von Holdt B, Kartzinel R, van Oers K, Verhoeven K, Ouyang J. Changes in the rearing environment cause reorganization of molecular networks associated with DNA methylation. J Anim Ecol. 2023;92(3):648–664. PMID: 36567635

Do T, Thokkadam A, Leach R, Link J. Phenotype-Guided Comparative Genomics Identifies the Complete Transport Pathway of the Antimicrobial Lasso Peptide Ubonodin in . ACS Chem Biol. 2022;17(8):2332–2343. PMCID: PMC9454059

Fauser F, Vilarrasa-Blasi J, Onishi M, Ramundo S, Patena W, Millican M, Osaki J, Philp C, Nemeth M, Salomé P, Li X, Wakao S, Kim R, Kaye Y, Grossman A, Niyogi K, Merchant S, Cutler S, Walter P, Dinneny J, Jonikas M, Jinkerson R. Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii. Nat Genet. 2022;54(5):705–714. PMCID: PMC9110296

Qin Y, Kernan K, Fan Z, Park H-J, Kim S, Canna S, Kellum J, Berg R, Wessel D, Pollack M, Meert K, Hall M, Newth C, Lin J, Doctor A, Shanley T, Cornell T, Harrison R, Zuppa A, Banks R, Reeder R, Holubkov R, Notterman D, Dean M, Carcillo J. Machine learning derivation of four computable 24-h pediatric sepsis phenotypes to facilitate enrollment in early personalized anti-inflammatory clinical trials. Crit Care. 2022;26(1):128. PMCID: PMC9077858

Klibaite U, Kislin M, Verpeut J, Bergeler S, Sun X, Shaevitz J, Wang S. Deep phenotyping reveals movement phenotypes in mouse neurodevelopmental models. Mol Autism. 2022;13(1):12. PMCID: PMC8917660

Kernan K, Ghaloul-Gonzalez L, Vockley J, Lamb J, Hollingshead D, Chandran U, Sethi R, Park H-J, Berg R, Wessel D, Pollack M, Meert K, Hall M, Newth C, Lin J, Doctor A, Shanley T, Cornell T, Harrison R, Zuppa A, Banks R, Reeder R, Holubkov R, Notterman D, Dean M, Carcillo J. Prevalence of Pathogenic and Potentially Pathogenic Inborn Error of Immunity Associated Variants in Children with Severe Sepsis. J Clin Immunol. 2022;42(2):350–364. PMCID: PMC8720168

Hussmann J, Ling J, Ravisankar P, Yan J, Cirincione A, Xu A, Simpson D, Yang D, Bothmer A, Cotta-Ramusino C, Weissman J, Adamson B. Mapping the genetic landscape of DNA double-strand break repair. Cell. 2021;184(22):5653–5669.e25. PMCID: PMC9074467

Quinn J, Jones M, Okimoto R, Nanjo S, Chan M, Yosef N, Bivona T, Weissman J. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science. 2021;371(6532). PMCID: PMC7983364

Wong A, Sealfon R, Theesfeld C, Troyanskaya O. Decoding disease: from genomes to networks to phenotypes. Nat Rev Genet. 2021;22(12):774–790. PMCID: 6786975

Chini C, Peclat T, Warner G, Kashyap S, Espindola-Netto J, de Oliveira G, Gomez L, Hogan K, Tarragó M, Puranik A, Agorrody G, Thompson K, Dang K, Clarke S, Childs B, Kanamori K, Witte M, Vidal P, Kirkland A, De Cecco M, Chellappa K, McReynolds M, Jankowski C, Tchkonia T, Kirkland J, Sedivy J, van Deursen J, Baker D, van Schooten W, Rabinowitz J, Baur J, Chini E. CD38 ecto-enzyme in immune cells is induced during aging and regulates NAD and NMN levels. Nat Metab. 2020;2(11):1284–1304. PMCID: PMC8752031

Mor D, Sohrabi S, Kaletsky R, Keyes W, Tartici A, Kalia V, Miller G, Murphy C. Metformin rescues Parkinson’s disease phenotypes caused by hyperactive mitochondria. Proc Natl Acad Sci U S A. 2020;117(42):26438–26447. PMCID: PMC7585014

Aiello-Couzo N, Kang Y. A bridge between melanoma cell states. Nat Cell Biol. 2020;22(8):913–914. PMID: 32753670

Garrison C, Singh-Varma A, Pastino A, Steele J, Kohn J, Murthy S, Schwarzbauer J. A multilayered scaffold for regeneration of smooth muscle and connective tissue layers. J Biomed Mater Res A. 2021;109(5):733–744. PMCID: PMC7855544

Kaletsky R, Murphy C. Transcriptional Profiling of C. elegans Adult Cells and Tissues with Age. Methods Mol Biol. 2020;2144:177–186. PMID: 32410035

