3/7/23 - session recording

Madeleine Duran
Kamimoto, K., Stringa, B., Hoffmann, C.M. et al. Dissecting cell identity via network inference and in silico gene perturbation. Nature (2023). https://doi.org/10.1038/s41586-022-05688-9

Shruti Jain
Yen, Michelle, et al. Facile discovery of surrogate cytokine agonists. Cell 185.8 (2022): 1414-1430.

2/28/23 - session recording

Lizzie Plender
Zhang et al. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. 2020 Science.

Devin Schweppe
Yu, L., Kang, X., Li, F. et al. Unidirectional single-file transport of full-length proteins through a nanopore. Nat Biotechnol (2023).

2/14/23 - session recording

Malvika Tejura
Reed, et al. Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device. Science. 13 Oct 2022. Vol 378, Issue 6616, pp. 186-192.

Mu Yang
Binder, J., Ursu, O., Bologa, C. et al. Machine learning prediction and tau-based screening identifies potential Alzheimer’s disease genes relevant to immunity. Commun Biol 5, 125 (2022). https://doi.org/10.1038/s42003-022-03068-7

2/7/23 - session recording

Connor Kubo
Guibentif, Carolina et al. Diverse Routes toward Early Somites in the Mouse Embryo. Developmental cell vol. 56,1 (2021): 141-153.e6. doi:10.1016/j.devcel.2020.11.013

David Lee
Klumpe et al. The context-dependent, combinatorial logic of BMP signaling. Cell Sys. 2022

1/31/23 - session recording

Phil Abitua
Yamaguchi, N., Zhang, Z., Schneider, T. et al. Rear traction forces drive adherent tissue migration in vivo. Nat Cell Biol 24, 194–204 (2022).

Syd Sattler
Wattrus, et al. Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality. Science 22 Sep 2022, Vol 377, Issue 6613, pp. 1413-1419.

1/24/23 - session recording

Hunter Colegrove
Schenk, et al. (2022). Homeostasis limits keratinocyte evolution. PNAS

Elliott Swanson
Battaglia, S., Dong, K., Wu, J. et al. Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements. Nat Genet 54, 1504–1513 (2022).

1/17/23 -

Alison Feder
Mariana Harris, Nandita R Garud. Enrichment of Hard Sweeps on the X Chromosome in Drosophila melanogaster. Molecular Biology and Evolution, Volume 40, Issue 1, January 2023, msac268.

Luana Paleologu
Tóth K, Földi I, Mihály J. A Comparative Study of the Role of Formins in Drosophila Embryonic Dorsal Closure. Cells. 2022;11(9):1539.

1/10/23 -

Maya Lewinsohn
Karras, P., Bordeu, I., Pozniak, J. et al. A cellular hierarchy in melanoma uncouples growth and metastasis. Nature 610, 190–198 (2022).

1/3/23 -

Lea Starita
Siwei Chen, et al. A genome-wide mutational constraint map quantified from variation in 76,156 human genomes. bioRxiv 2022.03.20.485034; doi: https://doi.org/10.1101/2022.03.20.485034

Ben Mallory
Sahu, B., Hartonen, T., Pihlajamaa, P. et al. Sequence determinants of human gene regulatory elements. Nat Genet 54, 283–294 (2022).

12/6/22 - session recording

Brook Nunn
Marshall, S.M., Mathis, C., Carrick, E. et al. Identifying molecules as biosignatures with assembly theory and mass spectrometry. Nat Commun 12, 3033 (2021). https://doi.org/10.1038/s41467-021-23258-x

Austin Gabel
Weiss, J.M., Hunter, M.V., Cruz, N.M. et al. Anatomic position determines oncogenic specificity in melanoma. Nature 604, 354–361 (2022). https://doi.org/10.1038/s41586-022-04584-6

11/29/22

Anna Bakhtina
Mund, A., Coscia, F., Kriston, A. et al. Deep Visual Proteomics defines single-cell identity and heterogeneity. Nat Biotechnol 40, 1231–1240 (2022).

11/22/22 - session recording

Morgan Hamm
Cascading regime shifts within and across scales. Rocha et al. Science 2018.

Zorian Thornton
Dugan H, et al. Preexisting immunity shapes distinct antibody landscapes after influenza virus infection and vaccination in humans. Science Translational Medicine. 9 Dec 2020. Vol 12, Issue 573

11/15/22 - session recording

Hannah Jordt
Monroe J, et al. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature. 3 Feb 2022. Vol 602: 101-105.

11/1/22 - session recording

Conor Camplisson
Efficient algorithms for designing maximally sized orthogonal DNA sequence libraries. Gokul Gowri, Kuanwei Sheng, Peng Yin. bioRxiv 2022.07.11.499592; doi: https://doi.org/10.1101/2022.07.11.499592

Xavi Guitart
Pascarella G, et al. Recombination of repeat elements generates somatic complexity in human genomes. Cell. 2022 Aug 4;185(16):3025-3040.e6. doi: 10.1016/j.cell.2022.06.032. Epub 2022 Jul 25. PMID: 35882231.

10/25/22 - session recording

Lilian Heil
Brian D. Reed, et al. Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device. Science. 13 Oct 2022. Vol 378, Issue 6616. pp. 186-192

Wei Yang
Haotian Guo, et al. Spatial engineering of E. coli with addressable phase-separated RNAs. Vol. 185, Issue 20, P3823-3837.E23, September 29, 2022.

10/18/22

Atom Lesiak
Jonathan Chernoff. How much is my paper worth? Molecular Biology of the Cell. Vol. 30, No. 23 Published Online: 31 Oct 2019. https://doi.org/10.1091/mbc.E19-08-0458

10/11/22 - session recording

Sophie Moggridge
Maxwell, et al. Ubiquitination is essential for recovery of cellular activities after heat shock. Science. 25 Jun 2021. Vol 372, Issue 6549

Sriram Pendyala
Oren, Y., Tsabar, M., Cuoco, M.S. et al. Cycling cancer persister cells arise from lineages with distinct programs. Nature 596, 576–582 (2021). https://doi.org/10.1038/s41586-021-03796-6

10/4/22 - Mary-Claire King

Mary-Claire King
Mora-Bermúdez F, Kanis P, Macak D, Peters J, Naumann R, Xing L, Sarov M, Winkler S, Oegema CE, Haffner C, Wimberger P, Riesenberg S, Maricic T, Huttner WB, Pääbo S. Longer metaphase and fewer chromosome segregation errors in modern human than Neanderthal brain development. Sci Adv. 2022 Jul 29;8(30):eabn7702. PMID: 35905187

and

Pinson A, Xing L, Namba T, Kalebic N, Peters J, Oegema CE, Traikov S, Reppe K, Riesenberg S, Maricic T, Derihaci R, Wimberger P, Pääbo S, Huttner WB. Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals. Science. 2022 Sep 9;377(6611):eabl6422. PMID: 36074851.

3/8/22 - session recording

Melih Yilmaz
Rives A, Meier J, Sercu T, et al. Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. Proc Natl Acad Sci U S A. 2021;118(15):e2016239118. doi:10.1073/pnas.2016239118

3/1/22 - session recording

Leah Anderson
Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae. Molly Brothers, Jasper Rine. eLife 2022;11:e75653 DOI: 10.7554/eLife.75653

Jay Shendure
Paulsen, B., Velasco, S., Kedaigle, A.J. et al. Autism genes converge on asynchronous development of shared neuron classes. Nature 602, 268–273 (2022). https://doi.org/10.1038/s41586-021-04358-6

2/22/22 - session recording

Tony Li
Rurik, et al. CAR T cells produced in vivo to treat cardiac injury. Science. 6 Jan 2022, Vol 375, Issue 6576, pp. 91-96.

Chris McGann

2/15/22 - session recording

Elena Romero
Einkauf KB, Osborn MR, Gao C, Sun W, Sun X, Lian X, Parsons EM, Gladkov GT, Seiger KW, Blackmer JE, Jiang C, Yukl SA, Rosenberg ES, Yu XG, Lichterfeld M. Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses. Cell. 2022 Jan 20;185(2):266-282.e15. doi: 10.1016/j.cell.2021.12.011. Epub 2022 Jan 12. PMID: 35026153. 

Taylor Real
Genetic studies of human–chimpanzee divergence using stem cell fusions. Janet H. T. Song, Rachel L. Grant, Veronica C. Behrens, Marek Kučka, Garrett A. Roberts Kingman, Volker Soltys, Yingguang Frank Chan, David M. Kingsley Proceedings of the National Academy of Sciences Dec 2021, 118 (51) e2117557118; DOI: 10.1073/pnas.2117557118

2/8/22 - session recording

Judit Villen
Benson, S., de Moliner, F., Fernandez, A. et al. Photoactivatable metabolic warheads enable precise and safe ablation of target cells in vivo. Nat Commun 12, 2369 (2021).

Gabrielle Ferra
Oziolor, E. M., N. M. Reid, S. Yair, K. M. Lee, S. Guberman VerPloeg, P. C. Bruns, J. R. Shaw, A. Whitehead, and C. W. Matson (2019). Adaptive introgression enables evolutionary rescue from extreme environmental pollution. Science 364:455–457.

2/1/22 - session recording

Bob Waterston
Hajdinjak, et al., Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature volume 592, pages253–257 (2021)

and

Prufer et al., A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia. Nature Ecology & Evolution volume 5, pages820–825 (2021)

1/25/22 - session recording

David Hawkins
Squair, J.W., Gautier, M., Kathe, C. et al. Confronting false discoveries in single-cell differential expression. Nat Commun 12, 5692 (2021). https://doi.org/10.1038/s41467-021-25960-2

Lincoln Harris
Arisdakessian, C., Poirion, O., Yunits, B. et al. DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data. Genome Biol 20, 211 (2019). https://doi.org/10.1186/s13059-019-1837-6

1/18/22 - session recording

Chris Hsu
Myers, S.A., Wright, J., Peckner, R. et al. Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling. Nat Methods 15, 437–439 (2018).

Aidan Keith
A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program. Celia Alda-Catalinas, Danila Bredikhin, Irene Hernando-Herraez, Fátima Santos, Oana Kubinyecz, Mélanie A. Eckersley-Maslin, Oliver Stegle, Wolf Reik. Cell Systems, Volume 11, Issue 1, P25-41.E9, July 6, 2020

1/11/22 - session recording

Doug Fowler
Saturation variant interpretation using CRISPR prime editing. Steven Erwood, Teija M.I. Bily, Jason Lequyer, Joyce Yan, Nitya Gulati, Reid A. Brewer, Liangchi Zhou, Laurence Pelletier, Evgueni A. Ivakine, Ronald D. Cohn
bioRxiv 2021.05.11.443710; doi: https://doi.org/10.1101/2021.05.11.443710

Cassia Wagner
Band, G., Leffler, E.M., Jallow, M. et al. Malaria protection due to sickle haemoglobin depends on parasite genotype. Nature (2021).

1/4/22 -

Alexis Chang
Martinez-Val, A., Bekker-Jensen, D.B., Steigerwald, S. et al. Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution. Nat Commun 12, 7113 (2021).
session recording

12/7/21 -

Shawn Fayer
Robinson, P.S., Coorens, T.H., Palles, C., Mitchell, E., Abascal, F., Olafsson, S., Lee, B.C., Lawson, A.R., Lee-Six, H., Moore, L. and Sanders, M.A., 2021. Increased somatic mutation burdens in normal human cells due to defective DNA polymerases. Nature genetics, 53(10), pp.1434-1442.

Sam Regalado
Kvon EZ, Kamneva OK, Melo US, Barozzi I, Osterwalder M, Mannion BJ, Tissières V, Pickle CS, Plajzer-Frick I, Lee EA, Kato M, Garvin TH, Akiyama JA, Afzal V, Lopez-Rios J, Rubin EM, Dickel DE, Pennacchio LA, Visel A., 2016. Progressive Loss of Function in a Limb Enhancer during Snake Evolution. Cell 167(3):633-642.e11. 

11/30/21 -

Phoebe Parrish
Ferran Muiños, Francisco Martínez-Jiménez, Oriol Pich, Abel Gonzalez-Perez & Nuria Lopez-Bigas. In silico saturation mutagenesis of cancer genes. Nature. 2021 Aug; 596(7872): 428-432. doi: https://doi.org/10.1038/s41586-021-03771-1. 

Chengxiang Qiu
Matsuda et al. Species-specific segmentation clock periods are due to differential biochemical reaction speeds. Science (2020)

11/23/21 -

Mike MacCoss
Leung SK, Jeffries AR, Castanho I, Jordan BT, Moore K, Davies JP, Dempster EL, Bray NJ, O'Neill P, Tseng E, Ahmed Z, Collier DA, Jeffery ED, Prabhakar S, Schalkwyk L, Jops C, Gandal MJ, Sheynkman GM, Hannon E, Mill J. Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing. Cell Rep. 2021 Nov 16;37(7):110022. doi: 10.1016/j.celrep.2021.110022. PMID: 34788620.

and

Smith LM, Agar JN, Chamot-Rooke J, Danis PO, Ge Y, Loo JA, Paša-Tolić L, Tsybin YO, Kelleher NL; Consortium for Top-Down Proteomics. The Human Proteoform Project: Defining the human proteome. Sci Adv. 2021 Nov 12;7(46):eabk0734. doi: 10.1126/sciadv.abk0734. Epub 2021 Nov 12. PMID: 34767442.

Michelle Noyes
Yakubu, AM & Chen, YP. Ensuring privacy and security of genomic data and functionalities. Briefings in Bioinformatics 21.

11/16/21 -

Robin Aguilar
Bury, et al. Alpha-satellite RNA transcripts are repressed by centromere–nucleolus associations. eLife 2020;9:e59770.

Brian Beliveau
Huang et al. Spatial organization of transcribing loci during early genome activation in Drosophila. Current Biology 2021

11/9/21 -

Eliza Barkan
Hussmann, Ling, Ravisankar, et al. Mapping the genetic landscape of DNA double-strand break repair. Cell, Volume 184, Issue 22, 2021. https://doi.org/10.1016/j.cell.2021.10.002.

Sam Smukowski
Swarnkar, S., Avchalumov, Y., Espadas, I., Grinman, E., Liu, X., Raveendra, B.L., Zucca, A., Mediouni, S., Sadhu, A., Valente, S., Page, D., Miller, K., Puthanveettil, S.V., 2021. Molecular motor protein KIF5C mediates structural plasticity and long-term memory by constraining local translation. Cell Reports 36, 109369. https://doi.org/10.1016/j.celrep.2021.109369

11/2/21 -

Sayeh Gorjifard
Wang, X., Aguirre, L., Rodríguez-Leal, D. et al. Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. Nat. Plants 7, 419–427 (2021). https://doi.org/10.1038/s41477-021-00898-x

Alan Min
Liu, H., Zhou, J., Tian, W. et al. DNA methylation atlas of the mouse brain at single-cell resolution. Nature 598, 120–128 (2021). https://doi.org/10.1038/s41586-020-03182-8

10/26/21 -

Hyeon-Jin Kim
Ng, A.H.M., Khoshakhlagh, P., Rojo Arias, J.E. et al. A comprehensive library of human transcription factors for cell fate engineering. Nat Biotechnol 39, 510–519 (2021). https://doi.org/10.1038/s41587-020-0742-6

10/19/21 -

Bonny Brewer
Loss of the fragile X syndrome protein FMRP results in misregulation of nonsense-mediated mRNA decay.
Tatsuaki Kurosaki, Naoto Imamachi, Christoph Pröschel, Shuhei Mitsutomi, Rina Nagao, Nobuyoshi Akimitsu, Lynne E. Maquat
Nat Cell Biol. 2021 January ; 23(1): 40–48. doi:10.1038/s41556-020-00618-1.

10/12/21 -

Sam Miller
Cayetano Pleguezuelos-Manzano, et al. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli. Nature volume 580, pages269–273 (2020)

Jim Thomas

10/5/21 -

Mary-Claire King
Choudhury A, Aron S, Botigué LR, Sengupta D, Botha G, Bensellak T, Wells G, Kumuthini J, Shriner D, Fakim YJ, Ghoorah AW, Dareng E, Odia T, Falola O, Adebiyi E, Hazelhurst S, Mazandu G, Nyangiri OA, Mbiyavanga M, Benkahla A, Kassim SK, Mulder N, Adebamowo SN, Chimusa ER, Muzny D, Metcalf G, Gibbs RA; TrypanoGEN Research Group, Rotimi C, Ramsay M; H3Africa Consortium, Adeyemo AA, Lombard Z, Hanchard NA. High-depth African genomes inform human migration and health. Nature. 2020 Oct; 586(7831):741-748.

