NEW: The ChIPseeqer paper is out and highlighted as

Olivier Elemento, PhD, Associate Professor
Acting Director, Englander Institute for Precision Medicine
Associate Director, Institute for Computational Biomedicine
Co-Assistant Dean for Scientific Computing
Co-Leader, Genetics, Epigenetics and Systems Biology Program, Meyer Cancer Center
Yanwen Jiang, PhD, postdoctoral research associate.
Project: experimental/computational characterization of transcriptional networks in normal and malignant B cells
Jacob Glass, MD, PhD, medical oncology fellow
Project: Computational analysis of DNA methylation profiles
Mark Carty, graduate student (Tri-I CBM program)

Project: graph-theoretical and statistical analysis of chromatin interactions in cancer
Matt Teater, graduate student (PBSB graduate program)
Project: CTCF- and lncRNA-based regulation in normal and malignant cells
David Redmond, graduate student (tri-I CBM graduate program)
Project: cancer genome evolution, whole cancer genome assembly, regulatory mutations
Kenneth Eng, MS, Precision Medicine pipeline guru.
Project: cancer exome/genome pipeline development
Heng Pan, graduate student (PBSB graduate program)
Project: epigenomic evolution in lymphoma
Katie Gayvert, graduate student (Tri-I CBM graduate program)
Project: drug repositioning, prediction of drug combinations using machine learning
Wei Du, graduate student (PBSB graduate program)
Project: computational and mathematical approaches for precision medicine, virtual cancer cells
Arielle Messer, graduate student (PBSB graduate program).
Project: virtual prostate cancer cells, metastasis
Omar Aly, laboratory technician and manager
Project: signalling, proteomics, reverse phase protein array
Akanksha Verma, MS, Graduate Student (Tri-I CBM program).
Project: comprehensive RNA-seq analytics pipeline
Linda Huang, MS, Bioinformatics analysist
Project: virtual drug discovery and precision medicine
Alex Sigaras, MS, Research Associate
Project: data visualization using AR and VR including Hololens
Andrew Schaumberg, rotation student (tri-I CBM).
Project: post-translational modification prediction using machine learning
Usama Mukhtar, rotation student (PBSB).
Project: cancer genomics
Neel Madhukar, graduate student (tri-I CBM).
Project: precision therapeutics
Charles Murphy, graduate student (tri-I CBM).
Project: mouse precision medicine (co-advised with Lew Cantley)
Asaf Poran, graduate student (PBSB).
Project: single cell RNAseq and immune repertoires
Ashley Doane, graduate student (tri-I CBM).
Project: reconstructing regulatory circuits using ATAC-seq
Sophia Roshal, software engineerign intern
Project: Hololens apps
Former members:
Antoine Assaf, summer student, Lycee Francais of New York
Project: Google Glasses for Precision Medicine
Han Yuan, rotation student (tri-I CBM).
Project: epigenomic deconvolution using machine learning
Stephanie Hyland, rotation student (tri-I CBM).
Project: cancer pheWAS
Balvir Kunar, rotation student (PBSB).
Project: reconstructing regulatory networks in endothelial cells
Eugenia (Jenny) Giannopoulou, PhD, postdoctoral research associate.
Project: computational approaches for ChIP-seq data analysis, regulatory network inference and visualization
Currently Assistant Professor at City University of New York
Hyunwoo Cho, rotation student (PBSB graduate program)
Project: immune escape and the shaping of cancer mutation spectrum
Priya Vijay, rotation student (Tri-I CBM graduate program)
Project: identifying anticancer compounds with unknown MoA
Joshua Finer, summer student, CUNY Queens
Project: mathematical modeling of cancer pathways
Roie Rennert, summer student, Penn State
Project: cancer pharmacogenomics
Lauren Fairchild, rotation student (Tri-I CBM graduate program)
Project: lcnRNA function discovery
Tamar Melman, rotation student (Tri-I CBM graduate program)
Project: machine learnign approaches to predicting structural breakpoints
Jin-Hyun Ju, rotation student (PBSB graduate program)
