Publications

  1. Khera R, Mortazavi BJ, Sangha V, Warner F, Patrick Young H, Ross JS, Shah ND, Theel ES, Jenkinson WG, Knepper C, Wang K, Peaper D, Martinello RA, Brandt CA, Lin Z, Ko AI, Krumholz HM, Pollock BD, Schulz WL. A multicenter evaluation of computable phenotyping approaches for SARS-CoV-2 infection and COVID-19 hospitalizations. NPJ Digit Med. 2022 Mar 8; 5 (1):27 Epub 2022 Mar 08
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  2. Ashrafzadeh-Kian S, Campbell MR, Jara Aguirre JC, Walsh J, Kumanovics A, Jenkinson G, Rinaldo P, Snyder MR, Algeciras-Schimnich A. Role of immune mediators in predicting hospitalization of SARS-CoV-2 positive patients. Cytokine. 2022 Feb; 150:155790 Epub 2021 Dec 25
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  3. Rangan A, Hein MS, Jenkinson WG, Koganti T, Aleff RA, Hilker CA, Blommel JH, Porter TR, Swanson KC, Lundquist P, Nguyen PL, Shi M, He R, Viswanatha DS, Jen J, Klee EW, Kipp BR, Hoyer JD, Wieben ED, Oliveira JL. Improved Characterization of Complex beta-Globin Gene Cluster Structural Variants Using Long-Read Sequencing. J Mol Diagn. 2021 Dec; 23 (12):1732-1740
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  4. Sankaranarayanan S, Balan J, Walsh JR, Wu Y, Minnich S, Piazza A, Osborne C, Oliver GR, Lesko J, Bates KL, Khezeli K, Block DR, DiGuardo M, Kreuter J, O'Horo JC, Kalantari J, Klee EW, Salama ME, Kipp B, Morice WG, Jenkinson G. COVID-19 Mortality Prediction From Deep Learning in a Large Multistate Electronic Health Record and Laboratory Information System Data Set: Algorithm Development and Validation. J Med Internet Res. 2021 Sep 28; 23(9):e30157.
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  5. Roden AC, Vrana JA, Koepplin JW, Hudson AE, Norgan AP, Jenkinson G, Yamaoka S, Ebihara H, Monroe R, Szabolcs MJ, Majumdar R, Moyer AM, Garcia JJ, Kipp BR. Comparison of In Situ Hybridization, Immunohistochemistry, and Reverse Transcription-Droplet Digital Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Testing in Tissue. Arch Pathol Lab Med. 2021 Jul 1; 145 (7):785-796
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  6. Koldobskiy MA, Jenkinson G, Abante J, Rodriguez DiBlasi VA, Zhou W, Pujadas E, Idrizi A, Tryggvadottir R, Callahan C, Bonifant CL, Rabin KR, Brown PA, Ji H, Goutsias J, Feinberg AP. Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis. Nat Biomed Eng. 2021 Apr; 5 (4):360-376 Epub 2021 Apr 15
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  7. Klee EW, Cousin MA, Pinto E Vairo F, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN. Impact of integrated translational research on clinical exome sequencing. Genet Med. 2021 Mar; 23 (3):498-507 Epub 2020 Nov 04
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  8. Balan J, Jenkinson G, Nair A, Saha N, Koganti T, Voss J, Zysk C, Barr Fritcher EG, Ross CA, Giannini C, Raghunathan A, Kipp BR, Jenkins R, Ida C, Halling KC, Blackburn PR, Dasari S, Oliver GR, Klee EW. SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA. Front Genet. 2021; 12:739054. Epub 2021 Oct 22.