Ryan Carlson
Akbari P et al. Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity. Science. 2021 Jul 2;373(6550):eabf8683. doi: 10.1126/science.abf8683. PMID: 34210852.

 

12/8/20 -

Taylor Wang, WiGS Social Education Chair 
AlShebli, Bedoor, Kinga Makovi, and Talal Rahwan. "The association between early career informal mentorship in academic collaborations and junior author performance." Nature communications 11.1 (2020): 1-8.
presentation recording

3/10/20 -

Josh Cuperus
Weiberg, et al. Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways. Science 04 Oct 2013.

Cai, et al. Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes. Science 08 Jun 2018.

Sayeh Gorjifard
In vivo RNA editing of point mutations via RNA-guided adenosine deaminases (Nature Methods)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395520/

A cytosine deaminase for programmable single-base RNA editing. (Science)

https://www.ncbi.nlm.nih.gov/pubmed/31296651?dopt=Abstract

3/3/20 -

Allie Greaney
Adaptive substitutions underlying cardiac glycoside insensitivity in insects exhibit epistasis in vivo: https://elifesciences.org/articles/48224

Genome editing retraces the evolution of toxin resistance in the monarch butterfly: https://www.nature.com/articles/s41586-019-1610-8.pdf?draft=collection

M.K. Raghuraman
Morafraile, E. C., C. Hanni, G. Allen, T. Zeisner, C. Clarke et al., 2019 Checkpoint inhibition of origin firing prevents DNA topological stress. Genes Dev 33:1539-1554.

2/25/20 -

Maitreya Dunham
Engineered symbionts activate honey bee immunity and limit pathogens. Science 367: 573-576. PMID: 32001655

2/18/20 -

Kelley Harris
Mostafavi, et al. Variable prediction accuracy of polygenic scores within an ancestry group. eLife 2020;9:e48376.

Hyeon-Jin Kim
Chen X, et al. High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing. Cell 179, 772-786 (2019)

2/11/20 -

Sam Smukowski
Marcus Davidsson, Gang Wang, Patrick Aldrin-kirk, Tiago Cardoso, Sara Nolbrant, Morgan Hartnor, Janitha Mudannayake, Malin Parmar, and Tomas Bjorklund. A systematic capsid evolution approach performed in vivo for the design of AAV vectors with tailored properties and tropism. Proceedings of the National Academy of Sciences, December 26, 2019, Vol 116, no 52, pgs 27053-27062.

2/4/20 -

Robin Aguilar
Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade.
J.S. Sproul, D.E. Khost, D.G. Eickbush, S. Negm, X. Wei, I. Wong, A.M. Larracuente. bioRxiv 846238; doi: https://doi.org/10.1101/846238

Phoebe Parrish
Sanson, et al. Optimization of AsCas12a for combinatorial genetic screens in human cells. biorxiv.

1/28/20 -

Evan Eichler
Olalde I, et al. The genomic history of the Iberian Peninsula over the past 8000 years. Science 2019.

Michelle Noyes
 F. Wu, et al. A comparison of humans and baboons suggests germline mutation rates do not track cell divisions.

1/14/20 -

Ryan Carlson
Abramovs, Brass, Tassabehji. GeVIR is a continuous gene-level metric that uses variant distribution patterns to prioritize disease candidate genes. Nature Genetics, 23 December 2019.

Chengxiang Qiu
Mor Nitzan et al. Gene expression cartography. Nature (2019)

1/7/20 -

John Stamatoyannopoulos
Satpathy, A.T., Granja, J.M., Yost, K.E. et al.Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat Biotechnol 37, 925–936 (2019) doi:10.1038/s41587-019-0206-z

12/3/19 -

April Lo
Yonemitsu et al. A single clonal lineage of transmissible cancer identified in two marine mussel species in South America and Europe. eLife. November 2019. 

Bianca Ruiz
Alexander C. Reis, Sean M. Halper, Grace E. Vezeau, Daniel P. Cetnar, Ayaan Hossain, Phillip R. Clauer and Howard M. Salis. Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays. Nature Biotechnology, October 2019.

11/26/19 -

Emma Hoppe
Xue et al. Hybrid decay: A transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize. Genetics 213 (2019): 143-160.

Alberto Rivera
Welker et al. 2019. Enamel proteome shows that Gigantopithecus was an early diverging pongine. Nature.

11/19/19 -

Anthony Valente
Gessulat, S., Schmidt, T., Zolg, D.P. et al. Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nat Methods 16, 509–518 (2019) doi:10.1038/s41592-019-0426-7

Mitchell Vollger

The primary paper will be:

Chin C-S, Khalak A. 2019. Human Genome Assembly in 100 Minutes. bioRxiv. doi:10.1101/705616

But the overall topic will be the concept of "Minimizers", and I will briefly discuss the following papers:

Roberts M, Hayes W, Hunt BR, Mount SM, Yorke JA. 2004. Reducing storage requirements for biological sequence comparison. Bioinformatics 20:3363–3369. doi:10.1093/bioinformatics/bth408

Schleimer S, Wilkerson DS, Aiken A. 2003. Winnowing: Local Algorithms for Document FingerprintingProceedings of the 2003 ACM SIGMOD International Conference on Management of Data, SIGMOD ’03. New York, NY, USA: ACM. pp. 76–85. doi:10.1145/872757.872770  

Berlin K, Koren S, Chin C-S, Drake JP, Landolin JM, Phillippy AM. 2015. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 33:623–630. doi:10.1038/nbt.3238

Li H. 2015. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. arXiv [q-bioGN].  

Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100. doi:10.1093/bioinformatics/bty191

11/12/19 -

Nick Hasle
Kula, et al. "T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes". Cell. Volume 178, Issue 4, 8 August 2019, Pages 1016-1028.e13

Sanjay Srivatsan
Gao et al. Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution. Science 363, 245 (2019)

11/5/19 -

Andria Ellis
Anazole, A. et al. Search-and-replace genome editing without double stranded breaks or donor DNA. Nature (2019)

10/29/19 -

Cindy Yeh
Yang, Y., Servedio, M.R., & Richards-Zawacki, C.L. Imprinting sets the stage for speciation. Nature. 2 Oct 2019.

Anna Minkina
RETRACTED: Wei & Nielsen. CCR5-∆32 is deleterious in the homozygous state in humans. Nature Medicine 25, pages 909–910 (2019)

Maier et al. No statistical evidence for an effect of CCR5-∆32 on lifespan in the UK Biobank cohort. BioRxiv (Oct. 2019)

10/22/19 -

Gesine Cauer
Schlissel, G. and Rine, J., 2019. The nucleosome core particle remembers its position through DNA replication and RNA transcription. Proceedings of the National Academy of Sciences, p.201911943.

Ian Smith
Wroblewska, A., Dhainaut, M., et al.  Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens. Cell, Volume 175, Issue 4, 1141-1155

10/15/19 -

Martin Mathay
May KL, et al. 2019. Identification of a stress response monitoring lipoprotein trafficking to the outer membrane. mBio 10(3)

Jared Mohr
Huang G, Voet A, Maglia G. FraC nanopore with adjustable diameter identify the mass of opposite-charge peptides with 44 dalton resolution. Nature Communications (2019).

10/8/19 -

Mary Kuhner

Original paper:

White et al. (2011)  Comparison of adaptive pacing therapy, cognitive behaviour therapy,
graded exercise therapy, and specialist medical care for chronic fatigue syndrome (PACE):
a randomised trial.  Lancet. 2011;377(9768):823–36.

Response:

Wilshire CE, Kindlon T, Courtney R, Matthees A, Tuller D, Geraghty K, Levin B.
Rethinking the treatment of chronic fatigue syndrome—a reanalysis and evaluation
of findings from a recent major trial of graded exercise and CBT. BMC Psychol.
2018;6(1):6.

Rebuttal:

Sharpe M, Goldsmith KA, Chalder T. The PACE trial of treatments for chronic
fatigue syndrome: a response to WILSHIRE et al. BMC Psychol. 2019;7:15.

Response to rebuttal:

Wilshire CE, Kindlon T.  Sharpe, Goldsmith and Chalder fail to restore
confidence in the PACE trial findings.  BMC Phychol 2019; 7:19.

Bill Noble

Hie, et al. Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape. Cell Systems. Volume 8, Issue 6, 26 June 2019, Pages 483-493.e7

10/1/19 -

Mary-Claire King

Sone J, Mitsuhashi S, Fujita A, Mizuguchi T, Hamanaka K, Mori K, Koike H, Hashiguchi A, Takashima H, Sugiyama H, Kohno Y, Takiyama Y, Maeda K, Doi H, Koyano S, Takeuchi H, Kawamoto M, Kohara N, Ando T, Ieda T, Kita Y, Kokubun N, Tsuboi Y, Katoh K, Kino Y, Katsuno M, Iwasaki Y, Yoshida M, Tanaka F, Suzuki IK,  Frith MC, Matsumoto N, Sobue G. Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease.  Nat Genet. 51:1215-1221, 2019 PMID: 31332381.

Ishiura H, Shibata S, Yoshimura J, Suzuki Y, Qu W, Doi K, Almansour MA, Kikuchi JK, Taira M, Mitsui J, Takahashi Y, Ichikawa Y, Mano T, Iwata A, Harigaya Y, Matsukawa MK, Matsukawa T, Tanaka M, Shirota Y, Ohtomo R, Kowa H, Date H, Mitsue A, Hatsuta H, Morimoto S, Murayama S, Shiio Y, Saito Y, Mitsutake A, Kawai M, Sasaki T, Sugiyama Y, Hamada M, Ohtomo G, Terao Y, Nakazato Y, Takeda A, Sakiyama Y, Umeda-Kameyama Y, Shinmi J, Ogata K, Kohno Y, Lim SY, Tan AH, Shimizu J, Goto J, Nishino I, Toda T, Morishita S, Tsuji S. Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease. Nat Genet. 51: 1222-1232, 2019 PMID: 31332380.

 

4/23/19 -

Nick Hasle
Xindong Liu, et al. Genome-wide analysis identifies NR4A1 as a key mediator of T cell dysfunction. Nature 567, 525–529 (2019).

Mitchell Vollger
Rachel Sherman et al. Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nature Genetics 51, 30-35 (2019).

4/16/19 -

Gesine Cauer
Zink, F., Magnusdottir, D.N., Magnusson, O.T., Walker, N.J., Morris, T.J., Sigurdsson, A., Halldorsson, G.H., Gudjonsson, S.A., Melsted, P., Ingimundardottir, H. and Kristmundsdottir, S., 2018. Insights into imprinting from parent-of-origin phased methylomes and transcriptomes. Nature Genetics, 50(11), p.1542.

Kate Dusenbury
Faber, M. S., Wrenbeck, E. E., Azouz, L. R., Steiner, P. J., & Whitehead, T. A. (2019). Impact of initial protein stability on local fitness landscapes. BioRxiv, 590398. https://doi.org/10.1101/590398

4/9/19 -

Emma De Neef
Weiss et al. "Genetic dissection of interspecific differences in yeast thermotolerance". Nature Genetics (2018)

Will DeWitt
Geometry of the Sample Frequency Spectrum and the Perils of Demographic Inference. Zvi Rosen, Anand Bhaskar, Sebastien Roch and Yun S. Song. GENETICS Early online July 31, 2018

4/2/19 -

Alberto Rivera
Edger P.P., et al., Origin and evolution of the octoploid strawberry genome, Nature Genetics (2019)

3/12/19 -

Jolie Carlisle
Q. Raza, et al. Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila. PlOS Genetics 14 Feb 2019.

Chris Large
Kukekova, A. V., et al. Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nature Ecology & Evolution (2018). 

3/5/19 -

Michael Goldberg -

Sarah Hilton
Barrett et al., Linking a mutation to survival in wild mice. Science. 2019 Feb 1;363(6426):499-504. doi: 10.1126/science.aav3824. 

2/26/19 -

Florence Chardon
N. Matharu, et al. CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency. Science 18 Jan 2019.

2/19/19 -

David Bacsik
Blauwkamp, et al. "Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease". Nature Microbiology.

Deanna Plubell
Dan, K. et al., DNA nanodevices map enzymatic activity in organelles. Nature Nanotechnology (2019)

2/12/19 -

Andy Lin
Computer Security, Privacy, and DNA Sequencing:Compromising Computers with Synthesized DNA, Privacy Leaks, and More. 2017 USENIX Security Symposium

Ian Smith
Wroblewska, A., Dhainaut, M., et al.  Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens. Cell, Volume 175, Issue 4, 1141-1155

2/5/19 -

Danielle Faivre
Mehta, A. P. et al. Bacterial Genome Containing Chimeric DNA–RNA Sequences. J. Am. Chem. Soc. 140, 11464–11473 (2018).

Danny Lawrence
Parameswaran et al. Intrahost Selection Pressures Drive Rapid Dengue Virus Microevolution in Acute Human Infections. Cell Host & Microbe.

1/29/19 -

Khrystyna North
Hoban et al. "The microbiome regulates amygdala-dependent fear recall." Molecular Psychiatry (2018)

David Read
"Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks",
K.M. Cherry and L. Qian. Nature, July 2018. Pg 370 - 376

1/22/19 -

Anthony Valente
AJ Riesselman, JB Ingraham, and DS Marks. Deep generative models of genetic variation capture the effects of mutations. Nature Methods, September 2018.

1/15/19 -

Anna Minkina
Hannezo et al. (2017) A unifying theory of branching morphogenesis. Cell 171, 242-255

Jonathan Packer
"Morris et al. An atlas of genetic influences on osteoporosis in humans and mice. Nature Genetics, 2018."

1/8/19 -

April Lo
Kyrou, K. et al. "A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes." Nature Biotechnology (2018)

Eliah Overbey
A case study on transferring basic science research to the clinic: The process of creating the first FDA-approved RNA interference drug.

Featuring: 
Ledford, H. (2018). Gene-silencing technology gets first drug approval after 20-year wait. Nature,560(7718), 291-292. doi:10.1038/d41586-018-05867-7

Adams, D. et al. (2018). Patisiran, an RNAi Therapeutic, for Hereditary Transthyretin Amyloidosis. The New England Journal of Medicine. doi:10.1056/NEJMoa1716153

11/27/18 -

Kyle Hess
Wang J, et al. A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

11/20/18 -

Nick Popp
Richardson, C.D., et al. CRISPR–Cas9 genome editing in human cells occurs via the Fanconi anemia pathway. Nature Genetics. 50: 1132–1139 (2018).

11/13/18 -

Martin Mathay
Rang, CU. et al. Minicells as a Damage Disposal Mechanism in Escherichia coli. mSphere. 3(5): e00428-18. 

Jared Mohr
Swaminathan, J. et al. Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures. Nature Biotechnology (2018). 

11/6/18 -

Bianca Ruiz
Catherine G Triandafillou, Christopher D Katanski, Aaron R Dinner, D. Allan Drummond. Transient intracellular acidification regulates the core transcriptional heat shock response.

10/23/18 -

Juhye Lee
Ilardo, M.A., et al. Physiological and Genetic Adaptations to Diving in Sea Nomads. Cell, Volume 173, Issue 3, 569-580.

Cindy Yeh
Gautier, M., Yamaguchi, J. et al. The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird. Current Biology (2018).

10/9/18 -

Ken Jean-Baptiste
Schilinger and Paulitz. Natural Suppression of Rhizoctonia Bare Patch in a Long-Term No-Till Cropping Systems Experiment.

Poudel, et al. Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management.

10/2/18 -

Mary-Claire King
Abelson JC et al. Prediction of acute myeloid leukemia risk in healthy individuals. Nature 559:400-404, 2018. PMID: 29988082

5/22/18 -

Andria Ellis
Srivastava et al. Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation. bioRxiv, posted online 5/8/2018.

Eliah Overbey
Global transcriptomic analysis suggests carbon dioxide as an environmental stressor in spaceflight: A systems biology GeneLab case study. Beheshti, A. (2018).  Scientific Reports,8(1). doi:10.1038/s41598-018-22613-1

5/9/18 -

Rebecca Martin
Dawe et al. A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize. Cell. DOI: https://doi.org/10.1016/j.cell.2018.03.009

Hannah Pliner
Myhrvold et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science 27 Apr 2018: Vol. 360, Issue 6387, pp. 444-448.

