2024

A best-match approach for gene set analyses in embedding spaces

Li L, Dannenfelser R, Cruz C, Yao V

Genome Research. 2024 Oct 11.

[Preprint] Disentangling associations between complex traits and cell types with seismic

Lai Q, Dannenfelser R, Roussarie J, Yao V

bioRxiv. 2024 May.

A cell autonomous regulator of neuronal excitability modulates tau in Alzheimer’s disease vulnerable neurons

Rodriguez-Rodriguez P, Arroyo-Garcia LE, Tsagkogianni C, Li L, Wang W, Végvári Á, Salas-Allende I, Plautz Z, Cedazo-Minguez A, Sinha SC, Troyanskaya OG, Flajolet M, Yao V, Roussarie J

Brain. 2024 Mar.
2023

Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer

Dannenfelser R, Yao V

Pacific Symposium on Biocomputing 2024. 2023 Dec.

Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts

Dannenfelser R, Zhong J, Zhang R, Yao V

NeurIPS 2023 Datasets and Benchmarks Spotlight. 2023 Sep.

Joint embedding of biological networks for cross-species functional alignment

Li L, Dannenfelser R, Zhu Y, Hejduk N, Segarra S, Yao V

Bioinformatics. 2023 Aug.

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis

Brewer RC, Lanz TV, Hale CR, Sepich-Poore GD, Martino C, Swafford AD, Carroll TS, Kongpachith S, Blum LK, Elliott SE, Blachere NE, Parveen S, Fak J, Yao V, Troyanskaya OG, Frank MO, Bloom MS, Jahanbani S, Gomez AM, Iyer R, Ramadoss NS, Sharpe O, Chandrasekaran S, Kelmenson LB, Wang Q, Wong H, Torres HL, Wiesen M, Graves DT, Deane KD, Holers VM, Knight R, Darnell RB, Robinson WH, Orange DE

Science Translational Medicine. 2023 Feb.
2022

Current progress and open challenges for applying deep learning across the biosciences

Sapoval N, Aghazadeh A, Nute MG, Antunes DA, Balaji A, Baraniuk R, Barberan CJ, Dannenfelser R, Dun C, Edrisi M, Elworth RAL, Kille B, Kyrillidis A, Nakhleh L, Wolfe CR, Yan Z, Yao V, Treangen TJ

Nature Communications. 2022 Apr.
2021

[Preprint] Neuron-Glia Signaling Regulates the Onset of the Antidepressant Response

Yao V, Aly A, Kalik S, Gresack J, Wang W, Handler A, Schaefer A, Troyanskaya OG, Greengard P, Chottekalapanda RU

bioRxiv. 2021 Jul.
2020

Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies

Dannenfelser R*, Allen GM*, VanderSluis B, Koegel AK, Levinson S, Stark SR, Yao V, Tadych A, Troyanskaya OG, Lim W

Cell Systems. 2020 Sep.

RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares

Orange DE*, Yao V*, Sawicka K, Fak J, Frank MO, Parveen S, Blachere NE, Hale C, Zhang F, Raychaudhuri S, Troyanskaya OG, Darnell RB

New England Journal of Medicine. 2020 Jul.

Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis

Roussarie JP*, Yao V*, Rodriguez-Rodriguez P, Oughtred R, Rust J, Plautz Z, Kasturia S, Albornoz C, Wang W, Schmidt EF, Dannenfelser R, Tadych A, Brichta L, Barnea-Cramer A, Heintz N, Hof PR, Heiman M, Dolinski K, Flajolet M, Troyanskaya OG, Greengard P

Neuron. 2020 Jun.
2019

Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons

Sargin D, Chottekalapanda RU, Perit KE, Yao V, Chu D, Sparks DW, Kalik S, Power SK, Troyanskaya OG, Schmidt EF, Greengard P, Lambe EK

Molecular Psychiatry. 2019 Aug.
2018

An integrative tissue-network approach to identify and test human disease genes

Yao V*, Kaletsky R*, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG

Nature Biotechnology. 2018 Oct.

Enabling Precision Medicine through Integrative Network Models

Yao V*, Wong AK*, Troyanskaya OG

Journal of Molecular Biology. 2018 Sep.

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression

Kaletsky R*, Yao V*, Williams A, Runnels AM, Tadych A, Zhou S, Troyanskaya OG, Murphy CT

PLoS Genetics. 2018 Aug.