VARIANT EFFECTS SEMINAR SERIES (VESS)
An early career scientist led seminar series sponsored by the Atlas of Variant Effects Alliance
In this series, early-career scientists from around the globe share and discuss their research related to interpreting human genetic variation.
Seminars are held on the 1st Tuesday each month from 9-10am Pacific (4-5pm UTC) timezone converter (Add these events to your calendar )
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PREVIOUS SPEAKERS are listed below
2024
Gonzalo Benegas
Pronouns: He/Him
University of California
Presentation Date: November 5th 2024
An alignment-based DNA language model for genome-wide variant effect prediction
Gonzalo Benegas is a postdoc at the University of California at Berkeley working with Yun S. Song. He did his undergraduate studies at the University of Buenos Aires and his graduate studies at UC Berkeley. Gonzalo is interested in genomic language models as a new machine learning tool for interpreting non-coding variants.
Social: @gsbenegas
Moez Dawood
Pronouns: He/Him
Baylor College of Medicine
Presentation Date: November 5th 2024
Using Multiplexed Functional Data to Reduce Variant Classification Inequities in Underrepresented Populations
Moez is a MD/PhD student from the Baylor College of Medicine in Houston,TX, USA and is mentored by Dr. Richard Gibbs and Dr. Jim Lupski. Moez uses saturation genome editing to study rare disease and mRNA surveillance.
Social: @MoezDawood
Saori Sakaue
Pronouns: She/Her
Harvard Medical School and Broad Institute
Presentation Date: October 1st 2024
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles
Saori is a physician scientist currently working as an Instructor with Dr. Soumya Raychaudhuri’s lab at Harvard Medical School and Broad Institute. She is interested in developing integrative analytical methods with population-scale genetics and multi-modal single-cell genomics data to define causal mechanisms of autoimmune diseases. She will be joining the department of Genome Sciences at University of Washington as an Assistant Professor in 2025.
Social: @saorisakaue
Priyanka Bajaj
Pronouns: She/Her
UCSF
Presentation Date: October 1st 2024
Structural and functional determinants inferred from deep mutational scans
Priyanka did her Ph.D. from Molecular Biophysics Unit, Indian Institute of Science under Prof. Raghavan Vardarajan. Her Ph.D. work involved developing high-throughput screens for measuring the mutational sensitivity of the toxin component of the toxin-antitoxin system of E. coli. She carried out deep mutational scans of the site-saturation mutagenesis library and synonymous codon substitution library of the toxin gene in operonic context to understand mutational effects on protein activity, stability and co-translational folding. Currently Priyanka is undergoing her postdoctoral training under James Fraser and Willow Coyote-Maestas at UCSF. She has generated novel-types of re-combinatorial libraries of fusion proteins with the goal to determine the structural basis of fusion protein oncogenesis.
Social: @Priyank67495046
Annique Claringbould
Pronouns: She/Her
University Medical Center (Rotterdam)
Presentation Date: September 3rd, 2024 (1st speaker)
Leveraging single-cell transcriptomics to study complex diseases
Annique Claringbould studied life sciences in Utrecht in the Netherlands, continued her studies at Imperial College London and did her PhD at the University Medical Centre Groningen, where she studied the effect of genetic variants on gene expression. In her postdoc at EMBL in Heidelberg, Annique constructed gene regulatory networks, and she has recently started at the university medical centre in Rotterdam. Her research focus is understanding disease through gene regulation and genetics.
Social: @AnniqueC
Craig Markin
University of Manchester
Presentation Date: September 3rd, 2024 (2nd speaker)
Developing and deploying high-throughput quantitative microfluidics for understanding mutational effects in enzymes
Craig Markin is a Fellow in the Manchester Institute of Biotechnology and the Division of Molecular and Cellular Function at the University of Manchester. His group's research is focused on understanding the molecular and physical basis of protein and enzyme function with the goal of addressing the two challenges of making enzyme design and engineering more rational and understanding the biological consequences of disease variants. In his postdoctoral work with Profs. Dan Herschlag and Polly Fordyce at Stanford University, Craig led the development of HT-MEK (High-Throughput Microfluidic Enzyme Kinetics), a novel microfluidics-based assay to express, purify, and quantitatively measure a variety of kinetic and thermodynamic constants for >1000 enzyme variants in parallel. In his graduate work with Prof. Leo Spyracopoulos at the University of Alberta, Craig studied the molecular mechanisms of polyubiquitin chain synthesis and their subsequent recognition by partner proteins in the DNA damage response with the aim of understanding how the kinetics and thermodynamics of these processes dictate biological outcomes.