5/8/18 -

Danny Lawrence
Parameswaran P, et al. Intrahost Selection Pressures Drive Rapid Dengue Virus Microevolution in Acute Human Infections. Cell Host Microbe. 2017 Sep 13;22(3):400-410.e5. doi: 10.1016/j.chom.2017.08.003.

4/24/18 -

Kyle Hess
Franzmann, et al. Phase separation of a yeast prion protein promotes cellular fitness. Science Vol. 359, Issue 6371

Chris Large
Akera, et al. Spindle asymmetry drives non-Mendelian chromosome segregation. Science 358, 668-672 (2017).

4/17/18 -

Anja Ollodart
Voyles, et al. Shifts in disease dynamics in a tropical amphibian assemblage are not due to pathogen attenuation. Sciene. 30 Mar 2018 : 1517-1519

Bianca Ruiz
Acevedo, et al. Changes in global translation elongation or initiation rates shape the proteome via the Kozak sequence. Scientific Reports volume 8, Article number: 4018(2018). doi:10.1038/s41598-018-22330-9

4/10/18 -

Jolie Carlisle
VanKuren, N. W. & Long, M. Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. Nat Ecol Evol 2, 705–712 (2018).

Steven Lee
Lisa Bastarache, et al. Phenotype risk scores identify patients with unrecognized Mendelian disease patterns. Science 16 Mar 2018 : 1233-1239

4/3/18 -

Emily Killingbeck -

Harkins CP, Pichon B, Doumith M, Parkhill J, Westh H, Tomasz A, de Lencastre H, Bentley SD, Kearns AM, Holden MTG. Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice. Genome Biol 2017 07/20;18(1):130.

Alberto Rivera -

Patel et al (2018).  DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins.  Cell 173, 221–233

3/27/18 -

Judit Villen

Piazza I, Kochanowski K, Cappelletti V, Fuhrer T, Noor E, Sauer U, Picotti P (2018). A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication. Cell 172: 358–372.e23.

Sanjay Srivatsan

A fungal pathogen that robustly manipulates the behavior of Drosophila melanogaster in the laboratory. Carolyn Elya, Tin Ching Lok, Quinn E Spencer, Hayley McCausland, Ciera C Martinez, Michael B Eisen bioRxiv 232140; doi: https://doi.org/10.1101/232140

3/6/18 -

Clara Amorosi

Lindsey AR, Rice DW, Bordenstein SR, Brooks AW, Bordenstein SR, Newton IL. (2018). Evolutionary genetics of cytoplasmic incompatibility genes cifA and cifB in prophage WO of Wolbachia. Genome biology and evolution.

Andy Lin

Black O, Cody R, et al. Identification of polymers and organic gunshot residue in evidence from 3D-printed firearms using DART-mass spectrometry: A feasibility study

2/27/18 -

Serena Liu

Du et al., "Genome-wide identification of interferon-sensitive mutations enables influenza vaccine design." Science 359, 290-296 (2018).

Colin Manoil

Kolata, Why is this bacterium hiding in human tumors? New York Times, Nov 23, 2017

Bullman et al, Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer, Science 358, 1443 (2017)

2/20/18 -

Sarah Hilton
Pastuzyn, E. D., Day, C. E., Kearns, R. B., Kyrke-Smith, M., Taibi, A. V., McCormick, J., & Briggs, J. A. (2018). The neuronal gene Arc encodes a repurposed retrotransposon Gag protein that mediates intercellular RNA transfer. Cell, 172(1), 275-288.

Mitchell Vollger
Sergej Nowoshilow el al. The axolotl genome and the evolution of key tissue formation regulators. Nature 554.

2/13/18 -

Martin Mathay
McCabe, AL. et al. Conformational Changes That Coordinate the Activity of BamA and BamD Allowing Beta-Barrel Assembly. J. Bacteriol. 199, 20 (2017).

Jared Mohr
Guo, H., Bueler, S. A. & Rubinstein, J. L. Atomic model for the dimeric F₀ region of mitochondrial ATP synthase. Science 358, 936-940 (2017).

2/6/18 -

April Lo
McGranahan et al. Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution. Cell (2017).

Anna Minkina
Falk et al. Heterochromatin drives organization of conventional and inverted nuclei. bioRxiv, posted online 1/9/2018.

1/30/18 -

Abby Keller
Gibeaux et al. Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus. Nature 553, 337–341

1/23/18 -

Molly Gasperini
Identification of Pre-Existing Adaptive Immunity to Cas9 Proteins in Humans. Carsten T. Charlesworth et al. bioRxiv posted online Jan. 5, 2018;

1/16/18 -

Maitreya Dunham
Emanuel Schmid-Siegert, Namrata Sarkar, et al. Low number of fixed somatic mutations in a long-lived oak tree. Nature Plants 3, 926–929 (2017).

Jonathan Packer
Shaffer et al. Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Nature (2017).

1/9/18 -

Ian Smith
Lobingier et al. An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Cell (2017).

12/5/17 -

Claudia Espinoza
Sadiya Khan, Sanjiv Shah, et al. A null mutation in SERPINE1 protects against biological aging in humans. Science Advances 15 Nov 2017: EAAO1617.

Anthony Valente
Clift et al., A Method for the Acute and Rapid Degradation of Endogenous Proteins. Cell. January 11, 2018

11/28/17 -

Ken Jean-Baptiste
Gaudelli, Nicole M., Alexis C. Komor, Holly A. Rees, Michael S. Packer, Ahmed H. Badran, David I. Bryson, and David R. Liu. 2017. “Programmable Base Editing of A•T to G•C in Genomic DNA without DNA Cleavage.” Nature, October. https://doi.org/10.1038/nature24644.

Cox, David B. T., Jonathan S. Gootenberg, Omar O. Abudayyeh, Brian Franklin, Max J. Kellner, Julia Joung, and Feng Zhang. 2017. “RNA Editing with CRISPR-Cas13.” Science, October. https://doi.org/10.1126/science.aaq0180.

Cindy Yeh
Murray et al. Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science, 17 Nov 2017.

11/21/17 -

Madeleine Geisheker
Tobias Hirsch, Tobias Rothoeft, Norbert Teig et al. Regeneration of the entire human epidermis using transgenic stem cells. Nature (2017). doi :10.1038/nature24487

11/14/17 -

Celeste Berg
Hong Ma, Nuria Marti-Gutierrez, Sang-Wook Park, et al. Correction of a pathogenic gene mutation in human embryos. Nature (2017) doi:10.1038/nature23305

Katherine Xue
Starr, Picton, and Thornton. 2017. Alternative evoltuionary histories in the sequence space of an ancient protein. Nature: doi:10.1038/nature23902

Starr et al. 2017. Pervasive contingency and entrenchment in a billion years of Hsp90 evolution. bioRxiv.

11/7/17 -

Lindsay Pino

Direct-to-Consumer Canine Genetic Testing:

E. Ostrander, et al. "Demographic history, selection and functional diversity of the canine genome". Nature Reviews Genetics 2017.

10/31/17 -

Emma Hoppe
Jin, Eser, Struhl, & Churchman (2017). The Ground State and Evolution of Promoter Region Directionality. Cell, 170(5): 889-898.e10.https://doi.org/10.1016/j.cell.2017.07.006

Khrystyna North
Schwendner, P. et al. Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing. Microbiome 5, 129 (2017).

10/24/17 -

Damon May
"Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9", Niu et al., Science 2017

10/17/17 -

Bill Noble
Michal Kosinski, Yilun Wang. Deep neural networks are more accurate than humans at detecting sexual orientation from facial images. https://osf.io/zn79k/

10/10/17 -

Amanda Larson
Chaitanya L et al. 2017. Bringing colour back after 70 years: Predicting eye and hair colour from skeletal remains of World War II victims using the HIrisPlex system. Forensic Science Int Genet. 26: 48-57

Walsh S et al. 2017. Global skin colour prediction from DNA. Hum Genet. 136(7):847-863

10/3/17 -

Sebé-Pedrós A, et al. High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation. Dev Cell. 2016 Oct 24;39(2):186-197. doi: 10.1016/j.devcel.2016.09.019. Epub 2016 Oct 13.

A useful review: Sebé-Pedrós A, et al. The origin of Metazoa: a unicellular perspective. Nat Rev Genet. 2017 Aug;18(8):498-512. doi: 10.1038/nrg.2017.21. Epub 2017 May 8.

5/30/17 -

Colby Samstag -

Cytosolic proteostasis through importing of misfolded proteins into mitochondria.
Linhao Ruan, Chuankai Zhou, Erli Jin, Andrei Kucharavy, Ying Zhang, Zhihui Wen, Laurence Florens & Rong Li

5/23/17 -

Jason Klein
Chen, Capellini, et al. Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton. PLOS Genetics.

Phil Green
Tomasetti C et al. (2017) Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention. Science 355 : 1330-1334.

5/16/17 -

Greg Findlay
Erlich, Y., Zielinski, D.  DNA Fountain enables a robust and efficient storage architecture. Science 355 (6328), 950-954.

Seungsoo Kim
Takahashi et al. (2017) Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells. Science 356: 503-508.

5/9/17 -

Eliah Overbey
Castro-Wallace et al. Nanopore DNA Sequencing and Genome Assembly on the International Space Station. bioRxiv (2016).
http://biorxiv.org/content/early/2016/09/27/077651

5/2/17 -

Max Dougherty
Saleheen et al. 2007. Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity. Nature https://www.ncbi.nlm.nih.gov/pubmed/28406212

Steven Lee
Dongjun Chung, et al. graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture. PLOS Computational Biology.

4/25/17 -

Vijay Ramani
Zhao, Wang, Beadell et al, "m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition," Nature (2017)

4/18/17 -

Anne Clark
Li D, Azoulay P, and Sampat BN (2017). The applied value of public investments in biomedical research. Science 356:78-81.

Andy Lin
Sattar SA, et al. Decontamination of indoor air to reduce the risk of airborne infections: Studies on survival and inactivation of airborne pathogens using an aerobiology chamber. Am J Infect Control. 2016 Oct 1;44(10):e177-e182. doi: 10.1016/j.ajic.2016.03.067. Epub 2016 Jun 30.

Sattar SA, et al. Airborne pathogens inside automobiles for domestic use: Assessing in-car air decontamination devices using Staphylococcus aureus as the challenge. Applied and Environmental Microbiology.

4/11/17 -

Emily Killingbeck
CD32a is a marker of a CD4 T-cell HIV reservoir harbouring replication-competent proviruses. Descours, B. et al. Nature 543, 564–567 (2017).

Brian Searle
Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state. Snijder J, Schuller JM, Wiegard A, Lössl P, Schmelling N, Axmann IM, Plitzko JM, Förster F, Heck AJ. Science. 2017 Mar 17;355(6330):1181-1184. doi: 10.1126/science.aag3218.

4/4/17 -

Alex Eng
Thomou, Thomas, et al. "Adipose-derived circulating miRNAs regulate gene expression in other tissues." Nature (2017).

John Lazar
Teves, Sheila S., et al. "A dynamic mode of mitotic bookmarking by transcription factors." Elife 5 (2016): e22280.

3/28/17 -

Claudia Espinoza
Bachner-Melman R, Dina C, Zohar AH, Constantini N, Lerer E, et al. (2005) AVPR1a and SLC6A4 Gene Polymorphisms Are Associated with Creative Dance Performance. PLOS Genetics 1(3): e42. doi: 10.1371/journal.pgen.0010042

Madeleine Geisheker
Rogers RL & Slatkin M. (2017). Excess of genomic defects in a wooly mammoth on Wrangel island. PLOS Genet 13(3): e1006601. doi:10.1371/journal.pgen.1006601.

Juhye Lee
Reid, N. M. The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science 354, 2016.

3/7/17 -

Jim Bruce
Vinothkumar, KR, et al. “Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy”. Proceedings of the National Academy of Sciences, November 8, 2016, vol. 113, 12709–12714.

Andrew Hill

Hannah Pliner
Halpern, KB, et al., Singe-cell spatial reconstruction reveals global division of labour in the mammalian liver, Nature 542, 352–356 (16 February 2017)

2/28/17 -

Molly Gasperini
Fulco, C. P., Munschauer, M., Anyoha, R., Munson, G., Sharon, R., Perez, E. M., … Jesse, M. (2016). Supplementary Materials for Systematic mapping of functional enhancer - promoter connections with. Science, 354(6313), 769–773. http://doi.org/10.1126/science.aag2445

2/21/17 -

Serena Liu
Zheng, J.H. et al. "Two-step enhanced cancer immunotherapy with engineered Salmonella typhimurium secreting heterologous flagellin." Sci. Transl. Med. 9, eaak9537 (2017).

Leo Pallanck
Elimination of paternal mitochondria in mouse embryos occurs through autophagic degradation dependent on PARKIN and MUL1.
Rojansky R, Cha MY, Chan DC. Elife. 2016 Nov 17;5. pii: e17896.

2/14/17 -

Sarah Hilton
Cognition-mediated evolution of low-quality floral nectars. Vladislav Nachev, Kai Petra Stich, Clemens Winter, Alan Bond, Alan Kamil and York Winter (January 5, 2017). Science 355 (6320), 75-78. [doi: 10.1126/science.aah4219]

Xiaojie Qiu
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

Dissecting Immune Circuits by Linking CRISPR- Pooled Screens with Single-Cell RNA-Seq

2/7/17 -

Ken Chen
Wu, J. et al. Interspecies Chimerism with Mammalian Pluripotent Stem Cells. Cell 168, 473–486.e15 (2017).

Mike Doud
Structured States of Disordered Proteins from Genomic Sequences Toth-Petroczy, Agnes et al. Cell, Volume 167 , Issue 1 , 158 - 170.e12
http://dx.doi.org/10.1016/j.cell.2016.09.010

1/31/17 -

Khrystyna Dilai
Loh et al.,"Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types." Cell 166.2 (2016): 451-67.

Evan Eichler
Ju XC, Hou QQ, Sheng AL, et al. The hominoid-specific gene TBC1D3 promotes generation of basal neural progenitors and induces cortical folding in mice. Elife. 2016 Aug 9;5. pii: e18197. doi: 10.7554/eLife.18197.

1/24/17 -

Debbie Nickerson
Astle WJ, Elding H, Jiang T et al. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease. Cell. 2016 Nov 17;167(5):1415-1429.e19. doi: 10.1016/j.cell.2016.10.042.

Chen, L., Ge, B. et al. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell. 2016 Nov 17;167(5):1398-1414.e24. doi: 10.1016/j.cell.2016.10.026.

Tim Durham
Lu, C. P., L. Polak, B. E. Keyes, and E. Fuchs. “Spatiotemporal Antagonism in Mesenchymal-Epithelial Signaling in Sweat versus Hair Fate Decision.” Science 354, no. 6319 (December 23, 2016): aah6102-aah6102. doi:10.1126/science.aah6102.

1/17/17 -

Jolie Carlisle
William H. Hudson, Bradley R. Kossmann, Ian Mitchelle S. de Vera, Shih-Wei Chuo, Emily R. Weikum, Geeta N. Eick, Joseph W. Thornton, Ivaylo N. Ivanov, Douglas J. Kojetin, and Eric A. Ortlund. "Distal substitutions drive divergent DNA specificity among paralogous transcription factors 
through subdivision of conformational space". PNAS 2016 113 (2) 326-331; published ahead of print December 29, 2015, 
doi:10.1073/pnas.1518960113

Heather Machkovech
Swart, E. C., Serra, V., Petroni, G., & Nowacki, M. (2016). Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination. Cell, 166(3), 691–702.

1/10/17 -

Colin McNally
Hackett et al. Systems-level analysis of mechanisms regulating yeast metabolic flux. Science, 2016.

Cecilia Noecker
Worobey et al. (2016). 1970s and “Patient 0” HIV-1 genomes illuminate early HIV/AIDS history in North America. Nature.

1/3/17 -

Anja Ollodart
"The escalatory Red Queen: Population extinction and replacement following arms-race dynamics in poplar rust" 
A. Persoons, K. J. Hayden, B. Fabre, P. Frey, S. De Mita, A. Tellier and F. Halkett. Molecular Ecology Dec 2016 

Jonathan Packer
Berry DC, Jiang Y, Arpke RW, Close EL, Uchida A, Reading D, Berglund ED, Kyba M, Graff JM. Cellular Aging Contributes to Failure of Cold-Induced Beige Adipocyte Formation in Old Mice and Humans. Cell Metabolism 25 (2016): 1-16.