Project: uncovering synthetic lethal weaknesses in cancer cells
Gabriel Barcia-Duran, rotation student (PBSB graduate program)
Project: detecting chromatin-associated lncRNAs in cancer
Ta-tsen (David) Soong, PhD, postdoctoral research associate.
Project: revealing cancer mutations using deep sequencing
Currently research scientist at GSK
Patrick Grinaway, rotation student (PBSB graduate program)
Project: identifying functional protein-DNA interactions
Elisa Araldi, NYU visiting graduate student
Project: exosome miRNA analysis using deep sequencing
Jan Dlabal, summer student (Lycee Francais)
Project: rich immersive and interactive visualization of 3D chromosome structure
Alicia Subtil-Rodriguez, visiting scientist (Centro Andaluz de BiologĂ­a Molecular y Medicina Regenerativa, Sevilla, Spain)
Project: ChIP-seq analysis of chromatin organizing proteins
Alex Ivanov, research scientist
Project: fundamental principles of drug resistance mutations
Chichao Chen, rotation student (PBSB graduate program)
Project: improving accuracy of massive shRNA screens
Guanshi Wang, rotation student (BCMB graduate program)
Project: cancer mutation detection in single cell deep sequencing
Yuheng Lu, rotation student (PBSB graduate program)
Project: cancer mutation detection using deep sequencing
David Kuo, rotation student (PBSB graduate program)
Project: discovering functional targets of transcription factors
Huimin Geng, PhD, postdoctoral research associate.
Project: the impact of DNA methylation on gene expression in normal B cells and lymphomas
Currently Assistant Professor at UCSF
Michal Novemsky, summer student (MS Computer Science, NYU)
Project: predicting drug sensitivity in lymphoma patients
Yogesh Saletore, rotation student (Tri-I CBM graduate program)
Project: detecting nucleosome relocalization in B cells
Sol Shenker, rotation student (Tri-I CBM graduate program)
Project: using computer vision to measure cancer cell phenotypes
Abishek M, rotation student (PBSB graduate program)
Project: 3D reconstruction of chromosome structur e
Hector Acaron, summer student (Biomedical Engineering, Cornell Ithaca)
Project: systems biology of endothelial cells
Brandon Giglio, undergraduate student (Hunter College)
Project: discovering novel non-coding RNAs in B cells
Danica Chiu, rotation student (Pharmacology graduate program)
Project: decoding the enhancer regulatory code in B cells
Irene Stevens, undergraduate student (Hunter College)
Project: global enhancer analysis from ChIPseq data
Alex Root, rotation student (PBSB graduate program)
Project: detecting aberrant transcription factor activity in cancer cells
Kaiming Li, rotation student (BCMB Allied graduate program)
Project: detecting CNVs using deep sequencing data
Sheng Li, rotation student (PBSB graduate program)
Project: understanding EZH2 deregulation
Jaaved Mohammed, rotation student (Tri-I CBM graduate program)
Project: cancer mutation detection using deep sequencing
Sayan Mondal, rotation student (PBSB)
Project: predicting GPCR oligomerization using genomic data integration


Group meetings:
Group meetings are held every Thursday at 1pm, in the ICB Conference room. We have joint lab meetings with Jason Mezey's group here at Weill.


Collaborators:
- Ari Melnick, WCMC, transcriptional networks and epigenetic mechanisms in normal and malignant B cells
- Shahin Rafii, WCMC, endothelial cell biology
- Thomas Fahey, WCMC/NYPH, thyroid cancer
- Tarun Kapoor, RU, cancer drug targets
- Scott Ely, WCMC, automated image analysis in multiple myeloma
- Jon Licht, Nothwestern U, Multiple Myeloma
- Mark Rubin, WCMC, prostate cancer
- David Lyden, WCMC, metastasis and exosome
- David Rickman, WCMC, chromatin interactions in prostate cancer
- Christina Leslie, MSKCC, miRNA activity in cancer
- Christopher Mason, WCMC, variant analysis and epitranscriptome
- Jason Banfelder, WCMC, 3D visualization of genomic data
- Tim McGraw, WCMC, metabolomics of cancer-associated fibroblasts