First Year Rotation Talks
June 10, 2026 1:00 pm – 4:00 pm | Foege Auditorium
Past Research Reports
2026
Sahar Attar
June 5, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Ben Mallory, Alex Robertson, Conor Kelly
Conor Kelly | Beliveau Lab
“Mapping the protein and chromatin landscape of nuclear condensates with CUT&Hyb”
Ben Mallory | Starita Lab, Stergachis Lab
“Plasmid POCA: A Targeted Proteomics Approach for Identifying Regulatory Element-Binding Proteins”
Alex Robertson | Feder Lab
“Cooperative interactions between measles viruses facilitate spread in the brain”
May 29, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Justin Sanders, Shengqi Hang
Shengqi Hang | Noble Lab
“Decoding single-molecule transcription factor occupancy from Fiber-seq with deep learning”
Justin Sanders | Noble Lab
“Pre-trained spectrum representations generalize to novel downstream tasks in mass spectrometry proteomics”
May 22, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Shruti Jain, Cliff Rostomily
Shruti Jain | Baker Lab, Shendure Lab
“Expanding the Toolkit of Signal-Responsive Recorders for Capturing Developmental Pathway Dynamics”
Cliff Rostomily | Trapnell Lab
May 15, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Bria Metzger, Manali Sawant, Katie Partington
Bria Metzger | Abitua Lab
“Mechanical regulation of β-catenin during self-organized symmetry breaking in killifish”
Katie Partington | Fowler Lab
“Variant in situ sequencing (VIS-seq) visually phenotypes thousands of LMNA variants”
Manali Sawant | Fowler Lab
“CellCode: Mapping How Cell-Extrinsic Signals Program T Cell Fate”
May 8, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Sean Perez, Hank Cheng, Catherine Sniezek
Hank Cheng | Stergachis Lab
“Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions”
Sean Perez | Abitua Lab
“Investigating the role of JAK/STAT Signaling in Killifish Diapause & Axis Formation”
Catherine Sniezek | Schweppe Lab
May 1, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Iris Jia, Elliott Swanson
Iris Jia | Feder Lab
“Genetic drivers of Pseudomonas aeruginosa persistence in the Cystic Fibrosis lung after CFTR modulator therapy”
Elliott Swanson | Stergachis Lab
“Mapping comprehensive single-cell chromatin fiber architectures at scale”
April 24, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Marazzano Colon, Olivia Waltner
Marazzano Colon | Trapnell Lab “Using MorphSeq to Disentangle Incomplete Penetrance”
Olivia Waltner | Trapnell Lab “Lateral plate mesoderm specification”
April 17, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Evan McDermot, Rachel Powell
Evan McDermot | MacPherson Lab
Rachel Powell | Dunham Lab
April 10, 2026 2:00 pm – 3:00 pm | Foege Auditorium
Sophia Gibson, Monika Perez
Sophia Gibson | Miller Lab, Starita Lab
Monika Perez | Beliveau Lab
April 3, 2026 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation talks
March 18, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Connor Kubo, Dustin Mullaney
Connor Kubo | Shendure Lab
Dustin Mullaney | Harris Lab, Srivatsan Lab “Capsule Based Genome Sequencing and Lineage Tracing”
March 13, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Lizzie Plender
Lizzie Plender | Bloom Lab, Eichler Lab “Cryptic structural variation in the mucin pangenome and disease implications”
March 6, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Stephen Gonzalez, Riku Yasutomi
Stephen Gonzalez | Trapnell Lab “Zebrafish meningeal cell-types repress chondrogenesis via Osr1 “
Riku Yasutomi | Trapnell Lab, Moens Lab “Developmental mechanisms underlying facial motor neuron diversification”
February 27, 2026 3:15 pm – 4:15 pm | Health Sciences K-069
Matt Chaw, Lucas Kerr, Joe Min
Matt Chaw | Srivatsan Lab
Lucas Kerr | Srivatsan Lab
Joe Min | Baker Lab, Queitsch / Cuperus Lab “Mining for gain-of-function candidates by using ML-based methods to redesign native enzymes”
February 20, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Caroline Kikawa, Syd Sattler
Caroline Kikawa | Bloom Lab “Near real-time data on the human neutralizing antibody landscape to influenza virus”
Syd Sattler | Abitua Lab “Immune Cells Ahead of Schedule: an evolutionary decoupling of immune cell fate from the mesoderm”
February 13, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Caleb Carr, Ariana Farrell
Caleb Carr | Bloom Lab
Ariana Farrell | Shendure Lab “Multiplex discovery of synthetic receptors for cell contact and ligand sensing”
February 6, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Clare Booth
Clare Booth | Abitua Lab “Setting up for axis formation in killifish: new insights into the early embryo”
January 30, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Connor Finkbeiner, Allie Kreitman
Connor Finkbeiner | Setty Lab
Allie Kreitman | Feder Lab “Detection of intra-tumor selection using phylogenetics”
January 23, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Abby McGee, Jenny Nathans, Qi Yu
Abby McGee | Shendure Lab “Building a locus-scale MPRA”
Jenny Nathans | Shendure Lab “Autobiographical recording to generate event decorated lineage trees”
Qi Yu | Shendure Lab
January 16, 2026 3:00 pm – 4:00 pm | Foege Auditorium
Sanjay Kottapalli
Sanjay Kottapalli | Shendure Lab “Bayesian inference of continuous cellular signaling histories from sequential genomic event records”
