People - Gillis Lab

Contact:
jgillis@cshl.edu
(516) 422-4041

Jesse Gillis

Associate Professor

Stanley Institute for Cognitive Genomics

Jesse Gillis completed his undergraduate in Biophysics (2001) at the University of Toronto, where he also received his PhD in Neuroscience (2007), working with Frances Skinner. His post-doctoral training was with Paul Pavlidis at the University of British Columbia at the Centre for High-throughput Biology. There, he focused on meta-analysis of expression data, and particularly co-expression analysis, which infers functionality between genes based on shared expression profiles, a form of network analysis. It was during his post-doctoral training that he became more broadly interested in network-based methods for interrogating gene function and problems associated with genes of high prior probability (multifunctionality) and robustness as well as overfitting. Jesse joined CSHL in 2012 with a central focus on improving network analysis for better characterization of neuropsychiatric data. Lately, the lab has extended its interest in network analysis to co-expression within single cell RNA-seq.

Google Scholar: https://scholar.google.com/citations?hl=en&user=N7GhB1IAAAAJ

Current Lab Members

Stephan Fischer

Postdoctoral Fellow

Stephan Fischer joined the Gillis lab as a postdoc in 2018. Stephan received an Engineering degree in Bioscience from INSA de Lyon (France) and a Master’s degree in Computer Science from Lyon University. In 2013, he obtained a PhD in Applied Mathematics from INSA de Lyon, working on understanding how indirect selection may produce wide ranges of genome sizes and architectures. He completed a first post-doc at the National Institute for Agronomical Research in Jouy-en-Josas (France), working on optimal resource allocation in bacterial metabolism. For his current research, Stephan is investigating statistical properties of single cell RNA sequencing datasets, in particular the connection between cell types and co-expression structures.

Risa Karakida Kawaguchi

Postdoctoral fellow

Risa Karakida Kawaguchi obtained her Bachelor’s degree at the Department of Bioinformatics and Systems Biology, University of Tokyo in 2012 and M.Sc. at the Department of Computational Biology, University of Tokyo in 2014. Her Ph.D. work was supervised by Prof. Hisanori Kiryu at the University of Tokyo, focusing on the prediction of transcriptome-wide RNA secondary structure to reveal RNA structural constraints. She was awarded a JSPS Research Fellowship (DC1) for this project and received her Ph.D. degree in 2017 with the Dean’s Award for Excellence. Working as a JSPS Postdoctoral Fellow at National Institute of Advanced Industrial Science and Technology Japan, she applied the combination of machine learning and statistical modeling to extract biological knowledge from multi-omics or heterogeneous data. She joined the Gillis lab as a postdoctoral fellow in 2019 and her current hope is to discover a hidden structure involved in an inter-omics network beyond stochastic fluctuations and systematic biases.

GitHub: https://github.com/carushi

Hamsini Suresh

Postdoctoral fellow

Hamsini Suresh joined the Gillis lab as a postdoc in 2019. Her PhD work was on modelling the interactions of single cells with their microenvironment using a novel statistical mechanics framework that she developed with her thesis advisor Prof. Vikram S Deshpande at the University of Cambridge. In 2015, she completed her Bachelors (Hons) and Masters degrees in Mechanical Engineering and Product Design at the Indian Institute of Technology Madras, India. Her research interests include cell mechanics, image processing, functional genomics, and machine learning.

LinkedIn: https://www.linkedin.com/in/hamsini-suresh/

Sukalp Muzumdar

Postdoctoral fellow

Sukalp Muzumdar joined the Gillis lab as a postdoc in 2019. Sukalp received an engineering degree in Biotechnology from VIT University in India, and a Master’s degree in Microbiology and Immunology at the ETH Zürich in Switzerland. In 2019 he obtained a PhD from the ETH Zürich, working on investigating the molecular basis of wound healing and rare disease and novel therapies. For his postdoctoral research, Sukalp is involved in investigating the pathogenesis of rare hematological disorders using single-cell transcriptomics and developing innovative computational analysis techniques with the ultimate aim of establishing novel therapeutic modalities. Sukalp is partially funded by the Swiss National Science Foundation through a postdoctoral fellowship for this work.

LinkedIn: https://www.linkedin.com/in/sukalp/

Ruchi Lohia

Postdoctoral fellow

Ruchi’s hometown is Darbhanga, India. She completed her Bachelors of Engineering in Biotechnology from Manipal Institute of Technology, Manipal, India in 2012. In 2019, she earned her PhD in computational biology while working in Grace Brannigan’s group at Rutgers University. As a graduate student, she used Molecular Dynamics simulation to investigate tertiary contacts in intrinsically disordered proteins. Ruchi joined the Gillis lab in May 2020. She aims to investigate the relationship between protein sequence, structure and its expression in RNA-seq datasets.

LinkedIn : https://www.linkedin.com/in/ruchi-lohia

Shaina Lu

Graduate Student WSBS

Shaina Lu is a CSHL graduate student co-advised by Jesse Gillis and Tony Zador. Shaina is broadly interested in computational and systems approaches to biology. Her current work focuses on the meta-analysis of spatial gene expression in the mouse brain, with the ultimate goal of integrating it with neuronal connectivity. Prior to graduate school, Shaina graduated from Swarthmore College in 2016 where she received a Bachelor of Arts with a major in biology and a minor in computer science with high honors. During that time, she was fortunate to work on a variety of research projects ranging from avian phylogenetics to pathogen genomics.

