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Kathleen Jagodnik, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Bartal A, Jagodnik KM, Chan SJ, Babu MS, Dekel S. Identifying women with postdelivery posttraumatic stress disorder using natural language processing of personal childbirth narratives. Am J Obstet Gynecol MFM. 2022 Dec 09; 5(3):100834. PMID: 36509356.
    Citations:    Fields:    
  2. Bartal A, Jagodnik KM, Chan SJ, Babu MS, Dekel S. Identifying Women with Post-Delivery Posttraumatic Stress Disorder using Natural Language Processing of Personal Childbirth Narratives. medRxiv. 2022 Aug 30. PMID: 36093354; PMCID: PMC9460977.
    Citations:    
  3. Bartal A, Jagodnik KM. Progress in and Opportunities for Applying Information Theory to Computational Biology and Bioinformatics. Entropy (Basel). 2022 Jul 03; 24(7). PMID: 35885148; PMCID: PMC9323281.
    Citations:    
  4. Xie Z, Kropiwnicki E, Wojciechowicz ML, Jagodnik KM, Shu I, Bailey A, Clarke DJB, Jeon M, Evangelista JE, V Kuleshov M, Lachmann A, Parigi AA, Sanchez JM, Jenkins SL, Ma'ayan A. Getting Started with LINCS Datasets and Tools. Curr Protoc. 2022 Jul; 2(7):e487. PMID: 35876555; PMCID: PMC9326873.
    Citations:    Fields:    Translation:HumansCells
  5. Evangelista JE, Clarke DJB, Xie Z, Lachmann A, Jeon M, Chen K, Jagodnik KM, Jenkins SL, Kuleshov MV, Wojciechowicz ML, Schürer SC, Medvedovic M, Ma'ayan A. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Res. 2022 May 07. PMID: 35524556; PMCID: PMC9252724.
    Citations: 4     Fields:    
  6. Kropiwnicki E, Lachmann A, Clarke DJB, Xie Z, Jagodnik KM, Ma'ayan A. DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. BMC Bioinformatics. 2022 Feb 19; 23(1):76. PMID: 35183110; PMCID: PMC8858480.
    Citations:    Fields:    Translation:Cells
  7. Bartal A, Jagodnik KM. Role-Aware Information Spread in Online Social Networks. Entropy (Basel). 2021 Nov 19; 23(11). PMID: 34828240; PMCID: PMC8618065.
    Citations:    
  8. Kropiwnicki E, Evangelista JE, Stein DJ, Clarke DJB, Lachmann A, Kuleshov MV, Jeon M, Jagodnik KM, Ma'ayan A. Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. Database (Oxford). 2021 03 31; 2021. PMID: 33787872; PMCID: PMC8011435.
    Citations: 7     Fields:    Translation:HumansCells
  9. Clarke DJB, Jeon M, Stein DJ, Moiseyev N, Kropiwnicki E, Dai C, Xie Z, Wojciechowicz ML, Litz S, Hom J, Evangelista JE, Goldman L, Zhang S, Yoon C, Ahamed T, Bhuiyan S, Cheng M, Karam J, Jagodnik KM, Shu I, Lachmann A, Ayling S, Jenkins SL, Ma'ayan A. Appyters: Turning Jupyter Notebooks into data-driven web apps. Patterns (N Y). 2021 Mar 12; 2(3):100213. PMID: 33748796; PMCID: PMC7961182.
    Citations: 21     
  10. Xie Z, Bailey A, Kuleshov MV, Clarke DJB, Evangelista JE, Jenkins SL, Lachmann A, Wojciechowicz ML, Kropiwnicki E, Jagodnik KM, Jeon M, Ma'ayan A. Gene Set Knowledge Discovery with Enrichr. Curr Protoc. 2021 Mar; 1(3):e90. PMID: 33780170; PMCID: PMC8152575.