Jingyou Rao
Pimentel lab, University of California
Presentation Date: August 6th 2024
Modeling Growth-based Deep Mutational Scanning Counts with Rosace
Modeling Deep Mutational Scanning with position and mean-variance shrinkage
Jingyou is a Computer Science PhD candidate under Pimentel lab at University of California, Los Angeles. Her research focuses on building experiment-driven statistical tools for perturbation experiments, including deep mutational scanning
Social: @JingyouR
Ayesha Muhammad
Pronouns: She/Her
Second-year resident physician, University of Michigan
Presentation Date: August 6th 2024
Multiplexed assays of the IKs channel complex
Ayesha Muhammad (she/her) is a resident physician in the Department of Anesthesiology at the University of Michigan. In 2023, she graduated from Vanderbilt University with an MD and a PhD in Human Genetics completed in the lab of Dr. Dan Roden. Her dissertation ("Addressing Challenges to Genomic Medicine: Effects of Rare and Common Variation on Arrhythmia and Pharmacogenetic Phenotypes"), which was partially funded by an American Heart Association predoctoral grant, featured multiplexed assays of KCNE1 variant trafficking and function. She has presented her research at many national and international conferences and was the Vanderbilt University School of Medicine Founder's Medalist in 2023. She hopes to pursue a career as a physician-scientist upon completion of her clinical training.
Social: @ayeshamyar
Matthew Durrant
Patrick Hsu Lab, Arc Institute
Presentation Date: July 2nd 2024
(co-presenting with Nicholas Perry)
“Bridge RNAs direct programmable recombination of target and donor DNA”
Matt Durrant received his PhD from Stanford University in 2020, working in the labs of Ami Bhatt and Stephen Montgomery on computationally characterizing mobile genetic elements. He continued on to a short postdoc in the lab of Patrick Hsu at UC Berkeley, where he discovered and characterized new large serine recombinases (LSRs) that could efficiently integrate DNA cargos into the genomes of human cells. He then transitioned to a senior scientist position in the Hsu Lab at the Arc Institute, where he continues his work with a focus on programmable recombinases and genome design.
Social: @mgdurrant
Nicholas Perry
Presentation Date: July 2nd 2024
(co-presenting with Matthew Durrant)
“Bridge RNAs direct programmable recombination of target and donor DNA”
Nicholas Perry is a current PhD student in the UC Berkeley - UCSF Joint Bioengineering program. He is conducting his research in Patrick Hsu's Lab at the Arc Institute, focusing on discovery and characterization of programmable recombinases.
Social: @ntperry13
Arjun Aditham
Pronouns: He/Him
Jesse Bloom Lab, Fred Hutchinson Cancer Center
Presentation Date: July 2nd, 2024
“Deep mutational scanning reveals mutational constraints of the Rabies virus glycoprotein”
WATCH RECORDING (forthcoming)
Arjun received his PhD in Bioengineering from Stanford University working in Polly Fordyce's Lab, where he developed high-throughput platforms for measuring Transcription Factor-DNA binding affinities. He then transitioned to a postdoctoral position at Jesse Bloom's Lab. Outside of Lab, Arjun enjoys educational outreach, running, plane spotting, and listening to podcasts.
Social: @arjunine
Raquel Cuella Martin
Pronouns: She/Her
Department of Human Genetics, McGill University
Presentation Date: June 4th 2024
“Precision genome editing to study protein function”
Raquel Cuella Martin is an Assistant Professor at the Department of Human Genetics at McGill University. Her lab applies cutting-edge large-scale precision genome editing to address outstanding mechanistic questions in the DNA damage response and their association with human disorders. Raquel undertook her Ph.D. studies at Dr. JR. Chapman’s lab at the Wellcome Center for Human Genetics (University of Oxford). During this time, Raquel described the mechanistic role of the DNA repair protein 53BP1 in optimal p53 tumor suppressor responses. In her postdoctoral work as an EMBO long-term fellow at the Ciccia lab (Columbia University), she used CRISPR-dependent base editing to perform genetic screens at nucleotide resolution and functionalize DNA variants at scale. Such an approach allowed her to identify loss-, gain- and separation-of-function mutations, and new functional domains in DNA damage response proteins, and to functionalize variants of uncertain significance in cancer predisposition syndromes.
Social: @raquel_cuella
Max Staller
Pronouns: He/Him
Staller Lab, University of California, Berkeley
Presentation Date: June 4th 2024
“Evolution of transcriptional activation domains”
Recording not available as per speaker’s preference
Max’s lab experience began with Sean Connolly and Jorge Benach at Stony Brook University. Max graduated from Princeton University with a major in Molecular Biology and a minor in Quantitative and Computational Biology, completing a senior thesis with David Botstein. Max completed graduate studies in the Systems Biology program at Harvard University, where he worked with Angela DePace. Max pursued his postdoctoral work at Washington University in St. Louis working with Barak Cohen and Rohit Pappu. Outside of lab, Max enjoys hiking, skiing and cooking.
Social: @maxvstaller
Anna Axakova
Pronouns: She/Her
The Roth Lab, University of Toronto
Presentation Date: May 7th 2024
“Systematically and proactively testing variant effects for the autoimmune regulator gene”
Anna Axakova is a Molecular Genetics PhD candidate at the University of Toronto.
