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Li Shen, PhD
img_Li Shen
PROFESSOR | Neuroscience
212-659-8622
email
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]
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).

BS, Fudan University

PhD, Nanyang Technological University

Postdoc, University of California San Diego

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

110
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

Serotonin Transporter-dependent Histone Serotonylation in Placenta Contributes to the Neurodevelopmental Transcriptome. Jennifer C. Chan, Natalia Alenina, Ashley M. Cunningham, Aarthi Ramakrishnan, Li Shen, Michael Bader, Ian Maze. Journal of Molecular Biology

Circulating myeloid-derived MMP8 in stress susceptibility and depression. Flurin Cathomas, Hsiao Yun Lin, Kenny L. Chan, Long Li, Lyonna F. Parise, Johana Alvarez, Romain Durand-de Cuttoli, Antonio V. Aubry, Samer Muhareb, Fiona Desland, Yusuke Shimo, Aarthi Ramakrishnan, Molly Estill, Carmen Ferrer-Pérez, Eric M. Parise, C. Matthias Wilk, Manuella P. Kaster, Jun Wang, Allison Sowa, William G. Janssen, Sara Costi, Adeeb Rahman, Nicolas Fernandez, Matthew Campbell, Filip K. Swirski, Eric J. Nestler, Li Shen, Miriam Merad, James W. Murrough, Scott J. Russo. Nature

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Icahn (East) Building Floor 10 Room 20D

1425 Madison Ave

New York, NY 10029

212-659-8622

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.