Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Last Name
Institution

Arjun Krishnan

TitleAssociate Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BIOMED Informatics Gen Ops

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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. Price A, Rasolofomanana-Rajery S, Manpearl K, Robertson CE, Krebs NF, Frank DN, Krishnan A, Hendricks AE, Tang M. Network-based representation learning reveals the impact of age and diet on the gut microbial and metabolomic environment of U.S. infants in a randomized controlled feeding trial. bioRxiv. 2025 Sep 04. PMID: 40475488.
      View in: PubMed
    2. Cortes KG, Sundar S, Gehrke S, Manpearl K, Lin J, Korn DR, Caufield H, Schaper K, Reese J, Koirala K, Hunter LE, Carter EK, DeLuca M, Krishnan A, Mungall C, Haendel M. Improving Biomedical Knowledge Graph Quality: A Community Approach. ArXiv. 2025 Aug 29. PMID: 40909156.
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    3. Breunig S, Lee YH, Karlson EW, Krishnan A, Lawrence JM, Schaffer LS, Grotzinger AD. Examining the genetic links between clusters of immune-mediated diseases and psychiatric disorders. Transl Psychiatry. 2025 Jul 21; 15(1):252. PMID: 40691433.
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    4. Samart K, Buskirk L, Tonielli A, Krishnan A, Ravi J. Integrative transcriptome-based drug repurposing in tuberculosis. bioRxiv. 2025 Jun 02. PMID: 40501823.
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    5. Abdill RJ, Graham SP, Rubinetti V, Ahmadian M, Hicks P, Chetty A, McDonald D, Ferretti P, Gibbons E, Rossi M, Krishnan A, Albert FW, Greene CS, Davis S, Blekhman R. Integration of 168,000 samples reveals global patterns of the human gut microbiome. Cell. 2025 Feb 20; 188(4):1100-1118.e17. PMID: 39848248.
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    6. Yuan H, Hicks P, Ahmadian M, Johnson KA, Valtadoros L, Krishnan A. Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata. Brief Bioinform. 2024 Nov 22; 26(1). PMID: 39710433.
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    7. Pividori M, Sadeeq S, Krishnan A, Stranger BE, Gignoux CR. Uncovering hidden gene-trait patterns through biclustering analysis of the UK Biobank. bioRxiv. 2024 Nov 11. PMID: 39605717.
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    8. Yuan H, Mancuso CA, Johnson K, Braasch I, Krishnan A. Computational strategies for cross-species knowledge transfer and translational biomedicine. ArXiv. 2024 Aug 16. PMID: 39184546.
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    9. Zitnik M, Li MM, Wells A, Glass K, Morselli Gysi D, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, Bozdag S, Chen DZ, Cowen L, Devkota K, Gitter A, Gosline SJC, Gu P, Guzzi PH, Huang H, Jiang M, Kesimoglu ZN, Koyuturk M, Ma J, Pico AR, Pr?ulj N, Przytycka TM, Raphael BJ, Ritz A, Sharan R, Shen Y, Singh M, Slonim DK, Tong H, Yang XH, Yoon BJ, Yu H, Milenkovic T. Current and future directions in network biology. Bioinform Adv. 2024; 4(1):vbae099. PMID: 39143982.
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    10. Gomez-Cano F, Rodriguez J, Zhou P, Chu YH, Magnusson E, Gomez-Cano L, Krishnan A, Springer NM, de Leon N, Grotewold E. Prioritizing Maize Metabolic Gene Regulators through Multi-Omic Network Integration. bioRxiv. 2024 Jul 24. PMID: 38464086.
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    11. Breunig S, Lee YH, Karlson EW, Krishnan A, Lawrence JM, Schaffer LS, Grotzinger AD. Examining the Genetic Links between Clusters of Immune-mediated Diseases and Psychiatric Disorders. medRxiv. 2024 Jul 19. PMID: 39072040.
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    12. Mancuso CA, Johnson KA, Liu R, Krishnan A. Joint representation of molecular networks from multiple species improves gene classification. PLoS Comput Biol. 2024 Jan; 20(1):e1011773. PMID: 38198480.
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    13. Palande S, Kaste JAM, Roberts MD, Segura Abá K, Claucherty C, Dacon J, Doko R, Jayakody TB, Jeffery HR, Kelly N, Manousidaki A, Parks HM, Roggenkamp EM, Schumacher AM, Yang J, Percival S, Pardo J, Husbands AY, Krishnan A, Montgomery BL, Munch E, Thompson AM, Rougon-Cardoso A, Chitwood DH, VanBuren R. Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants. PLoS Biol. 2023 Dec; 21(12):e3002397. PMID: 38051702.
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    14. Mancuso CA, Liu R, Krishnan A. PyGenePlexus: a Python package for gene discovery using network-based machine learning. Bioinformatics. 2023 02 03; 39(2). PMID: 36721325.
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    15. Liu R, Hirn M, Krishnan A. Accurately modeling biased random walks on weighted networks using node2vec. Bioinformatics. 2023 01 01; 39(1). PMID: 36688699.
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    16. Hawkins NT, Maldaver M, Yannakopoulos A, Guare LA, Krishnan A. Systematic tissue annotations of genomics samples by modeling unstructured metadata. Nat Commun. 2022 11 08; 13(1):6736. PMID: 36347858.