January 9, 2026 3:00 pm – 4:00 pm | Foege Auditorium
2025
first year rotation talks
December 10, 2025 1:00 pm – 2:00 pm | Foege Auditorium
Ayomikun Akinrinade, Karl Young
Ayomikun Akinrinade | McCrone Lab “Detecting the drivers of transmission heterogeneity in large viral outbreaks”
Karl Young | Trapnell Lab “Comparing Molecular Features of Development Across Vertebrate Models”
December 5, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Chris Oliveira, Morgan Wu
Chris Oliveira | Stergachis Lab “Targeted somatic mutation quantification with deaminase-assisted PCR (daPCR)”
Morgan Wu | Trapnell Lab “Large Language Model-Assisted Developmental Genetics”
November 21, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Alex Donny, Megan Taylor
Alex Donny | Termini Lab “Interrogating syndecan-2-mediated hematopoietic stem cell self-renewal”
Megan Taylor | Dunham Lab “Industrial Yeast Engineering with Prime Editing”
November 14, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Ben Cohen Stillman, Jyoti Rai
Ben Cohen Stillman | Stergachis Lab “Targeted single cell mapping of the regulatory consequences of engineered deletions”
Jyoti Rai | Trapnell Lab “The PRDM gene family in cell differentiation and development”
November 7, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Leah McDermott, Carlo Melendez
Leah McDermott | Bruce Lab “Uncovering the Mitochondrial Permeability Transition Pore: A Structural Interactome Approach”
Carlo Melendez | Noble Lab “Representation Learning and Cross-Modal Imputation for Multiomics”
October 31, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Rachael Hu, Anna Leipertz
Rachael Hu | Villen Lab “Signal initiation at the cell surface”
Anna Leipertz | Queitsch / Cuperus Lab “Improving plant biotechnology for a climate resilient future”
October 24, 2025 3:15 pm – 4:15 pm | Health Sciences K-069
Carina Biar, Zanny Ham
Carina Biar | Shendure Lab “Understanding the grammar within and between regulatory elements”
Zanny Ham | Dunham Lab “Uncovering genes driving fitness phenotypes in S. cerevisiae “
October 17, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Kyle Brandt
Kyle Brandt | Schweppe Lab “Toward Genomics Scale with Quantitative Proteomics”
October 10, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Yash Sonthalia
Yash Sonthalia | Noble Lab, Pinglay Lab
October 3, 2025 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation talks
June 11, 2025 1:30 pm – 2:30 pm | Foege Auditorium
Lincoln Harris, Justin Sanders
Lincoln Harris | Noble Lab “One Weird Trick! Solve your missingness issues by imputing retention times!”
Justin Sanders | Noble Lab “A procedure for controlling the false discovery rate of de novo peptide sequencing”
June 6, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Shruti Jain, Aidan Keith
Shruti Jain | Baker Lab, Shendure Lab
Aidan Keith | Shendure Lab
May 30, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Hunter Colegrove, Conor Kelly
Hunter Colegrove | Feder Lab “TP53 second-hit mutations in Li-Fraumeni syndrome: tissue-specific burdens and a recurrent hotspot”
Conor Kelly | Beliveau Lab “Towards compartmentalized chromatin proteomic profiling with CUT&Hyb”
May 23, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Joe Min, Elliott Swanson
Joe Min | Baker Lab, Queitsch / Cuperus Lab “Leveraging evolutionary sequence information in structure-based protein design methods for native enzyme thermostabilization”
Elliott Swanson | Stergachis Lab “Comprehensive diploid chromatin map of a single cell using deaminase-assisted fiber-seq (DAF-seq)”
May 16, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Monika Perez, Bo Wen
Monika Perez | Beliveau Lab
Bo Wen | MacCoss Lab, Noble Lab “Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics”
May 9, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Sahar Attar, Jenny Nathans, Connor Kubo
Sahar Attar | Beliveau Lab, Schweppe Lab
Jenny Nathans | Shendure Lab “Towards a signal and cell-type decorated lineage tree in a model of early mammalian development”
Connor Kubo | Hamazaki Lab, Shendure Lab
May 2, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Hank Cheng, Cliff Rostomily
Hank Cheng | Stergachis Lab “Identifying pathogenic variants that cause Mendelian conditions using long-read transcript sequencing”
Cliff Rostomily | Trapnell Lab
April 25, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Malvika Tejura, Riku Yasutomi
Malvika Tejura | Fowler Lab, Starita Lab
Riku Yasutomi | Moens Lab, Trapnell Lab “Developmental mechanisms underlying the functional diversification of facial motor neurons”
April 18, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Ben Mallory, Taylor Real
Ben Mallory | Starita Lab, Stergachis Lab “Single-molecule chromatin architecture of transiently transfected plasmid constructs in mammalian cells”
Taylor Real | Eichler Lab, Stergachis Lab “The functional fate of human-specific NOTCH2NL duplications”
April 11, 2025 12:30 pm – 1:30 pm | Health Sciences K-069
Stephen Gonzalez, Syd Sattler
Stephen Gonzalez | Trapnell Lab “Single-cell reverse genetics reveals a TF required for meningeal connective tissue specification”
Syd Sattler | Abitua Lab “Flexibility in development: The novel adaptation of immune cell specification in killifish”