Gonzalo Parra
Pronouns: He/Him
Barcelona Supercomputing Center
Presentation Date: May 7th 2024
“Local Energetic Frustration Through Time and Species”
Gonzalo Parra is an Argentine scientist who got a Bioinformatics degree from Universidad Nacional de Entre Rios followed by a Ph.D. from Buenos Aires University in Argentina. He was an EMBO postdoctoral researcher in the group of Dr. Johannes Soeding at the Max Planck Institute for Biophysical Chemistry in Goettingen, Germany. Then moved to work as a postdoctoral researcher in the group of Prof. Oliver Stegle at the European Molecular Biology Laboratory and the German Cancer Research Center in Germany. Since 2021, Gonzalo works at the Barcelona Supercomputing Center where he tries to understand the molecular mechanisms behind protein evolution, stability, function and dynamics both in healthy conditions as in disease. In addition, Gonzalo participates in multiple international forums to make science a more equal, diverse and inclusive environment. Gonzalo is currently a member of the International Society for Computational Biology (ISCB) Board of Directors, he is one of the co-chairs of the ISCB 3DSig COSI, a member of the ISCB EDI committee, a steering committee member of the 3DBioinfo Elixir community, a member of the advisory board of the Bioinfo4Women programme and a Working Group lead within the Machine Learning for Non Globular Proteins COST action.
Ian Hoskins
Pronouns: he/him
Cenik Lab, UT Austin
Presentation Date: April 2nd 2024
“Integrated multiplexed assays of variant effect reveal cis-regulatory determinants of catechol-O-methyltransferase gene expression”
Ian Hoskins was raised in Colorado and received his Bachelor’s of Science in Integrative Biology with a minor in Chemistry from The University of Colorado at Denver. He entered the biotechnology sector and worked at Enzymatics, Inc. and ArcherDX, Inc. between 2013 and 2018 developing genomic assays and software for clinical cancer research. Ian was admitted in The University of Texas at Austin Microbiology graduate program in 2018 and joined the lab of Dr. Can Cenik as his supervisor’s first graduate student.
Gabriella Estevam
Pronouns: she/her
Fraser Lab, UCSF
Presentation Date: April 2nd 2024
“Exploring the landscape of MET kinase domain mutations and inhibitor resistance”
Gabriella is a recent alum of the Fraser Lab at UCSF, where she studied the phenotypic and resistance landscape of the MET receptor tyrosine kinase. Her research focused on deciphering kinase domain regulatory motifs and resistance mechanisms to tyrosine kinase inhibitors. Additionally, she studied the relationship between the MET kinase domain and juxtamembrane.
Social: @GabbyEstevam
Ben Livesey
Pronouns: he/him
Marsh Lab, The University of Edinburgh
Presentation Date: March 5th 2024
“Independent benchmarking of variant effect predictors with deep mutational scanning datasets.”
Dr. Benjamin Livesey is a postdoctoral researcher currently working at the Institute of Genetics and Cancer at The University of Edinburgh. Over the course of his PhD and postdoc, Ben has worked towards finding an unbiased method to assess the performance of computational variant effect predictors.
Social: @BenLivesey6
Clare Bycroft
Pronouns: She/her
Affiliation: Google DeepMind
Presentation Date: March 5th 2024
“Accurate proteome-wide missense variant effect prediction with AlphaMissense.”
Recording not available as per speaker’s preference
Dr. Clare Bycroft is a research scientist at Google DeepMind with a background in human genetics. She has a particular focus on ensuring the utility of deep learning models in real-world settings. Previously, Clare worked at Genomics PLC, an Oxford-based biotech using human genetics data to propose new therapeutic targets; and during her PhD (University of Oxford), she curated the first tranche of the UK Biobank genotyping data set.
Sriram Pendyala
Fowler Lab, University of Washington
Presentation Date: February 6th 2024
“Multiplexed Optical Screening of protein variant localization”
Sriram majored in Chemistry and Physics in Boston and is now an MSTP student in Doug Fowler’s lab at Seattle’s UW Genome Sciences developing technology to study protein variation using microscopy. He also works on screening cytokine treatments in T-cells to develop better cell therapies. His hobbies include biking, hiking, and skiing.
Phillip Huss
Pronouns: he/him
Raman Lab, University of Wisconsin-Madison
Presentation Date: February 6th 2024
“Understanding and engineering bacteriophages by exploring sequence-function landscapes”
Phil is a postdoctoral fellow in the Raman lab at the University of Wisconsin-Madison where he studies bacteriophage host interactions. He investigates how genetic perturbations influence the sequence-function landscape of phages and their bacterial hosts. His current research extends his doctoral work using large unbiased libraries of phage variants with the goal of engineering programmable synthetic phages for diverse biotechnology applications.
Social: @phil_huss
Nadav Brandes
Ye Lab, UCSF
Presentation Date: January 9th, 2024
“Large language models of protein sequences are accurate, effective and general variant effect predictors”
Dr. Nadav Brandes obtained his PhD in Computer Science from the Hebrew University of Jerusalem, and is currently a Cancer Research Institute (CRI) and European Molecular Biology Organization (EMBO) postdoctoral fellow at University of California, San Francisco (UCSF). His research focuses on the development of machine and deep learning approaches to study the effect of genetic variation on human traits and diseases.
Social: @BrandesNadav
King Hung
Pronouns: he/him
Chang Lab, Stanford University
Presentation Date: January 9th, 2024
“Oncogenes outside chromosomes”
King Hung is a PhD candidate at Stanford University. His research focuses on the regulation of gene expression and organization of the genome in disease and development. His recent work with Howard Chang at Stanford aims to uncover mechanisms of oncogene upregulation on extrachromosomal DNA in human cancer.
