Personal information

Biography

I am interested in developing machine learning methods to tackle biology-related problems. I started as a wet-lab biologist in undergrad, where I used a combination to experimental approaches – including imaging, biochemistry, cell biology – to study autophagy in human cell lines and yeast. My graduate work is focused on integrating large scale biological datasets and applying network-based approaches to predict context-specific disease genes and pathways in neurodevelopmental and neurodegenerative diseases and disorders. During my postdoc studies, I am working on integrating and translating multi-omics single cell profiles across data modality, time and species.

Activities

Employment (1)

University of Washington: Seattle, US

2020-02-01 to present | Postdoctoral fellow (Genome Sciences)
Employment
Source: Self-asserted source
Ran Zhang

Education and qualifications (1)

Princeton University: Princeton, NJ, US

2012-09-01 to 2019-09-01 | PhD (Molecular Biology)
Education
Source: Self-asserted source
Ran Zhang

Works (18)

Astrocyte-derived extracellular matrix proteins regulate synapse remodeling in stress-induced depression

2024-12-30 | Preprint
Contributors: Ran Zhang; Patricia Rodriguez-Rodriguez; Lucian Medrihan; Jerry C. Chang; Tatiana Ferraro; Pedro Del Cioppo Vasques; Wei Wang; Caroline Menard; Flurin Cathomas; Kenny L. Chan et al.
Source: check_circle
Crossref

Multi-condition and multi-modal temporal profile inference during mouse embryonic development

2024-03-04 | Preprint
Contributors: Ran Zhang; Chengxiang Qiu; Gala Filippova; Gang Li; Jay Shendure; Jean-Philippe Vert; Xinxian Deng; Christine Disteche; William Stafford Noble
Source: check_circle
Crossref

Cross-species imputation and comparison of single-cell transcriptomic profiles

2023-10-20 | Preprint
Contributors: Ran Zhang; Mu Yang; Jacob Schreiber; Diana R. O’Day; James M. A. Turner; Jay Shendure; Christine M. Disteche; Xinxian Deng; William Stafford Noble
Source: check_circle
Crossref

LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis

Bioinformatics
2023-07-01 | Journal article
Contributors: Laetitia Meng-Papaxanthos; Ran Zhang; Gang Li; Marco Cuturi; William Stafford Noble; Jean-Philippe Vert; Anthony Mathelier
Source: check_circle
Crossref

MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes

2023-03-20 | Preprint
Contributors: Daniel Mar; Ilona M. Babenko; Ran Zhang; William Stafford Noble; Oleg Denisenko; Tomas Vaisar; Karol Bomsztyk
Source: Self-asserted source
Ran Zhang

Semi-supervised Single-Cell Cross-modality Translation Using Polarbear

2022 | Book chapter
Contributors: Ran Zhang; Laetitia Meng-Papaxanthos; Jean-Philippe Vert; William Stafford Noble
Source: check_circle
Crossref

Identifying genes and pathways linking astrocyte regional specificity to Alzheimer’s disease susceptibility

2022-11-17 | Preprint
Contributors: Ran Zhang; Margarete Knudsen; Pedro Del Cioppo Vasques; Alicja Tadych; Patricia Rodriguez-Rodriguez; Paul Greengard; Jean-Pierre Roussarie; Ana Milosevic; Olga Troyanskaya
Source: check_circle
Crossref

Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning

Journal of Computational Biology
2022-11-01 | Journal article
Contributors: Ran Zhang; Laetitia Meng-papaxanthos; Jean-philippe Vert; William Stafford Noble
Source: check_circle
Crossref

LSMMD-MA: Scaling multimodal data integration for single-cell genomics data analysis

2022-03-25 | Preprint
Contributors: Laetitia Meng-Papaxanthos; Ran Zhang; Gang Li; Marco Cuturi; William Stafford Noble; Jean-Philippe Vert
Source: check_circle
Crossref

Semi-supervised single-cell cross-modality translation using Polarbear

2021-11-19 | Other
Contributors: Ran Zhang; Laetitia Meng-Papaxanthos; Jean-Philippe Vert; William Stafford Noble
Source: check_circle
Crossref

Presenilin 1 phosphorylation regulates amyloid-β degradation by microglia

Molecular Psychiatry
2021-10 | Journal article
Contributors: Jose Henrique Ledo; Thomas Liebmann; Ran Zhang; Jerry C. Chang; Estefania P. Azevedo; Eitan Wong; Hernandez Moura Silva; Olga G. Troyanskaya; Victor Bustos; Paul Greengard
Source: check_circle
Crossref

Tissue-specific enhancer functional networks for associating distal regulatory regions to disease.

Cell systems
2021-03-08 | Journal article
Source: Self-asserted source
Ran Zhang

Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development.

PloS one
2020-08-21 | Journal article
Source: Self-asserted source
Ran Zhang

Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder

Nature Neuroscience
2016-11-01 | Journal article
Contributors: Arjun Krishnan; Ran Zhang; Victoria Yao; Chandra L Theesfeld; Aaron K Wong; Alicja Tadych; Natalia Volfovsky; Alan Packer; Alex Lash; Olga G Troyanskaya
Source: check_circle
Crossref

Genome-wide characterization of genetic and functional dysregulation in autism spectrum disorder

2016-06-09 | Preprint
Contributors: Arjun Krishnan; Ran Zhang; Victoria Yao; Chandra L. Theesfeld; Aaron K. Wong; Alicja Tadych; Natalia Volfovsky; Alan Packer; Alex Lash; Olga G. Troyanskaya
Source: check_circle
Crossref

Understanding multicellular function and disease with human tissue-specific networks.

Nature genetics
2015-04-27 | Journal article
Source: Self-asserted source
Ran Zhang

Targeted exploration and analysis of large cross-platform human transcriptomic compendia.

Nature methods
2015-01-12 | Journal article
Source: Self-asserted source
Ran Zhang

Atg5 regulates late endosome and lysosome biogenesis.

Science China. Life sciences
2013-12-23 | Journal article
Source: Self-asserted source
Ran Zhang

Peer review (2 reviews for 2 publications/grants)

Review activity for Journal of Molecular Biology. (1)
Review activity for Nature machine intelligence. (1)