Pavel P Kuksa, PhD, Computer Science
Research Assistant Professor of Pathology and Laboratory Medicine
Department: Pathology and Laboratory Medicine
Contact information
Richards Medical Research Laboratories
3700 Hamilton Walk
Philadelphia, PA 19104
3700 Hamilton Walk
Philadelphia, PA 19104
Lab: 215-573-3114
Email:
pkuksa@upenn.edu
pkuksa@upenn.edu
Publications
Links
Search PubMed for articles
Personal website
ORCID
Math Genealogy
Google scholar page
DBLP
NCBI bibliography
Search PubMed for articles
Personal website
ORCID
Math Genealogy
Google scholar page
DBLP
NCBI bibliography
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.
Permanent linkBS (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.
Description of Research Expertise
algorithmssequence analysis and modeling
high-throughput sequencing data analysis
functional genomics
chromatin interaction data modeling and analysis
web servers and databases
Selected Publications
Pavel P. Kuksa*, Matei Ionita*, Luke Carter, Jeffrey Cifello, Prabhakaran Gangadharan, Kaylyn Clark, Otto Valladares, Yuk Yee Leung, Li-San Wang: BTS: a scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across >1,000s of omics datasets. Bioinformatics 41(10), Oct 2025 Notes: https://doi.org/10.1093/bioinformatics/btaf509.Farid Rajabli, Penelope Benchek, Giuseppe Tosto, Nicholas Kushch, Jin Sha, Katrina Bazemore, Congcong Zhu, Wan-Ping Lee, Jacob Haut, Kara L. Hamilton-Nelson, Nicholas R. Wheeler, Yi Zhao, John J. Farrell, Michelle A. Grunin, Yuk Yee Leung, Pavel P. Kuksa, Donghe Li, Eder Lucio da Fonseca, Jesse B. Mez, Ellen L. Palmer, Jagan Pillai, Richard M. Sherva, Yeunjoo E. Song, Xiaoling Zhang, Takeshi Ikeuchi, Taha Iqbal, Omkar Pathak, Otto Valladares, Dolly Reyes-Dumeyer, Amanda B. Kuzma, Erin Abner, Larry D. Adams, Perrie M. Adams, Alyssa Aguirre, Marilyn S. Albert, Roger L. Albin, Mariet Allen, Lisa Alvarez, Liana G. Apostolova, Steven E. Arnold, Sanjay Asthana, Craig S. Atwood, Sanford Auerbach, Gayle Ayres, Clinton T. Baldwin, Robert C. Barber, Lisa L. Barnes, Sandra Barral, Thomas G. Beach, James T. Becker, Gary W. Beecham, Duane Beekly, Bruno A. Benitez, David Bennett, John Bertelson, Thomas D. Bird, Deborah Blacker, Bradley F. Boeve, James D. Bowen, Adam Boxer, James Brewer, James R. Burke, Jeffrey M. Burns, Joseph D. Buxbaum, Nigel J. Cairns, Laura B. Cantwell, Chuanhai Cao, Christopher S. Carlson, Cynthia M. Carlsson, Regina M. Carney, Minerva M. Carrasquillo, Scott Chasse, Marie-Francoise Chesselet, Nathaniel A. Chin, Helena C. Chui, Jaeyoon Chung, Suzanne Craft, Paul K. Crane, David H. Cribbs, Elizabeth A. Crocco, Carlos Cruchaga, Michael L. Cuccaro, Munro Cullum, Eveleen Darby, Barbara Davis, Philip L. De Jager, Charles DeCarli, John DeToledo, Malcolm Dick, Dennis W. Dickson, Beth A. Dombroski, Rachelle S. Doody, Ranjan Duara, NIlüfer Ertekin-Taner, Denis A. Evans, Kelley M. Faber, Thomas J. Fairchild, Kenneth B. Fallon, David W. Fardo, Martin R. Farlow, Victoria Fernandez-Hernandez, Steven Ferris, Robert P. Friedland, Tatiana M. Foroud, Matthew P. Frosch, Brian Fulton-Howard, Douglas R. Galasko, Adriana Gamboa, Marla Gearing, Daniel H. Geschwind, Bernardino Ghetti, John R. Gilbert, Rodney C.P. Go, Alison M. Goate, Thomas J. Grabowski, Neill R. Graff-Radford, Robert C. Green, John H. Growdon, Hakon Hakonarson, James Hall, Ronald L. Hamilton, Oscar Harari, John Hardy, Lindy E. Harrell, Elizabeth Head, Victor W. Henderson, Michelle Hernandez, Timothy Hohman, Lawrence S. Honig, Ryan M. Huebinger, Matthew J. Huentelman, Christine M. Hulette, Bradley T. Hyman, Linda S. Hynan, Laura Ibanez, Gail P. Jarvik, Suman Jayadev, Lee-Way Jin, Kim Johnson, Leigh Johnson, M. Ilyas Kamboh, Anna