Social: @kinglhung
2023
Carlos Marti-Gomez
McCandlish Lab, CSHL
Presentation Date: December 5th, 2023
“Understanding complex genotype-phenotype maps”
I am a postdoctoral researcher at Cold Spring Harbor Laboratory in the McCandlish lab. My research focuses on the study of complex combinatorial genotype-phenotype maps to study the genetic architecture of different molecular phenotypes, e.g. rna, protein interactions; and their consequences for long-term molecular evolution. With this aim, I also develop computational tools to facilitate the inference and visualization of complex genotype-phenotype maps from different types of data, which may be of interest to the community (https://gpmap-tools.readthedocs.io/en/latest/).
Social: @cmarti_ga
Juannan Zhou
University of Florida
Presentation Date: December 5th 2023
“Modeling higher-order genetic interactions in sequence-function relationships”
Dr. Juannan Zhou completed his PhD training in the area of evolutionary biology. He worked in the McCandlish lab at the Cold Spring Harbor Laboratory from 2017 to 2021, with a focus on development of theoretical and computational methods for modeling sequence-function relationships. He joined the Department of Biology at the University of Florida in Fall 2021. His current research directions include developing machine learning methods for modeling genotype phenotype maps, the genetic architecture of complex traits, and experimental evolution.
Social: @keitokiddo
Willow Coyote-Maestas
Assistant Professor, UCSF
Presentation Date: November 7th 2023
“Bridging the gap between pharmacogenomics and transporter biophysics using mutational scanning”
Willow Coyote-Maestas is an Assistant Professor in Bioengineering and Therapeutic Sciences at University of California, San Francisco. His lab focused on building biophysical, molecular, and cellular understanding of the secret life of membrane proteins. They build and apply scalable technologies to learn how membrane proteins underlie our physiology, what goes awry in disease, and how to better treat these diseases with therapeutics.
Social: @willowcoyote
Raehoon Jeong
Bulyk Lab, Harvard Medical School
Presentation Date: November 7th 2023
“Blood cell traits’ GWAS loci colocalization with variation in PU.1 genomic occupancy prioritizes causal noncoding regulatory variants”
Raehoon Jeong is a Bioinformatics and Integrative Genomics PhD student in the Bulyk Lab at Harvard Medical School. He earned his Bachelor’s degree at Swarthmore College in Mathematics and Computer Science, and he will soon defend his dissertation at Harvard in August. Raehoon is interested in applying statistical genetics and machine learning approaches to better understand how genetic variants affect gene expression and cause diseases.
Megan Buckley
Findley Lab, Crick Institute
Presentation Date: October 3rd 2023
“Resolving the functional spectrum of pathogenic alleles across VHL”
Megan graduated in Biochemistry from the University of Oxford, where in her final year she joined Doug Higgs’s lab researching gene regulation at the alpha-globin locus. After completing her studies in 2020, Megan joined Greg Findlay at the Francis Crick Institute in London, researching in functional genomics. Megan worked at the Crick for 2 years before beginning her PhD at Cambridge in October 2022, now working in chromatin and epigenetics.
Social: @megan_buckley01
Adrine de Souza
Roth Lab, University of Toronto
Presentation Date: October 3rd 2023
“Large-scale testing of nearly all possible AGXT missense variant effects in the reference allele and in a double mutant background (the minor allele: Pro11Leu, Ile340Met)”
Adrine is a PhD student at The University of Toronto in the Department of Molecular Genetics. Supervised by Dr. Fritz Roth, she is leading to large-scale variant effect testing of the VHL and AGXT genes. Using VAMP-seq and yeast complementation assays she is providing evidence for variant interpretation of renal cell carcinoma, VHL disease and Primary Hyperoxaluria Type I patients. Adrine completed undergraduate studies in Biotechnology in Brazil and participated in an exchange program in Boston. She is interested in scientific communication, implementation of evidence-based care and teaching.
Social: @adrinedesouza
Florian Wünneman
Schapiro Lab, Heidelberg University
Presentation Date: September 5th 2023
“Using multimodal CRISPR perturbations to prioritize coronary artery disease risk loci in vascular endothelial cells”
Florian is an expert in cardiovascular disease and functional genomics, currently working as a Postdoc in the group of Denis Schapiro at the Institute for Computational Biomedicine in Heidelberg. He acquired his PhD from the University of Muenster working together with the group of Dr. Gregor Aldenfinger at the CHU Ste Justine research center in Montreal, working on congenital heart disease. Following his PhD, Florian joined the lab of Guillaume Lettre at the Montreal Heart Institute, where he focused on the genetic architecture of complex cardiovascular diseases using functional genomics tools, such as pooled CRISPR screens. In his talk, Florian will share insights on how to utilize different CRISPR perturbations to investigate genetic loci associated with complex cardiovascular phenotypes.
