Han E, Lee S, Hoshino S, Seyedsayamdost M. Targeted Discovery of Cryptic Metabolites with Antiproliferative Activity. ACS Chem Biol. 2022;17(11):3121–3130. PMID: 36228140

Clark K, Seyedsayamdost M. Bioinformatic Atlas of Radical SAM Enzyme-Modified RiPP Natural Products Reveals an Isoleucine-Tryptophan Crosslink. J Am Chem Soc. 2022;144(39):17876–17888. PMID: 36128669

Weiner B, Pyo A, Meir Y, Wingreen N. Motif-pattern dependence of biomolecular phase separation driven by specific interactions. PLoS Comput Biol. 2021;17(12):e1009748. PMCID: PMC8751999

Covington B, Seyedsayamdost M. MetEx, a Metabolomics Explorer Application for Natural Product Discovery. ACS Chem Biol. 2021;16(12):2825–2833. PMCID: PMC9090437

King S, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS Comput Biol. 2021;17(11):e1009560. PMCID: PMC8601562

Zhou J, Troyanskaya O. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021;18(11):1317–1321. PMCID: PMC8959118

Kloosterman A, Cimermancic P, Elsayed S, Du C, Hadjithomas M, Donia M, Fischbach M, van Wezel G, Medema M. Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides. PLoS Biol. 2020;18(12):e3001026. PMCID: PMC7794033

Montalbán-López M, Scott T, Ramesh S, Rahman I, van Heel A, Viel J, Bandarian V, Dittmann E, Genilloud O, Goto Y, Burgos M, Hill C, Kim S, Koehnke J, Latham J, Link J, Martínez B, Nair S, Nicolet Y, Rebuffat S, Sahl H-G, Sareen D, Schmidt E, Schmitt L, Severinov K, Süssmuth R, Truman A, Wang H, Weng J-K, van Wezel G, Zhang Q, Zhong J, Piel J, Mitchell D, Kuipers O, van der Donk W. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep. 2021;38(1):130–239. PMCID: PMC7864896

Stern T, Shvartsman S, Wieschaus E. Template-based mapping of dynamic motifs in tissue morphogenesis. PLoS Comput Biol. 2020;16(8):e1008049. PMCID: PMC7442231

Federspiel J, Cook K, Kennedy M, Venkatesh S, Otter C, Hofstadter W, Beltran P, Cristea I. Mitochondria and Peroxisome Remodeling across Cytomegalovirus Infection Time Viewed through the Lens of Inter-ViSTA. Cell Rep. 2020;32(4):107943. PMCID: PMC8489195

Sealfon R, Mariani L, Kretzler M, Troyanskaya O. Machine learning, the kidney, and genotype-phenotype analysis. Kidney Int. 2020;97(6):1141–1149. PMCID: PMC8048707

Cabreros I, Storey J. A Likelihood-Free Estimator of Population Structure Bridging Admixture Models and Principal Components Analysis. Genetics. 2019;212(4):1009–1029. PMCID: PMC6707457

Wang R, Zheng J, Shao X, Ishii Y, Roy A, Bello A, Lee R, Zhang J, Wind-Rotolo M, Feng Y. Development of a prognostic composite cytokine signature based on the correlation with nivolumab clearance: translational PK/PD analysis in patients with renal cell carcinoma. J Immunother Cancer. 2019;7(1):348. PMCID: PMC6907258

Arguello E, Leach R, Kleiner R. Selection with a Site-Specifically Modified RNA Library Reveals the Binding Preferences of N-Methyladenosine Reader Proteins. Biochemistry. 2019;58(31):3386–3395. PMCID: PMC6684389

Bushin L, Clark K, Pelczer I, Seyedsayamdost M. Charting an Unexplored Streptococcal Biosynthetic Landscape Reveals a Unique Peptide Cyclization Motif. J Am Chem Soc. 2018;140(50):17674–17684. PMID: 30398325

Zhou J, Schor I, Yao V, Theesfeld C, Marco-Ferreres R, Tadych A, Furlong E, Troyanskaya O. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. PLoS Genet. 2019;15(9):e1008382. PMCID: PMC6779412

Durán A, Greco T, Vollmer B, Cristea I, Grünewald K, Topf M. Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PLoS Biol. 2019;17(6):e3000316. PMCID: PMC6594648