April 4, 2025 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation talks
March 19, 2025 1:30 pm – 2:30 pm | Foege Auditorium
Erik Bergstrom, Luana Paleologu
Erik Bergstrom | Queitsch / Cuperus Lab
Luana Paleologu | Berg Lab
March 14, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Sophia Gibson
Sophia Gibson | Miller Lab, Starita Lab “Long read sequencing for evaluating tandem repeats and episignatures”
March 7, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Gabby Ferra, Alex Robertson
Gabby Ferra | Dunham Lab, Harris Lab “Double Trouble: Using DMS Library Errors to Explore CYP2D6 Double Mutants in Saccharomyces cerevisiae”
Alex Robertson | Feder Lab “When Less is More: Tuning Antiviral Neutralization Delays Poliovirus Resistance Evolution”
February 28, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Connor Finkbeiner, Shengqi Hang
Connor Finkbeiner | Setty Lab “Desynchronization Between Gene Expression and Chromatin States Sheds Light on Mechanisms Driving Cell-State Change”
Shengqi Hang | Noble Lab “A Deep Learning Approach for Predicting Gene Expression from Genomic Sequences and Chromatin Structure”
February 21, 2025 12:30 pm – 1:30 pm | Health Sciences K-069
Leah Anderson, Iris Jia
Leah Anderson | Dunham Lab “Student-driven evolution experiments reveal recurrent pathways of antifungal resistance”
Iris Jia | Feder Lab “Regional lung properties and bacterial migration shape Pseudomonas aeruginosa persistence during CFTR modulator
therapy”
February 14, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Chris Hsu, Evan McDermot
Chris Hsu | MacCoss Lab “Method development for low input spatial proteomics”
Evan McDermot | MacPherson Lab “Roles for SOX4 and other transcription factors in small cell lung cancer chemotherapy response”
February 7, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Caleb Carr, Caroline Kikawa
Caleb Carr | Bloom Lab “Pseudovirus deep mutational scanning of the Lassa virus glycoprotein complex”
Caroline Kikawa | Bloom Lab “High- throughput neutralization measurements correlate strongly with
evolutionary success of human influenza strains”
January 31, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Lizzie Plender, Qi Yu
Lizzie Plender | Bloom Lab, Eichler Lab “A tale of two mucins: MUC4 and MUC20 structural genetic variation and severe cystic fibrosis”
Qi Yu | Shendure Lab “generating a lineage recording mouse model to study mammalian development”
January 24, 2025 3:00 pm – 4:00 pm | Foege Auditorium
David Lee, Tony Li, Olivia Waltner
David Lee | Baker Lab, Shendure Lab “Building a toolkit of de novo designed binders for bone morphogenetic proteins and receptors”
Tony Li | Shendure Lab “Designing biological sensors for cell recording”
Olivia Waltner | Trapnell Lab “Lateral Plate Mesoderm Specification”
January 17, 2025 3:00 pm – 4:00 pm | Foege Auditorium
Bria Metzger, Elena Romero
Bria Metzger | Abitua Lab “Mechanical inputs in the self-organization of annual killifish”
Elena Romero | Feder Lab “Learning from the intersection of HIV genetics and demography”
January 10, 2025 3:00 pm – 4:00 pm | Foege Auditorium
2024
Lucas Kerr
Lucas Kerr | Srivatsan Lab “Towards a scalable single cell genome & transcriptome co-assay”
December 6, 2024 12:30 pm – 1:30 pm | Health Sciences K-069
Rachel Powell, Catherine Sniezek
Rachel Powell | Dunham Lab “Characterization of Saccharomyces centromeric sequences to engineer a Saccharomyces -wide CEN “
Catherine Sniezek | Schweppe Lab “Bridging the gap: proteomics for testing of engineered minibinders”
November 22, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Marazzano Colon, Sean Perez
Marazzano Colon | Trapnell Lab
Sean Perez | Abitua Lab “Investigating the role of TOR regulation in annual killifish diapause”
November 15, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Sanjay Kottapalli, Abby McGee
Sanjay Kottapalli | Shendure Lab “A simulation and inference framework for cellular signaling histories with ENGRAM”
Abby McGee | Shendure Lab “Multiplex functional dissection of long-range gene regulation”
November 8, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Zachary Amador, Matthew Chaw
Zachary Amador | Pinglay Lab, Stergachis Lab “Integrating Recombinase, Transcriptome and Epigenome Technologies to Study the Grammar of DNA”
Matthew Chaw | Srivatsan Lab “multiplex enzyme photometry”
November 1, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Conor Camplisson, Alexis Chang
Conor Camplisson | Beliveau Lab “Technology development for simple, bright labeling of cell types in tissues”
Alexis Chang | Villen Lab “Phosphoproteomics of multicellular interactions – new organism, new obstacles”
October 25, 2024 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation talks:
Evan McDermot, Abby McGee, Sean Perez, Rachel Powell, Olivia Waltner
June 4, 2024 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation talks:
Zachary Amador, Matthew Chaw, Marazzano Colon, Sanjay Kottapalli, Catherine Sniezek, Lucas Kampman
May 31, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Taylor Real, Elena Romero
Taylor Real | Eichler Lab, Stergachis Lab “The genomic and functional fate of human-specific NOTCH2NL duplications”
Elena Romero | Feder Lab “Disentangling distinct origins of HIV-1 resistance to bNAb monotherapy”
May 24, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Alexis Chang
