Li Shen | Mount Sinai

Biography

Research Topics

Bioinformatics, Biomedical Informatics, Computational Biology, Epigenomics, Image Analysis, Mathematical Modeling of Biomedical Systems, Mathematical and Computational Biology

Multi-Disciplinary Training Area

Artificial Intelligence and Emerging Technologies in Medicine [AIET], Genetics and Genomic Sciences [GGS], Neuroscience [NEU]

Dr. Shen joined Mount Sinai in 2009 with a Ph.D. in computer science. He is currently a professor of bioinformatics with dual appointments at the department of Neuroscience and the department of Artificial Intelligence and Human Health. He has made contributions to large-scale sequencing analysis, bioinformatic tools development and machine learning applications to medical imaging and epigenomics. His current research interests include the applications of machine learning in healthcare and genomics. He has more than 100 publications with >12,000 total citations. See his Google scholar page for a full list of his publications. Visit Li Shen's Laboratory of Bioinformatics for more information on his research activities.

Download the CV

Dr. Shen joined Mount Sinai in 2009 with a Ph.D. in computer science. He is currently a professor of bioinformatics with dual appointments at the department of Neuroscience and the department of Artificial Intelligence and Human Health. He has made contributions to large-scale sequencing analysis, bioinformatic tools development and machine learning applications to medical imaging and epigenomics. His current research interests include the applications of machine learning in healthcare and genomics. He has more than 100 publications with >12,000 total citations. See his Google scholar page for a full list of his publications. Visit Li Shen's Laboratory of Bioinformatics for more information on his research activities.

Download the CV

Research

Machine learning

Dr. Shen has made many contributions to machine learning applications in medical imaging and epigenomics, including breast cancer detection and risk prediction using mammograms and automated genome annotation using ChIP-seq.

Large-scale next-generation sequencing data analysis

From 2009-present, the Shen lab has analyzed 10,000s of NGS samples with a total storage of more than 100 TB. The results have generated numerous publications in top-tier journals, such as Nature, Science, Neuron, Nature Neuroscience and Genome Biology. The Shen lab has also produced some of the most popular bioinformatic tools, such as ngs.plot (data mining and visualization of NGS data), diffReps (ChIP-seq differential analysis) and GeneOverlap (gene lists overlapping analysis).

Education

BS, Fudan University

PhD, Nanyang Technological University

Postdoc, University of California San Diego

Honors & Awards

2022

Google Cloud Research Innovator

Google

2019

4D Technology Development

Icahn School of Medicine at Mount Sinai

2006

Interfaces in Science Award

Burroughs Wellcome Funds

2000

ViaVoice National Campus Application Contest Excellence Prize

IBM

Publications

8

Publications

Selected Publications

Chromatin accessibility and H3K9me3 landscapes reveal long-term epigenetic effects of fetal-neonatal iron deficiency in rat hippocampus. Shirelle X. Liu, Aarthi Ramakrishnan, Li Shen, Jonathan C. Gewirtz, Michael K. Georgieff, Phu V. Tran. BMC Genomics

DeepRegFinder: deep learning-based regulatory elements finder. Aarthi Ramakrishnan, George Wangensteen, Sarah Kim, Eric J. Nestler, Li Shen. Bioinformatics Advances

CREB Binding at the Zfp189 Promoter Within Medium Spiny Neuron Subtypes Differentially Regulates Behavioral and Physiological Adaptations Over the Course of Cocaine Use. Collin D. Teague, Joseph A. Picone, William J. Wright, Caleb J. Browne, Gabriella M. Silva, Rita Futamura, Angélica Minier-Toribio, Molly E. Estill, Aarthi Ramakrishnan, Freddyson J. Martinez-Rivera, Arthur Godino, Eric M. Parise, Kyra H. Schmidt, Nathalia V. Pulido, Zachary S. Lorsch, Jee Hyun Kim, Li Shen, Rachael L. Neve, Yan Dong, Eric J. Nestler, Peter J. Hamilton. Biological Psychiatry

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Office Locations

Icahn (East) Building Floor 10 Room 20D

1425 Madison Ave

New York, NY 10029

212-659-8622

Industry Relationships

Physicians and scientists on the faculty of the Icahn School of Medicine at Mount Sinai often interact with pharmaceutical, device, biotechnology companies, and other outside entities to improve patient care, develop new therapies and achieve scientific breakthroughs. In order to promote an ethical and transparent environment for conducting research, providing clinical care and teaching, Mount Sinai requires that salaried faculty inform the School of their outside financial relationships.

Dr. Shen has not yet completed reporting of Industry relationships.

Mount Sinai's faculty policies relating to faculty collaboration with industry are posted on our website. Patients may wish to ask their physician about the activities they perform for companies.

Physicians and scientists on the faculty of the Icahn School of Medicine at Mount Sinai often interact with pharmaceutical, device, biotechnology companies, and other outside entities to improve patient care, develop new therapies and achieve scientific breakthroughs. In order to promote an ethical and transparent environment for conducting research, providing clinical care and teaching, Mount Sinai requires that salaried faculty inform the School of their outside financial relationships.

Dr. Shen has not yet completed reporting of Industry relationships.

Mount Sinai's faculty policies relating to faculty collaboration with industry are posted on our website. Patients may wish to ask their physician about the activities they perform for companies.