    Citations: 346     Fields:    Translation:HumansAnimals
  11. Jeon M, Jagodnik KM, Kropiwnicki E, Stein DJ, Ma'ayan A. Prioritizing Pain-Associated Targets with Machine Learning. Biochemistry. 2021 05 11; 60(18):1430-1446. PMID: 33606503.
    Citations: 1     Fields:    Translation:Humans
  12. Kuleshov MV, Stein DJ, Clarke DJB, Kropiwnicki E, Jagodnik KM, Bartal A, Evangelista JE, Hom J, Cheng M, Bailey A, Zhou A, Ferguson LB, Lachmann A, Ma'ayan A. The COVID-19 Drug and Gene Set Library. Patterns (N Y). 2020 Sep 11; 1(6):100090. PMID: 32838343; PMCID: PMC7381899.
    Citations: 36     
  13. Bartal A, Lachmann A, Clarke DJB, Seiden AH, Jagodnik KM, Ma'ayan A. EnrichrBot: Twitter bot tracking tweets about human genes. Bioinformatics. 2020 06 01; 36(12):3932-3934. PMID: 32277816; PMCID: PMC7320605.
    Citations: 2     Fields:    Translation:Humans
  14. Kuleshov MV, Clarke DJB, Kropiwnicki E, Jagodnik KM, Bartal A, Evangelista JE, Zhou A, Ferguson LB, Lachmann A, Ma'ayan A. The COVID-19 Gene and Drug Set Library. Res Sq. 2020 May 13. PMID: 32702729; PMCID: PMC7336700.
    Citations:    
  15. Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z, Silverstein MC, Schilder BM, Robasky K, Castillo C, Idaszak R, Ahalt SC, Williams J, Schurer S, Cooper DJ, de Miranda Azevedo R, Klenk JA, Haendel MA, Nedzel J, Avillach P, Shimoyama ME, Harris RM, Gamble M, Poten R, Charbonneau AL, Larkin J, Brown CT, Bonazzi VR, Dumontier MJ, Sansone SA, Ma'ayan A. FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources. Cell Syst. 2019 11 27; 9(5):417-421. PMID: 31677972; PMCID: PMC7316196.
    Citations: 13     Fields:    Translation:Humans
  16. Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma'ayan A. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 2019 07 02; 47(W1):W212-W224. PMID: 31114921; PMCID: PMC6602523.
    Citations: 145     Fields:    Translation:Humans
  17. Wang Z, He E, Sani K, Jagodnik KM, Silverstein MC, Ma'ayan A. Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. Bioinformatics. 2019 04 01; 35(7):1247-1248. PMID: 30169739; PMCID: PMC6449747.
    Citations: 8     Fields:    Translation:HumansCells
  18. Stathias V, Koleti A, Vidovic D, Cooper DJ, Jagodnik KM, Terryn R, Forlin M, Chung C, Torre D, Ayad N, Medvedovic M, Ma'ayan A, Pillai A, Schürer SC. Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. Sci Data. 2018 06 19; 5:180117. PMID: 29917015; PMCID: PMC6007090.
    Citations: 14     Fields:    Translation:HumansAnimals
  19. Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma'ayan A. Massive mining of publicly available RNA-seq data from human and mouse. Nat Commun. 2018 04 10; 9(1):1366. PMID: 29636450; PMCID: PMC5893633.
    Citations: 211     Fields:    Translation:HumansAnimalsCells
  20. Torre D, Krawczuk P, Jagodnik KM, Lachmann A, Wang Z, Wang L, Kuleshov MV, Ma'ayan A. Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses. Sci Data. 2018 02 27; 5:180023. PMID: 29485625; PMCID: PMC5827688.
    Citations: 4     Fields:    
  21. Koleti A, Terryn R, Stathias V, Chung C, Cooper DJ, Turner JP, Vidovic D, Forlin M, Kelley TT, D'Urso A, Allen BK, Torre D, Jagodnik KM, Wang L, Jenkins SL, Mader C, Niu W, Fazel M, Mahi N, Pilarczyk M, Clark N, Shamsaei B, Meller J, Vasiliauskas J, Reichard J, Medvedovic M, Ma'ayan A, Pillai A, Schürer SC. Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. Nucleic Acids Res. 2018 01 04; 46(D1):D558-D566. PMID: 29140462.