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    17. Hickey SL, McKim A, Mancuso CA, Krishnan A. A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities. Front Pharmacol. 2022; 13:995459. PMID: 36313344.
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    18. Mancuso CA, Bills PS, Krum D, Newsted J, Liu R, Krishnan A. GenePlexus: a web-server for gene discovery using network-based machine learning. Nucleic Acids Res. 2022 07 05; 50(W1):W358-W366. PMID: 35580053.
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    19. Johnson KA, Krishnan A. Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data. Genome Biol. 2022 01 03; 23(1):1. PMID: 34980209.
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    20. Samart K, Tuyishime P, Krishnan A, Ravi J. Reconciling multiple connectivity scores for drug repurposing. Brief Bioinform. 2021 11 05; 22(6). PMID: 34013329.
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    21. Jensen M, Tyryshkina A, Pizzo L, Smolen C, Das M, Huber E, Krishnan A, Girirajan S. Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion. Genome Med. 2021 10 18; 13(1):163. PMID: 34657631.
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    22. Liu R, Krishnan A. PecanPy: a fast, efficient and parallelized Python implementation of node2vec. Bioinformatics. 2021 Oct 11; 37(19):3377-3379. PMID: 33760066.
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    23. Pizzo L, Lasser M, Yusuff T, Jensen M, Ingraham P, Huber E, Singh MD, Monahan C, Iyer J, Desai I, Karthikeyan S, Gould DJ, Yennawar S, Weiner AT, Pounraja VK, Krishnan A, Rolls MM, Lowery LA, Girirajan S. Functional assessment of the "two-hit" model for neurodevelopmental defects in Drosophila and X. laevis. PLoS Genet. 2021 04; 17(4):e1009112. PMID: 33819264.
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    24. Mancuso CA, Canfield JL, Singla D, Krishnan A. A flexible, interpretable, and accurate approach for imputing the expression of unmeasured genes. Nucleic Acids Res. 2020 12 02; 48(21):e125. PMID: 33074331.
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    25. Liu R, Mancuso CA, Yannakopoulos A, Johnson KA, Krishnan A. Supervised learning is an accurate method for network-based gene classification. Bioinformatics. 2020 06 01; 36(11):3457-3465. PMID: 32129827.
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    26. Lee YS, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, Kristensen VN, Dolinski K, Theesfeld CL, Troyanskaya OG. A Computational Framework for Genome-wide Characterization of the Human Disease Landscape. Cell Syst. 2019 02 27; 8(2):152-162.e6. PMID: 30685436.
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    27. Pizzo L, Jensen M, Polyak A, Rosenfeld JA, Mannik K, Krishnan A, McCready E, Pichon O, Le Caignec C, Van Dijck A, Pope K, Voorhoeve E, Yoon J, Stankiewicz P, Cheung SW, Pazuchanics D, Huber E, Kumar V, Kember RL, Mari F, Curró A, Castiglia L, Galesi O, Avola E, Mattina T, Fichera M, Mandarà L, Vincent M, Nizon M, Mercier S, Bénéteau C, Blesson S, Martin-Coignard D, Mosca-Boidron AL, Caberg JH, Bucan M, Zeesman S, Nowaczyk MJM, Lefebvre M, Faivre L, Callier P, Skinner C, Keren B, Perrine C, Prontera P, Marle N, Renieri A, Reymond A, Kooy RF, Isidor B, Schwartz C, Romano C, Sistermans E, Amor DJ, Andrieux J, Girirajan S. Rare variants in the genetic background modulate cognitive and developmental phenotypes in individuals carrying disease-associated variants. Genet Med. 2019 04; 21(4):816-825. PMID: 30190612.
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    28. Wong AK, Krishnan A, Troyanskaya OG. GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. Nucleic Acids Res. 2018 07 02; 46(W1):W65-W70. PMID: 29800226.
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    29. Iyer J, Singh MD, Jensen M, Patel P, Pizzo L, Huber E, Koerselman H, Weiner AT, Lepanto P, Vadodaria K, Kubina A, Wang Q, Talbert A, Yennawar S, Badano J, Manak JR, Rolls MM, Krishnan A, Girirajan S. Pervasive genetic interactions modulate neurodevelopmental defects of the autism-associated 16p11.2 deletion in Drosophila melanogaster. Nat Commun. 2018 06 29; 9(1):2548. PMID: 29959322.
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    30. Rangan AV, McGrouther CC, Kelsoe J, Schork N, Stahl E, Zhu Q, Krishnan A, Yao V, Troyanskaya O, Bilaloglu S, Raghavan P, Bergen S, Jureus A, Landen M. A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data. PLoS Comput Biol. 2018 05; 14(5):e1006105. PMID: 29758032.
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    31. Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG. Understanding multicellular function and disease with human tissue-specific networks. Nat Genet. 2015 Jun; 47(6):569-76. PMID: 25915600.
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    32. Zhu Q, Wong AK, Krishnan A, Aure MR, Tadych A, Zhang R, Corney DC, Greene CS, Bongo LA, Kristensen VN, Charikar M, Li K, Troyanskaya OG. Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nat Methods. 2015 Mar; 12(3):211-4, 3 p following 214. PMID: 25581801.
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