Alexis Chang | Villen Lab “Phosphoproteomics of multicellular interactions – new organism, new obstacles”
May 17, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Chris McGann
Chris McGann | Schweppe Lab
May 10, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Syd Sattler, Malvika Tejura
Syd Sattler | Abitua Lab “The evolution of a novel immune lineage in the annual killifish”
Malvika Tejura | Fowler Lab, Starita Lab “Clinical variant interpretation using functional and computational data”
May 3, 2024 3:00 pm – 4:00 pm | Foege Auditorium
David Lee, Jenny Nathans
David Lee | Baker Lab, Shendure Lab “De novo design of receptor-specific bone morphogenetic proteins”
Jenny Nathans | Shendure Lab “Spatially resolved lineage and signaling history of human skin development”
April 26, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Shruti Jain, Candice Young
Shruti Jain | Baker Lab, Shendure Lab “Modulating Interferon Lambda Receptor Dimer Geometry by De Novo Protein Design for Improved Signaling”
Candice Young | Harris Lab “The Influence of MUTYH on Germline and Somatic Mutagenesis Across Species”
April 19, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Elliott Swanson
Elliott Swanson | Stergachis Lab “Haplotype-resolved view of normal and pathogenic gene regulation”
April 12, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Hunter Colegrove, Lizzie Plender
Hunter Colegrove | Feder Lab “Modeling as a guide to epithelial gene therapy”
Lizzie Plender | Bloom Lab, Eichler Lab “Structural and genetic variation in the secreted mucin MUC5AC”
April 5, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Leah Anderson, Ben Mallory
Leah Anderson | Dunham Lab “Utilizing experimental evolution to study freeze-thaw tolerance in S. cerevisiae “
Ben Mallory | Starita Lab, Stergachis Lab “Chromatinization of Transfected Plasmid DNA in Mammalian Cells”
March 29, 2024 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation talks:
Zachary Amador, Matthew Chaw, Marazzano Colon, Evan McDermot, Olivia Waltner Foege Auditorium
March 12, 2024 12:30 pm – 1:30 pm | Foege Auditorium
first year rotation talks:
Sanjay Kottapalli, Abby McGee, Sean Perez, Rachel Powell, Catherine Sniezek
March 8, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Chris Hsu
Chris Hsu | MacCoss Lab “Massively parallel targeted proteomics for low input samples” 12:30, K-069 (usual 3:30 time reserved for Medical Genetics Stamatoyannopoulos Lecture)
March 1, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Gabby Ferra
Gabby Ferra | Dunham Lab, Harris Lab “Deep mutational scan of the pharmacogene CYP2D6 in Saccharomyces cerevisiae “
February 23, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Luke Zhu
Luke Zhu | Harris Lab “Mutator allele detection in whole-genome sequencing datasets”
February 16, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Xavi Guitart
Xavi Guitart | Eichler Lab “The evolution and variation of primate specific segmental duplication gene families: TBC1D3”
February 2, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Aidan Keith, Qi Yu
Aidan Keith | Shendure Lab “Investigating TFs that drive chromatin accessibility changes via a CRISPRa approach”
Qi Yu | Shendure Lab
January 26, 2024 3:00 pm – 4:00 pm | Foege Auditorium
Caleb Carr, Caroline Kikawa
Caleb Carr | Bloom Lab “Pseudovirus deep mutational scanning of Lassa virus glycoprotein”
Caroline Kikawa | Bloom Lab “Next-generation sequencing-based neutralization assays to forecast influenza virus clade growth”
January 5, 2024 3:00 pm – 4:00 pm | Foege Auditorium
2023
first year rotation talks:
Marazzano Colon, Abby McGee, Sean Perez, Rachel Powell, Olivia Waltner
December 12, 2023 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation talks:
Zachary Amador, Matthew Chaw, Sanjay Kottapalli, Evan McDermot, Catherine Sniezek
December 8, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Hank Cheng, Riku Yasutomi
Hank Cheng | Stergachis Lab “Long-read transcript sequencing to discover splicing variants”
Riku Yasutomi | Moens Lab, Trapnell Lab “Single-cell analysis of cranial motor neuron development”
December 1, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Sahar Attar, Cliff Rostomily
Sahar Attar | Beliveau Lab, Schweppe Lab “Enhancing Visualization of Small Targets and Probing Subcellular Interactions”
Cliff Rostomily | Trapnell Lab topic tba
November 28, 2023 12:30 pm – 1:30 pm | Foege Auditorium
Stephen Gonzalez, Bo Wen
Stephen Gonzalez | Trapnell Lab “Investigating the role of BMP receptors in cell computation in-vivo”
Bo Wen | MacCoss Lab, Noble Lab “An AI-powered all-in-one search engine for proteomics”
November 17, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Joe Min, Monika Perez
Joe Min | Baker Lab, Queitsch / Cuperus Lab “Deep Learning-Based Methods for Native Protein Redesign to Make Thermotolerant Plants”
Monika Perez | Beliveau Lab “Where’s Waldo? A probing question”
November 3, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Sophia Gibson, Tongqiu (Iris) Jia
Sophia Gibson | Miller Lab, Starita Lab – “Genome-wide population-scale characterization of repetitive elements and methylation using long-read sequencing”
Tongqiu (Iris) Jia | Feder Lab – “Intra-host phylogeography reveals the importance of space in Pseudomonas aeruginosa lung persistence”
