[Accepted RECOMB 2024] Enhancing gene set analysis in embedding spaces: a novel best-match approach
Li L, Dannenfelser R, Cruz C, Yao V
bioRxiv. 2023 Nov 22.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 22.[Preprint] The proto-oncogene DEK regulates neuronal excitability and tau accumulation in Alzheimer′s disease vulnerable neurons
Rodriguez-Rodriguez P, Arroyo-Garcia LE, Li L, Tsagkogianni C, Wang W, Salas-Allende I, Plautz Z, Cedazo-Minguez A, Sinha S, Troyanskaya OG, Flajolet M, Yao V, Roussarie JP
bioRxiv. 2022 May.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 1.[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.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 11.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 16.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 29.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.Enabling Precision Medicine through Integrative Network Models
Yao V*, Wong AK*, Troyanskaya OG
Journal of Molecular Biology. 2018 Sep 14.