Clark K, Bushin L, Seyedsayamdost M. Aliphatic Ether Bond Formation Expands the Scope of Radical SAM Enzymes in Natural Product Biosynthesis. J Am Chem Soc. 2019;141(27):10610–10615. PMID: 31246011

Giovannucci A, Friedrich J, Gunn P, Kalfon J, Brown B, Koay S, Taxidis J, Najafi F, Gauthier J, Zhou P, Khakh B, Tank D, Chklovskii D, Pnevmatikakis E. CaImAn an open source tool for scalable calcium imaging data analysis. Elife. 2019;8. PMCID: PMC6342523

Zhou J, Park C, Theesfeld C, Wong A, Yuan Y, Scheckel C, Fak J, Funk J, Yao K, Tajima Y, Packer A, Darnell R, Troyanskaya O. Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. Nat Genet. 2019;51(6):973–980. PMCID: PMC6758908

Wang S-W, Bitbol A-F, Wingreen N. Revealing evolutionary constraints on proteins through sequence analysis. PLoS Comput Biol. 2019;15(4):e1007010. PMCID: PMC6502352

Seyedsayamdost M. Toward a global picture of bacterial secondary metabolism. J Ind Microbiol Biotechnol. 2019;46(3-4):301–311. PMCID: PMC6779422

Chen K, Cofer E, Zhou J, Troyanskaya O. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019;16(4):315–318. PMCID: PMC7148117

Moon K, Xu F, Zhang C, Seyedsayamdost M. Bioactivity-HiTES Unveils Cryptic Antibiotics Encoded in Actinomycete Bacteria. ACS Chem Biol. 2019;14(4):767–774. PMCID: PMC6813803

Liszczak G, Muir T. Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter. Angew Chem Int Ed Engl. 2019;58(13):4144–4162. PMCID: PMC6748390

DiMaio D, Dermody T, Enquist L. Reductio ad Intellectum. Annu Rev Virol. 2018;5(1):ii-iv. PMID: 30265630

Sigoillot F, Lyman S, Huckins J, Adamson B, Chung E, Quattrochi B, King R. A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nat Methods. 2012;9(4):363–6. PMCID: PMC3482495

Wong A, Krishnan A, Troyanskaya O. GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. Nucleic Acids Res. 2018;46(W1):W65-W70. PMCID: PMC6030827

Davis K, Schramma K, Hansen W, Bacik J, Khare S, Seyedsayamdost M, Ando N. Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition. Proc Natl Acad Sci U S A. 2017;114(39):10420–10425. PMCID: PMC5625900

Donnelly A, Murphy G, Digianantonio K, Hecht M. A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli. Nat Chem Biol. 2018;14(3):253–255. PMID: 29334382

Ioffe M, Berry M. The structured ’low temperature’ phase of the retinal population code. PLoS Comput Biol. 2017;13(10):e1005792. PMCID: PMC5654267

Villoutreix P, Andén J, Lim B, Lu H, Kevrekidis I, Singer A, Shvartsman S. Synthesizing developmental trajectories. PLoS Comput Biol. 2017;13(9):e1005742. PMCID: PMC5619836

Hristov B, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017;5(3):221–229.e4. PMCID: PMC5997485

Calhoun A, Murthy M. Quantifying behavior to solve sensorimotor transformations: advances from worms and flies. Curr Opin Neurobiol. 2017;46:90–98. PMCID: PMC5765764

Lu Y, Xie S, Zhang W, Zhang C, Gao C, Sun Q, Cai Y, Xu Z, Xiao M, Xu Y, Huang X, Wu X, Liu W, Wang F, Kang Y, Zhou T. Twa1/Gid8 is a β-catenin nuclear retention factor in Wnt signaling and colorectal tumorigenesis. Cell Res. 2017;27(12):1422–1440. PMCID: PMC5717399

vonHoldt B, Shuldiner E, Koch I, Kartzinel R, Hogan A, Brubaker L, Wanser S, Stahler D, Wynne C, Ostrander E, Sinsheimer J, Udell M. Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs. Sci Adv. 2017;3(7):e1700398. PMCID: PMC5517105

Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics. 2017;33(16):2471–2478. PMCID: PMC5870623

Misra M, Audoly B, Shvartsman S. Complex structures from patterned cell sheets. Philos Trans R Soc Lond B Biol Sci. 2017;372(1720). PMCID: PMC5379023

Beltran P, Federspiel J, Sheng X, Cristea I. Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. Mol Syst Biol. 2017;13(3):922. PMCID: PMC5371729