M. Karydas, Mindy J. Katz, John S. Kauwe, Jeffrey A. Kaye, C. Dirk Keene, Aisha Khaleeq, Masataka Kikuchi, Ronald Kim, Janice Knebl, Neil W. Kowall, Joel H. Kramer, Walter A. Kukull, Frank M. LaFerla, James J. Lah, Eric B. Larson, Alan Lerner, James B. Leverenz, Allan I. Levey, Andrew P. Lieberman, Richard B. Lipton, Mark Logue, Oscar L. Lopez, Kathryn L. Lunetta, Constantine G. Lyketsos, Douglas Mains, Flanagan E. Margaret, Daniel C. Marson, Eden RR. Martin, Frank Martiniuk, Deborah C. Mash, Eliezer Masliah, Paul Massman, Arjun Masurkar, Wayne C. McCormick, Susan M. McCurry, Andrew N. McDavid, Stefan McDonough, Ann C. McKee, Marsel Mesulam, Bruce L. Miller, Carol A. Miller, Joshua W. Miller, Thomas J. Montine, Edwin S. Monuki, John C. Morris, Shubhabrata Mukherjee, Amanda J. Myers, Trung Nguyen, Thomas Obisesan, Sid O’Bryant, John M. Olichney, Marcia Ory, Raymond Palmer, Joseph E. Parisi, Henry L. Paulson, Valory Pavlik, David Paydarfar, Victoria Perez, Elaine Peskind, Ronald C. Petersen, Helen Petrovitch, Aimee Pierce, Marsha Polk, Wayne W. Poon, Huntington Potter, Liming Qu, Mary Quiceno, Joseph F. Quinn, Ashok Raj, Murray Raskind, Eric M. Reiman, Barry Reisberg, Joan S. Reisch, John M. Ringman, Erik D. Roberson, Monica Rodriguear, Ekaterina Rogaeva, Howard J. Rosen, Roger N. Rosenberg, Donald R. Royall, Marwan Sabbagh, A. Dessa Sadovnick, Mark A. Sager, Mary Sano, Andrew J. Saykin, Julie A. Schneider, Lon S. Schneider, William W. Seeley, Susan H. Slifer, Scott Small, Amanda G. Smith, Janet P. Smith, Joshua A. Sonnen, Salvatore Spina, Peter St George-Hyslop, Takiyah D. Starks, Robert A. Stern, Alan B. Stevens, Stephen M. Strittmatter, David Sultzer, Russell H. Swerdlow, Rudolph E. Tanzi, Jeffrey L. Tilson, John Q. Trojanowski, Juan C. Troncoso, Magda Tsolaki, Debby W. Tsuang, Vivianna M. Van Deerlin, Linda J. van Eldik, Jeffery M. Vance, Badri N. Vardarajan, Robert Vassar, Harry V. Vinters, Jean-Paul Vonsattel, Sandra Weintraub, Kathleen A. Welsh-Bohmer, Patrice L. Whitehead, Ellen M. Wijsman, Kirk C. Wilhelmsen, Benjamin Williams, Jennifer Williamson, Henrik Wilms, Thomas S. Wingo, Thomas Wisniewski, Randall L. Woltjer, Martin Woon, Clinton B. Wright, Chuang-Kuo Wu, Steven G. Younkin, Chang-En Yu, Lei Yu, Xiongwei Zhu, Brian W. Kunkle, William S. Bush, Akinori Miyashita, Goldie S. Byrd, Li-San Wang, Lindsay A. Farrer, Jonathan L. Haines, Richard Mayeux, Margaret A. Pericak-Vance, Gerard D. Schellenberg, Gyungah R. Jun, Christiane Reitz, Adam C. Naj, on behalf of Alzheimer’s Disease Genetics Consortium (ADGC): Multi-ancestry genome-wide meta-analysis of 56,241 individuals identifies known and novel cross-population and ancestry-specific associations as novel risk loci for Alzheimer’s disease. Genome Biology 26(1): 210, July 2025 Notes: doi: https://doi.org/10.1186/s13059-025-03564-z.
Amanda Kuzma, Otto Valladares, Emily Greenfest-Allen, Heather Nicaretta, Maureen Kirsch, Youli Ren, Zivadin Katanic, Heather White, Andrew Wilk, Lauren Bass, Jascha Brettschneider, Luke Carter, Jeffrey Cifello, Wei-Hsuan Chuang, Kaylyn Clark, Prabhakaran Gangadharan, Jacob Haut, Pei-Chuan Ho, Wenhwai Horng, Taha Iqbal, Yumi Jin, Peter Keskinen, Alexis Lerro Rose, Michelle K Moon, Joseph Manuel, Liming Qu, Flawless Robbins, Naveensri Saravanan, Jin Sha, Sam Tate, Yi Zhao, Alzheimer’s Disease Sequencing Project, Laura Cantwell, Jake Gardner, Shin-Yi Chou, Jung-Ying Tzeng, William Bush, Adam Naj, Pavel Kuksa, Wan-Ping Lee, Yuk Yee Leung, Gerard Schellenberg, Li-San Wang: NIAGADS: a data repository for Alzheimer's disease and related dementia genomics. Alzheimer's & Dementia 21(6): e70255, Jun 2025 Notes: https://doi.org/10.1002/alz.70255.
