All Stories

  1. LC-PLM: Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers

    Article • October 2024, Cold Spring Harbor Laboratory Press

    Zichen Wang

  2. GraphStorm: All-in-one Graph Machine Learning Framework for Industry Applications

    Article • August 2024, ACM (Association for Computing Machinery)

    Zichen Wang

  3. EGGNet, a Generalizable Geometric Deep Learning Framework for Protein Complex Pose Scoring

    Article • ACS Omega, February 2024, American Chemical Society (ACS)

    Zichen Wang

  4. EGGNet, a generalizable geometric deep learning framework for protein complex pose scoring

    Article • March 2023, Cold Spring Harbor Laboratory Press

    Zichen Wang

  5. In-hospital use of ACE inhibitors/angiotensin receptor blockers associates with COVID-19 outcomes in African American patients

    Article • Journal of Clinical Investigation, October 2021, American Society for Clinical Investigation

    Zichen Wang

  6. LM-GVP: A Generalizable Deep Learning Framework for Protein Property Prediction from Sequence and Structure

    Article • September 2021, Cold Spring Harbor Laboratory Press

    Zichen Wang

  7. Improving Pre-eclampsia Risk Prediction by Modeling Individualized Pregnancy Trajectories Derived from Routinely Collected Electronic Medical Record Data

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Zichen Wang

  8. Improving postpartum hemorrhage risk prediction using longitudinal electronic medical records

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Zichen Wang

  9. A comprehensive digital phenotype for postpartum hemorrhage

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Zichen Wang

  10. Hospitalised COVID-19 patients of the Mount Sinai Health System: a retrospective observational study using the electronic medical records

    Article • BMJ Open, October 2020, BMJ

    Zichen Wang

  11. Analysis of hospitalized COVID-19 patients in the Mount Sinai Health System using electronic medical records (EMR) reveals important prognostic factors for improved clinical outcomes

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Zichen Wang

  12. Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects

    Article • JACC Basic to Translational Science, April 2020, Elsevier

    Zichen Wang

  13. Dermal sheath contraction powers stem cell niche relocation during hair cycle regression

    Article • Science, December 2019, American Association for the Advancement of Science

    Zichen Wang

  14. The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways

    Article • Scientific Data, October 2019, Springer Science + Business Media

    Zichen Wang, Dave Bridges

  15. Habenular TCF7L2 links nicotine addiction to diabetes

    Article • Nature, October 2019, Springer Science + Business Media

    Jessica Ables, Zichen Wang

  16. Single-cell immune landscape of human atherosclerotic plaques

    Article • Nature Medicine, October 2019, Springer Science + Business Media

    Zichen Wang

  17. ChEA3: transcription factor enrichment analysis by orthogonal omics integration

    Article • Nucleic Acids Research, May 2019, Oxford University Press (OUP)

    Zichen Wang

  18. Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells

    Article • Nature Cell Biology, April 2019, Springer Science + Business Media

    Zichen Wang

  19. Predicting opioid dependence from electronic health records with machine learning

    Article • BioData Mining, January 2019, Springer Science + Business Media

    Zichen Wang

  20. Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent

    Article • Developmental Cell, January 2019, Elsevier

    Zichen Wang

  21. Mining data and metadata from the gene expression omnibus

    Article • Biophysical Reviews, December 2018, Springer Science + Business Media

    Zichen Wang

  22. Temporal proteomic profiling of postnatal human cortical development

    Article • Translational Psychiatry, December 2018, Springer Science + Business Media

    Zichen Wang

  23. Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming

    Article • Cell Reports, December 2018, Elsevier

    Zichen Wang

  24. Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures

    Article • Bioinformatics, August 2018, Oxford University Press (OUP)

    Zichen Wang

  25. SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling

    Article • Nature Communications, August 2018, Springer Science + Business Media

    Zichen Wang

  26. Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease

    Article • Journal of the American Society of Nephrology, August 2018, American Society of Nephrology