12/6/16 -

Willie Swanson
Maria Chikina, Joseph D. Robinson, Nathan L. Clark Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals Mol Biol Evol (2016) 33 (9): 2182-2192 first published online June 21, 2016 doi:10.1093/molbev/msw112

11/29/16 -

Mary-Claire King
Chatterjee S, Kapoor A, Akiyama JA, Auer DR, Lee D, Gabriel S, Berrios C, Pennacchio LA, Chakravarti A. Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network in Hirschsprung Disease. Cell 167(2):355-368, 2016

Abigail Keller
Chakrabortee, S., Byers, J. S., Jones, S., Garcia, D. M., Bhullar, B., Chang, A., et al. (2016). Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits. Cell, 167(2), 369–381.e12. http://doi.org/10.1016/j.cell.2016.09.017

 

11/22/16 -

Mike MacCoss
Nixon-Abell J, Obara CJ, Weigel AV, Li D, Legant WR, Xu CS, Pasolli HA, Harvey K, Hess HF, Betzig E, Blackstone C, Lippincott-Schwartz J. Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER. Science. 2016 Oct 28;354(6311).

Amanda Watts
de Keijser et al. "Differential reporting of mixed DNA profiles and its impact on jurists' evaluation of evidence. An international analysis". Forensic Sci Int Genet, 2016.

Gill P. "Analysis and implications of the miscarriages of justice of Amanda Knox and Raffaele Sollecito." Forensic Sci Int Genet, 2016

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Katherine Xue
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Sonia Ting:
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Anna Brosius
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Michael Duyzend
Alsford, S. et al. (2012). High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature, 482: 232-236.

5/1/12 -

Max Libbrecht
Heterozygote advantage as a natural consequence of adaptation in diploids
Diamantis Sellis, Benjamin J. Callahan, Dmitri A. Petrov, and Philipp W. Messera

Matthew Snyder
Zhang, L., Hou, D., Chen, X., Li, D. et al. (2012).  Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA.  Cell Research 22: 107-126.  doi:10.1038/cr.2011.158

4/24/12 -

Max Press
Pocock et al. ( 2012).  The Robustness and Restoration of a Network of Ecological Networks. Science 335: 973-977

4/17/12 -

Matt Maurano
Djuranovic S, Nahvi A, Green R. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science. 2012 Apr 13;336(6078):237-40.

Bazzini AA, Lee MT, Giraldez AJ. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science. 2012 Apr 13;336(6078):233-7. Epub 2012 Mar 15.

Akash Kumar
Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Elizabeth A Manrao, Ian M Derrington, Andrew H Laszlo, Kyle W Langford, Matthew K Hopper, Nathaniel Gillgren, Mikhail Pavlenok, Michael Niederweis & Jens H Gundlach. Nature Biotechnology 30,349–353 (2012). Published online: 25 March 2012 | doi:10.1038/nbt.2171

4/10/12 -

Sharon Greenblum
Morran, L. T., Schmidt, O. G., Gelarden, I. A., Parrish, R. C., & Lively, C. M. (2011). Running with the Red Queen: host-parasite coevolution selects for biparental sex. Science, 333(6039), 216-8.

Morris, J. J., Lenski, R. E., & Zinser, E. R. (2012). The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss. mBio, 3(2).

Blake Hovde
Evolution of increased complexity in a molecular machine. Finnigan GC, Hanson-Smith V, Stevens TH, Thornton JW.
Nature. 2012 Jan 9;481(7381):360-4.

4/3/12 -

Katrina Claw
Jiang P et al. (2012) Major taste loss in carnivorous mammals. PNAS Early Edition.

William Edelman
Xu, X., Coats, J. K., Yang, C. F., Wang, A., Ahmed, O. M., Alvarado, M., Izumi, T., et al. (2012). Modular Genetic Control of Sexually Dimorphic Behaviors. Cell, 148(3), 596–607. Elsevier Inc. doi:10.1016/j.cell.2011.12.018

3/27/12 -

Jacob Kitzman
Garrett and Rosenthal. (2012). RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses,Science 335, 848-851.

Alessandra Sullivan
Immobilization of Proteins in the Nucleolus by Ribosomal Intergenic Spacer Noncoding RNA. Timothy E. Audas, Mathieu D. Jacob, Stephen Lee. Molecular Cell - 27 January 2012 (Vol. 45, Issue 2, pp. 147-157)

3/6/12 -

Keolu Fox
A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes. MacArthur, D. Science, 17 February 2012

Joe Hiatt
A logic-gated nanorobot for targeted transport of molecular payloads. Douglas SM, Bachelet I, Church GM. Science. 2012 Feb 17;335(6070):831-4.

2/28/12 -

Alejandro Wolf-Yadlin
The mTOR-Regulated Phosphoproteome Reveals a Mechanism of mTORC1-Mediated Inhibition of Growth Factor Signaling. Peggy P. Hsu, et al. Science 10 June 2011: Vol. 332 no. 6035 pp. 1317-1322. DOI: 10.1126/science.1199498

Xander Nuttle
The Majority of Animal Genes Are Required for Wild-Type Fitness. Arun K. Ramani, et al. Cell, Volume 148, Issue 4, 792-802, 17 February 2012

2/21/12 -

Anna Brosius
Predicting mutation outcome from early stochastic variation in genetic interaction partners, Burga et al., Nature, 2011

Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans, Casanueva et al., Science, 2012

Nik Krumm
Detecting Novel Associations in Large Data Sets. David N. Reshef, et al.
Science 16 December 2011: 1518-1524.

2/14/12 -

Leslie Kim
Wongsrikeao P et al. (2011) Antiviral restriction factor transgenesis in the domestic cat. Nature Methods 8, 853-9.

Benjamin Vernot
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Li Ding, et al. Nature (2012) doi:10.1038/nature10738

2/7/12 -

Tzitziki Lemus-Vergara
Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling. Seung Chul Shin, Sung-Hee Kim, Hyejin You, Boram Kim, Aeri C. Kim, et al. Science 4  2011:334  (6056), 670-674.

Aaron Miller
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Rachel Mackelprang, Mark P. Waldrop, Kristen M. DeAngelis, Maude M. David, Krystle L. Chavarria, Steven J. Blazewicz, Edward M. Rubin & Janet K. Jansson. Nature 480, 368–371 (15 December 2011). doi:10.1038/nature10576

1/31/12 -

Ben Whiddon
Daily JL et al. (2011) Adeno-Associated Virus-Mediated Rescue of the Cognitive Defects in a Mouse Model for Angelman Syndrome. PLoS ONE 6
(12): e27221. doi:10.1371/journal.pone.0027221

Huang H, Allen JA et al. (2011) Topoisomerase inhibitors unsilence the dormant allele of Ube3a in neurons. Nature advance online publication. doi:10.1038/nature10726

Caitlin Connelly
Meyer JR, Dobias DT, Weitz JS, Barrick JE, Quick RT, Lenski RE (2012) Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda. Science 35:428-432. doi:10.1126/science.1214449

1/24/12 -

Josh Burton
van Bakel H et al (2011). "The draft genome and transcriptome of Cannabis sativa". Genome Biology 12:R102.

Peter Sudmant
Lewis JE, DeGusta D, Meyer MR, Monge JM, Mann AE, et al. (2011) The Mismeasure of Science: Stephen Jay Gould versus Samuel George Morton on Skulls and Bias. PLoS Biol 9(6): e1001071. doi:10.1371/journal.pbio.1001071

1/17/12 -

Matt Rich
Kim, EB, et al. (2011) Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 479, 223-227

1/10/12 -

Tanya Grancharova
Kane et al. (2011) Successful Transmission of a Retrovirus Depends on the Commensal Microbiota. Science 334: 245-249. 

Kuss et al. (2011) Intestinal Microbiota Promote Enteric Virus Replication and Systemic Pathogenesis. Science 334: 249-252. 

Rachel Diederich
Rand DG, Arbesman S, Christakis NA (2011) Dynamic social networks promote cooperation in experiments with humans. Proc. Natl. Acad. Sci. 108:19193-19198

1/3/12 -

Keisha Carlson
Weinhold, A and Baldwin, I.T. (2011) Trichome-derived O-acyl sugars are a first meal for caterpillars that tags them for predation. PNAS 108:7855-7859.

Gilardoni, PA et al. (2011) Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory. The Plant Cell. 23:3512-3532.

Jennifer McCreight
Ghaderi, D et al. (2011) Sexual selection by female immunity against paternal antigens can fix loss of function alleles. PNAS 108:17743-17748.

12/6/11 -

Chad Weisbrod
Avian-Type Receptor-Binding Ability Can Increase Influenza Virus Pathogenicity in Macaques. Tokiko Watanabe et. al. J. Virol. 2011, 85(24) Published Ahead of Print September 2011.

11/29/11 -

Stan Fields:
Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes.
del Alamo M, Hogan DJ, Pechmann S, Albanese V, Brown PO, Frydman J.
PLoS Biol. 2011 Jul;9(7):e1001100. Epub 2011 Jul 12.

Ray Monnat:
Sarkies P, Murat P, Phillips LG, Patel KJ, Balasubramanian S, Sale
JE.(2011) FANCJ coordinates two pathways that maintain epigenetic stability at G-quadruplex DNA. Nucleic Acids Res. 2011 Oct 22. [Epub ahead of print] doi:10.1093/nar/gkr868

11/22/11 -

Jeff Vierstra
Synergic reprogramming of mammalian cells by combined exposure to mitotic Xenopus egg extracts and transcription factors. PNAS 2011 108 (42) 17331-17336

11/15/11 -

Leslie Emery
Variants of the protein PRDM9 differentially regulate a set of human meiotic recombination hotspots highly active in African populations. Ingrid L. Berg, Rita Neumann, Shriparna Sarbajna, Linda Odenthal-Hesse, Nicola J. Butler, and Alec J. Jeffreys. PNAS. 2011. 108:30 (12378-12383). 

Adam Gordon
Bos KI, Schuenemann VJ, Golding GB, Burbano HA et al. A draft genome of Yersinia pests from victims of the Black Death. Nature 478, 506–510 (27 October 2011)

11/8/11 -

Melody Palmer
Daniel R. G. Price, Rebecca P. Duncan, Shuji Shigenobu, and Alex C. C. Wilson. Genome Expansion and Differential Expression of Amino Acid Transporters at the Aphid/Buchnera Symbiotic Interface
Mol. Biol. Evol. 2011 : msr140v2-msr140.

Andrew Stergachis
Lin, C., Smith, E. R., Takahashi, H., Lai, K. C., Martin-Brown, S., Florens, L., Washburn, M. P., et al. (2010). AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Molecular Cell, 37(3), 429-37.

10/25/11 -

Jarrett Egertson
Correction of Sickle Cell Disease in Adult Mice by Interference with Fetal Hemoglobin Silencing. Jian Xu, Cong Peng, Vijay G. Sankaran, Zhen Shao, Erica B. Esrick, Bryan G. Chong, Gregory C. Ippolito, Yuko Fujiwara, Benjamin L. Ebert, Philip W. Tucker,
and Stuart H. Orkin. Science 13 October 2011: 1211053 Published online 13 October 2011 [DOI:10.1126/science.1211053]

Sam Lancaster
Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Diego Libkinda, Chris Todd Hittingerb, Elisabete Valériod, Carla Gonçalvesd, Jim Doverb, Mark Johnstonb, Paula Gonçalvesd, and José Paulo Sampaiod. PNAS.

10/11/11 -

Bill Noble:

A Modern History Theory of Functions
Peter Godfrey-Smith
Noûs
Vol. 28, No. 3 (Sep., 1994), pp. 344-362

Jennifer Andrie:

Reed RD, Papa R, Martin A, Hines HM, Counterman BA, Pardo-Diaz C, Jiggins CD, Chamberlain NL, Kronforst MR, Chen R, Halder G, Nijhout HF, McMillan WO (2011) optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry. Science 333(6046):1137-1141. doi: 10.1126/science.1208227

10/4/11 -

Mary-Claire King:

Hitchins MP, Rapkins RW, Kwok CT, Srivastava S, Wong JJ, Khachigian LM, Polly P, Goldblatt J, Ward RL. Dominantly Inherited Constitutional Epigenetic Silencing of MLH1 in a Cancer-Affected Family Is Linked to a Single Nucleotide Variant within the 5'UTR. Cancer Cell. 2011 Aug 16;20(2):200-13. PubMed PMID: 21840485

5/31/11 -

Jennifer Wagner

Mariela Jaskelioff, Florian L. Muller, Ji-Hye Paik, Emily Thomas, Shan Jiang, Andrew C. Adams, Ergun Sahin, Maria Kost-Alimova, Alexei Protopopov, Juan Cadiñanos, James W. Horner, Eleftheria Maratos-Flier & Ronald A. DePinho. 2011. Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice. Nature, 469: 102–106. doi:10.1038/nature09603

Ergün Sahin, Simona Colla, Marc Liesa, Javid Moslehi, Florian L. Müller, Mira Guo, Marcus Cooper, Darrell Kotton, Attila J. Fabian, Carl Walkey, Richard S. Maser, Giovanni Tonon, Friedrich Foerster, Robert Xiong, Y. Alan Wang, Sachet A. Shukla, Mariela Jaskelioff, Eric S. Martin, Timothy P. Heffernan, Alexei Protopopov, Elena Ivanova, John E. Mahoney, Maria Kost-Alimova, Samuel R. Perry, Roderick Bronson, Ronglih Liao, Richard Mulligan, Orian S. Shirihai, Lynda Chin1, & Ronald A. DePinho1. 2011. Telomere dysfunction induces metabolic and mitochondrial compromise. Nature, 470: 359–365. doi:10.1038/nature09787

Benjamin Vernot

Brain Evolution Triggers Increased Diversification of Electric Fishes http://www.sciencemag.org/content/332/6029/583.full

5/24/11 -

Matt Rich

Latty, T. et al. Structure and formation of ant transportation networks. J R Soc Interface (2011)

Tero, A. et al. Rules for biologically inspired adaptive network design. Science 327, 439-442 (2010).

Alexander Nuttle

Second-order selection for evolvability in a large Escherichia coli population. Woods et al. Science 18 March 2011:
Vol. 331 no. 6023 pp. 1433-1436. PMID: 21415350

5/17/11 -

Max Press

Kamura et al. "Pkd1l1 complexes with Pkd2 on motile cilia and functions to establish the left-right axis." Development 138: 1121-1129 (2011)

Field et al. "Pkd1l1 establishes left-right asymmetry and physically interacts with Pkd2."  Development 138: 1131-1142 (2011)

Jeff Staples

Holm, H. et al. (2011). A rare variant in MYH6 is associated with high risk of sick sinus syndrome. Nat. Gen. 43(4):316-20.

5/10/11 -

Tanya Grancharova

Deltcheva E et al. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 471(31): 602-607.

Jennifer McCreight

Atkinson (2011) Phonemic diversity supports a serial founder effect model of language expansion from Africa. Science 332: 346-348.

Dunn et al (2011) Evolved structure of language shows lineage-specific trends in word-order universals. Nature

5/3/11 -

William Edelman

McLean, C. Y. et al. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471, 216-219, doi:10.1038/nature09774 (2011).

Keolu Fox

Ancient Voyaging and Polynesian Origins. Martin B. Richards et al. AJHG vol. 88 issue 2

4/26/11 -

Josh Burton

Edan E, Geva-Zatorsky N, Issaeva I, Cohen A, Dekel E, Danon T, Cohen L, Mayo A, Alon U.  "Proteome Half-Life Dynamics in Living Human Cells."  Science 11 February 2011: Vol. 331 no. 6018 pp. 764-768

Akash Kumar

A Virophage at the Origin of Large DNA Transposons Matthias G. Fischer1 and Curtis A. Suttle1,2,3* Science advance online publication doi: 10.1126/science.1199412 (2011).

