Pavel P. Kuksa, PhD, Computer Science
Research Assistant Professor of Pathology and Laboratory MedicinePerelman 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 Scientist, NEC Laboratories America, 2011-2014
Postdoctoral Researcher, University of Pennsylvania, 2014-2019
Awards and Honors
Reviewers' Choice Abstract Award, American Society of Human Genetics, 2023
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
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
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
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
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
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
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
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
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
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