Ashford P, Hernandez A, Greco T, Buch A, Sodeik B, Cristea I, Grünewald K, Shepherd A, Topf M. HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. Mol Cell Proteomics. 2016;15(9):2939–53. PMCID: PMC5013309

Gopalan P, Hao W, Blei D, Storey J. Scaling probabilistic models of genetic variation to millions of humans. Nat Genet. 2016;48(12):1587–1590. PMCID: PMC5127768

Adolfsen K, Brynildsen M. A Kinetic Platform to Determine the Fate of Hydrogen Peroxide in Escherichia coli. PLoS Comput Biol. 2015;11(11):e1004562. PMCID: PMC4636272

Gorenshteyn D, Zaslavsky E, Fribourg M, Park C, Wong A, Tadych A, Hartmann B, Albrecht R, García-Sastre A, Kleinstein S, Troyanskaya O, Sealfon S. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity. 2015;43(3):605–14. PMCID: PMC4753773

Ochoa A, Storey J, Llinás M, Singh M. Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PLoS Comput Biol. 2015;11(11):e1004509. PMCID: PMC4648515

Seyedsayamdost M, Cleto S, Carr G, Vlamakis H, Vieira M, Kolter R, Clardy J. Mixing and matching siderophore clusters: structure and biosynthesis of serratiochelins from Serratia sp. V4. J Am Chem Soc. 2012;134(33):13550–3. PMCID: PMC3424848

Medema M, Kottmann R, Yilmaz P, Cummings M, Biggins J, Blin K, de Bruijn I, Chooi Y, Claesen J, Coates C, Cruz-Morales P, Duddela S, Düsterhus S, Edwards D, Fewer D, Garg N, Geiger C, Gomez-Escribano J, Greule A, Hadjithomas M, Haines A, Helfrich E, Hillwig M, Ishida K, Jones A, Jones C, Jungmann K, Kegler C, Kim H, Kötter P, Krug D, Masschelein J, Melnik A, Mantovani S, Monroe E, Moore M, Moss N, Nützmann H-W, Pan G, Pati A, Petras D, Reen J, Rosconi F, Rui Z, Tian Z, Tobias N, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel A, Balibar C, Balskus E, Barona-Gómez F, Bechthold A, Bode H, Borriss R, Brady S, Brakhage A, Caffrey P, Cheng Y-Q, Clardy J, Cox R, De Mot R, Donadio S, Donia M, van der Donk W, Dorrestein P, Doyle S, Driessen A, Ehling-Schulz M, Entian K-D, Fischbach M, Gerwick L, Gerwick W, Gross H, Gust B, Hertweck C, Höfte M, Jensen S, Ju J, Katz L, Kaysser L, Klassen J, Keller N, Kormanec J, Kuipers O, Kuzuyama T, Kyrpides N, Kwon H-J, Lautru S, Lavigne R, Lee C, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell D, Moore B, Moreira L, Müller R, Neilan B, Nett M, Nielsen J, O’Gara F, Oikawa H, Osbourn A, Osburne M, Ostash B, Payne S, Pernodet J-L, Petricek M, Piel J, Ploux O, Raaijmakers J, Salas J, Schmitt E, Scott B, Seipke R, Shen B, Sherman D, Sivonen K, Smanski M, Sosio M, Stegmann E, Süssmuth R, Tahlan K, Thomas C, Tang Y, Truman A, Viaud M, Walton J, Walsh C, Weber T, van Wezel G, Wilkinson B, Willey J, Wohlleben W, Wright G, Ziemert N, Zhang C, Zotchev S, Breitling R, Takano E, Glöckner F. Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol. 2015;11(9):625–31. PMCID: PMC5714517

Toettcher J, Gong D, Lim W, Weiner O. Light-based feedback for controlling intracellular signaling dynamics. Nat Methods. 2011;8(10):837–9. PMCID: PMC3184382

Wühr M, Freeman R, Presler M, Horb M, Peshkin L, Gygi S, Kirschner M. Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. Curr Biol. 2014;24(13):1467–1475. PMCID: PMC4090281

Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for collective behavior in a large network of sensory neurons. PLoS Comput Biol. 2014;10(1):e1003408. PMCID: PMC3879139

da Silveira R, Berry M. High-fidelity coding with correlated neurons. PLoS Comput Biol. 2014;10(11):e1003970. PMCID: PMC4238954