    Citations: 53     Fields:    Translation:Humans
  22. Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Syst. 2018 01 24; 6(1):13-24. PMID: 29199020.
    Citations: 145     Fields:    Translation:HumansCells
  23. Jagodnik KM, Koplev S, Jenkins SL, Ohno-Machado L, Paten B, Schurer SC, Dumontier M, Verborgh R, Bui A, Ping P, McKenna NJ, Madduri R, Pillai A, Ma'ayan A. Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. J Biomed Inform. 2017 07; 71:49-57. PMID: 28501646; PMCID: PMC5545976.
    Citations: 14     Fields:    Translation:Humans
  24. Jagodnik KM, Thomas PS, van den Bogert AJ, Branicky MS, Kirsch RF. Training an Actor-Critic Reinforcement Learning Controller for Arm Movement Using Human-Generated Rewards. IEEE Trans Neural Syst Rehabil Eng. 2017 10; 25(10):1892-1905. PMID: 28475063; PMCID: PMC7523734.
    Citations: 6     Fields:    Translation:Humans
  25. Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma'ayan A. GEN3VA: aggregation and analysis of gene expression signatures from related studies. BMC Bioinformatics. 2016 Nov 15; 17(1):461. PMID: 27846806; PMCID: PMC5111283.
    Citations: 11     Fields:    Translation:HumansAnimalsCells
  26. Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF, Gundersen GW, Rouillard AD, Jenkins SL, Feldmann AS, Hu KS, McDermott MG, Duan Q, Clark NR, Jones MR, Kou Y, Goff T, Woodland H, Amaral FMR, Szeto GL, Fuchs O, Schüssler-Fiorenza Rose SM, Sharma S, Schwartz U, Bausela XB, Szymkiewicz M, Maroulis V, Salykin A, Barra CM, Kruth CD, Bongio NJ, Mathur V, Todoric RD, Rubin UE, Malatras A, Fulp CT, Galindo JA, Motiejunaite R, Jüschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, Pérez-García V, Ma'ayan A. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nat Commun. 2016 Sep 26; 7:12846. PMID: 27667448; PMCID: PMC5052684.
    Citations: 127     Fields:    
  27. Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016 07 08; 44(W1):W90-7. PMID: 27141961; PMCID: PMC4987924.
    Citations: 3065     Fields:    Translation:Humans
  28. Jagodnik KM, Blana D, van den Bogert AJ, Kirsch RF. An optimized proportional-derivative controller for the human upper extremity with gravity. J Biomech. 2015 Oct 15; 48(13):3692-700. PMID: 26358531; PMCID: PMC4600679.
    Citations: 1     Fields:    Translation:Humans
  29. Jagodnik KM, van den Bogert AJ. Optimization and evaluation of a proportional derivative controller for planar arm movement. J Biomech. 2010 Apr 19; 43(6):1086-91. PMID: 20097345; PMCID: PMC3853125.
    Citations: 9     Fields:    Translation:Humans
  30. Thomas P, Branicky M, van den Bogert A, Jagodnik K. Application of the Actor-Critic Architecture to Functional Electrical Stimulation Control of a Human Arm. Proc Innov Appl Artif Intell Conf. 2009; 2009:165-172. PMID: 20689654; PMCID: PMC2916188.
    Citations: 2     
  31. Thomas PS, Branicky M, van den Bogert A, Jagodnik K. Creating a Reinforcement Learning Controller for Functional Electrical Stimulation of a Human Arm. Yale Workshop Adapt Learn Syst. 2008; 49326:1-6. PMID: 22081795; PMCID: PMC3212874.
    Citations: 2     
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.