Social: @Flowuenne
Xiaoyi Li
Shendure Lab, UW
Presentation Date: September 5th 2023
“Chromatin context-dependent regulation and epigenetic manipulation of prime editing”
Xiaoyi is a postdoctoral fellow in the Jay Shendure Lab in the department of Genome Sciences at the University of Washington. She earned her Bachelor’s degree at Tsinghua University and received a PhD at Memorial Sloan Kettering Cancer Center. Xiaoyi is interested in developing new molecular tools to dissect the roles of the epigenome in genome engineering and gene regulation.
Social: @XiaoyiLi10
William Bakhache
Laboratory of Viral Diseases, NIH-NIAID
Presentation Date: August 1st 2023
“Deep Insertional Screening reveals hotspots for the insertion of useful tags in the non-polio Enterovirus, EV-A71”
William Bakhache is a postdoctoral fellow at the Quantitative Virology and Evolution Unit (QVEU) at the Laboratory of Viral Diseases (NIH-NIAID, Bethesda MD, main campus) under the supervision of Patrick Dolan, Ph.D. At the QVEU, William is developing approaches to explore the mutational landscape of viral proteins. In his talk, William will share his unpublished work related to investigating the tolerance of a variety of insertion sequences in viral proteomes.
Social: @WBakhache
Haider Inam
Pritchard Lab, Penn State University
Presentation Date: August 1st 2023
“Quantifying resistance to targeted anticancer therapies in BCR-ABL using an error-corrected DMS workflow”
Haider is a PhD student Biomedical Engineering in the Pritchard Lab at Penn State University. His work focuses on quantifying drug resistance to targeted anticancer therapeutics at scale. Variants of uncertain drug resistance in cancer are an analogous problem to VUS, but face unique technical barriers in DMS screens. To overcome these barriers, Haider built a scalable duplex sequencing workflow that enables deep error-corrected sequencing of variant libraries. He then applied this workflow to study resistance to targeted therapies in the BCR-ABL fusion protein. This workflow is able to successfully detect and quantify known resistant variants, as well as rare variants of unknown drug resistance in BCR-ABL. In this way, DMS screens can identify drug resistance variants long before they are seen in the clinic. This prospective detection of drug resistant variants can help guide clinical treatment decision-making as well as prioritize mutants to study for drug discovery efforts.
Social: @HaiderInam
Florence Chardon
Shendure and Starita Labs, University of Washington
Presentation Date: June 6th 2023
“Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements”
Florence is a PhD student in the Shendure and Starita labs in the department of Genome Sciences at the University of Washington. After receiving her B.S. in chemistry at UC Berkeley, Florence spent three years at Genentech working in monoclonal antibody therapeutic development before starting graduate school. The focus of her PhD is developing novel multiplex single-cell and bulk functional genomics sequencing-based technologies to study and better understand gene regulatory architecture and the consequences of genetic variation in numerous different in vitro cell culture models. The main application of this work relates to understanding and identifying both proximal and distal regulatory regions that regulate neurodevelopment and autism disorder risk genes with a goal of helping develop gene therapies for these disorders.
Social: @FloChardon
John Morris
Sanjana and Lappalainen Labs, NYGC
Presentation Date: June 6th 2023
“Beyond GWAS: Massively parallel genome engineering to pinpoint causal variants and target genes”
Dr. John Morris is a human geneticist and genome engineer. He earned his Bachelor's degree in Biology at the University of Western Ontario, then went on to complete a Ph.D. in Human Genetics at McGill University, in the lab of Brent Richards. His PhD focused on identifying the genetic determinants of osteoporosis through genome-wide association studies of bone traits in large-scale biobanks. He is currently a Postdoctoral Fellow at the New York Genome Center and New York University, in the labs of Neville Sanjana and Tuuli Lappalainen, where has developed single-cell pooled CRISPR screens to study noncoding GWAS loci. John's postdoctoral work linking GWAS variants to genes and functions, STING-seq, expands our ability to understand mechanisms underlying GWAS loci. John's achievements have been recognized by multiple agencies, as he was awarded both a CIHR Banting Fellowship and NHGRI K99 Fellowship, and was a 2021 winner of the ASHG Charles J. Epstein Excellence Award.
Social: @johnomix
Ohanna Cavalcanti L. Bezerra
Dalla Lana School of Public Health, University of Toronto
Presentation Date: May 2nd 2023
“Signatures of natural selection affecting disease risk in admixed population”
After studying Biomedicine from the Federal University of Rio de Janeiro State (UNIRIO) for her bachelor’s degree, Ohanna received a master's and PhD degree in Cellular and Molecular Biology from the Oswaldo Cruz Foundation (FIOCRUZ/Brazil). Her dissertation focused on the Genetic Epidemiology of Infectious Diseases. Currently, she is a Postdoc of the CANSSI Ontario STAGE HostSeq Project in Dalla Lana School of Public Health at University of Toronto, studying genetics and epigenetics of complex traits.
Warren van Loggerenberg
Roth lab, University of Toronto
Presentation Date: May 2nd 2023
“Variant effect mapping for acute hepatic porphyrias”
Warren is a postdoctoral researcher at the University of Toronto in the laboratory of Dr. Frederick Roth. His research focuses on using multiplexed assays to measure the functional impact of missense variants across human disease genes associated with neurodegenerative, immune and metabolic disorders. Warren completed his PhD at the University of Guelph under the supervision of Dr. Ross N. Nazar. His PhD research focused on the structure, synthesis and regulation of eukaryotic ribosomes in normal and oncogenic tissues.
