Pavel P Kuksa, PhD, Computer Science

faculty photo
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
Lab: 215-573-3114
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.
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Description of Research Expertise

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

Selected Publications

Kuksa PP, Greenfest-Allen E, Cifello J, Ionita M, Wang H, Issen H, Cheng PL, Lee WP, Wang LS, Leung YY.: Scalable approaches for functional analyses of whole-genome sequencing non-coding variants. Human Molecular Genetics Aug 9 2022 Notes: No issue or volume.

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.

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.

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.

Amlie-Wolf A, Kuksa PP, Lee CY, Mlynarski E, Leung YY, Wang LS.: Using INFERNO to Infer the Molecular Mechanisms Underlying Noncoding Genetic Associations. Methods Mol Biol 2254: 73-91, Jan 2021 Notes: No issue number.

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.: SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants. Bioinformatics 36(12): 3879-3881, Jun 2020.

Kuksa PP, Li F, Kannan S, Gregory BD, Leung YY, Wang LS.: HiPR: High-throughput probabilistic RNA structure inference. Comput Struct Biotechnol J 18: 1539-1547, Jun 2020 Notes: No issue number.

Kuksa PP, Amlie-Wolf A, Hwang YC, Valladares O, Gregory BD, Wang LS.: HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions. NAR Genom Bioinform 2(2): lqaa022, Jun 2020.

Kuksa PP, Amlie-Wolf A, Katanić Ž, Valladares O, Wang LS, Leung YY.: DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. Bioinformatics 35(6): 1033-1039, Mar 2019.

Amlie-Wolf A, Tang M, Mlynarski EE, Kuksa PP, Valladares O, Katanic Z, Tsuang D, Brown CD, Schellenberg GD, Wang LS.: INFERNO: inferring the molecular mechanisms of noncoding genetic variants. Nucleic Acids Res 46(17): 8740-8753, Sep 2018.

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Last updated: 11/11/2022
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