October 27, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Erik Bergstrom, Conor Kelly
Erik Bergstrom | Schweppe Lab “Scalable proteomics with massively multiplexed sample barcodes”
Conor Kelly | Beliveau Lab “Leveraging in situ hybridization for multiomic tool development”
October 20, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Connor Finkbeiner
Connor Finkbeiner | Setty Lab
“Uncovering the connections and dynamics of chromatin and expression landscapes during differentiation using single-cell data”
October 13, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Alex Robertson
Alex Robertson | Feder Lab “Poliovirus Modeling Reveals Pathways to Antiviral Resistance Evolution”
October 6, 2023 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation presentations
Stephen Gonzalez, Conor Kelley, Monika Perez, Clifford Rostomily, Bo Wen, Qi Yu
June 6, 2023 12:30 pm – 1:30 pm | Foege Auditorium
first year rotation presentations:
Sahar Attar, Erik Bergstrom, Connor Finkbeiner, Sophia Gibson, Iris Jia, Joe Min
June 2, 2023 3:00 pm – 4:00 pm | K-069
Alexis Chang
Alexis Chang | Villen Lab
May 26, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Chase Suiter
Chase Suiter | Shendure Lab “Combinatorial mapping of E3 ubiquitin ligases to their substrate proteins”
May 23, 2023 12:30 pm – 1:30 pm | Foege Auditorium
Anna Bakhtina, Wei Yang
Anna Bakhtina | Bruce Lab “Quantitative interactomics connects protein structure, function, and aging”
Wei Yang | Shendure Lab “a molecular recorder for cell-cell interaction”
May 19, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Morgan Hamm
Morgan Hamm | Queitsch/Cuperus Lab, Trapnell Lab “Analyzing high coverage Fiber-seq data in Arabidopsis”
May 16, 2023 12:30 pm – 1:30 pm | Foege Auditorium
Sophie Moggridge
Sophie Moggridge | Villen Lab “Stressed out and phosphorylated: Exploring signalling in membraneless condensates”
May 12, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Sam Smukowski
Sam Smukowski | Valdmanis Lab “RNA mislocalization to synapses is a key feature of Alzheimer’s Disease”
May 9, 2023 12:30 pm – 1:30 pm | Foege Auditorium
Conor Camplisson
Conor Camplisson | Beliveau Lab “Probe technology development for advanced in situ multiplexing”
May 5, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Chris Hsu
Chris Hsu | MacCoss Lab “Massively parallel targeted proteomics for low input samples”
May 2, 2023 12:30 pm – 1:30 pm | Foege Auditorium
Kevin Thornton
Kevin Thornton | Queitsch/Cuperus Lab “rDNA copy number modulates yeast fitness and stress”
April 25, 2023 12:30 pm – 1:30 pm | Foege Auditorium
Sayeh Gorjifard
Sayeh Gorjifard | Queitsch-Cuperus Lab “Terminators: Rise of the Plant Machines”
April 14, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Zorian Thornton
Zorian Thornton | Matsen Lab “Simulating influenza sequences under a model of host cross-immunity”
April 7, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Michelle Noyes, Taylor Real
Michelle Noyes | Eichler Lab “Toward a more comprehensive de novo rate across the human genome”
Taylor Real | Eichler Lab, Stergachis Lab “Evolution and genomic variation of human-specific NOTCH2NL duplications”
April 4, 2023 12:30 pm – 1:30 pm | Foege Auditorium
Madeleine Duran
Madeleine Duran | Trapnell Lab “Differential analysis of cellular composition in single-cell perturbation experiments”
March 31, 2023 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation presentations:
Sahar Attar, Erik Bergstrom, Connor Finkbeiner, Sophia Gibson, Stephen Gonzalez, Iris Jia
March 14, 2023 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation presentations:
Conor Kelley, Joseph Min, Monika Perez, Clifford Rostomily, Bo Wen, Qi Yu
March 10, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Tony Li, Elena Romero
Tony Li | Shendure Lab “Understanding mammalian cis-regulatory evolution in developmental enhancers with deep learning approaches”
Elena Romero | Feder Lab “Elevated HIV viral load is associated with higher intra-host recombination rate in vivo “
March 3, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Luke Zhu
Luke Zhu | Harris Lab “A tree-based algorithm for identifying mutator alleles from genetic variation data”
February 24, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Gabby Ferra
Gabby Ferra | Dunham & Harris Labs, “A deep mutational scan of CYP2D6 in Saccharomyces cerevisiae “
February 17, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Leah Anderson
Leah Anderson | Dunham Lab “Investigating the genetic basis of freeze-thaw tolerance in yeast”
February 10, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Lincoln Harris
Lincoln Harris | Noble Lab “Evaluating methodological approaches for imputing missing values in quantitative proteomics”
February 3, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Sriram Pendyala
Sriram Pendyala | Fowler Lab “Decoding the language of cytokine communication in CD8 T-cells”
January 27, 2023 3:00 pm – 4:00 pm | Foege Auditorium
Caleb Carr, Caroline Kikawa
Caleb Carr | “Complete mapping of mutations to the Lassa virus glycoprotein that escape antibody neutralization”
Caroline Kikawa | “Mapping epitopes of flavivirus broadly neutralizing antibodies”
January 13, 2023 3:00 pm – 4:00 pm | Foege Auditorium
2022