    Zichen Wang, Sandeep Mallipattu

  27. eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

    Article • Nucleic Acids Research, May 2018, Oxford University Press (OUP)

    Zichen Wang

  28. Brain microstructural injury occurs in patients with RRMS despite ‘no evidence of disease activity’

    Article • Journal of Neurology Neurosurgery & Psychiatry, March 2018, BMJ

    Zichen Wang

  29. Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses

    Article • Scientific Data, February 2018, Nature

    Zichen Wang

  30. L1000FWD: fireworks visualization of drug-induced transcriptomic signatures

    Article • Bioinformatics, February 2018, Oxford University Press (OUP)

    Zichen Wang

  31. Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age

    Article • Journal of Biomedical Informatics, December 2017, Elsevier

    Zichen Wang

  32. Transcriptomic analysis uncovers novel synergistic mechanisms in combination therapy for lupus nephritis

    Article • Kidney International, November 2017, Elsevier

    Zichen Wang

  33. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

    Article • Cell Systems, November 2017, Elsevier

    Zichen Wang

  34. Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling

    Article • Nature Communications, October 2017, Nature

    Zichen Wang

  35. Differential cytokine contributions of perivascular haematopoietic stem cell niches

    Article • Nature, February 2017, Nature

    Zichen Wang

  36. Integrative Analysis of Sex-Specific microRNA Networks Following Stress in Mouse Nucleus Accumbens

    Article • Frontiers in Molecular Neuroscience, December 2016, Frontiers

    Zichen Wang

  37. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

    Article • Nature Communications, September 2016, Nature

    Zichen Wang, Vicente Perez-Garcia

  38. Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration

    Article • Nature Neuroscience, August 2016, Nature

    Zichen Wang

  39. L1000CDS2: LINCS L1000 characteristic direction signatures search engine

    Article • npj Systems Biology and Applications, August 2016, Nature

    Zichen Wang

  40. An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

    Article • F1000Research, July 2016, Faculty of 1000, Ltd.

    Zichen Wang, Dr. Avi Ma'ayan

  41. Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production

    Article • Scientific Reports, May 2016, Nature

    Zichen Wang

  42. Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma

    Article • Oncotarget, March 2016, Impact Journals, LLC

    Zichen Wang

  43. Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles

    Article • Cell Reports, March 2016, Elsevier

    Zichen Wang

  44. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

    Article • Database, January 2016, Oxford University Press (OUP)

    Zichen Wang

  45. Reprint of “Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction”

    Article • Computational Biology and Chemistry, December 2015, Elsevier

    Zichen Wang

  46. Publisher's Note: Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction

    Article • Computational Biology and Chemistry, October 2015, Elsevier

    Zichen Wang

  47. An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin

    Article • Developmental Cell, September 2015, Elsevier

    Zichen Wang, Dr. Avi Ma'ayan

  48. Dynamics of the discovery process of protein-protein interactions from low content studies

    Article • BMC Systems Biology, June 2015, Springer Science + Business Media

    Zichen Wang, Dr. Avi Ma'ayan

  49. Dynamic Phosphorylation of CENP-A at Ser68 Orchestrates Its Cell-Cycle-Dependent Deposition at Centromeres

    Article • Developmental Cell, January 2015, Elsevier

    Zichen Wang

  50. Histone H3.3 and its proteolytically processed form drive a cellular senescence programme

    Article • Nature Communications, November 2014, Nature

    Zichen Wang, Dr. Avi Ma'ayan

  51. Lean Big Data integration in systems biology and systems pharmacology

    Article • Trends in Pharmacological Sciences, September 2014, Elsevier

    Zichen Wang, Dr. Avi Ma'ayan

  52. Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets

    Article • Bioinformatics, August 2014, Oxford University Press (OUP)

    Zichen Wang

  53. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Zichen Wang, Dr. Avi Ma'ayan

  54. Arabidopsis CSLD1 and CSLD4 are required for cellulose deposition and normal growth of pollen tubes

    Article • Journal of Experimental Botany, July 2011, Oxford University Press (OUP)

    Zichen Wang