4/19/11 -

Joe Felsenstein

Loytynoja, A. and N. Goldman. 2008. A model of evolution and structure for multiple sequence alignment. Philosophical Transactions of the Royal Society. 363: 3913-3919. doi:10.1098/rstb.2008.0170

Nik Krumm

Using induced pluripotent stem cells to investigate cardiac phenotypes in Timothy syndrome
Yazawa et al. Nature 471, 230–234 (10 March 2011)
doi:10.1038/nature09855

Modelling the long QT syndrome with induced pluripotent stem cells
Itzhaki et al. Nature 471, 225–229 (10 March 2011)

4/12/11 -

Leslie Emery

Castro-Prieto A., Wachter, B., & Sommer, S. 2011. Cheetah paradigm revisited: MHC diversity in the world's largest free-ranging population. Mol Biol Evol. 28(4): 1455-1468.

Rupali Patwardhan

Science. 2010 Sep 3;329(5996):1175-80. Spiroindolones, a potent compound class for the treatment of malaria.
Rottmann M, McNamara C, Yeung BK, Lee MC, Zou B, Russell B, Seitz P, Plouffe DM, Dharia NV, Tan J, Cohen SB, Spencer KR, González-Páez GE, Lakshminarayana SB, Goh A, Suwanarusk R, Jegla T, Schmitt EK, Beck HP, Brun R, Nosten F, Renia L, Dartois V, Keller TH, Fidock DA, Winzeler EA, Diagana TT.

4/5/11 -

Colin Manoil

Three-dimensional structure of tropism-switching Bordetella bacteriophage.
Dai W, Hodes A, Hui WH, Gingery M, Miller JF, Zhou ZH.
Proc Natl Acad Sci U S A. 2010 107:4347-52.

Diversity-generating retroelement homing regenerates target sequences for repeated rounds of codon rewriting and protein diversification.
Guo H, Tse LV, Barbalat R, Sivaamnuaiphorn S, Xu M, Doulatov S, Miller JF. Mol Cell. 2008 31:813-23.

M.K. Raghuraman

Stephens, P.J., et al. (2011). Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144,
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Kloosterman, W.P., et al. (2011). Chromothripsis as a mechanism 
driving complex de novo structural rearrangements in the germline. 
Hum Mol Genet. (EPub)

3/29/11 -

Ray Monnat

Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site.
Letessier A, Millot GA, Koundrioukoff S, Lachags AM, Vogt N, Hansen RS, Malfoy B, Brison O, Debatisse M. Nature. 2011 Feb 3;470(7332):120-3. Epub 2011 Jan 23.

Jacob Kitzman

Nature. 2009 Aug 27;460(7259):1127-31. Epub 2009 Aug 5.
L1 retrotransposition in human neural progenitor cells.
Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu Y, Lovci MT, Morell M, O'Shea KS, Moran JV, Gage FH.

and

Nature. 2010 Nov 18;468(7322):443-6.
L1 retrotransposition in neurons is modulated by MeCP2.
Muotri AR, Marchetto MC, Coufal NG, Oefner R, Yeo G, Nakashima K, Gage FH

3/8/11 -

Rose Okamoto

Desjardins JK, Klausner JQ, Fernald RD. Female genomic response to mate information.
Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):21176-80. Epub 2010 Nov 24

Dan Skelly

Culler SJ, Hoff KG, Smolke CD (2010) Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330:1251-1255

 

3/1/11 -

Katrina Claw

Brock DA, Douglas TE, Queller DC, and Strassmann JE (2011) Primitive agriculture in a social amoeba. Nature 469: 393-396.

Sharon Greenblum

G. Sharon, D. Segal, J. M. Ringo, A. Hefetz, I. Zilber-Rosenberg, E. Rosenberg. Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.1009906107

and

Miller WJ, Ehrman L, Schneider D, 2010 Infectious Speciation Revisited: Impact of Symbiont-Depletion on Female Fitness and Mating Behavior of Drosophila paulistorum. PLoS Pathog 6(12): e1001214. doi:10.1371/journal.ppat.1001214

2/22/11 -

Alessandra Oddone

Circadian clocks in human red blood cells. Nature. 2011 Jan 27;469(7331):498-503. O'Neill JS, Reddy AB.

Nate Peters

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis. Science 329, 336 (2010). T. Kondo, S. Plaza, J. Zanet, E. Benrabah, P. Valenti, Y. Hashimoto, S. Kobayashi, F. Payre,Y. Kageyama.

2/15/11 - Andrew Stergachis

Andrew Stergachis

Anderson, K. et al. Genetic variegation of clonal architecture and propagating cells in leukaemia. Nature advance online publication (2010).
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09650.html

2/11/11 -

Blake Hovde

"Predicting protein structures with a multiplayer online game."
Cooper S, Khatib F, Treuille A, Barbero J, Lee J, Beenen M, Leaver-Fay A, Baker D, Popović Z, Players F.
Nature. 2010 Aug 5;466(7307):756-60.

Aaron Miller

Gao Q, Jin K, Ying S-H, Zhang Y, Xiao G, et al. 2011 Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic FungiMetarhizium anisopliae and M. acridum. PLoS Genet 7(1): e1001264. doi:10.1371/journal.pgen.1001264

2/8/11 -

Tzitziki Lemus-Vergara

Kalinka AT, Varga KM, Gerrard DT, Preibisch S, Corcoran DL, Jarrells J, Ohler U, Bergman CM, Tomancak P. Gene expression divergence recapitulates the developmental hourglass model. Nature. 2010 Dec 9;468(7325):811-4.

and

Domazet-Lošo T, Tautz D. A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature. 2010 Dec 9;468(7325):815-8.

Joe Hiatt

Nature. 2010 Aug 12;466(7308):835-40.
Mammalian microRNAs predominantly act to decrease target mRNA levels.
Guo H, Ingolia NT, Weissman JS, Bartel DP.

2/1/11 -

Caitlin Connelly

Effect of Direct-to-Consumer Genomewide Profiling to Assess Disease Risk. Bloss CS, Schork NJ, Topol EJ. N Engl J Med. 2011 Jan 12

Willingness-to-pay for predictive tests with no immediate treatment implications: a survey of US residents. Neumann PJ, Cohen JT, Hammitt JK, Concannon TW, Auerbach HR, Fang C, Kent DM. Health Econ. 2010 Dec 28

Renee George

Bellott et al. Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature, Vol. 466, No. 7306. (11 July 2010), pp. 612-616.

1/25/11 -

Anna Brosius

Virus-Plus-Susceptibility Gene Interaction Determines Crohn's Disease Gene Atg16L1 Phenotypes in Intestine, Ken Cadwell, Khushbu K. Patel, Nicole S. Maloney, Ta-Chiang Liu, Aylwin C.Y. Ng, Chad E. Storer, Richard D. Head, Ramnik Xavier, Thaddeus S. Stappenbeck, Herbert W. Virgin, Cell, Volume 141, Issue 7, 1135-1145, 25 June 2010

Evelyn Vincow

Early heart failure in the SMNDelta7 model of spinal muscular atrophy and correction by postnatal scAAV9-SMN delivery (2010). Bevan AK, Hutchinson KR, Foust KD, Braun L, McGovern VL, Schmelzer L, Ward JG, Petruska JC, Lucchesi PA, Burghes AH, Kaspar BK. Hum Mol Genet 19(20):3895-905.

Arrhythmia and cardiac defects are a feature of spinal muscular atrophy model mice (2010). Heier CR, Satta R, Lutz C, DiDonato CJ. Hum Mol Genet 19(20):3906-18.

1/18/11 -

John Stamatoyannopoulos

Carone BR, Fauquier L, Habib N, Shea JM, Hart CE, Li R, Bock C, Li C, Gu H, Zamore PD, Meissner A, Weng Z, Hofmann HA, Friedman N, Rando OJ. Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell. 2010 Dec 23;143(7):1084-96.

Ben Whiddon

EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda.
Shilpi Aggarwal et al. Proc Natl Acad Sci U S A. 2010 November 2; 107 (44):18961-6.

 

1/14/11 -

Melody Rynerson

Sex-Specific Parent-of-Origin Allelic Expression in the Mouse Brain .
Christopher Gregg, Jiangwen Zhang, James E. Butler, David Haig, and Catherine Dulac (6 August 2010) Science 329 (5992), 682.

Andy Itsara

A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. Lowry DB, Willis JH. PLoS Biol. 2010 Sep 28;8(9). pii: e1000500

1/11/11 -

Stan Fields:
Quantitative reactivity profiling predicts functional cysteines in proteomes.
Weerapana E, Wang C, Simon GM, Richter F, Khare S, Dillon MB, Bachovchin DA, Mowen K, Baker D, Cravatt BF.
Nature. 2010 Dec 9;468:790-5.

Ray Malfavon-Borja

Katzourakis A, Gifford RJ, 2010 Endogenous Viral Elements in Animal Genomes. PLoS Genet 6(11): e1001191. doi:10.1371/journal.pgen.1001191

1/4/11 -

Sarah Ng

Molecular basis of infrared detection by snakes. Elena O. Gracheva, Nicholas T. Ingolia, Yvonne M. Kelly, Julio F.Cordero-Morales, Gunther Hollopeter, Alexander T. Chesler, Elda E.
Sánchez, John C. Perez, Jonathan S. Weissman & David Julius. Nature 464, 1006-1011 (15 April 2010)

Chad Weisbrod

Wolfe-Simon, F., Blum, J., Kulp, T., Gordon, G., Hoeft, S., Pett-Ridge, J., Stolz, J., Webb, S., Weber, P., Davies, P., Anbar, A., & Oremland, R. (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus Science DOI: 10.1126/science.1197258

 

12/7/10 -

Willie Swanson

Christakis NA, Fowler JH, 2010 Social Network Sensors for Early Detection of Contagious Outbreaks. PLoS ONE 5(9): e12948.doi:10.1371/journal.pone.0012948

11/30/10 -

Jim Thomas

Mol Biol Evol. 2010 Feb;27(2):225-33. Epub 2009 Sep 30. Retracing evolution of red fluorescence in GFP-like proteins from Faviina corals. Field SF, Matz MV.

Cailyn Spurrell

Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme, Wallace BD, Wang H, Lane KT, Scott JE, Orans J, Koo JS, Venkatesh M, Jobin C, Yeh LA, Mani S, Redinbo MR. Science 5 November 2010: Vol. 330 no. 6005 pp. 831-835

11/16/10 -

Leo Pallanck

Van Ham TJ, et al (2010) Identification of MOAG-4/SERF as a regulator of age-related proteotoxicity. Cell 142: 601.

Matt Maurano

van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Most "dark matter" transcripts are associated with known genes. PLoS Biol. 2010 May 18;8(5):e1000371.

11/9/10 -

Mike MacCoss

DE Lieberman et al., Foot strike patterns and collision forces in habitually barefoot versus shod runners Nature 463, 531-535 (2010) doi:10.1038/nature08723

Sean Schneider

Kirkness, E.F., Haas, B.J., Sun, W., Braig, H.R., Perotti, M.A., Clark, J.M. et al. (2010) Genome sequences of the human body louse and its primary endosymbiont provides insights into the permanent parasitic lifestyle. Proc Natl Acad Sci USA, doi:10.1073/pnas.1003379107

The International Aphid Genomics Consortium 2010 Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol 8(2): e1000313. doi:10.1371/journal.pbio.1000313

11/2/10 -

Bill Noble

Global profiling of proteolysis during rupture of P. falciparum from the host erythrocyte.
Paul W. Bowyer, Gabriel M. Simon, Benjamin F. Cravatt and Matthew Bogyo. Molecular & Cellular Proteomics. 2010.

Celeste Berg

The role of recently derived FT paralogs in sunflower domestication.
Blackman BK, Strasburg JL, Raduski AR, Michaels SD, Rieseberg LH.
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10/26/10 -

Keisha Carlson

"Gut inflammation provides a respiratory electron acceptor for Salmonella." Sebastian E. Winter, Parameth Thiennimitr, Maria G. Winter, Brian P. Butler, Douglas L. Huseby,Robert W. Crawford, Joseph M. Russell, Charles L. Bevins, L. Garry Adams, Renée M. Tsolis, John R. Roth & Andreas J. Bäumler. Nature 467, 426-429 (23 September 2010).

Rachel Diederich

"Long- and short-term selective forces on malaria parasite genomes." Nygaard S, Braunstein A, Malsen G, Van Dongen S, Gardner PP, Krogh A, Otto TD, Pain A, Berriman M, McAuliffe J, Dermitzakis ET, Jeffares DC. PLoS Genet. 6(9): e1001099 (9 September 2010)

10/19/10 -

Mary-Claire King:

Genovese G, Friedman DJ, Ross MD, Lecordier L, Uzureau P, Freedman BI,
Bowden DW, Langefeld CD, Oleksyk TK, Uscinski Knob AL, Bernhardy AJ,
Hicks PJ, Nelson GW, Vanhollebeke B, Winkler CA, Kopp JB, Pays E, Pollak
MR. Association of trypanolytic ApoL1 variants with kidney disease in
African Americans. Science 329: 841-845, 2010. Epub 2010 Jul 15.

Jeff Vierstra:

Rohs et al. The role of DNA shape in protein-DNA recognition. Nature (2009) vol. 461 (7268) pp. 1248-1253

Meijsing et al. DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity. Science (2009) vol. 324 (5925) pp. 407-410

10/12/10 -

Peter Sudmant:

Qian, Wenfeng; Liao, Ben-Yang; Chang, Andrew Ying-Fei; Zhang, Jianzhi, Maintenance of duplicate genes and their functional redundancy by reduced expression Trends in genetics : TIG doi:10.1016/j.tig.2010.07.002 (volume 26 issue 10 pp.425 - 430)

DeLuna A, Springer M, Kirschner MW, Kishony R, 2010 Need-Based Up-Regulation of Protein Levels in Response to Deletion of Their Duplicate Genes. PLoS Biol 8(3): e1000347. doi:10.1371/journal.pbio.1000347

Jarett Egertson:

Taniguchi, Yuichi, Paul J. Choi, Gene-Wei Li, Huiyi Chen, Mohan Babu, Jeremy Hearn, Andrew Emili, and X. S. Xie. "Quantifying E. Coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells." Science 329 (2010): 533-37

Laurent, Jon, et. al. "Protein Abundances Are More Conserved than mRNA Abundances across Diverse Taxa." Proteomics (2010). (Accepted for Publication)

10/5/10 -

Cait Rippey:

"The Right to Ignore Genetic Status of Late Onset Genetic Disease in the Genomic Era"
A. Erez, K. Plunkett, V.R. Sutton, and A.L. McGuire
American Journal of Medical Genetics
2010 Jul 152A(7):1774-80

Alex Nord:

Choate KA, Lu Y, Zhou J, Choi M, Elias PM, Farhi A, Nelson-Williams C, Crumrine D, Williams ML, Nopper AJ, Bree A, Milstone LM, Lifton RP. Mitotic Recombination in Patients with Ichthyosis Causes Reversion of Dominant Mutations in KRT10. Science. 2010 Aug 26. [Epub ahead of print]

6/1/10 -

Rose Okamoto
Williams, A.H., G. Valdez, V. Moresi, X. Qi, J. McAnally, J.L. Elliot, R. Bassel-Duby, J.R. Sanes, and E.N. Olson. 2009 MicroRNA-206 Delays ALS Progression and Promotes Regeneration of Neuromuscular Synapses in Mice. Science 326: 1549-1554.

Jeff Vierstra
Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells.
Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC.
Science. 2010 May 14;328(5980):872-5. Epub 2010 Apr 22.

Small RNA duplexes function as mobile silencing signals between plant cells.
Dunoyer P, Schott G, Himber C, Meyer D, Takeda A, Carrington JC, Voinnet O.
Science. 2010 May 14;328(5980):912-6. Epub 2010 Apr 22.

5/25/10 -

Aaron Miller
A Draft Sequence of the Neanderthal Genome. Richard E. Green, et al. Science 328, 710 (2010);

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture. Hernán A. Burbano, et al. Science 328, 723 (2010);

Alessandra Oddone
Therapeutic silencing of miR-10b inhibits metastasis in a mouse mammary tumor model. Li Ma, Ferenc Reinhardt, Elizabeth Pan, Jürgen Soutschek, Balkrishen Bhat, Eric G Marcusson, Julie Teruya-Feldstein, George W Bell, Robert A Weinberg
Nature Biotechnology 28, 341-347 (28 March 2010) doi:10.1038/nbt.1618 Research

5/18/10 -

Blake Hovde
Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat. Seluanov A, Hine C, Azpurua J, Feigenson M, Bozzella M, Mao Z, Catania KC, Gorbunova V. Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19352-7. Epub 2009 Oct 26.