Sahar Attar, Connor Finkbeiner, Sophia Gibson, Stephen Gonzalez, Iris Jia
Sahar Attar, Connor Finkbeiner, Sophia Gibson, Stephen Gonzalez, Iris Jia | first year rotation presentations:
December 9, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Jenny Nathans, Malvika Tejura
Jenny Nathans | “Multi-targeting large serine recombinases as novel tools for genomic engineering”
Malvika Tejura | “Guiding Clinical Variant Interpretation Using Functional and Computational Data”
November 18, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Ben Mallory, Elliott Swanson
Ben Mallory | “Principles of chromatin organization along transfected plasmid DNA”
Elliott Swanson | “Regulatory element cooperativity along individual chromatin fibers”
November 4, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Lizzie Plender, Syd Sattler
Lizzie Plender | “Genetic Variation in MUC5AC and its Association with Influenza Infection”
Syd Sattler | “Old Cell, New Trick? Macrophage-like Cells in Early Annual Killifish Embryos”
October 28, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Connor Kubo, David Lee
Connor Kubo | “Defining the roles of genes in early human development”.
David Lee | “Parsing the pleiotropy of bone morphogenic proteins”
October 21, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Hunter Colegrove, Shruti Jain
Hunter Colegrove | “Modeling as a guide to epithelial gene therapy”
Shruti Jain | “Computational design and characterization of de novo cytokines”
October 14, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Luana Paleologu
Luana Paleologu | “Tube Goldberg Machine: investigating a novel signaling pathway using fly egg tubes as a model system”
October 7, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Eliza Barkan
Eliza Barkan | “Whole-embryo chemical transcriptomics at single-cell resolution reveals dependencies between cell types and signaling pathways”
September 30, 2022 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation presentations: Shruti Jain, Lizzie Plender, Sydney Sattler,
first year rotation presentations: Shruti Jain, Lizzie Plender, Sydney Sattler, Elliott Swanson
June 7, 2022 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation presentations: Hunter Colegrove, Connor Kubo, David Lee, Ben
first year rotation presentations: Hunter Colegrove, Connor Kubo, David Lee, Ben Mallory, Malvika Tejura now changed back to 3:15, Foege Auditorium
June 3, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Mu Yang, Hanna Liao
Mu Yang
Hanna Liao
May 31, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Sayeh Gorjifard, Michelle Noyes
Sayeh Gorjifard | “Terminator 4: The End of all Genes”
Michelle Noyes | “A more comprehensive assessment of de novo variation using long read sequencing”
May 27, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Flo Chardon, Chengxiang Qiu
Flo Chardon | “Identification of enhancers to rescue haploinsufficiency via a CRISPRa-QTL approach”
Chengxiang Qiu | “Leveraging single-cell sequencing to understand the cellular trajectories of mouse embryogenesis”
May 24, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Anna Bakhtina
Anna Bakhtina | “Mitochondrial Interactome remodeling in aged muscle”
May 20, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Conor Camplisson, Miranda Mudge
Conor Camplisson | “Probe technology development for multiplexed in situ detection”
Miranda Mudge | “Utilizing microbiome peptides to forecast harmful algal blooms”
May 17, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Gabe Boyle, Zorian Thornton
Gabe Boyle | “Mass spectrometry on visually distinct cell populations”
Zorian Thornton | “Modeling viral escape from polyclonal antibodies using deep mutational scanning data”
May 13, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Sam Smukowski
Sam Smukowski | “Investigating the importance of the synaptic-localized transcriptome in Alzheimer’s Disease”
May 10, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Madeleine Duran, Lilian Heil
Madeleine Duran | “Differential analysis of cellular composition in single-cell perturbation experiments”
Lilian Heil | “Robust peptide quantitation for low input proteomics with massively parallel targeted data acquisition”
May 6, 2022 3:00 pm – 4:00 pm | Foege Auditorium
David Read
David Read | “Single cell study of age- and sex-dependent differences in the human heart”
May 3, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Xavi Guitart, Sophie Moggridge
Xavi Guitart | “Investigating the human variation of segmental duplication gene families: TBC1D3”
Sophie Moggridge | “Interrogating protein variant dysfunction using multidimensional proteomics”
April 29, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Robin Aguilar
Robin Aguilar | “Visualizing repetitive DNA in situ with Tigerfish”
April 22, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Rachel Wellington
Rachel Wellington | “Single Cell Analysis of Human Hematopoietic Development From Induced Pluripotent Stem Cells”
April 15, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Abbey Thorpe
Abbey Thorpe | “Characterization of prostate cancer genomes by long-range sequencing”
April 12, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Hyeon-Jin Kim
Hyeon-Jin Kim | “Linking nuclear morphology and chromatin dynamics during mouse embryonic development”
