Clustering short time series gene expression data. - Jason Ernst; Gerard J. Nau; Ziv Bar-Joseph (ISMB (Supplement of Bioinformatics), 2005)

STEM: a tool for the analysis of short time series gene expression data. - Jason Ernst; Ziv Bar-Joseph (BMC Bioinform., 2006)

Algorithms and Implementation for Interconnection Graph Problem. - Hongbing Fan; Christian Hundt 001; Yu-Liang Wu; Jason Ernst (COCOA, 2008)

Customized Reconfigurable Interconnection Networks for multiple application SOCS. - Hongbing Fan; Jason Ernst; Yu-Liang Wu (FPL, 2008)

Impact of the solvent capacity constraint on E. coli metabolism. - Alexei Vázquez; Qasim K. Beg; Marcio A. de Menezes; Jason Ernst; Ziv Bar-Joseph; Albert-László Barabási; László G. Boros; Zoltán N. Oltvai (BMC Syst. Biol., 2008)

A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli. - Jason Ernst; Qasim K. Beg; Krin A. Kay; Gábor Balázsi; Zoltán N. Oltvai; Ziv Bar-Joseph (PLoS Comput. Biol., 2008)

Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome. - Jason Ernst; Manolis Kellis (RECOMB, 2011)

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. - Marcel H. Schulz; William E. Devanny; Anthony Gitter; Shan Zhong; Jason Ernst; Ziv Bar-Joseph (BMC Syst. Biol., 2012)

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State. - Nisha Rajagopal; Wei Xie; Yan Li; Uli Wagner 002; Wei Wang 051; John A. Stamatoyannopoulos; Jason Ernst; Manolis Kellis; Bing Ren (PLoS Comput. Biol., 2013)

Integrative analysis of 111 reference human epigenomes Open. - Roadmap Epigenomics Consortium; Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi Moussavi; Pouya Kheradpour; ZhiZhuo Zhang; Jianrong Wang; Michael J. Ziller; Viren Amin; et al. (Nat., 2015)

Using genomic annotations increases statistical power to detect eGenes. - Dat Duong; Jennifer Zou; Farhad Hormozdiari; Jae Hoon Sul; Jason Ernst; Buhm Han; Eleazar Eskin (Bioinform., 2016)

An integrative approach for fine-mapping chromatin interactions. - Artur Tomasz Jaroszewicz; Jason Ernst (Bioinform., 2020)

Marginal Contribution Feature Importance - an Axiomatic Approach for The Natural Case. - Amnon Catav; Boyang Fu; Jason Ernst; Sriram Sankararaman; Ran Gilad-Bachrach (CoRR, 2020)

M-ODD: A Standard Protocol for Reporting MANET Related Models, Simulations, and Findings. - Izabela Savic; Marshall Asch; Keefer Rourke; Fatemeh Safari; Patrick Houlding; Jeremie Fraeys de Veubeke; Jason Ernst; Daniel Gillis (ADHOCNETS/TRIDENTCOM, 2021)

Marginal Contribution Feature Importance - an Axiomatic Approach for Explaining Data. - Amnon Catav; Boyang Fu; Yazeed Zoabi; Ahuva Weiss-Meilik; Noam Shomron; Jason Ernst; Sriram Sankararaman; Ran Gilad-Bachrach (ICML, 2021)

Co-designing a community-led Internet assessment tool in Rigolet, Nunatsiavut, Canada. - Nic Durish; Rekkab Gill; Patrick Houlding; Charlie Flowers; Inez Shiwak; Jason Ernst; Daniel Gillis (ISTAS, 2021)

It's Time to Do Something: Mitigating the Negative Impacts of Computing Through a Change to the Peer Review Process. - Brent J. Hecht; Lauren Wilcox; Jeffrey P. Bigham; Johannes Schöning; Ehsan Hoque 001; Jason Ernst; Yonatan Bisk; Luigi De Russis; Lana Yarosh; Bushra Anjum; Danish Contractor; Cathy Wu 002 (CoRR, 2021)

A Review of AI-based MANET Routing Protocols. - Fatemeh Safari; Izabela Savic; Herb Kunze; Jason Ernst; Daniel Gillis (WiMob, 2023)

A Novel Cross-Layer Adaptive Fuzzy-Based Ad Hoc On-Demand Distance Vector Routing Protocol for MANETs. - Fatemeh Safari; Herb Kunze; Jason Ernst; Daniel Gillis (IEEE Access, 2023)

A framework for group-wise summarization and comparison of chromatin state annotations. - Ha Vu; Zane Koch; Petko Fiziev; Jason Ernst (Bioinform., 2023)