Tzitziki Lemus Vergara
Zhao D, McBride D, Nandi S, McQueen HA, McGrew MJ, Hocking PM, Lewis PD, Sang HM, Clinton M: Somatic sex identity is cell autonomous in the chicken. Nature, 464(7286):237-242.

5/11/10 -

Adam Gordon
Selective loss of polymorphic mating types is associated with rapid phenotypic evolution during morphic speciation.
Corl A, Davis AR, Kuchta SR, and Sinervo B. PNAS. 2010 March 2.

Sharon Greenblum
Hehemann, J.-H. et al.Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota.  Nature 464, 908-912 (2010).

5/4/10 -

Caitlin Connelly
De Grassi A, Segala C, Iannelli F, Volorio S, Bertario L, et al. (2010) Ultradeep Sequencing of a Human Ultraconserved Region Reveals Somatic and Constitutional Genomic Instability. PLoS Biol 8(1): e1000275. doi:10.1371/journal.pbio.1000275

Rachel Diederich
Horie, M. et al. Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 463, 84-7

4/27/10 -

Andrew Stergachis
Metabolic syndrome and altered gut microbiota in mice lacking toll-like receptor 5.
Vijay-Kumar, M., J. D. Aitken, F. A. Carvalho, T. C. Cullender, S. Mwangi, S. Srinivasan, S. V. Sitaraman, R. Knight, R. E. Ley, and A. T. Gewirtz. Science. 2010 Mar 4. [Epub ahead of print]

Chad Weisbrod
Full Dynamic Range ProteomeAnalysis of S. cerevisiaeby Targeted Proteomics Paola Picotti,1 Bernd Bodenmiller,1 Lukas N. Mueller,1 Bruno Domon,1 and Ruedi Aebersold Cell 138, 795–806, August 21, 2009

4/20/10 -

Anna Brosius
Inferring tumor progression from genomic heterogeneity.
Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J, Wigler M. Genome Resesarch, 2010

Joe Hiatt
PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice.
Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, Przeworski M, Coop G, de Massy B.
Science. 2009 Dec 31. [Epub ahead of print]

Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination. Myers S, Bowden R, Tumian A, Bontrop RE, Freeman C, Macfie TS, McVean G, Donnelly P. Science. 2009 Dec 31. [Epub ahead of print]

Prdm9 Controls Activation of Mammalian Recombination Hotspots. Parvanov ED, Petkov PM, Paigen K. Science. 2009 Dec 31. [Epub ahead of print]

4/13/10 -

Matt Maurano
Sharma SV, Lee DY, Li B, Quinlan MP, Takahashi F, Maheswaran S, McDermott U, Azizian N, Zou L, Fischbach MA, Wong KK, Brandstetter K, Wittner B, Ramaswamy S, Classon M, Settleman J. A Chromatin-Mediated
Reversible Drug-Tolerant State in Cancer Cell Subpopulations. Cell. 2010 Apr 2;141(1):69-80

Jarrett Egertson
Odorant reception in the malaria mosquito Anopheles gambiae. Allison F. Carey, Guirong Wang, Chih-Ying Su, Laurence J. Zwiebel, and John R. Carlson. Nature 464 March 2010: 66-71

4/6/10 -

Ben Whiddon
"An NGF-responsive element targets myo-inositol monophosphatase-1 mRNA to sympathetic neuron axons." Andreassi C, Zimmermann C, Mitter R, Fusco S, Devita S, Saiardi A, Riccio A. Nat Neurosci. 2010 Mar;13
(3):291-301. Epub 2010 Jan 31

Jacob Kitzman -
Regulation of Alternative Splicing by Histone Modifications
Reini F. Luco, Qun Pan, Kaoru Tominaga, Benjamin J. Blencowe, Olivia M. Pereira-Smith, and Tom Misteli. Science 19 February 2010: 996-1000.

3/30/10 -

Leslie Emery
Ecological adaptation determines functional mammalian olfactory subgenomes.  Sara Hayden, Michael Bekaert, Tess A. Crider, Stefano Mariani, William J. Murphy, and Emma C. Teeling.  Genome Res. 2010 20: 1-9 originally published online December 1, 2009.

Keisha Carlson
"H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis." S. Vinod Kumar and Philip A. Wigge. Cell 140: 136-147, January 8, 2010.

3/9/10 -

Ryan Emerson
Ancestry and Pathology in King Tutankhamun's Family.
Zahi Hawass, PhD; Yehia Z. Gad, MD; Somaia Ismail, PhD; Rabab Khairat, MSc; Dina Fathalla, MSc; Naglaa Hasan, MSc; Amal Ahmed, BPharm; Hisham Elleithy, MA; Markus Ball, MSc; Fawzi Gaballah, PhD; Sally Wasef, MSc; Mohamed Fateen, MD; Hany Amer, PhD; Paul Gostner, MD; Ashraf Selim, MD; Albert Zink, PhD; Carsten M. Pusch, PhD. JAMA. 2010;303(7):638-647.

James Thompson
"Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli." Blount ZD, Borland CZ, Lenski RE. Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):7899-906. Epub 2008 Jun 4. http://www.pnas.org/content/105/23/7899.long

"Genome evolution and adaptation in a long-term experiment with Escherichia coli." Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF. Nature. 2009 Oct 29;461(7268):1243-7. Epub 2009 Oct 18. http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html

3/2/10 -

Katrina Claw
Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer. Yingguang Frank Chan, Melissa E. Marks, Felicity C. Jones, Guadalupe Villarreal, Jr., Michael D. Shapiro, Shannon D. Brady, Audrey M. Southwick, Devin M. Absher, Jane Grimwood, Jeremy Schmutz, Richard M. Myers, Dmitri Petrov, Bjarni Jónsson, Dolph Schluter, Michael A. Bell, and David M. Kingsley (10 December 2009)
Science [DOI: 10.1126/science.1182213]

Stepwise Modification of a Modular Enhancer Underlies Adaptation in a Drosophila Population
Mark Rebeiz, John E. Pool, Victoria A. Kassner, Charles F. Aquadro, and Sean B. Carroll (18 December 2009)
Science 326 (5960), 1663. [DOI: 10.1126/science.1178357]

Peter Sudmant
Olga Fehér, Haibin Wang, Sigal Saar, Partha P. Mitra & Ofer Tchernichovski. De novo establishment of wild-type song culture in the zebra finch. Nature 459, 564-568 (28 May 2009) | doi:10.1038/nature07994; Published online 3 May 2009

2/23/10 -

Dan Skelly
Raj A, Rifkin SA, Andersen E, van Oudenaarden A (2010) Variability in gene expression underlies incomplete penetrance. Nature 463:913-918

Cailyn Spurrell
George L. Sen, Jason A. Reuter, Daniel E. Webster, Lilly Zhu & Paul A. Khavari, DNMT1 maintains progenitor function in self-renewing somatic tissue. Nature 463, 563-567 (28 January 2010)

2/16/10 -

Colin Manoil
Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5883-8. Epub 2009 Mar 17.
Evolution of virulence in epidemic community-associated methicillin-resistant Staphylococcus aureus. Li M, Diep BA, Villaruz AE, Braughton KR, Jiang X, DeLeo FR, Chambers HF, Lu Y, Otto M.

M. K. Raghuraman
K. Si, Y. Choi, E. White-Grindley, A. Majumdar, and E. Kandel.
2010. Aplysia CPEB Can Form Prion-like Multimers in Sensory Neurons
that Contribute to Long-Term Facilitation. Cell 140: 421-435.

2/9/10 -

Joe Felsenstein
Christiansen, F. B. and O. Frydenberg. 1977. Selection-mutation balance for two nonallelic recessives producing an inferior double homozygote. American Journal of Human Genetics 29(2): 195-207.

and

Walsh, J. B. 1995. How often do duplicated genes evolve new functions? Genetics 139: 421-428.

Oliver Serang
"Solving a Hamiltonian Path Problem with a bacterial computer." Jordan Baumgardner, Karen Acker, Oyinade Adefuye, Samuel Thomas Crowley, Will DeLoache, James O Dickson, Lane Heard, Andrew T Martens, Nickolaus Morton, Michelle Ritter, Amber Shoecraft, Jessica Treece, Matthew Unzicker, Amanda Valencia, Mike Waters, a. Malcolm Campbell, Laurie J. Heyer, Jeffrey L. Poet, Todd T. Eckdahl. Journal of Biological Engineering (2009)

2/2/10 -

Sean Schneider
Origins and evolution of a transmissible cancer. Rebbeck CA, Thomas R, Breen M, Leroi AM, Burt A. Evolution 2009 Sep 63(9):2340-9

Andy Itsara
d'Erfurth I, Jolivet S, Froger N, Catrice O, Novatchkova M, et al. (2009) Turning Meiosis into Mitosis. PLoS Biol 7(6): e1000124. doi:10.1371/journal.pbio.1000124

1/26/10 -

Alex Nord
Large, rare chromosomal deletions associated with severe early-onset obesity. Bochukova EG, Huang N, Keogh J, Henning E, Purmann C, Blaszczyk K, Saeed S, Hamilton-Shield J, Clayton-Smith J, O'Rahilly S, Hurles ME, Farooqi IS. Nature. 2009 Dec 6. [Epub ahead of print]

Evelyn Vincow
Novel repression of Kcc2 transcription by REST-RE-1 controls developmental switch in neuronal chloride. Yeo M, Berglund K, Augustine G, Liedtke W. J Neurosci. 2009 Nov 18;29(46):14652-62.

1/19/10 -

Maitreya Dunham

Kevin Roach

1/12/10 -

John Stamatoyannopoulos
"2009: The Year in Epigenetics"

Alan Rubin
Heger P, Marin B, Schierenberg E. (2009) Loss of the insulator protein CTCF during nematode evolution. BMC Mol Biol, 10: 84.

1/5/10 -

Rupali Patwardhan
Somatic Sex Reprogramming of Adult Ovaries to Testes by FOXL2 Ablation. Uhlenhaut et. al, Cell, Volume 139, Issue 6, 1130-1142, 11 December 2009

Renee George
Peterson BK, Hare EE, Iyer VN, Storage S, Conner L, et al. (2009) Big Genomes Facilitate the Comparative Identification of Regulatory Elements. PLoS ONE 4(3): e4688. doi:10.1371/journal.pone.0004688

12/8/09 -

Phil Green
Lister R et al. Human DNA methylomes at base resolution show widespread epigenomic differences, Nature 462, 315-322 (Nov 19, 2009).

Willie Swanson
Evolution 63-10: 2487–2490
Adaptionism - 30 Years After Gould and Lewontin
Rasmus Nielsen

Nature 462, 213-217 (12 November 2009) | doi:10.1038/nature08549 Human-specific transcriptional regulation of CNS development genes by FOXP2
Genevieve Konopka, Jamee M. Bomar, Kellen Winden, Giovanni Coppola, Zophonias O. Jonsson, Fuying Gao, Sophia Peng, Todd M. Preuss, James A. Wohlschlegel & Daniel H. Geschwind

12/1/09 -

Ray Monnat
Hanna J, Saha K, Pando B, van Zon J, Lengner CJ, Creyghton MP, van Oudenaarden A, Jaenisch R. (2009) Direct cell reprogramming is a stochastic process amenable to acceleration. Nature. 2009 Nov 8. [Epub
ahead of print].

Stan Fields
Systems-level dynamic analyses of fate change in murine embryonic stem cells.
Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, Macarthur BD, Lachmann A, Rozov R, Ma'ayan A, Boyer LA, Troyanskaya OG, Whetton AD, Lemischka IR. Nature. 2009 462:358-362.

11/24/09 -

Sara Di Rienzi
Antoine Martin, Christelle Troadec, Adnane Boualem, Mazen Rajab, Ronan Fernandez, Halima Morin, Michel Pitrat, Catherine Dogimont, Abdelhafid Bendahmane. A transposon-induced epigenetic change leads to sex determination in melon. 2009. Nature vol. 461 (7267) pp. 1135-8

Melody Rynerson
Chaperonin overexpression promotes genetic variation and enzyme evolution
Nobuhiko Tokuriki, Dan S. Tawfik
Nature 459, 668-673 (4 June 2009) doi:10.1038/nature08009

11/17/09 -

Leo Pallanck
Edgar D, Shabalina I, Camara Y, Wredenberg A, Calvaruso MA, Nijtmans L, Nedergaard J, Cannon
B, Larsson NG, Trifunovic A. (2009) Random point mutations with major effects on protein-coding genes are the driving force behind premature aging in mtDNA mutator mice. Cell Metab 10(2):131-8.

Kyle Siebenthall
Mets, DG and Meyer BJ. 2009. Condensins Regulate Meiotic DNA Break Distribution, thus Crossover Frequency, by Controlling Chromosome Structure. Cell 139, 73-86.

11/10/09 -

Cait Rippey
Nature. 2009 Oct 15;461(7266):947-55. Asymmetric centrosome inheritance maintains neural progenitors in the neocortex. Wang X, Tsai JW, Imai JH, Lian WN, Vallee RB, Shi SH.

Sayer Herin
Predicting new molecular targets for known drugs
Michael J. Keiser, Vincent Setola, John J. Irwin, Christian Laggner, Atheir I. Abbas, Sandra J. Hufeisen, Niels H. Jensen, Michael B. Kuijer, Roberto C. Matos, Thuy B. Tran, Ryan Whaley, Richard A. Glennon, Jerome Hert, Kelan L. H. Thomas, Douglas D. Edwards, Brian K. Shoichet & Bryan L. Roth doi:10.1038/nature08506

11/3/09 -

Celeste Berg -

Genotype Analysis Identifies the Cause of the "Royal Disease"
Rogaev EI, Grigorenko AP, Faskhutdinova G, Kittler EL, Moliaka YK.
Science. 2009 Oct 8. [Epub ahead of print]DOI: 10.1126/science.1180660

Nick Coley -

Gene Therapy for Dopamine Replacement in Parkinson´s Disease. Anders Björklund, Tomas Björklund, Deniz Kirik. Science Translational Medicine. 14 October 2009 Vol 1 Issue 2

Dopamine Gene Therapy for Parkinson's Disease in a Nonhuman Primate Without Associated Dyskinesia. Béchir Jarraya, et al. Sci Transl Med 1, 2ra4 (2009)

10/27/09 -

Ray Malfavon-Borja -

Sasaki E, Suemizu H, Shimada A, Hanazawa K, Oiwa R, Kamioka M, Tomioka I, Sotomaru Y, Hirakawa R, Eto T, Shiozawa S, Maeda T, Ito M, Ito R, Kito C, Yagihashi C, Kawai K, Miyoshi H, Tanioka Y, Tamaoki N, Habu S, Okano H, Nomura T. Generation of transgenic non-human primates with germline transmission. Nature. 2009 May 28;459(7246):523-7.

Sarah Ng -

Architecture and secondary structure of an entire HIV-1 RNA genome. Watts JM, Dang KK, Gorelick RJ, Leonard CW, Bess JW Jr, Swanstrom R, Burch CL, Weeks KM. Nature. 2009 Aug 6;460(7256):711-6.

10/20/09 -

Lisa Beutler

Tumours with PI3K activation are resistant to dietary restriction.
Kalaany NY, Sabatini DM. Nature. 2009 Apr 9;458(7239):725-31. Epub 2009 Mar 11.

10/13/09 -

Bonny Brewer

Coat variation in the domestic dog is governed by variants in three genes.
Cadieu E, Neff MW, Quignon P, Walsh K, Chase K, Parker HG, Vonholdt BM, Rhue A, Boyko A, Byers A, Wong A, Mosher DS, Elkahloun AG, Spady TC, André C, Lark KG, Cargill M, Bustamante CD, Wayne RK, Ostrander EA.Science. 2009 Oct 2;326(5949):150-3. Epub 2009 Aug 27.

An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs.
Parker HG, VonHoldt BM, Quignon P, Margulies EH, Shao S, Mosher DS, Spady TC, Elkahloun A, Cargill M, Jones PG, Maslen CL, Acland GM, Sutter NB, Kuroki K, Bustamante CD, Wayne RK, Ostrander EA.
Science. 2009 Aug 21;325(5943):995-8. Epub 2009 Jul 16.

