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

January 25, 2021

mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge

M. Meyer, Y. Wang, D. Edwards, G. Smith, A. Rubenstein, P. Ramanathan, C. Mire, C. Pietzch, X. Chen, Y. Ge, W. Cheng, C. Henry, A. Woods, L. Ma, G. Stewart-Jones, K. Bock, M. Minai, B. Nagata, S. Periasamy, P. Shi, B. Graham, I. Moore, I. Ramos, O. Troyanskaya, E. Zaslavsky, A. Carfi, S. Sealfon, A. Bukreyev

The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase…

bioRxiv 2021.01.25.428136

January 18, 2021

Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk

C. Park, J. Zhou, A. Wong, K. Chen, C. Theesfeld, R. Darnell, O. Troyanskaya

Despite the strong genetic basis of psychiatric disorders, the underlying molecular mechanisms are largely unmapped. RNA-binding proteins (RBPs) are responsible…

Nature Genetics

January 11, 2021

Identifying intracellular signaling modules and exploring pathways associated with breast cancer recurrence

X. Chen, J. Gu, A. Neuwald, L. Hilakivi-Clarke, R. Clarke, J. Xuan

Exploring complex modularization of intracellular signal transduction pathways is critical to understanding aberrant cellular responses during disease development and drug…

Scientific Reports

News & Announcements

November 10, 2020

Finding Signals in the Noise with HumanBase By Susan Reslewic Keatley, Ph.D.

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

March 2021

04 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
11 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
18 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
25 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting

April 2021

01 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
08 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
15 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
22 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting
29 Thu
- Meeting 1:00 - 2:00 PM
  Genomics Group Meeting

May 2021

06 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…

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,…

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.

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.

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