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  9. Jenkinson G, Li YI, Basu S, Cousin MA, Oliver GR, Klee EW. LeafCutterMD: an algorithm for outlier splicing detection in rare diseases. Bioinformatics. 2020 Nov 1; 36 (17):4609-4615
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  10. Koldobskiy MA, Abante J, Jenkinson G, Pujadas E, Tetens A, Zhao F, Tryggvadottir R, Idrizi A, Reinisch A, Majeti R, Goutsias J, Feinberg AP. A Dysregulated DNA Methylation Landscape Linked to Gene Expression in MLL-Rearranged AML. Epigenetics. 2020 Aug; 15 (8):841-858 Epub 2020 Feb 29
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  11. Oliver GR, Jenkinson G, Klee EW. Computational Detection of Known Pathogenic Gene Fusions in a Normal Tissue Database and Implications for Genetic Disease Research. Front Genet. 2020; 11:173 Epub 2020 Feb 28
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  12. Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, Vitaterna MH, Afkarian M, Afshinnekoo E, Ahadi S, Ambati A, Arya M, Bezdan D, Callahan CM, Chen S, Choi AMK, Chlipala GE, Contrepois K, Covington M, Crucian BE, De Vivo I, Dinges DF, Ebert DJ, Feinberg JI, Gandara JA, George KA, Goutsias J, Grills GS, Hargens AR, Heer M, Hillary RP, Hoofnagle AN, Hook VYH, Jenkinson G, Jiang P, Keshavarzian A, Laurie SS, Lee-McMullen B, Lumpkins SB, MacKay M, Maienschein-Cline MG, Melnick AM, Moore TM, Nakahira K, Patel HH, Pietrzyk R, Rao V, Saito R, Salins DN, Schilling JM, Sears DD, Sheridan CK, Stenger MB, Tryggvadottir R, Urban AE, Vaisar T, Van Espen B, Zhang J, Ziegler MG, Zwart SR, Charles JB, Kundrot CE, Scott GBI, Bailey SM, Basner M, Feinberg AP, Lee SMC, Mason CE, Mignot E, Rana BK, Smith SM, Snyder MP, Turek FW. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science. 2019 Apr 12; 364 (6436)
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  13. Jenkinson G, Abante J, Koldobskiy MA, Feinberg AP, Goutsias J. Ranking genomic features using an information-theoretic measure of epigenetic discordance. BMC Bioinformatics. 2019 Apr 8; 20 (1):175 Epub 2019 Apr 08
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  14. Oliver GR, Tang X, Schultz-Rogers LE, Vidal-Folch N, Jenkinson WG, Schwab TL, Gaonkar K, Cousin MA, Nair A, Basu S, Chanana P, Oglesbee D, Klee EW. A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PLoS One. 2019; 14 (10):e0223337 Epub 2019 Oct 02
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  15. Jenkinson G, Abante J, Feinberg AP, Goutsias J. An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data. BMC Bioinformatics. 2018 Mar 7; 19 (1):87 Epub 2018 Mar 07
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  16. Jenkinson G, Pujadas E, Goutsias J, Feinberg AP. Potential energy landscapes identify the information-theoretic nature of the epigenome. Nat Genet. 2017 May; 49 (5):719-729 Epub 2017 Mar 27
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  17. Jenkinson G, Goutsias J. Intrinsic noise induces critical behavior in leaky Markovian networks leading to avalanching. PLoS Comput Biol. 2014 Jan; 10 (1):e1003411 Epub 2014 Jan 09
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  18. Goutsias J, Jenkinson G. Markovian Dynmaics on Complex Reaction Networks Physics Reports. 2013; 529(2):199-264.
  19. Jenkinson G, Goutsias J. Statistically testing the validity of analytical and computational approximations to the chemical master equation. J Chem Phys. 2013 May 28; 138 (20):204108
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  20. Jenkinson G, Goutsias J. Numerical integration of the master equation in some models of stochastic epidemiology. PLoS One. 2012; 7 (5):e36160 Epub 2012 May 02
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  21. Jenkinson G, Goutsias J. Thermodynamically consistent model calibration in chemical kinetics. BMC Syst Biol. 2011 May 6; 5:64 Epub 2011 May 06
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  22. Jenkinson G, Zhong X, Goutsias J. Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems. BMC Bioinformatics. 2010 Nov 5; 11:547 Epub 2010 Nov 05
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