Yuk Yee Leung, Wan-Ping Lee, Amanda B Kuzma, Heather Nicaretta, Otto Valladares, Prabhakaran Gangadharan, Liming Qu, Yi Zhao, Youli Ren, Po-Liang Cheng, Pavel P Kuksa, Hui Wang, Heather White, Zivadin Katanic, Lauren Bass, Naveen Saravanan, Emily Greenfest-Allen, Maureen Kirsch, Laura Cantwell, Taha Iqbal, Nicholas R Wheeler, John J. Farrell, Congcong Zhu, Shannon L Turner, Tamil I Gunasekaran, Pedro R Mena, Jimmy Jin, Luke Carter, Alzheimer’s Disease Sequencing Project, Xiaoling Zhang, Badri N Vardarajan, Arthur Toga, Michael Cuccaro, Timothy J Hohman, William S Bush, Adam C Naj, Eden Martin, Clifton Dalgard, Brian W Kunkle, Lindsay A Farrer, Richard P Mayeux, Jonathan L Haines, Margaret A Pericak-Vance, Gerard D Schellenberg, Li-San Wang: Alzheimer’s Disease Sequencing Project Release 4 Whole Genome Sequencing Dataset. Alzheimer's & Dementia 21(5): e70237, May 2025 Notes: doi: 10.1002/alz.70237.
Kurt Farrell, Jack Humphrey, Timothy Chang, Yi Zhao, Yuk Yee Leung, Pavel P. Kuksa, Vishakha Patil, Wan-Ping Lee, Amanda B. Kuzma, Otto Valladares, Laura B. Cantwell, Hui Wang, Ashvin Ravi, Claudia De Sanctis, Natalia Han, Thomas D. Christie, Robina Afzal, Shrishtee Kandoi, Kristen Whitney, Margaret M. Krassner, Hadley Ressler, SoongHo Kim, Diana Dangoor, Megan A. Iida, Alicia Casella, Ruth H. Walker, Melissa J. Nirenberg, Alan E. Renton, Bergan Babrowicz, Giovanni Coppola, Towfique Raj, Günter U. Höglinger, Ulrich Müller, Lawrence I. Golbe, Huw R. Morris, John Hardy, Tamas Revesz, Tom T. Warner, Zane Jaunmuktane, Kin Y. Mok, Rosa Rademakers, Dennis W. Dickson, Owen A. Ross, Li-San Wang, Alison Goate, Gerard Schellenberg, Daniel H. Geschwind, PSP Genetics Study Group, John F. Crary & Adam Naj: Genetic, transcriptomic, histological, and biochemical analysis of progressive supranuclear palsy implicates glial activation and novel risk genes. Nature Communications 15(1): 7880, Sept 2024 Notes: [2024 Publication of the Year Award, International Society to Advance Alzheimer’s Research and Frontotemporal Dementia and Related Disorders PIA]
Greenfest-Allen E, Valladares O, Kuksa PP, Gangadharan P, Lee WP, Cifello J, Katanic Z, Kuzma AB, Wheeler N, Bush WS, Leung YY, Schellenberg G, Stoeckert CJ Jr, Wang LS.: NIAGADS Alzheimer's GenomicsDB: A resource for exploring Alzheimer's disease genetic and genomic knowledge. Alzheimers Dement. 20(2): 1123-1136, Feb 2024 Notes: https://doi.org/10.1002/alz.13509 [Top viewed article]
Jeffrey Cifello*, Pavel P. Kuksa*, Naveensri Saravanan, Otto Valladares, Li-San Wang, Yuk Yee Leung: hipFG: High-throughput harmonization and integration pipeline for functional genomics data. Bioinformatics. Tobias Marschall (eds.). 39(11): btad673, Nov 2023 Notes: https://doi.org/10.1093/bioinformatics/btad673.
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.: New insights into the genetic etiology of Alzheimer's disease and related dementias. Nature Genetics 54(4): 412-436, Apr 2022 Notes: The citation lists over 100 authors. The FEDS system does not have the capability to include all names.
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.: Alzheimer's Disease Variant Portal: A Catalog of Genetic Findings for Alzheimer's Disease. J Alzheimers Dis 86(1): 461-477, Mar 2022.
Kuksa PP, Leung YY, Gangadharan P, Katanic Z, Kleidermacher L, Amlie-Wolf A, Lee CY, Qu L, Greenfest-Allen E, Valladares O, Wang LS.: FILER: a framework for harmonizing and querying large-scale functional genomics knowledge. NAR Genom Bioinform 4(1): lqab123, Jan 2022.