People

Rong Chen

Principal Investigator

Rong Chen is the Director of Clinical Genome Informatics and Assistant Professor at the department of Genetic and Genomics Sciences in Icahn School of Medicine at Mount Sinai. Dr. Chen has developed many databases, software, and patents to drive precision medicine and clinical diagnosis using next generation sequencing and integrative genomics at Icahn School of Medicine at Mount Sinai, Personalis, Stanford University, and Quest Diagnostics. He built a startup company called Personalis to interpret personal genome and exome sequences for clinical diagnosis, and sit in the advisor board for several genome informatics companies, including LifeMap Solutions, Bina Technologies, and Tute Genomics. Dr. Chen received his B.S. in Chemical Physics from University of Science and Technology in China, his M.S. in Structure Biology from Chinese Academy of Sciences, and his Ph.D. in Bioinformatics from Boston University. More in his linkedinGoogleScholar, and NIH Biosketch

Faculty

Shuyu Dan Li

Associate Professor

Dan Li’s primary research interests focus on applying genomics, genetics and integrative data analysis to further our understanding of disease mechanisms and to develop biomarkers for personalized medicine.  Dan received his Ph.D. in Cell & Molecular Biology from University of Texas Southwestern Medical Center at Dallas, and a M.S. in Computer Sciences from University of Texas at Dallas.  Prior to Mount Sinai, Dan made significant contributions to delineating novel oncogenic pathways in hepatocellular carcinomas (HCCs) through whole genome sequencing and integrative genomic data analysis, which led to several seminal publications on Nature Genetics and Genome Research.  He also developed a predictive biomarker for a standard care drug for non-small cell lung cancer based on a bioinformatics approach. The marker was subsequently validated in clinic and a patent application was filed where Dan was named as a co-inventor.  Dan is well published (selected publication) and served on National Cancer Institute Special Emphasis Panel on Integrative Cancer Biology Program and Center for Cancer Systems Biology.

Staff

Andrew Uzilov

Biomedical Informatics Research Scientist

Andrew Uzilov is a bioinformatics scientist with an RNA focus, recently specializing in RNA-Seq methods development and applications. He received double-majored in Biochemistry and Computer Science at University of Rochester and earned a PhD in Bioinformatics and Biomolecular Engineering from UC Santa Cruz. Prior to Mt Sinai, he worked to develop an RNA-Seq bioinformatics infrastructure for Cancer Therapeutics Innovation Group, a cancer genomics startup in San Francisco. More in his linkedin.

Marc Fink

Senior Scientist

Marc Fink is a cell biologist with a focus on cancer signaling networks and systems biology.  Currently, he is focused on developing novel approaches to integrate signaling network information and pharmacogenomics data into tailored cancer therapy protocols. Prior to Mt Sinai, he worked on the signaling network and development of drug resistance in HER2-positive breast cancers in the Dept. of Biomedical Sciences at LIU Post.  He obtained his B.S. from Queens College-CUNY in chemistry, Ph.D. in Biomedical Sciences from the Icahn School of Medicine at Mount Sinai, and he did his PostDoc at Weill Cornell Medical College.

Robert Küffner

Group leader clinical informatics

Robert Kueffner heads scientific programming and computational data analysis projects supporting wet lab and clinical groups. He develops innovative next generation sequencing (NGS) and multi-omics based analytics based on machine learning (ML), advanced statistics and natural language processing for genomics, transcriptomics and epidemiology applications. Approaches and tools resulting from this research have been applied in many projects to provide systematic bioinformatics support; e.g. for the pre-processing, analysis and integration of large-scale NGS datasets. Supervising large international consortia, he brings together ML techniques commonly applied from bioinformatics to marketing analytics, including techniques for multivariate, survival and longitudinal data analysis. They also led to the generation and implementation of novel approaches for the detection of biomarkers by analyzing massive clinical data via ML. Dr. Küffner received his PhD in molecular biology in 1998 at the Heinrich-Heine Universität Düsseldorf, Germany and habilitated 2010 in computer science at the Ludwig-Maximilians Universität München, Germany.

Xiang Zhou

Data group leader

Dr. Zhou Xiang. Data leader in Chen Lab, got Computational Biology in Columbia University, New York, NY  in 2011. Over ten years’ experience in Information Technology and 5 years' project management experience as well as  5 years’ experience in supporting science and clinical research. Developed clinical trial management system which greatly improved research assistants’ efficiency in identifying and managing enrolled patients

 

Hui Li

Senior computer scientist

Hui Li got PhD in Beijing University of Technology from China.  He is a senior computer scientist of 19 years software and hardware development experience, 10 years of academic research in machine learning, graph theory, Bayesian network, the genetic algorithm, decision tree, support vector machines, artificial neural networks, HMM and 8 years of bioinformatics tool and smart electronic equipment application implementation experience. He is interested in big data analysis, high performance parallel computing, 3D protein structure visualization and embedded hardware development. In his current position at Mount Sinai, he will lead software team to develop clinical and personalized cancer medicine tool.