LinkedIn: https://www.linkedin.com/in/shaina-lu-09ab87a5
GitHub: https://github.com/shainalu

Benjamin Harris

Graduate Student WSBS

Ben Harris did his undergraduate studies at Colgate University, receiving a Bachelors of Arts in Biology and Computer Science with honors in both disciplines. His undergraduate biology thesis was on redefining cancer testis antigens (CTAs) using the GTEx and TCGA RNAseq data. It was a continuation of his work as an URP in Dr. Mickey Atwal’s lab. Ben joined the Gillis Lab in the summer of 2018 as a graduate student. He thesis work focuses on understanding cells types through co-expression networks. In particular, he is interested in differential co-expression across cell types throughout development. He also is developing an interest in the quirky traits of Naked Mole Rats.

Twitter: @b_harris_12

Jonathan Werner

Graduate Student WSBS

For his undergraduate studies, Jonathan Werner graduated Summa Cum Laude from the University of Maryland Baltimore County (UMBC) in 2018 with a Bachelor of Science in Bioinformatics and Computational Biology and was also awarded a NSF GRFP fellowship. While at UMBC, his research primarily focused on investigating the cellular mechanisms that shape the early forebrain in zebrafish embryos. For his graduate studies, Jonathan joined the Gillis Lab in the summer of 2019 to pursue computational training in his broader interests of developmental lineage tracing and gene network dynamics. His current project focuses on the use of x-chromosomal inactivation patterns as a means for whole-organismal lineage tracing and investigating sex chromosomal dosage compensation as a mechanism for sex differences across developmental processes and in disease prevalence.

Michael Passalacqua

Graduate Student WSBS

Michael Passalacqua joined the Gillis lab as a graduate student in 2020, after working with the Center for Cell and Gene Therapy at Baylor College of Medicine in Houston. While there, he worked on improving the efficiency of non-viral transformation of human T-cells. He completed his undergraduate work at Rice University, where he studied pexophagy and peroxisome genesis in Arabidopsis in the Bartel Lab. Michael is interested in studying the development of genetic diversity in plants, and how regulatory changes can drive changes in coexpression during plant development. When not working, he loves cooking, tabletop games, foraging, and kayaking.

Twitter: @NomadicScience

Nathan Fox

Computational Science Developer

Nathan Fox joined the Gillis Lab in August 2019, shortly after graduating from the University of Miami. He graduated with a B.S. in Biochemistry & Molecular Biology and Computer Science. At UM, Nathan worked on a variety of projects including machine learning feature selection, discrete stochastic modeling, and a brief foray into bacterial bench work. Generally, he is interested in computational biology, and software engineering. At CSHL, Nathan analyzes scRNA-seq data and builds large-scale pipelines for Hi-C and ChIP-seq meta-analysis. In his free time, he likes to cook, hike, birdwatch, and read fantasy novels.

GitHub: https://github.com/nathancfox
LinkedIn: https://www.linkedin.com/in/nathan-fox-811596164/

John Lee

Computational Science Developer

John Lee joined the Gillis lab in October 2019 after spending a few years at UMass Amherst, first as an undergraduate, with BS degrees in Applied Mathematics and Biology, followed by graduate work in Mathematics. In his time there, he worked toward understanding Nonlinear Waves in the context of Granular Crystals and Bose-Einstein Condensations. Broadly, in the Gillis lab, his research interests have shifted to utilizing gene co-expression networks and other methods to predict protein function and structure.

Linkedin: https://www.linkedin.com/in/jlee44327
ResearchGate: https://www.researchgate.net/profile/John_Lee183

John Hover

Computational Science Developer

John Hover joined the Gillis Lab in October 2019, after 14 years at Brookhaven National Laboratory doing software engineering for large-scale distributed computing in support of physics experiments at BNL and the Large Hadron Collider (LHC). Prior to that he received an M.S. in Computer Science from Stony Brook University while working in the Gail Mandel lab. There he aided in bioinformatic studies of degenerate transcription factor binding sites. His undergraduate area of study was in Biological Anthropology at New College of Florida, with a thesis concerning human evolutionary genetics and the cognitive science of language. His current focus is on gaining expertise in the full range of bioinformatics tools and statistical methods, using gene co-expression networks to predict gene function, and exploring cross-species co-expression.

Github: https://github.com/jhover/
Google Scholar: https://scholar.google.com/citations?user=eW-7aBEAAAAJ
LinkedIn: https://www.linkedin.com/in/john-hover-4938705/

Noah Sobel

Summer Student

Noah Sobel is a part of the CSHL undergraduate research program for the summer of 2021. He is a rising senior at Johns Hopkins University majoring in biophysics and minoring in visual arts. His current work focuses on DNA methylation patterns in single cell sequencing data. Noah has also worked on a project focused on multi-domain protein folding as an undergraduate. In his free time, he likes to rock climb, ski, and play board games.

Former Lab Members

Wim Verleyen

Former: Postdoctoral Fellow
Current: Senior Data Scientist at United Technologies

Maria Nattestad

Former: WSBS Rotation Student
Current: Data Visualization Team Lead at DNAnexus

Jenelys Ruiz

Former: WSBS Rotation Student
Current: WSBS Graduate Student in Jessica Tollkuhn’s Lab

Manthan Shah

Former: Computational Science Developer

Sara Ballouz

Former: Postdoctoral Fellow
Current: Group Leader at the Garvan-Weizmann Centre for Cellular Genomics

Conor Cremin

Former: Visiting Doctoral Student
Current: Doctoral Student at the University of Hong Kong

Maggie Crow

Former: Postdoctoral Fellow
Current: Bioinformatics Scientist at Genentech

Summer Students

Melanie Weber

Robert Baraldi

Maya Talukdar