Before formal publication in a scholarly journal, scientific and medical articles are traditionally “peer reviewed.” In this process, the journal’s editors take advice from various experts—called “referees”—who have assessed the paper and may identify weaknesses in its assumptions, methods, and conclusions. Typically a journal will only publish an article once the editors are satisfied that the authors have addressed referees’ concerns.

Because this process can be lengthy, authors use the bioRxiv service to make their manuscripts available as “preprints” before peer review, allowing other scientists to see, discuss, and comment on the findings immediately. Readers should therefore be aware that articles on bioRxiv have not been finalized by authors, might contain errors, and report information that has not yet been accepted or endorsed in any way by the scientific or medical community.

Epigenome-based Splicing Prediction using a Recurrent Neural Network
D Lee, J Zhang, J Liu, M Gerstein (2020). bioRxiv.

To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq
J Xu, MM Kudron, A Victorsen, J Gao, HN Ammouri, FCP Navarro, L Gevirtzman, RH Waterston, KP White, V Reinke, M Gerstein (2019). bioRxiv.

TopicNet: a framework for measuring transcriptional regulatory network change
S Lou, T Li, X Kong, J Zhang, J Liu, D Lee, M Gerstein (2019). bioRxiv.

Private information leakage from functional genomics data: Quantification with calibration experiments and reduction via data sanitization protocols
G Gursoy, P Emani, OA Jolanki, C Brannon, A Harmanci, JS Strattan, A Miranker, M Gerstein (2019). bioRxiv.

Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts
G Gursoy, C Brannon, M Gerstein (2019). bioRxiv.

Quantum Computing at the Frontiers of Biological Sciences
PS Emani, J Warrell, AvAnticevic, S Bekiranov, M Gandal, MJ McConnell, G Sapiro, A Aspuru-Guzik, J Baker, M Bastiani, P McClure, J Murray, SN Sotiropoulos, J Taylor, G Senthil, T Lehner, MB Gerstein, AW Harrow (2019). arXiv.

FANCY: Fast Estimation of Privacy Risk in Functional Genomics Data
G Gursoy, F Navarro, M Gerstein (2019). bioRxiv.

LESSeq: Local event-based analysis of alternative splicing using RNA-Seq data
J Leng, CJF Cameron, S Oh, E Khurana, JP Noonan, MB Gerstein (2019). bioRxiv.

Cyclic and Multilevel Causation in Evolutionary Processes
J Warrell, M Gerstein (2019). bioRxiv.

SVFX: a machine-learning framework to quantify the pathogenicity of structural variants
S Kumar, A Harmanci, J Vytheeswaran, M Gerstein (2019). bioRxiv.

An integrative ENCODE resource for cancer genomics
J Zhang*, D Lee*, V Dhiman*, P Jiang*, J Xu*, P McGillivray*, H Yang*, J Liu, W Meyerson, D Clarke, M Gu, S Li, S Lou, J Xu, L Lochovsky, M Ung, L Ma, S Yu, Q Cao, A Harmanci, K Yan, A Sethi, G Gursoy, MR Schoenberg, J Rozowsky, J Warrell, P Emani, YT Yang, T Galeev, X Kong, S Liu, X Li, J Krishnan, Y Feng, JC Rivera-Mulia, J Adrian, JR Broach, M Bolt, J Moran, D Fitzgerald, V Dileep, T Liu, S Mei, T Sasaki, C Trevilla-Garcia, S Wang, Y Wang, C Zang, D Wang, R Klein, M Snyder, DM Gilbert, K Yip, C Cheng, F Yue, XS Liu, K White, M Gerstein (2019). bioRxiv.

STARRPeaker: Uniform processing and accurate identification of STARR-seq active regions
D Lee, M Shi, J Moran, M Wall, J Zhang, J Liu, D Fitzgerald, Y Kyono, L Ma, K White, M Gerstein (2019). bioRxiv.

Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients
S Lou, T Li, D Spakowicz, GL Chupp, M Gerstein (2019). bioRxiv.

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins
J Zhang, J Liu, D Lee, J Feng, L Lochovsky, S Lou, MR Schoenberg, M Gerstein (2018). bioRxiv.

A cross-organism framework for supervised enhancer prediction with epigenetic pattern recognition and targeted validation
A Sethi, M Gu, E Gumusgoz, L Chan, K Yan, J Rozowsky, I Barozzi, V Afzal, J Akiyama, I Plajzer-Frick, C Yan, C Pickle, M Kato, T Garvin, Q Pham, A Harrington, B Mannion, E Lee, Y Fukuda-Yuzawa, A Visel, DE Dickel, K Yip, R Sutton, LA Pennacchio, M Gerstein (2018). bioRxiv.

SigLASSO: a LASSO approach jointly optimizing sampling likelihood and cancer mutation signatures
S Li, FW Crawford, MB Gerstein (2018). bioRxiv.

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.
S Kumar, J Warrell, S Li, PD McGillivray, W Meyerson, L Salichos, A Harmanci, A Martinez-Fundichely, CWY Chan, MM Nielsen, L Lochovsky, Y Zhang, X Li, S Lou, JS Pedersen, C Herrmann, G Getz, E Khurana, MB Gerstein (2020). Cell.

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