Genomics

An immensely complex molecular network of interactions forms the foundation of human biology and disease. Genomic approaches provide a particularly illuminating window to biological systems, and when combined with advanced analysis allow us to learn and model this complexity.

The goal of CCB Genomics research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods for systems-level pathway modeling through integrative analysis of genome-scale datasets.

Research Highlights

August 2, 2021

Decoding disease: from genomes to networks to phenotypes

A. Wong, R. Sealfon, Chandra L. Theesfeld, O. Troyanskaya

Interpreting the effects of genetic variants is key to understanding individual susceptibility to disease and designing personalized therapeutic approaches. Modern…

Nature Reviews Genetics

July 22, 2021

ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements

X. Chen, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan

Transcription factors (TFs) often function as a module including both master factors and mediators binding at cis-regulatory regions to modulate…

PLOS Comuptational Biology

July 15, 2021

Machine learning methods to model multicellular complexity and tissue specificity

R. Sealfon, A. Wong, O. Troyanskaya

Experimental approaches to study tissue specificity enable insight into the nature and organization of the cell types and tissues that…

Nature Reviews Materials

News & Announcements

November 10, 2020

Finding Signals in the Noise with HumanBase By Susan Reslewic Keatley

October 23, 2020

Molecular Processes in Kidney Cells May ‘Prime’ Diabetics for COVID-19 Infection By Thomas Sumner

June 29, 2020

Plasticity May Make Neurons Vulnerable to Alzheimer’s Disease By Thomas Sumner

Upcoming Events

December 2021

02 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
09 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
16 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
23 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
30 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting

January 2022

06 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
13 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
20 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
27 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting

February 2022

03 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting

Software

GIANT

Genome-wide Scale functional interaction networks for 144 human tissues and cell types

DeepSEA

Deep learning-based algorithmic framework for predicting chromatin effects

Nano-Dissection

This server performs in silico nano-dissection, an approach we developed to identify genes with novel cell-lineage specific expression.

IMP 2.0

Integrative Multi-species Prediction

SEEK

Search-Based Exploration of Expression Compendium [Human]

KNNimpute

K-Nearest Neighbors Imputation

FNTM

Functional Networks of Tissues in Mouse

URSA(HD)

A data-driven perspective to your gene expression profile for human tissues and diseases.

humanbase

Data-driven predictions of gene expression, function, regulation, and interactions in human.

Sleipnir

Sleipnir Library for Computational Functional Genomics

Group Members

Olga Troyanskaya, Ph.D.

Deputy Director, Genomics

Olga Troyanskaya became deputy director for genomics in 2014 after working with CCB as a consultant since 2013. Troyanskaya is also a professor at the Lewis-Sigler Institute for Integrative Genomics and at the department of computer science at Princeton University, where she has been on…

Kathleen Chen

Guest Researcher

Kathleen is working on methods that analyze large-scale experimental data compendia in order to improve our understanding of how, and which, genes work together to produce a particular disease state.

Xi Chen, Ph.D.

Research Scientist, Genomics

Xi Chen joined the Flatiron Institute’s Center for Computational Biology in 2016 in the genomics group. Chen’s research focuses on developing algorithms for processing and statistical analysis of heterogeneous genomics data. He has a Ph.D. in electrical engineering from Virginia Polytechnic Institute and State University,…

Kara Dolinski, Ph.D.

Visiting Scholar

Kara Dolinski is Assistant Director at the Lewis-Sigler Institute for Integrative Genomics, and Director of its Genome Databases Group.

Julien Funk

Software Engineer, Genomics

Julien Funk joined the Simons Foundation in 2017 as a software engineer in Center for Computational Biology’s Genomics group.

Kiley Graim, Ph.D.

Guest Researcher

Kiley Graim is Assistant Professor in the Computer & Information Science & Engineering Department of the University of Florida. Dr. Graim received her Ph.D. in 2016 from the University of California, Santa Cruz, advised by Professor Josh Stuart.

Christopher Park, Ph.D.

Research Scientist, Genomics

Christopher Park joined the Center for Computational Biology in May of 2018 as a Research Scientist in the Genomics group.

Natalie Sauerwald, Ph.D.

Flatiron Research Fellow, Genomics

Natalie Sauerwald joined the genomics group at the Flatiron Institute in October 2020 to develop new methods for studying human diseases.

Rachel Sealfon, Ph.D.

Research Scientist, Genomics

Rachel Sealfon joined the foundation in 2016 as a research scientist in the center’s genomics group. She is applying data integration methods and prediction approaches to study functional genomic data.

Jerry Vinokurov, Ph.D.

Senior Software Engineer, Genomics

Jerry Vinokurov came to Simons in 2020 to work on the HumanBase project at the Center for Computational Biology.

Aaron Wong, Ph.D.

Data Scientist and Project Leader, Genomics

Aaron Wong joined the center’s Genomics Group in 2015 to develop algorithms and models for analyzing high-throughput biomedical data and to coordinate the development of a public database of human functional genomics.

Zijun Zhang, Ph.D.

Flatiron Research Fellow, Genomics

Zijun Frank Zhang joined the Flatiron Institute as a Research Fellow in 2019.

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