Kristin Ayers

Statistical Geneticist

Kristin Ayers is a statistical geneticist with a focus on genetic association studies. She earned her PhD in Biomathematics from UCLA working on methods for haplotype estimation and association. She did her Postdoc at Newcastle University in the UK focusing primarily on penalized regression methods for GWAS and rare variant analysis. A list of publications can be found here. At Mt Sinai, her current research projects involve the investigation of predicted functional variants in healthy and disease populations.

Chetanya Pandya

Biomedical Informatics Research Scientist

Chetanya Pandya is a bioinformatics scientist with a broad area of expertise ranging from software development to biochemistry. His undergraduate training is in Computer Science & Engineering from GGS Indraprastha University, New Delhi, India and he pursued his PhD in Bioinformatics from Boston University with Profs. Karen Allen and Yu Xia. Prior to Mount Sinai, he has worked at Defense Research & Development Organization (India), All India Institute of Medical Sciences, Wipro Infotech Limited, Indian Institute of Technology (Delhi), LeadInvent Technologies and Infinity Pharmaceuticals. At Mount Sinai, he’ll be working on developing bioinformatics techniques and performing analyses for several efforts including the Personalized Cancer Therapy study. For more info, check out LinkedIn.

Jon McCafferty

Bioinformatician II

Jon McCafferty is a bioinformatician with a focus on data analysis and software development.  He received his PhD in bioinformatics and computational biology from the University of North Carolina at Charlotte.  He previously worked in the informatics core at the Forsyth Institute in Boston Massachusetts, where he focused on using high-throughput technologies to profile human associated microbial communities and to characterize community structure, function and diversity.  He is interested in data mining and applying machine learning algorithms to genomic data.

Jinlian Wang

Bioinformatician II

Jinlian Wang is a bioinformatician with emphasizing on cancer omics data research and bioinformatics tool development. She did her PostDoc training at Lombardi Comprehensive Center, Georgetown University. Currently, she works at genetics testing lab with focus on development of genetic variants diagnosis supporting tool, clinical NGS pipeline dashboard and genetic lab management system. She is interested in diseases omics data integration, analysis and system biology.

Hong Lu

Bioinformatician

Hong Lu is a bioinformatician with a NGS focus specializing in NGS variant calling and QC method development. With over 14 years of NGS bioinformatics experience in supporting research and clinical  operations, he developed variant calling pipelines that improved  variant calling sensitivity and specificity.  He co-discovered a NGS quality filter algorithm method that is currently still in use in Ion Torrent sequencers.  He obtained his M.S.  in Biophysics and Biochemistry from University of Minnesota, Twin Cities.  More in his linkedin:  https://www.linkedin.com/in/hong-lu-03a8508

Umadevi Thirumurthi

Senior Scientist

Umadevi Thirumurthi (Uma) is a cancer biologist with over 6 years of experience focusing of Receptor Tyrosine kinase (RTK) signaling in cancer and identifying biomarkers for treatment efficacy and resistance to therapy. Currently she is focused on building a database for variants in cancer. Uma has a B.Tech in Industrial Biotechnology from PSG College of Technology in India, a Masters in Molecular Biotechnology from Wayne State University and a PhD in Cancer Biology from UT MD Anderson Cancer Center. After her PhD, she worked for Merrimack Pharmaceuticals in Cambridge, MA, where she worked on identifying novel pathways to target cancer stem cells to overcome resistance to SOC chemotherapy in triple negative breast cancers.

Elaine Janet, Hager

Cancer Knowledge Base Senior Scientist

Janet Hager obtained her BSc degree in Biology in the UK and joined the graduate program in Biology at the University of Virginia earning her Doctoral degree with Dr. Oscar Miller Jr. visualizing gene activity in Drosophila.  She completed her postdoctoral training at Stanford University and UCLA investigating muscle cell lineage in chicken limb development and early gene activation in mouse muscle satellite cells after injury. Returning to the east coast, she took a position at Yale University Medical School within the Keck Biotechnology Resource Lab and was the founding director of the Keck Microarray Resource. Following her experience at Yale she was a Senior Study Director and Product Manager, DNA Sequencing in a contract research company overseeing SNP discovery, resequencing and targeted genotyping projects. Janet joined the faculty at University of Connecticut Health Center in 2009 as Director of the Translational Genomics Core and established Illumina GAIIx and HiSeq 2000 high throughput next gen sequencing services. Most recently Janet transitioned into molecular diagnostics at Yale. Initially she was involved in validating and transferring a lab developed CML test to an international standard. Subsequently she was a clinical analyst in the tumor profiling lab and was responsible for curating somatic variants identified by next gen sequencing and preparing clinical reports.

Nicholas Hahner

Bioinformatician

Nick Hahner is a bioinformatician who focuses on data. He's been doing bioinformatics professionally since High School. He automates and chains tools together into data pipelines and stores results in cohesive and easily queried databases. He's got a Master of Science in Biomolecular Engineering and Bioinformatics from the University of California, Santa Cruz. After grad school he spent three and a half years working for a small startup formerly known as Cancer Therapeutics Innovation Group (CTIG). At CTIG he built NGS data pipelines, databases, accessioning interfaces, and provided bioinformatics support for designing and optimizing protocols for NGS. At Mount Sinai he'll be focusing on various tooling, databases, and other projects for their personalized cancer therapy efforts. His favorite hobby is building custom electronics with arduinos.  linkedin: https://www.linkedin.com/in/nick-hahner-79745044/ .