Social: @WarrenvanLogge1
Antje Rottner
AstraZeneca
Presentation Date: April 4th 2023
“From GWAS to Causal Genes – A CRISPR Screen for Type 2 Diabetes”
Antje completed her PhD in Medical Sciences at the University of Oxford and is currently working as a Postdoctoral fellow at AstraZeneca in Gothenburg, Sweden. In her PhD, supervised by Prof Anna Gloyn, she focused on identifying genes mediating Type 2 Diabetes risk and as part of her work, Antje developed the first genome-editing pipeline in an authentic human beta-cell model and performed a genome-wide CRISPR screen for human pancreatic beta-cell dysfunction. Since her MSc in Cell and Gene Therapy at the University College London, she has been fascinated by the insights gained from genetic studies to develop targeted or personalised therapies. Her postdoctoral work at AstraZeneca now builds on her interest in using genome editing to understand the molecular mechanisms underlying disease causing mutations.
Social: @antje_rottner
Samuele Cancelieri
Giugno Lab, University of Trento
Presentation Date: April 4th 2023
“Human genetic diversity alters off-target outcomes of therapeutic gene editing.”
Dr. Samuele Cancellieri is postdoctoral fellow at University of Trento. His work spans from software and algorithm development for CRISPR targets prediction using SNVs and INDELs, to genomic and transcriptomic analysis and data processing for identification of gene’s isoforms related to neuropsychiatric diseases.
Guillaume Butler-Laporte
Canadian Institutes for Health Research fellow at the University of Oxford
Presentation Date: March 7th, 2023
“Slowly unravelling the HLA: an application to vaccinology using the UK Biobank whole-exome sequencing.”
Guillaume is an infectious diseases clinician-scientist and currently a Canadian Institutes for Health Research fellow at the University of Oxford. He is a graduate of Brent Richards' genetic epidemiology lab at the Lady Davis Institute (McGill University), where he was actively involved in the genetic community's COVID-19 research response.
Social: @GBL_Unit
Dan Weiner and Ajay Nadig
Harvard Medical School
Presentation Date: March 7th, 2023
“Polygenic architecture of rare coding variation across 394,783 exomes.”
Dan Weiner is an MD/PhD candidate at Harvard Medical School. He recently defended his PhD in Bioinformatics and Integrative Genomics, focused on statistical and functional integration of common and rare genetic variation across complex traits and common diseases.
Social: @danweiner92
Ajay is an MD/PhD student at Harvard Medical School and the Massachusetts Institute of Technology. He is broadly interested in statistical and functional genomics, with particular emphasis on psychiatric and neurodevelopmental disorders. He is advised by Drs. Elise Robinson and Luke O'Connor at the Broad Institute.
Social: @NadigAjay
Nicholas Lue
Liau Lab, Harvard University
Presentation Date: Jan 10th, 2023
“Charting the activity landscape of DNMT3A through base editor scanning”
Nicholas Lue is a graduate student in the Chemical Biology Ph.D. program at Harvard University working in the laboratory of Prof. Brian Liau. His work focuses on applying interdisciplinary approaches, including genome editing and protein biochemistry, to study DNA Methyltransferase 3A, a key cancer target.
Social: @nicklue8
2022
Megan Le
Narasimhan Lab, University of Texas at Austin
Presentation Date: Dec 06 2022
“1,000 ancient genomes uncover 10,000 years of natural selection in Europe”
Megan is pursuing an integrated B.S. in Computer Science / M.S. in Computational Science, Engineering, and Mathematics at the University of Texas at Austin. She is a research assistant in the Narasimhan Lab analyzing time-stratified ancient DNA data to understand natural selection.
Social: @megankle
Sofia Battaglia
Bernstein Lab, DFCI and the Broad Institute
Presentation Date: Dec 06 2022
“Single-molecule regulatory landscapes”
Sofia Battaglia is a postdoctoral researcher in Brad Bernstein's group at the Dana Farber Cancer Institute (DFCI) and the Broad Institute. Her work focuses on developing and applying novel technologies for understanding long range interactions of regulatory elements of human complex loci, by leveraging ultralong-read epigenomic profiling on single DNA molecules. Prior to joining the Bernstein lab, Sofia did her PhD in the laboratory of Prof. Dr. Patrick Cramer at the Max-Planck-Institute (MPI) for Biophysical Chemistry in Göttingen and Munich University, studying the role of nascent mRNA in the recruitment of elongation factors to the transcription machinery.