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

Kyrchanova O, Maksimenko O, Ibragimov A, Sokolov V, Postika N, Lukyanova M, Schedl P, Georgiev P. The insulator functions of the polydactyl C2H2 zinc finger protein CTCF: Necessity versus sufficiency. Sci Adv. 2020;6(13):eaaz3152. PMCID: PMC7096168

Park J-D, Moon K, Miller C, Rose J, Xu F, Ebmeier C, Jacobsen J, Mao D, Old W, DeShazer D, Seyedsayamdost M. Thailandenes, Cryptic Polyene Natural Products Isolated from Using Phenotype-Guided Transposon Mutagenesis. ACS Chem Biol. 2020;15(5):1195–1203. PMCID: PMC9106368

Benson K, Hu W, Weller A, Bennett A, Chen E, Khetarpal S, Yoshino S, Bone W, Wang L, Rabinowitz J, Voight B, Soccio R. Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene. Proc Natl Acad Sci U S A. 2019;116(46):23232–23242. PMCID: PMC6859347

Carcillo J, Berg R, Wessel D, Pollack M, Meert K, Hall M, Newth C, Lin J, Doctor A, Shanley T, Cornell T, Harrison R, Zuppa A, Reeder R, Banks R, Kellum J, Holubkov R, Notterman D, Dean M, Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediatric Critical Care Research Network. A Multicenter Network Assessment of Three Inflammation Phenotypes in Pediatric Sepsis-Induced Multiple Organ Failure. Pediatr Crit Care Med. 2019;20(12):1137–1146. PMCID: PMC8121153

Itakura A, Chan K, Atkinson N, Pallesen L, Wang L, Reeves G, Patena W, Caspari O, Roth R, Goodenough U, McCormick A, Griffiths H, Jonikas M. A Rubisco-binding protein is required for normal pyrenoid number and starch sheath morphology in . Proc Natl Acad Sci U S A. 2019;116(37):18445–18454. PMCID: PMC6744930

Tandon D, Ressler K, Petticord D, Papa A, Jiranek J, Wilkinson R, Kartzinel R, Ostrander E, Burney N, Borden C, Udell M, vonHoldt B. Homozygosity for Mobile Element Insertions Associated with Could Predict Success in Assistance Dog Training Programs. Genes (Basel). 2019;10(6). PMCID: PMC6627829

Chan M, Smith Z, Grosswendt S, Kretzmer H, Norman T, Adamson B, Jost M, Quinn J, Yang D, Jones M, Khodaverdian A, Yosef N, Meissner A, Weissman J. Molecular recording of mammalian embryogenesis. Nature. 2019;570(7759):77–82. PMCID: PMC7229772

Aedo S, Orman M, Brynildsen M. Stationary phase persister formation in Escherichia coli can be suppressed by piperacillin and PBP3 inhibition. BMC Microbiol. 2019;19(1):140. PMCID: PMC6591824

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

Aedo S, Ma H, Brynildsen M. Checks and Balances with Use of the Keio Collection for Phenotype Testing. Methods Mol Biol. 2019;1927:125–138. PMID: 30788789

vonHoldt B, Kartzinel R, Huber C, Le Underwood V, Zhen Y, Ruegg K, Lohmueller K, Smith T. Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus. Nat Commun. 2018;9(1):4855. PMCID: PMC6242981

Kaletsky R, Yao V, Williams A, Runnels A, Tadych A, Zhou S, Troyanskaya O, Murphy C. Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PLoS Genet. 2018;14(8):e1007559. PMCID: PMC6105014

FitzGerald G, Botstein D, Califf R, Collins R, Peters K, Van Bruggen N, Rader D. The future of humans as model organisms. Science. 2018;361(6402):552–553. PMID: 30093589

Celià-Terrassa T, Kang Y. Metastatic niche functions and therapeutic opportunities. Nat Cell Biol. 2018;20(8):868–877. PMCID: 4161226

Rosenthal G, Schumer M, Andolfatto P. How the manakin got its crown: A novel trait that is unlikely to cause speciation. Proc Natl Acad Sci U S A. 2018;115(18):E4144-E4145. PMCID: PMC5939116

Aebersold R, Agar J, Amster J, Baker M, Bertozzi C, Boja E, Costello C, Cravatt B, Fenselau C, Garcia B, Ge Y, Gunawardena J, Hendrickson R, Hergenrother P, Huber C, Ivanov A, Jensen O, Jewett M, Kelleher N, Kiessling L, Krogan N, Larsen M, Loo J, Loo R, Lundberg E, MacCoss M, Mallick P, Mootha V, Mrksich M, Muir T, Patrie S, Pesavento J, Pitteri S, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff S, Smith L, Snyder M, Thomas P, Uhlén M, Van Eyk J, Vidal M, Walt D, White F, Williams E, Wohlschlager T, Wysocki V, Yates N, Young N, Zhang B. How many human proteoforms are there?. Nat Chem Biol. 2018;14(3):206–214. PMCID: PMC5837046

