UW Genome Sciences: GS Seminars

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

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

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

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

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.

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.

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

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

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.

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]

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

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

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

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).

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

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)

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.

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

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).

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

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).

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

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)

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.

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.

Stephens, P.J., et al. (2011). Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144,
27-40

Kloosterman, W.P., et al. (2011). Chromothripsis as a mechanism
driving complex de novo structural rearrangements in the germline.
Hum Mol Genet. (EPub)

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.

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.

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

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

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

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

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

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

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

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.

"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.

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.

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

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.

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

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.

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.

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.

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.

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

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

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.

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

Leo Pallanck

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

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

"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).

"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)

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.

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

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

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)

"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

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]

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.

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);

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.

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.

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

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

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

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.

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.

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

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)

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.

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)

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

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.

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

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

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

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.

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

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.

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

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.

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.

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.
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Ray Monnat
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Steve Salipante
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Troy Zerr
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Ryan Emerson
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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.

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Past Journal Club