PEOPLE

Pavel P. Kuksa, PhD, Computer Science

Research Assistant Professor of Pathology and Laboratory Medicine
Perelman School of Medicine at the University of Pennsylvania

Contact InformationRichards Medical Research Laboratories
3700 Hamilton Walk
Philadelphia, PA, 19104

Research Expertise

algorithms
sequence analysis and modeling
high-throughput sequencing data analysis
functional genomics
chromatin interaction data modeling and analysis
web servers and databases

Education

BS (Computer Engineering), Bauman Moscow State Technical University, 2002
MS (Computer and Information Sciences), Bauman Moscow State Technical University, 2004
MS (Computer Science), Rutgers University, 2010
PhD (Computer Science), Rutgers University, 2011

Specialty Certification

Postgraduate Training

Postdoctoral Researcher, NEC Laboratories America, 2011-2014
Postdoctoral Researcher, University of Pennsylvania, 2014-2019

Awards and Honors

Memberships and Professional Organizations

Institute for Biomedical Informatics (IBI), 2014 - 2023
NWO Dutch Research Council, 2015 - 2015
European Coordinated Research on Long-term Challenges in Information and Communication Sciences & Technologies ERA-Net (CHIST-ERA), 2015 - 2015
Marsden Fund, 2021 - Present
Institute for Biomedical Informatics (IBI), 2023 - Present
Institute for Translational Medicine and Therapeutics (ITMAT), 2023 - Present

Web Links


Selected Publications

Scalable approaches for functional analyses of whole-genome sequencing non-coding variants

Kuksa PP, Greenfest-Allen E, Cifello J, Ionita M, Wang H, Issen H, Cheng PL, Lee WP, Wang LS, Leung YY., Human Molecular Genetics 31(R1): R62-R72, 2022, PMID:35943817

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FILER: a framework for harmonizing and querying large-scale functional genomics knowledge

Kuksa PP, Leung YY, Gangadharan P, Katanic Z, Kleidermacher L, Amlie-Wolf A, Lee CY, Qu L, Greenfest-Allen E, Valladares O, Wang LS., NAR Genom Bioinform 4(1): lqab123, 2022, PMID:35047815

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New insights into the genetic etiology of Alzheimer's disease and related dementias

Bellenguez C, Küçükali F, Jansen IE, Kleineidam L, Moreno-Grau S, Amin N, Naj AC, Campos-Martin R, Grenier-Boley B, Andrade V, Holmans PA, Boland A, Damotte V, van der Lee SJ, Costa MR, Kuulasmaa T, Yang Q, de Rojas I, Bis JC, Yaqub A, Prokic I, Chapuis J, Ahmad S, Giedraitis V, Aarsland D, Garcia-Gonzalez P, Abdelnour C, Alarcón-Martín E, Alcolea D, Alegret M, Alvarez I, Álvarez V, Armstrong NJ, Tsolaki A, Antúnez C, Appollonio I, Arcaro M, Archetti S, Pastor AA, Arosio B, Athanasiu L, Bailly H, Banaj N, Baquero M, Barral S, Beiser A, Pastor AB, Below JE, Benchek P, Benussi L, Berr C, Besse C, Bessi V, Binetti G, Bizarro A, Blesa R, Boada M, Boerwinkle E, Borroni B, Boschi S, Bossù P, Bråthen G, Bressler J, Bresner C, Brodaty H, Brookes KJ, Brusco LI, Buiza-Rueda D, Bûrger K, Burholt V, Bush WS, Calero M, Cantwell LB, Chene G, Chung J, Cuccaro ML, Carracedo Á, Cecchetti R, Cervera-Carles L, Charbonnier C, Chen HH, Chillotti C, Ciccone S, Claassen JAHR, Clark C, Conti E, Corma-Gómez A, Costantini E, Custodero C, Daian D, Dalmasso MC, Daniele A, Dardiotis E, Dartigues JF, de Deyn PP, de Paiva Lopes K, de Witte LD, Debette S, Deckert J, Del Ser T, et al., Nature Genetics 54(4): 412-436, 2022, PMID:35379992

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Alzheimer's Disease Variant Portal: A Catalog of Genetic Findings for Alzheimer's Disease

Kuksa PP, Liu CL, Fu W, Qu L, Zhao Y, Katanic Z, Clark K, Kuzma AB, Ho PC, Tzeng KT, Valladares O, Chou SY, Naj AC, Schellenberg GD, Wang LS, Leung YY., J Alzheimers Dis 86(1): 461-477, 2022, PMID:35068457

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Using INFERNO to Infer the Molecular Mechanisms Underlying Noncoding Genetic Associations

Amlie-Wolf A, Kuksa PP, Lee CY, Mlynarski E, Leung YY, Wang LS., Methods Mol Biol 2254(): 73-91, 2021, PMID:33326071

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SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants

Kuksa PP, Lee CY, Amlie-Wolf A, Gangadharan P, Mlynarski EE, Chou YF, Lin HJ, Issen H, Greenfest-Allen E, Valladares O, Leung YY, Wang LS., Bioinformatics 36(12): 3879-3881, 2020, PMID:32330239

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HiPR: High-throughput probabilistic RNA structure inference

Kuksa PP, Li F, Kannan S, Gregory BD, Leung YY, Wang LS., Comput Struct Biotechnol J 18(): 1539-1547, 2020, PMID:32637050

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HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions

Kuksa PP, Amlie-Wolf A, Hwang YC, Valladares O, Gregory BD, Wang LS., NAR Genom Bioinform 2(2): lqaa022, 2020, PMID:32270138

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DASHR 2.0: integrated database of human small non-coding RNA genes and mature products

Kuksa PP, Amlie-Wolf A, Katanić Ž, Valladares O, Wang LS, Leung YY., Bioinformatics 35(6): 1033-1039, 2019, PMID:30668832

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INFERNO: inferring the molecular mechanisms of noncoding genetic variants

Amlie-Wolf A, Tang M, Mlynarski EE, Kuksa PP, Valladares O, Katanic Z, Tsuang D, Brown CD, Schellenberg GD, Wang LS., Nucleic Acids Res 46(17): 8740-8753, 2018, PMID:30113658

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