April 8, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Maya Lewinsohn, Cassia Wagner
Maya Lewinsohn | “Linking genotypic and phenotypic spatial heterogeneity in primary prostate cancer”
Cassia Wagner | “Antigenic exposure associated with development of malaria immunity”
April 5, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Morgan Hamm
Morgan Hamm | “Understanding regulatory DNA in plants with Fiber-seq”
April 1, 2022 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation presentations: Hunter Colegrove, Shruti Jain, Connor Kubo, D
first year rotation presentations: Hunter Colegrove, Shruti Jain, Connor Kubo, David Lee, Ben Mallory
March 15, 2022 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation presentations: Lizzie Plender, Sydney Sattler, Elliott Swans
first year rotation presentations: Lizzie Plender, Sydney Sattler, Elliott Swanson, Malvika Tejura
March 11, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Wei Yang
Wei Yang | “Decoding lineage specification in human gastrulation with an in vitro embryo model”
February 25, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Luke Zhu
Luke Zhu | “A tree-based algorithm for identifying mutator alleles from genetic variation data”
February 18, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Sam Hart, Phoebe Parrish
Sam Hart | “Centuries of cancer evolution under the sea: genome evolution of a contagious clam cancer”
Phoebe Parrish | “Enabling cancer drug target discovery through identification of synthetic lethal paralog pairs”
February 11, 2022 3:00 pm – 4:00 pm | Foege Auditorium
Shawn Fayer, Deanna Plubell
Shawn Fayer | “Multiplexed functional assay development in iPSC cardiomyocytes”
Deanna Plubell | “Peptide-level analysis suggests Alzheimer’s disease subtypes”
February 4, 2022 3:00 pm – 4:00 pm | Foege Auditorium
2021
first year rotation presentations
Lizzie Plender, Sydney Sattler, Shruti Jain
December 14, 2021 12:30 pm – 1:30 pm | Foege Auditorium
first year research presentations
Hunter Colegrove, Connor Kubo, David Lee, Ben Mallory, Elliott Swanson, Malvika Tejura
December 10, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Elena Romero
Elena Romero | “Quantifying the impact of viral load on HIV recombination rate”
December 3, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Lincoln Harris
Lincoln Harris | “Imputation of quantitative proteomics data with matrix factorization”
November 19, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Tony Li, Chris McGann
Tony Li | “Sequence-based modeling of cis-regulatory elements across mammalian species”
Chris McGann
November 12, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Chris Hsu, Aidan Keith
Chris Hsu | “Understanding locus-specific chromatin compositions through oligonucleotide spatial proteomics”
Aidan Keith
November 5, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Taylor Real
Taylor Real | “Human-specific evolution and regulatory architectures of segmental duplications associated with cortical brain
expansion”
October 29, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Leah Anderson, Alexis Chang
Leah Anderson | “Using experimental evolution to discover factors that influence freeze-thaw tolerance in yeast”
Alexis Chang | “Technological advancements to understand foundations of cellular communities”
October 22, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Gabrielle Ferra
Gabrielle Ferra | “Understanding the effects of evolution on polar bear introgression in brown bears”
October 15, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Ayse Dincer, Melih Yilmaz
Ayse Dincer | “Inferring peptide coefficients from quantitative mass spectrometry data”
Melih Yilmaz | “Mass spectrometry-based de novo peptide sequencing with deep learning”
October 8, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Austin Gabel, Candice Young
Austin Gabel | “High-throughput functional characterization of cancer specific alternative polyadenylation”
Candice Young | “The consequences of mutating an anti-mutator: how Mutyh protects genomic integrity”
October 1, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Chris Hsu, Chris McGann, Alexis Neuman, Luana Paleologu, Taylor Real, Abbey Thorpe
Chris Hsu, Chris McGann, Alexis Neuman, Luana Paleologu, Taylor Real, Abbey Thorpe | first year rotation talks:
June 8, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Leah Anderson, Gabrielle Ferra, Lincoln Harris, Aidan Keith, Tony Li, Elena Romero
Leah Anderson, Gabrielle Ferra, Lincoln Harris, Aidan Keith, Tony Li, Elena Romero | first year rotation talks:
June 4, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Dani Faivre, Mu Yang
Dani Faivre | “Comparing FAIMS and quadrupole gas phase fractionation”
Mu Yang | “Exploring X dosage compensation with non-negative matrix factorization”
June 1, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Emma Hoppe, Jose Pineda
Emma Hoppe | “Recursive splicing discovery using lariats in total RNA sequencing”
Jose Pineda
May 28, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Cindy Yeh
Cindy Yeh | “High-throughput functional analysis of natural variants in yeast”
May 25, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Ryan Carlson, Soyeon Showman
Ryan Carlson | “Projects in gene discovery for hereditary hearing loss.”