Social: @Sofi_Battaglia
Tyler Starr
Starr Lab, University of Utah
Presentation Date: Nov 01 2022
“Evolution of SARS-CoV-2 and related bat coronaviruses”
Tyler Starr is a NIH Pathway to Independence (K99) Fellow and an incoming Assistant Professor in the Department of Biochemistry at the University of Utah. Dr. Starr received his Ph.D. in Biochemistry and Molecular Biophysics from the University of Chicago, where he studied protein evolution in the lab of Dr. Joe Thornton. He then moved to the Fred Hutchinson Cancer Center to conduct postdoctoral research on viral evolution in the lab of Dr. Jesse Bloom. Dr. Starr’s research explores the evolutionary arms races between viruses and host factors involved in infection and immunity. Dr. Starr uses high-throughput “deep mutational scanning” assays to characterize the protein-protein interactions between viral glycoproteins, host receptors, and antiviral antibodies. These experiments reveal the biophysical details of protein sequence-structure-function relationships and provide maps for understanding viral evolution. Since 2020, Dr. Starr has applied these approaches to study SARS-CoV-2, informing ongoing efforts in viral forecasting and aiding in the development of vaccines and monoclonal antibodies to combat COVID-19. His lab will continue to extend these approaches to understand the deeper molecular evolutionary features that drive the emergence of animal viruses that spill over into humans and to inform the development of vaccines and antibodies that can treat or prevent future viral spillovers.
Social: @tylernstarr
Daniel Schraivogel
Steinmetz Lab, EMBL
Presentation Date: Oct 04 2022
“Genome-scale functional genomics screens with image-enabled cell sorting”
Dr. Daniel Schraivogel works as a research staff scientist in the laboratory of Dr. Lars Steinmetz at the European Molecular Biology Laboratory (EMBL). He develops and applies novel technologies in the functional genomics space, by combining high-throughput CRISPR/Cas9 genetic screens with complex readouts from single cells. These technologies aim to provide a better understanding of genotype-phenotype correlations in health and disease by scaling with the complexity of the human genome. Prior to joining EMBL, Daniel did his PhD in the laboratory of Prof. Dr. Gunter Meister at the Max-Planck-Institute (MPI) of Biochemistry in Munich and Regensburg University, studying the function of short non-coding RNAs and their associated proteins.
Social: @SchraivogelS
Roshni Patel
Pritchard Lab, Stanford University
Presentation Date: Sept 06 2022
“Genetic interactions drive heterogeneity in causal variant effect sizes”
Roshni is a PhD candidate in Jonathan Pritchard's group at Stanford University. Her work focuses on developing statistical methods for understanding the genetic architecture of human complex traits, often by leveraging data from multiple populations.
Social: @RoshniAPatel
Franco Izzo
Landau laboratory, Weill Cornell Medicine and the New York Genome Center
Presentation Date: Sept 06 2022
“Mapping genotypes to phenotypes through single cell resolution multi-modal approaches”
Dr. Franco Izzo is an Instructor of Molecular Biology in Medicine at Weill Cornell Medicine and the New York Genome Center. His research focuses on clonal hematopoiesis and myeloproliferative neoplasms, where he aims to link genotypes to phenotypes within human samples by applying single cell multi-omics. Dr. Izzo is supported by the American Society of Hematology Fellow-to-Faculty Scholar awards.
Social: @FrancoIzzo85
Jeffrey Calhoun
Carvill laboratory, Northwestern University
Presentation Date: Aug 02 , 2022
“mTORC1 functional assay reveals SZT2 loss-of-function variants and a founder in-frame deletion”
Jeff received a PhD in Cellular and Molecular Biology at the University of Michigan in 2013 under the mentorship of Dr. Lori Isom. For his postdoctoral training, he studied the genetics of epilepsy in mice and humans in the laboratories of Dr. Jennifer Kearney and Dr. Gemma Carvill. His research interests focus on improving the genetic diagnosis of epilepsy through genome sequencing, machine learning, and functional characterization of variants of uncertain significance.
Social: @calhoujd
Sarah Gersing
Hartmann-Petersen laboratory, University of Copenhagen
Presentation Date: Aug 02, 2022
“A comprehensive map of human glucokinase variant activity”
Sarah is a PhD student in Rasmus Hartmann-Petersen’s group at the University of Copenhagen. Her work focuses on characterizing the effects and mechanisms of variants in the human enzyme glucokinase using deep mutational scanning in yeast.
Social: @s_gersing
Matt Coelho
Garnett laboratory, Wellcome Sanger Institute
Presentation Date: June 07, 2022
“Base editing screens map mutations affecting IFNg signalling in cancer”
Matt is a postdoctoral researcher in the Garnett laboratory at the Wellcome Sanger Institute, Cambridge, UK. His research is focused on functional genomics strategies to understand molecular pathways involved in sensitivity to cancer immunotherapies. Matt has gained prior expertise in cancer immunotherapy in the laboratory of Julian Downward at the Francis Crick Institute, and CRISPR and base editing technologies at AstraZeneca.
Social: @mattcoelho3
Antonio Mollica
Cohn lab, University of Toronto
Presentation Date: May 03, 2022
“Identifying novel pathogenic mechanisms in brain development disorders”
Recording not available as per speaker’s preference
Antonio is a PhD candidate in Ronald Cohn’s laboratory at the Hospital for Sick Children in Toronto. He is interested in the challenges of gene discovery for rare genetic diseases. His work focuses on defining a novel role for variants causing complex brain development disorders.
Social: N/A
Marty Yang
Greenberg lab, Harvard Medical School
Presentation Date: April 5th, 2022
“Genetic dissection of enhancer function”
Marty is a Ph.D. student in Michael Greenberg’s laboratory at Harvard Medical School. His work focuses on using genetic variation to understand how transcription factors control cis-regulatory function in the native chromatin context.