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

Keenan S, Shvartsman S. Mechanisms and causality in molecular diseases. Hist Philos Life Sci. 2017;39(4):35. PMCID: PMC6445273

Pujol F, Hodgson T, Martinez-Corral I, Prats A-C, Devenport D, Takeichi M, Genot E, Mäkinen T, Francis-West P, Garmy-Susini B, Tatin F. Dachsous1-Fat4 Signaling Controls Endothelial Cell Polarization During Lymphatic Valve Morphogenesis-Brief Report. Arterioscler Thromb Vasc Biol. 2017;37(9):1732–1735. PMID: 28705793

Celià-Terrassa T, Liu D, Choudhury A, Hang X, Wei Y, Zamalloa J, Alfaro-Aco R, Chakrabarti R, Jiang Y-Z, Koh B, Smith H, DeCoste C, Li J-J, Shao Z-M, Kang Y. Normal and cancerous mammary stem cells evade interferon-induced constraint through the miR-199a-LCOR axis. Nat Cell Biol. 2017;19(6):711–723. PMCID: PMC5481166

Duncan J, Stoller M, Francl A, Tissir F, Devenport D, Deans M. Celsr1 coordinates the planar polarity of vestibular hair cells during inner ear development. Dev Biol. 2017;423(2):126–137. PMCID: PMC5369242

Anllo L, Schüpbach T. Signaling through the G-protein-coupled receptor Rickets is important for polarity, detachment, and migration of the border cells in Drosophila. Dev Biol. 2016;414(2):193–206. PMCID: PMC4887387

Kyrchanova O, Mogila V, Wolle D, Deshpande G, Parshikov A, Cleard F, Karch F, Schedl P, Georgiev P. Functional Dissection of the Blocking and Bypass Activities of the Fab-8 Boundary in the Drosophila Bithorax Complex. PLoS Genet. 2016;12(7):e1006188. PMCID: PMC4948906

Goyal Y, Jindal G, Pelliccia J, Yamaya K, Yeung E, Futran A, Burdine R, Schüpbach T, Shvartsman S. Divergent effects of intrinsically active MEK variants on developmental Ras signaling. Nat Genet. 2017;49(3):465–469. PMCID: PMC5621734

Ding Q, von Schaewen M, Hrebikova G, Heller B, Sandmann L, Plaas M, Ploss A. Mice Expressing Minimally Humanized CD81 and Occludin Genes Support Hepatitis C Virus Uptake In Vivo. J Virol. 2017;91(4). PMCID: PMC5286898

Jindal G, Goyal Y, Yamaya K, Futran A, Kountouridis I, Balgobin C, Schüpbach T, Burdine R, Shvartsman S. In vivo severity ranking of Ras pathway mutations associated with developmental disorders. Proc Natl Acad Sci U S A. 2017;114(3):510–515. PMCID: PMC5255624

Bhogal B, Plaza-Jennings A, Gavis E. Nanos-mediated repression of hid protects larval sensory neurons after a global switch in sensitivity to apoptotic signals. Development. 2016;143(12):2147–59. PMCID: PMC4920170

Orman M, Brynildsen M. Inhibition of stationary phase respiration impairs persister formation in E. coli. Nat Commun. 2015;6:7983. PMCID: PMC4530465

Jonikas M, Collins S, Denic V, Oh E, Quan E, Schmid V, Weibezahn J, Schwappach B, Walter P, Weissman J, Schuldiner M. Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum. Science. 2009;323(5922):1693–7. PMCID: PMC2877488

Li X, Zhang R, Patena W, Gang S, Blum S, Ivanova N, Yue R, Robertson J, Lefebvre P, Fitz-Gibbon S, Grossman A, Jonikas M. An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii. Plant Cell. 2016;28(2):367–87. PMCID: PMC4790863

vonHoldt B, Pollinger J, Earl D, Knowles J, Boyko A, Parker H, Geffen E, Pilot M, Jedrzejewski W, Jedrzejewska B, Sidorovich V, Greco C, Randi E, Musiani M, Kays R, Bustamante C, Ostrander E, Novembre J, Wayne R. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res. 2011;21(8):1294–305. PMCID: PMC3149496

Verhoeven K, vonHoldt B, Sork V. Epigenetics in ecology and evolution: what we know and what we need to know. Mol Ecol. 2016;25(8):1631–8. PMID: 26994410

Chung N, Storey J. Statistical significance of variables driving systematic variation in high-dimensional data. Bioinformatics. 2015;31(4):545–54. PMCID: PMC4325543

Seyedsayamdost M, Traxler M, Zheng S-L, Kolter R, Clardy J. Structure and biosynthesis of amychelin, an unusual mixed-ligand siderophore from Amycolatopsis sp. AA4. J Am Chem Soc. 2011;133(30):11434–7. PMCID: PMC3144690

Wagner E, Stolfi A, Choi Y, Levine M. Islet is a key determinant of ascidian palp morphogenesis. Development. 2014;141(15):3084–92. PMCID: PMC4197658