10/6/09 -

Mary-Claire King

Tuupanen S et al. The common colorectal cancer predisposition SNP
rs6983267 at chromosome 8q24 confers potential to enhanced Wnt
signaling. Nature Genetics 41:885-890, 2009. Epub Jun 28, 2009

Pomerantz MM et al. The 8q24 cancer risk variant rs6983267 shows
long-range interaction with MYC in colorectal cancer. Nature Genetics
41:882-884, 2009. Epub Jun 28, 2009

6/2/09 -

Sean Schneider
Fernandez AA, Morris MR. Mate choice for more melanin as a mechanism to maintain a functional oncogene. Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13503-7.

Peter Sudmant
Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis
Haifeng Shao, Lindsay C. Burrage, David S. Sinasac, Annie E. Hill, Sheila R. Ernest, William O'Brien, Hayden-William Courtland, Karl J. Jepsen, Andrew Kirby, E. J. Kulbokas, Mark J. Daly, Karl W. Broman, Eric S. Lander, and Joseph H. Nadeaua. PNAS December 16, 2008 vol. 105 no. 50 19910-19914

5/29/09 -

Graham McVicker
Lincoln, TA, Joyce, GF. Self-Sustained Replication of an RNA Enzyme. Science. 2009. Epub Jan 8

Max Robinson
Differential chromatin marking of introns and expressed exons by H3K36me3. P. Kolasinska-Zweirz, T. Down, I. Latorre, T. Liu, X S Liu, and J. Ahringer, Nature Genetics 41(3):376-81. (March 2009)

5/26/09 -

Matt Maurano
Solovei I, Kreysing M, Lanctôt C, Kösem S, Peichl L, Cremer T, Guck J, Joffe B. Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell. 2009 Apr 17;137(2):356-68.

Melody Rynerson
Cristina Grande & Nipam H. Patel. 2009. Nodal signalling is involved in left–right asymmetry in snails. Nature 457, 1007-1011

5/19/09 -

Leslie Emery
Brown DM, Brenneman RA, Koepfli KP, Pollinger JP, Mila B, Georgiadis NJ, Louis Jr EE, Grether GF, Jacobs DK, Wayne RK. 2007. Extensive population genetic structure in the giraffe. BMC Biology. 5:57.

Jacob Kitzman
Nature. 2009 Feb 5;457(7230):736-40. Epub 2008 Dec 14. Messenger RNA targeting to endoplasmic reticulum stress signalling sites. Aragón T, van Anken E, Pincus D, Serafimova IM, Korennykh AV, Rubio CA, Walter P.

5/12/09 -

Katrina Claw
Bézier A, Annaheim M, Herbinière J, Wetterwald C, Gyapay G, Bernard-Samain S, Wincker P, Roditin I,Heller M,Belghazi M, Pfister-Wilhem R, Periquet G, Dupuy C,Huguet E,Volkoff A, Lanzrein B, Drezen J. 2009. Polydnaviruses of Braconid Wasps Derive from an Ancestral Nudivirus. Science Vol. 323: 926-930.

Jarrett Egertson
Grzegorz Kudla, et. al. Coding-Sequence Determinants of Gene Expression in Escherichia coli. Science 324, 255(2009; DOI: 10.1126/science.1170160.

5/5/09 -

Ben Whiddon
Nicholas T. Ingolia, Sina Ghaemmaghami, John R. S. Newman, Jonathan S. Weissman. 10 April 2009 Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling. Science 324: 218-223.

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types
Cell, Volume 135, Issue 4, 14 November 2008, Pages 738-748.

Keisha Carlson
Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, and Bayley H. 2009. Continuous base identification for single-molecule nanopore DNA sequencing . Nat Nanotechnol. 4(4):265-70. Epub 2009 Feb.

4/28/09 -

Ryan Emerson
Snowdrift game dynamics and facultative cheating in yeast. Jeff Gore, Hyun Youk & Alexander van Oudenaarden. Nature advance online publication 6 April 2009 | doi:10.1038/nature07921

Sayer Herin
Mary E. Rumpho, Jared M. Worful, Jungho Lee, Krishna Kannan, Mary S. Tyler, Debashish Bhattacharya, Ahmed Moustafa, and James R. Manhart. Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. PNAS November 18, 2008 vol.105 no.46 17867-17871

4/21/09 -

Oliver Serang
Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. Wu Y, Bhat PR, Close TJ, Lonardi S. PLoS Genet 2008 Oct 4(10):e1000212.

Alan Rubin
Freckleton G, Lippman SI, Broach JR, Tavazoie S, 2009 Microarray Profiling of Phage-Display Selections for Rapid Mapping of Transcription Factor–DNA Interactions. PLoS Genet 5(4): e1000449.

4/14/09 -

Joe Felsenstein
Nozawa, M., Y. Suzuki, and M. Nei. 2009. Reliabilities of identifying positive selection by the branch-site and site-prediction methods. Proceedings of the National Academy of Sciences, Early Edition 1 April 2009.

Tom Pohl
Jin-Hee Han, Steven A. Kushner, Adelaide P. Yiu, Hwa-Lin (Liz) Hsiang, Thorsten Buch, Ari Waisman, Bruno Bontempi, Rachael L. Neve, Paul W. Frankland, Sheena A. Josselyn (2009). Selective Erasure of a Fear Memory. Science. 323, 1492-1496.

4/7/09 -

John Stamatoyannopoulos
Paynter NP et al. Cardiovascular disease risk prediction with and without knowledge of genetic variation at chromosome 9p21.3. Ann Intern Med. 150:65-72 (2009)

Eckman MH et al. Cost-effectiveness of using pharmacogenetic information in warfarin dosing for patients with nonvalvular atrial fibrillation. Ann Intern Med. 150:73-83 (2009)

Sara Di Rienzi
Mandel MJ, Wollenberg MS, Stabb EV, Visick KL, Ruby EG. A single regulatory gene is sufficient to alter bacterial host range. Nature 458, 215-218 (12 March 2009).

3/31/09 -

Dan Blick
Elhanan Borenstein and David C. Krakauer. An end to endless forms: Epistasis, phenotype distribution bias, and
non-uniform evolution. PLoS Computational Biology, 4(10), 2008.
http://www.stanford.edu/%7Eebo/pub/pnk_borens_pcb.pdf

Kevin Roach
Saleh, M. C. et al. The endocytic pathway mediates cell entry of dsRNA
to induce RNAi silencing. Nature Cell Biol. 8, 793–802 (2006) and

Saleh M.C. et al. Antiviral immunity in Drosophila requires systemic RNA
interference spread. Nature. 2009 Feb 8 (Epub ahead of print).

3/10/09 -

Max Boeck
Massive Horizontal Gene Transfer in Bdelloid Rotifers. Gladyshev EA, Meselson M, Arkhipova IR.
Science. 2008 May 30;320(5880):1210-3.

3/6/09 -

Ray Monnat
Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from
maternal blood. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16266-71.

and

Circulating mutant DNA to assess tumor dynamics.
Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, Thornton K,
Agrawal N, Sokoll L, Szabo SA, Kinzler KW, Vogelstein B, Diaz LA Jr. Nat Med. 2008 Sep;14(9):985-90.

Tom Nicholas
Sequencing the nuclear genome of the extinct woolly mammoth Miller, W. et al. (2008) Nature 456 387-392.

3/3/09 -

Maitreya Dunham
Gross JB, Borowsky R, Tabin CJ (2009) A Novel Role for Mc1r in the Parallel Evolution of Depigmentation in Independent Populations of the Cavefish Astyanax mexicanus. PLoS Genet 5(1): e1000326. doi:10.1371/journal.pgen.1000326

Renee George
Kin discrimination increases with genetic distance in a social amoeba.
Ostrowski EA, Katoh M, Shaulsky G, Queller DC, Strassmann JE.
PLoS Biol. 2008 Nov 25;6(11):e287.

2/24/09 -

Colin Manoil
An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.
Zender L, Xue W, Zuber J, Semighini CP, Krasnitz A, Ma B, Zender P, Kubicka S, Luk JM, Schirmacher P, McCombie WR, Wigler M, Hicks J, Hannon GJ, Powers S, Lowe SW.
Cell. 2008 Nov 28;135(5):852-64.

Sarah Ng
Repeatability of published microarray gene expression analyses. Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, Mangion J, Mehta T, Nitzberg M, Page GP, Petretto E, van Noort V. Nat Genet. 2009 Feb;41(2):149-55. Epub 2008 Jan 28.

2/17/09 -

Kyle Siebenthall
D'Angelo, MA, et al. 2008. Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells. Cell 136(2): 284-295.

Ray Malfavon-Borja
Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon. Anton A. Turanov, Alexey V. Lobanov, Dmitri E. Fomenko, Hilary G. Morrison, Mitchell L. Sogin, Lawrence A. Klobutcher, Dolph L. Hatfield, and Vadim N. Gladyshev. (9 January 2009). Science 323 (5911), 259.

2/10/09 -

Cailyn Spurrell

CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA, Luciano A. Marraffini and Erik J. Sontheimer Science 19 December 2008;322(5909):1843-5

Leslie Kim

Escape from X chromosome inactivation is an intrinsic property of the Jarid1c locus. Li N and Carrel L. PNAS. 2008 Nov 4; 44:17055-60.

2/3/09 -

Stan Fields

The spreading of disorder. Keizer K, Lindenberg S, Steg L. Science. 2008 Dec 12;322:1681-5

Geoff Findlay

1/27/09 -

Celeste Berg
Genetic structure along an elevational gradient in Hawaiian honeycreepers reveals contrasting evolutionary responses to avian malaria. Eggert LS, Terwilliger LA, Woodworth BL, Hart PJ, Palmer D, Fleischer RC. BMC Evol Biol. 2008 Nov 14;8:315.

Rupali Patwardhan
A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia.
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1/13/09 -

Jay Shendure
Eid J et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009 Jan 2;323(5910):133-8. Epub 2008 Nov 20.

Dan Skelly
Roper M, Pepper RE, Brenner MP, Pringle A. 2008. Explosively launched
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1/6/09 -

Jeff Kidd
Keinan A, Mullikin JC, Patterson N, Reich D. Accelerated genetic drift
on chromosome X during the human dispersal out of Africa.
Nat Genet. 2009 Jan;41(1):66-70. Epub 2008 Dec 21.

Hammer MF, Mendez FL, Cox MP, Woerner AE, Wall JD.
Sex-biased evolutionary forces shape genomic patterns of human
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Andy Itsara
Chen BT, Bowers MS, Martin M, Hopf FW, Guillory AM, Carelli RM, Chou JK,
and Bonci A. Cocaine but not natural reward self-administration nor passive cocaine
infusion produces persistent LTP in the VTA. Neuron 59:288-297 (2008).
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12/2/08 -

Phil Green
Bentley DR, et al. "Accurate whole human genome sequencing using reversible terminator chemistry", Nature 456, 53-59 (6 November 2008).

Willie Swanson
Jeremy Ginsberg, Matthew H. Mohebbi, Rajan S. Patel, Lynnette Brammer, Mark S. Smolinski & Larry Brilliant. Detecting influenza epidemics using search engine query data. In press at Nature, or see http://www.google.org/about/flutrends/how.html

11/25/08 -

Leo Pallanck
Narkar VA, Downes M, Yu RT, Embler E, Wang YX, Banayo E, Mihaylova
MM, Nelson MC, Zou Y, Juguilon H, Kang H, Shaw RJ, Evans RM. (2008)
AMPK and PPARdelta agonists are exercise mimetics. Cell 134(3):405-15.

Steve Salipante
The virophage as a unique parasite of the giant mimivirus. La Scola et al.
Nature. 2008 Aug 6

11/18/08 -

Bob Waterston
Marini NJ, Gin J, Ziegle J, Keho KH, Ginzinger D, Gilbert DA, Rine J.
The prevalence of folate-remedial MTHFR enzyme variants in humans.
Proc Natl Acad Sci U S A. 2008 105:8055-60.

Bonny Brewer
"Field Experiments with Transformed Plants Reveal the Sense of Floral Scents"
Danny Kessler, Klaus Gase, and Ian T. Baldwin. Science; August 29, 2008; Vol 321; 1200-1202.

11/4/08 -

Kristen Lewis
Heijmans BT, Tobi EW, Stein AD, Putter H, Blauw GJ, Susser ES, Slagboom PE, Lumey LH.
Persistent epigenetic differences associated with prenatal exposure to famine in humans. PNAS 2008 Nov 4; 105(44):17046-9.

James Thompson
Wilson, M.D., Barbosa-Morais, N.L., Schmidt, D., Conboy, C.M., Vanes, L., Tybulewicz, V.L.J. Fisher, E.M.C., Tavaré, S., and Odom. D.T. (2008) Species-Specific Transcription in Mice Carrying Human Chromosome 21. Science 322: 434-438.

10/28/08 -

Lisa Beutler
Qiao Zhou, Juliana Brown, Andrew Kanarek, Jayaraj Rajagopal, and Douglas A. Melton In vivo reprogramming of adult pancreatic exocrine cells to Beta-cells. Nature 2 Oct 2008

Caitlin Rippey
Frank MC, Everett DL, Fedorenko E, Gibson E.
Number as a cognitive technology: Evidence from Pirahã language and cognition. Cognition. 2008 Sep;108(3):819-24. Epub 2008 Jun 10.

and

Butterworth B, Reeve R, Reynolds F, Lloyd D.
Numerical thought with and without words: Evidence from indigenous Australian children. Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):13179-84. Epub 2008 Aug 29.

10/14/08 -

Bill Noble
Sabine Begall, Jaroslav Červený, Julia Neef, Oldřich Vojtěch, and Hynek Burda. Magnetic alignment in grazing and resting cattle and deer. PNAS September 9, 2008 vol. 105 no. 36 13451-13455.

Alex Nord
Gegear RJ, Casselman A, Waddell S, Reppert SM.
Cryptochrome mediates light-dependent magnetosensitivity in Drosophila. Nature. 2008 Aug 21;454(7207):1014-8. PubMed ID: 18641630

10/7/08 -

Diane Dickel
Am J Hum Genet. 2008 Jul;83(1):77-88. Influence of Friedreich ataxia GAA noncoding repeat expansions on pre-mRNA processing. Baralle M, Pastor T, Bussani E, Pagani F.

Matt Sandel
"Tools for studying the underlying causes of psychiatric illness" Or "One medical students misadventures with neuropsychiatry"

King-Casas B, Sharp C, Lomax-Bream L, Lohrenz T, Fonagy P, Montague PR. "The rupture and repair of cooperation in borderline personality disorder." Science. 2008 Aug 8;321(5890):806-10. PMID: 18687957

This is an associated "News + Views" article: http://www.sciencemag.org/cgi/content/full/321/5890/778

9/30/08 -

Mary-Claire King
Xu B, Roos JL, Levy S, van Rensburg EJ, Gogos JA, Karayiorgou M. Strong association of de novo copy number mutations with sporadic schizophrenia. Nat Genet. 2008 Jul; 40(7): 880-885. epub 30 May 2008

Stefansson H. et al. Large recurrent microdeletions associated with schizophrenia. Nature Advance online publication doi: 10.1038/nature07229 (2008).

The International Schizophrenia Consortium. Rare chromosomal deletions and duplications increase risk of schizophrenia Nature Advance online publication doi: 10.1038/ nature07239 (2008).

Rori Rohlfs
Homer N, Szelinger S, Redman M, Duggan D, Tembe W, et al. (2008) Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays. PLoS Genet 4(8)

6/3/08 -

Dan Skelly
Jaillon O, Bouhouche K, Gout J-F, et al. 2008. Translational control of intron splicing in eukaryotes. Nature 451(7176):359-362

Cailyn Spurrell
Saima Malik, Francis McGlone, Diane Bedrossian, and Alain Dagher, Ghrelin Modulates Brain Activity in Areas that Control Appetitive Behavior, Cell Metabolism, Vol 7, 400-409, 07 May 2008

5/27/08 -

Renee George
Nutritional Control of Reproductive Status in Honeybees via DNA Methylation
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Rupali Patwardhan
Eberle AB, Stalder L, Mathys H, Orozco RZ, Mühlemann O (2008) Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region. PLoS Biol 6(4): e92 doi:10.1371/journal.pbio.0060092

5/20/08 -

Ray Malfavon-Borja
Hirofumi Nariya and Masayori Inouye. MazF, an mRNA Interferase, Mediates Programmed Cell Death during Multicellular Myxococcus Development. Cell. 2008. Jan 11 ;132(1):55-66.