Meng Ma

Postdoc

Meng Ma is postdoc with a focus on data mining analysis on genome data. He obtained a PhD in computer science from University of Science and Technology of China. He did PostDoc in the University of North Carolina at Chapel Hill on gene alternative splicing regulatory mechanism study. His research areas are on (1) Mendelian diseases modifiers identification through clinical phenotypes. (2) The pathogenetic mechanism of diseases-associated variants at molecular level.

Aye Moe

Bioinformatics Engineer

Aye Sandar Moe is a bioinformatics engineering coming from software engineering background.   Aye graduated with a Bachelor degree in Computer Engineering from Polytechnic Institute of NYU and obtained a Masters Degree in Information Systems from New York University.   Prior to working at Mount Sinai, Aye worked as a software developer in Zoteca Inc and Goldman Sachs.  At Mount Sinai, she’ll be working on automating and optimization of the various processes and aspects involved in Personalized Cancer Therapy research study.  For more info, check out Aye’s LinkedIn.

Patricia Taik

Clinical Research Coordinator

Patricia Taik graduated with a B.A. in Biology from Hamilton College in May ‘16. She is a clinical research coordinator for the Personalized Cancer Therapy program, which specializes in the personalized cancer treatment by using genomic data analysis and next generation sequencing. She tracks patients information, maintains specimens and coordinates with bioinformaticians, geneticists, molecular and cell biologists, clinicians, research scientists, pathologist, and Genetic Core Sequencing Facility to ensure the smooth workflow of the samples in this program.

Students

Benjamin Glicksberg

PhD Student (Neruoscience)

Benjamin a PhD student in the Neruoscience program who is working under the tutelage of Dr. Rong Chen and Dr. Joel Dudley doing work related to bioinformatics and computational genetics. His research areas of interest include: genetic architecture of diseases,  comparing Mendelian and complex diseases; Electronic Medical Record (EMR) analysis, and psychiatric diseases. He graduated from Skidmore College in 2010 studying Neuroscience.

Alumni

Jörg Hakenberg

Biomedical Informatics Research Scientist

Jörg Hakenberg is a senior bioinformatics scientist with a focus on high-throughput sequencing analysis pipelines, algorithms, and literature mining. He obtained a PhD in computer science from Humboldt-Universität zu Berlin and worked as a postdoc for the Biotechnology Center of the TU Dresden and for Arizona State University. Prior to joining Mt Sinai, Jörg worked for Hoffmann-La Roche Pharmaceuticals as a Principal Scientist, supporting the oncology department with bioinformatics analysis, development of NGS pipelines, and molecular profiling of cancer cell lines. In Chen's lab, he is responsible for administration of large-scale bioinformatics databases and for software development, as well as curation of genetic variants. He is also working in the Resilience Project, aiming to identify buffering effects that lessen the manifestation of normally severe, early onset genetic disorders. See his homepage for details.Currently work at Illumina.

Wei Ding

Biomedical Informatics Research Scientist

Wei Ding’s current research is focused on the personalized medicine and systems biology of human diseases. Prior to joining Mt Sinai, he was a Principal Scientist at Schering-Plough and Merck, leading the biomarker research and –omics profiling efforts in both clinical and pre-clinical setting. He was an adjunct professor in the Department of Biological Sciences at the Kean University. Wei received his B.S from the University of Science and Technology of China, Ph.D. in Biophyiscs from the State University of New York at Stony Brook, and the postdoctoral training as a Fogarty Fellow in the National Center for Biotechnology Information (NCBI). More in his linkedin.

Wei-Yi Cheng

Bioinformatician

Wei-Yi Cheng is a bioinformatician with concentration on disease risk modeling. Wei-Yi has received a Ph.D. degree in Electrical Engineering from Columbia University, where his research focuses on development of genome-scale data mining algorithms for biological discovery and predictive modeling. Currently work at Roche

Chun Yee Lau

Clinical Research Coordinator

Chun Yee Lau is the clinical research coordinator for the Personalized Cancer Therapy program, which produces personalized treatment reports for cancer patients based on a constellation of next-generation sequencing and other high-throughput assays that try to determine the detailed molecular events driving the person’s cancer.  She works with many people, including the genetic counselor, clinicians in pathology, the Genomics Core Facility, the Tech Dev lab, the bioinformatics group, the immunotherapy group, and various collaborators, to make sure the specimens are flowing through smoothly through the pipeline. Previously, she worked as a research technician in Pathology at Beth Israel Deaconess Medical Center in Boston. She graduated from Hamilton College with a B.A. in biology.

Xintong Chen

PhD Student (Genetics and Genomic Science)

Xintong Chen is a PhD student in Department of Genetics and Genomic Sciences interested in clinical application of NGS.