Soyeon Showman | “Massively parallel functional characterization of CYP2D6 missense variants”
May 18, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Michael Goldberg, Michelle Noyes
Michael Goldberg | “Variation in germline de novo mutagenesis in human families”
Michelle Noyes
May 14, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Xingfan Huang, Chengxiang Qiu
Xingfan Huang | “Temporal dynamics of the regulatory landscape in Drosophila embryonic development”
Chengxiang Qiu | “Systematic reconstruction of the cellular trajectories of mammalian embryogenesis”
May 11, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Miranda Mudge, Rachel Wellington
Miranda Mudge | “Utilizing microbiome peptides to forecast harmful algal blooms”
Rachel Wellington
May 7, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Sam Regalado, Flo Chardon
Sam Regalado | “Elucidating the role of all TFs in early development with multiplexed CRISPR screens”
Flo Chardon | “Single-cell transcriptomics to assess gene function”
May 4, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Kyle Hess, Anthony Valente
Kyle Hess | “Proteome-wide mistranslation identifies functional amino acid residues in yeast”
Anthony Valente | “Phosphopedia 2.0. A modern targeted phosphoproteomics resource”
April 23, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Vanessa Nguyen, Gabe Boyle
Vanessa Nguyen | “Towards understanding Hsp90 chaperoning using deep mutational scanning”
Gabe Boyle
April 16, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Robin Aguilar, Phoebe Parrish
Robin Aguilar | “Visualizing repetitive DNA in situ with Tigerfish”
Phoebe Parrish | “Discovery of synthetic lethal and tumor suppressive paralog pairs in the human genome”
April 9, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Nick Popp, Jackson Tonnies
Nick Popp | “Towards a comprehensive characterization of missense variation in Factor IX”
Jackson Tonnies
April 2, 2021 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation talks
Leah Anderson, Gabrielle Ferra, Lincoln Harris, Chris Hsu, Aidan Keith, Tony Li
March 16, 2021 3:00 pm – 4:00 pm | Foege Auditorium
first year rotation talks
Chris McGann, Alexis Neuman, Luana Paleologu, Taylor Real, Elena Romero, Abbey Thorpe
March 12, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Anna Bakhtina, Wei Yang
Anna Bakhtina | “Quantitative interactome comparison of human cell lines”
Wei Yang | “Constructing a cell-fate map during human gastrulation”
March 5, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Sophie Moggridge, Zorian Thornton
Sophie Moggridge | “PGM1 variant annotation using mass spectrometry”
Zorian Thornton | “A deep learning framework for modeling deep mutational scanning data”
February 26, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Morgan Hamm, Lilian Heil
Morgan Hamm | “Decoding plant regulatory DNA with 300k random enhancers”
Lilian Heil | “The right tool for the job: balancing sensitivity and resolution in targeted proteomics”
February 19, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Xavi Guitart, Kianna Hales
Xavi Guitart | “Investigating the evolution and variation of gene families: TBC1D3”
Kianna Hales | “Self-supervised learning to denoise tandem mass spectra”
February 12, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Conor Camplisson, Madeleine Duran
Conor Camplisson | “paintshop.io: web server and pipeline for optimal FISH probe design”
Madeleine Duran | “Computational Methods for Studying Developmental Robustness with Single-Cell Genomics”
February 5, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Sam Smukowski, Cassia Wagner
Sam Smukowski | “Defects in synaptic-localized translation and its impact in neurodegenerative disease”
Cassia Wagner | “Impact of Spike D614G on the Washington State SARS-CoV-2 epidemic”
January 29, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Anna Minkina, Hyeon-Jin Kim
Anna Minkina
Hyeon-Jin Kim | “Studying nuclear architecture during mouse development”
January 22, 2021 3:00 pm – 4:00 pm | Foege Auditorium
Courtnee Clough
Courtnee Clough | “Coordinated mis-splicing of multiple mitochondrial iron metabolism genes causes ring sideroblast formation
in SF3B1-mutant MDS”
January 15, 2021 3:00 pm – 4:00 pm | Foege Auditorium