Social: @MartyYang
Shawn Fayer
Fowler and Starita labs, UW
Presentation Date: April 5th, 2022
“Closing the gap: Systematic integration of multiplexed functional data resolves variants of uncertain significance in BRCA1, TP53, and PTEN”
Shawn is a genetic counselor and PhD candidate at the University of Washington coadvised by Doug Fowler and Lea Starita. His work focuses on the clinical integration of multiplexed functional assay data and generation of multiplexible assays in pluripotent stem cells.
Social: @ShawnFayerGC
Haley Randolph
Barreiro lab, University of Chicago
Presentation Date: March 1st, 2022
“Genetic ancestry effects on the response to viral infection are pervasive but cell type specific”
Haley is a PhD candidate in Luis Barreiro's group at the University of Chicago. She works at the interface of genomics and immunology to understand how transcriptional and genetic variation influence differences in the immune response to pathogens across individuals.
Social: @he_randolph
André Faure
Lehner lab, Centre for Genomic Regulation
Presentation Date: March 1st, 2022
“Mapping the energetic and allosteric landscapes of protein binding domains”
André is a senior postdoc in Ben Lehner's group at the Centre for Genomic Regulation (CRG) in Barcelona. His work focuses on developing software for the analysis and modelling of deep mutational scanning (DMS) data in order to better understand how biological sequences encode biophysical properties.
Social: @aj4re
Oana Ursu
Regev Lab, Genentech
Presentation Date: February 1st, 2022
“Phenotyping coding variants in cancer using Perturb-seq”
Bio: Oana is a postdoc working with Prof. Aviv Regev at Genentech. She studies the molecular basis of cellular decisions and resulting cell states using pooled high-content screening, applied to profile the impact of coding variation in cancer (collaboration with JT Neal, Jesse Boehm at the Broad Institute).
Twitter: @oana__ursu
2021
Mafalda Dias & Jonathan Frazer (co-presenters)
Debora Marks Lab, Harvard
Presentation Date: December 7th, 2021
“Disease variant prediction with deep generative models of evolutionary data”
Bio(s): Mafalda and Jonathan are senior postdocs in Debora Marks’ group at Harvard Medical School. They work at the intersection of computational biology and machine learning, developing probabilistic models of sequence data with an emphasis on predicting risk of disease from genetic variation.
Twitter: @MafaldaFigDias
Twitter: @Jonnygfrazer
Mireia Seuma
Benedetta Bolognesi’s Lab at the Institute for Bioengineering of Catalunya (IBEC) in Barcelona
Presentation Date: December 7th, 2021
“Mapping amyloid nucleation by Deep mutational scanning”
Bio: Mireia is a PhD student in Benedetta Bolognesi’s Lab at the Institute for Bioengineering of Catalunya (IBEC) in Barcelona. We use deep mutational scanning to understand and predict how genetic variation impact amyloid formation in Alzheimer’s and other neurodegenerative diseases.
Twitter: @mseumaar
Jonas Koeppel
Leopold Parts lab, Cambridge, United Kingdom
Presentation Date: November 2nd, 2021
“Determinants of efficiency for writing small sequences into the genome using prime editing”
Bio: Jonas is a PhD student at the Wellcome Sanger Institute in Leopold Parts’ laboratory. He focuses on modelling structural variants in disease using synthetic genomics.
Twitter: @jonaskoeppel
Xiaoyan ‘Isaac’ Jia
贾小彦
Kitzman lab, Cambridge, University of Michigan
Presentation Date: November 2nd, 2021
“Systematic functional interrogation of the Lynch Syndrome gene MLH1 by deep mutational scanning”
Recording not available as per speaker’s preference
Bio: Isaac Jia is postdoc fellow in Jacob Kitzman's lab at University of Michigan, Ann Arbor, United States. He and colleagues in the Kitzman lab use high-throughput assays such as deep mutational scanning to produce functional evidence for Lynch Syndrome genetic variants. He will soon launch an independent lab in the Greater Bay Area Institute of Precision Medicine in Guangzhou, China.
Twitter: @jia_xiaoyan
Steven Erwood
Ronald Cohn lab, Toronto, Canada
Presentation Date: September 7th, 2021
“Saturation variant interpretation using prime editing”
Bio: Steven is a PhD student in Ronald Cohn’s laboratory at the Hospital for Sick Children in Toronto. He is interested in developing new methodologies for understanding genome variation, with a particular focus on CRISPR genome editing technologies
Twitter: @stevenerwood
Ferran Muiños
Nuria Lopez-Bigas lab, Barcelona, Spain
Presentation Date: September 7th, 2021
“Searching for cancer driver mutations with computational tools”
Bio: Ferran Muiños is a Postdoctoral Fellow at the Institute for Biomedical Research (IRB Barcelona) working in computational cancer genomics. His main research revolves around the characterization of mutational heterogeneity, the interplay between mutagenesis and selection in cancer, and the study of positional determinants of mutagenesis as well as DNA damage and repair
Twitter: @fmuinos