Declan Clarke, PhD
Associate Research ScientistCards
About
Research
Publications
2021
A novel signature predicts recurrence risk and therapeutic response in breast cancer patients
Tran QH, Than VT, Luu PL, Clarke D, Lam HN, Nguyen T, Nguyen D, Duy PQ, Phung D, Nguyen MN. A novel signature predicts recurrence risk and therapeutic response in breast cancer patients. International Journal Of Cancer 2021, 148: 2848-2856. PMID: 33586202, DOI: 10.1002/ijc.33512.Peer-Reviewed Original Research
2018
Network Analysis as a Grand Unifier in Biomedical Data Science
McGillivray P, Clarke D, Meyerson W, Zhang J, Lee D, Gu M, Kumar S, Zhou H, Gerstein M. Network Analysis as a Grand Unifier in Biomedical Data Science. Annual Review Of Biomedical Data Science 2018, 1: 1-28. DOI: 10.1146/annurev-biodatasci-080917-013444.Peer-Reviewed Original Research
2016
Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation
Clarke D, Sethi A, Li S, Kumar S, Chang RW, Chen J, Gerstein M. Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation. Structure 2016, 24: 826-837. PMID: 27066750, PMCID: PMC4883016, DOI: 10.1016/j.str.2016.03.008.Peer-Reviewed Original Research
2015
Reads meet rotamers: structural biology in the age of deep sequencing
Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M. Reads meet rotamers: structural biology in the age of deep sequencing. Current Opinion In Structural Biology 2015, 35: 125-134. PMID: 26658741, PMCID: PMC4751031, DOI: 10.1016/j.sbi.2015.11.003.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
2013
Localized structural frustration for evaluating the impact of sequence variants
Kumar S, Clarke D, Gerstein M. Localized structural frustration for evaluating the impact of sequence variants. Nucleic Acids Research 2013, 44: 10062-10073. PMID: 27915290, PMCID: PMC5137452, DOI: 10.1093/nar/gkw927.Peer-Reviewed Original Research
2012
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics 2012, 28: 2267-2269. PMID: 22743228, PMCID: PMC3426844, DOI: 10.1093/bioinformatics/bts368.Peer-Reviewed Original ResearchNovel insights through the integration of structural and functional genomics data with protein networks
Clarke D, Bhardwaj N, Gerstein MB. Novel insights through the integration of structural and functional genomics data with protein networks. Journal Of Structural Biology 2012, 179: 320-326. PMID: 22343087, PMCID: PMC4830681, DOI: 10.1016/j.jsb.2012.02.001.Peer-Reviewed Original Research
2011
Systematic control of protein interactions for systems biology
Bhardwaj N, Clarke D, Gerstein M. Systematic control of protein interactions for systems biology. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 20279-20280. PMID: 22160691, PMCID: PMC3251072, DOI: 10.1073/pnas.1118084109.Peer-Reviewed Original ResearchIntegration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions
Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Science 2011, 20: 1745-1754. PMID: 21826754, PMCID: PMC3218368, DOI: 10.1002/pro.710.Peer-Reviewed Original Research