Sarah Ng
Cell-to-Cell Stochastic Variation in Gene Expression is a Complex Genetic Trait. Juliet Ansel, Hélène Bottin, Camilo Rodriguez-Beltran, Christelle Damon, Muniyandi Nagarajan, Steffen Fehrmann, Jean François, Gaël Yvert PLoS Genetics, 4(4):e1000049

5/13/08 -

Alex Nord
Kleinman et al.. Sequence- and target-independent angiogenesis suppression by siRNA via TLR3. Nature. 2008 Apr 3;452(7187):591-7. PMID: 18368052

Sayer Herin
Reyeslamothe et al. Independent Positioning and Action of Escherichia coli Replisomes in Live Cells. Cell (2008) vol. 133 (1) pp. 90-102

5/6/08 -

Andy Itsara
"Superwobbling facilitates translation with reduced tRNA sets." Marcelo Rogalski, Daniel Kacher & Ralph Bock. Nat Struct Mol Biol. 2008 Feb;15(2):192-8. Epub 2008 Jan 13

Caitlin Rippey
Krishnan V, Han MH, Graham DL, Berton O, Renthal W, Russo SJ, Laplant Q, Graham A, Lutter M, Lagace DC, Ghose S, Reister R, Tannous P, Green TA, Neve RL, Chakravarty S, Kumar A, Eisch AJ, Self DW, Lee FS, Tamminga CA, Cooper DC, Gershenfeld HK, Nestler EJ. Molecular adaptations underlying susceptibility and resistance to social defeat in brain reward regions. Cell. 2007 Oct 19;131(2):391-404.

4/29/08 -

Josh Akey
Sturm RA, Duffy DL, Zhao ZZ, Leite FP, Stark MS, Hayward NK, Martin NG, Montgomery GW. (2008) A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. Am J Hum Genet. 82:424-431.

4/22/08 -

Mike MacCoss
Bacteria Subsisting on Antibiotics. Gautam Dantas, Morten O. A. Sommer, Rantimi D. Oluwasegun, and George M. Church. Science 4 April 2008: 100-103.

Colin Manoil
Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA, Collins JJ. A common mechanism of cellular death induced by bactericidal antibiotics. Cell. 2007 Sep 7;130(5):797-810.

4/15/08 -

Bob Waterston

Geoff Findlay
Ishibashi, K., K. Masuda, S. Naito, T. Meshi and M. Ishikawa. 2007.
An inhibitor of viral RNA replication is encoded by a plant resistance
gene. PNAS 104: 13833-13838.

4/8/08 -

James Thompson
"BLOSUM62 Miscalculations Improve Search Performance." Styczynski MP, Jensen KL, Rigoutsos I, Stephanopoulos G. Nat Biotechnol. 2008 Mar;26(3):274-5.

Troy Zerr
Huichen Feng, Masahiro Shuda, Yuan Chang, and Patrick S. Moore Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma Science. 22 February 2008 319: 1096-1100

4/1/08 -

Steve Salipante
Identification of host proteins required for HIV infection through a functional genomic screen. Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ. Science. 2008 Feb 15;319(5865):921-6.

Ryan Emerson
Lethargus is a Caenorhabditis elegans sleep-like state. Raizen DM, Zimmerman JE, Maycock MH, Ta UD, You Y-j, Sundaram MV, Pack AI. Nature. 2008 Jan 31;451(7178):569-72.

3/11/08 -

Bonny Brewer
A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans. AC Gomes, I Miranda, RM Silva, GR Moura, B Thomas, A Akoulitchev and MAS Santos. Genome Biology (2007) 8:R206.

Kristen Lewis
Sulem et al. 2007. Genetic determinants of hair, eye and skin pigmentation in Europeans. Nature Genetics 39, 1443 - 1452

3/4/08 -

Stan Fields
Nature. 2008 451:720-4. Rapid appearance and local toxicity of amyloid-beta plaques in a mouse model of Alzheimer's disease. Meyer-Luehmann M, Spires-Jones TL, Prada C, Garcia-Alloza M, de Calignon A, Rozkalne A, Koenigsknecht-Talboo J, Holtzman DM, Bacskai BJ, Hyman BT.

David Spencer
Two levels of protection for the B cell genome during somatic hypermutation Nature 451, 841-845 (14 February 2008)

2/26/08 -

Mike Hoopmann
Helgason A, et al. An association between the kinship and fertility of human couples. Science. 2008 Feb 8;319(5864):813-6.

Shameek Biswas
GTP-independent rapid and slow endocytosis at a central synapse Jianhua Xu et al. Nat Neurosci 11 (1), 45-53 (Jan 2008)

2/19/08 -

Jeff Kidd
Recent acceleration of human adaptive evolution. John Hawks, Eric T. Wang, Gregory M. Cochran, Henry C. Harpending, and Robert K. Moyzis.
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Alan Rubin
Maria Divina E. Deato and Robert Tjian. 2007. Switching of the core transcriptional machinery during myogenesis. Genes & Dev. 21:2137-2149.

2/12/08 -

Kyle Siebenthall
Takahashi et al., Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors, Cell (2007), doi:10.1016/j.cell.2007.11.019

Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells
Junying Yu, Maxim A. Vodyanik, Kim Smuga-Otto, Jessica Antosiewicz-Bourget, Jennifer L Frane, Shulan Tian, Jeff Nie, Gudrun A. Jonsdottir, Victor Ruotti, Ron Stewart, Igor I. Slukvin, and James A. Thomson (20 November 2007) Science [DOI: 10.1126/science.1151526]

2/5/08 -

Joe Felsenstein
Kaoru Fukami-Kobayashi, Yoshiaki Minezaki, Yoshio Tateno, and Ken Nishikawa. 2007. A tree of life based on protein domain organizations Molecular Biology and Evolution 24: 1181-1189.

Gregory P. Fournier and J. Peter Gogarten. 2007. Signature of a primitive genetic code in ancient protein lineages. Journal of Molecular Evolution 65 (4): 425-436.

Zhaoshi Jiang
Perfusion-decellularized matrix: using nature's platform to engineer a bioartificial heart. Harald C Ott, Thomas S Matthiesen, Saik-Kia Goh, Lauren D Black, Stefan M Kren, Theoden I Netoff & Doris A Taylor. Published online: 13 January 2008; doi:10.1038/nm1684 on Nature Medicine

1/29/08 -

Tom Nicholas

A functional circuit underlying male sexual behaviour in the female mouse brain.
KImchi T, Xu J, and Dulac C. Nature 448 (2007)

Sara Di Rienzi

Smith and Williams. 2006. Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus. PNAS. 103: 8564-8569.
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1/22/08 -

Oliver Serang
Clustering by Passing Messages Between Data Points
Brendan J. Frey, et al. Science 315, 972 (2007)
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Kevin Roach
M. Nowacki1, et al. RNA-mediated epigenetic programming a genome-rearrangement pathway. Nature 451, 153-158 (10 January 2008). doi:10.1038/nature06452
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1/15/08 -

Evan Eichler
Weiss et al. Association between Microdeletion and Microduplication
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Mary-Claire King
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Secondary mutations as a mechanism of cisplatin resistance in
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1/8/08 -

Brig Mecham
Lundmark F, Duvefelt K, et al
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Gregory SG, Schmidt S, Seth P, et al
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Matt Sandel
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12/4/07 -

Phil Green
U Bergthorsson, DI Andersson, JR Roth. Ohno's dilemma: Evolution of new genes under continuous selection. PNAS 104, 17004-17009 (2007).

Willie Swanson
Falling off the academic bandwagon. Women are more likely to quit at the postdoc to principal investigator transition. Elisabeth D. Martinez, Jeannine Botos, Kathleen M. Dohoney, Theresa M. Geiman, Sarah S. Kolla, Ana Olivera, Yi Qiu, Geetha Vani Rayasam, Diana A. Stavreva & Orna Cohen-Fix
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11/27/07 -

Dan Blick
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Stark et al. Nature, p. 219, 8 November 2007.

Carlos Araya
Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Livet J, Weissman TA, Kang H, Draft RW, Lu J, Bennis RA, Sanes JR, Lichtman JW. Nature 2007 Nov 1

11/20/07 -

Rori Rohlfs
Perry et al. Diet and the evolution of human amylase gene copy number variation. Nature Genetics. October 2007.

Diane Dickel
Kim J, Inoue K, Ishii J, Vanti WB, Voronov SV, Murchison E, Hannon G, Abeliovich A.
A MicroRNA feedback circuit in midbrain dopamine neurons. Science. 2007 Aug 31;317(5842):1220-4.

11/13/07 -

Celeste Berg
A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals
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Ancient DNA Reveals Neandertals With Red Hair, Fair Complexions. Elizabeth Culotta (26 October 2007). Science 318 (5850), 546.
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Leo Pallanck
Deleault NR, Harris BT, Rees JR, Supattapone S. (2007) Formation of native prions from minimal components in vitro. Proc Natl Acad Sci U S A. 104:9741-6.

11/6/07 -

Lisa Beutler
Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Ma L, Teruya-Feldstein J, Weinberg RA. Nature. 2007 Oct 11;449(7163):682-8. Epub 2007 Sep 26

Graham McVicker
Batada NN, Hurst LD. Evolution of chromosome organization driven by selection for reduced gene expression noise. Nature Genetics. August 2007

10/30/07 -

Angela Poole
Transvascular delivery of small interfering RNA to the central nervous system. Kumar P, Wu H, McBride JL, Jung KE, Kim MH, Davidson BL, Lee SK, Shankar P, Manjunath N. Nature. 2007 Jul 5; 448(7149): 39-43.

Nick Coley
Agger et al. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature Development 11 October 2007.

10/23/07 -

Jim Thomas
Global Dissemination of a Single Mutation Conferring White Pericarp in Rice Megan T. Sweeney, Michael J. Thomson, Yong Gu Cho, Yong Jin Park, Scott H. Williamson, Carlos D. Bustamante, Susan R. McCouch. PLoS Genetics, August 2007.

Max Boeck
Augmented Wnt Signaling in a Mammalian Model of Accelerated Aging. H. Liu, M. M Fergusson, R. M. Castilho, J. Liu, L. Cao, J. Chen, D. Malide, I. I. Rovira, D. Schimel, C. J. Kuo, J. S. Gutkind, P. M. Hwang, and T. Finkel Science 317 (5839), 803-806.

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10/16/07 -

Bill Noble
Checkers Is Solved. Schaeffer et al. Science 14 September 2007: Vol. 317. no. 5844, pp. 1518 - 1522

John Stamatoyannopoulos
Pagel M et al. Frequency of word-use predicts rates of lexical evolution throughout Indo-European history. Nature 449, 717-720 (2007)

Lieberman E et al. Quantifying the evolutionary dynamics of language. Nature 449:713-6 (2007)

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Mary Kuhner
Tulio de Oliveira, Oliver G. Pybus, Andrew Rambaut, Marco Salemi,
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10/2/07 -

Maynard Olson
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5/31/07 -

Oliver Serang
Wiring optimization can relate neuronal structure and function by Beth L. Chen, David H. Hall, and Dmitri B. Chklovskii. PNAS 103 (12): 4723-4728 (2006).

Kyle Siebenthall
Conboy MJ, Karasov AO and Rando TA. (2007) High incidence of non-random template strand segregation and asymmetric fate determination in dividing stem cells and their progeny. PLoS Biology 5 (5): e102.

5/24/07 -

Kevin Roach
Covalent modification of DNA regulates memory formation.
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Alan Rubin
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5/17/07 -

Ryan Emerson
Dierick HA & Greenspan RJ. Molecular analysis of flies selected for aggressive behavior. 2006. Nature Genetics 38: 1023-31.

Chris Murphy
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5/10/07 -

Dan Blick
Fontaneto D, Herniou EA, Boschetti C, Caprioli M, Melone G, et al.
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Sara DiRienzi
Pradel N, Santini CL, Bernadac A, Fukumori Y, and Wu LF. 2006. Biogenesis of actin-like bacterial cytoskeletal filaments destined for positioning prokaryotic magnetic organelles. PNAS: 103, pp. 17845-17849.

5/3/07 -

Nick Coley
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Will Sheffler
Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by
Mass Spectrometry. John M. Asara, Mary H. Schweitzer, Lisa M. Freimark, Matthew
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Accompanying article:

Analyses of Soft Tissue from Tyrannosaurus rex Suggest the Presence
of Protein. Mary Higby Schweitzer, Zhiyong Suo, Recep Avci, John M. Asara,
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Bonny Brewer
"Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila". Julius Brennecke, Alexei Aravin, Alexander Stark, Monica Dus, Manolis Kellis, Ravi Sachidanandam, and Gregory Hannon. Cell 128, 1089-1103, March 23, 2007.

James Ronald
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Joshua Akey
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Lisa Beutler
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Amanda Schivell
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Mike Hoopmann
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4/5/07 -

Kristen Lewis

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Carlos Araya
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3/8/07 -

David Spencer
"Reversal of Neurological Defects in a Mouse Model of Rett Syndrome"
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Steve Salipante
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2/28/07 -

Joe Felsenstein
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Troy Zerr
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Rori Rohlfs
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James Thompson
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2/15/07 -

Shameek Biswas
A "Silent" polymorphism in the MDR1 gene changes substrate specificity.Kimchi-Safraty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM. Science. 2007 Jan 26;315(5811):525-8.

Greg Finney
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Stan Fields
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Jeff Kidd
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Angela Poole
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Mike MacCoss
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M.K. Raghuraman
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Diane Dickel
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Graham McVicker
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Ray Monnat
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Ben Smith
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Mary-Claire King

Mutations in the gene encoding the synaptic scaffolding protein SHANK3
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Bob Waterston

"Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin". SM Johnson, FJ Tan, HL McCullough, DP Riordan and AZ Fire (2006). Genome Res. 16:1505-1516

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Phil Green
Two Dobzhansky-Muller Genes Interact to Cause Hybrid Lethality in Drosophila. Nicholas J. Brideau, Heather A. Flores, Jun Wang, Shamoni Maheshwari, Xu Wang, and Daniel A. Barbash. Science 314, 1292-1295. (24 November 2006).

Willie Swanson
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Bob Braun
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PDF

Brig Mecham
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Leo Pallanck
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Tom Nicholas
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Mark Enstrom
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Max Boeck
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Aaron Klammer
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Laura Certain
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Karen Chisholm
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Matt Sandel
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Joanna Kelley
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Jennifer Gogarten
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Carol Sibley
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Bonny Brewer
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Jeff Kidd
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Kristen Lewis
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Diane Dickel
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Max Boeck
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Shameek Biswas
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Geoff Findlay
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Zhaoshi Jiang
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Steve Salipante
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4/6/06 -

Mike MacCoss
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Josh Akey
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Stan Fields
High-Throughput Screening of Enzyme Libraries: In Vitro Evolution of a b-Galactosidase by
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Greg Finney
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Tobias Mann
Transient Homologous Chromosome Pairing Marks the Onset of X Inactivation.
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Mark Enstrom
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Angela Poole
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Will Sheffler
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2/23/06 -

Colin Manoil

Michael Boyle

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Joe Felsenstein
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Rokas, A., D. Kruger, and S. B. Carroll. 2005. Animal evolution and the
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David Spencer
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Celeste Berg
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Maynard Olson
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Divya Bhat
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Miller HC, Lambert DM.  Genetic drift outweighs balancing selection in shaping post-bottleneck major histocompatibility complex variation in New Zealand robins (Petroicidae).   Mol Ecol. 2004 Dec;13(12):3709-21.

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Aaron Hinz
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Bob Braun
"Is Snuppy Really a Clone?"

Lee BC , Kim MK, Jang G, Oh HJ, Yuda F, Kim HJ, Shamim MH, Kim JJ, Kang SK, Schatten G, Hwang WS. Dogs cloned from adult somatic cells. Nature. 2005 Aug 4;436(7051):641. Erratum in: Nature. 2005 Aug 25;436(7054):1102.

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Nathan Clark
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Mandy Schivell
The Inner Menace: HERV's and disease

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Cindy Desmarais
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Breck Byers
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T. Hirota, J.J. Lipp, J.-M. Peters.  Nature (22/29 December 05) 438: 1176-1180.  Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin.

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Mike Hoopmann
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Phil Green
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Chung-Ying Huang
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M. K. Raghuraman
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Jon Bleyhl
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Ben Smith
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Jay Shendure, et al. "Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome".  Science, Vol 309, Issue 5741, 1728-1732, 9 September 2005

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Willie Swanson
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Ross Centers
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Brig Mecham
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Ray Monnat
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