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Selected Publications

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  • Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey ALW, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A pan-cancer gene panel for childhood malignancies to enhance cancer monitoring and early detection. Clinical Cancer Research. 2024 Jul 24. doi: 10.1158/1078-0432.CCR-24-1063. PMID: 39047169.

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  • LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Allan TJ, Zalusky MP, Goffena J, Gibson SB, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel MN, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Gupta S, Jones EA, Weisz-Hubshman M, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT; Undiagnosed Diseases Network; Neale G, Carvill GL; University of Washington Center for Rare Disease Research; Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement. Nature Communications. 2024 Aug 6;15(1):6524. doi: 10.1038/s41467-024-50159-6. PMID: 39107278.

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  • Liu Y, Klein J, Bajpai R, Dong L, Tran Q, Kolekar P, Smith JL, Ries RE, Huang BJ, Wang YC, Alonzo TA, Tian L, Mulder HL, Shaw TI, Ma J, Walsh MP, Song G, Westover T, Autry RJ, Gout AM, Wheeler DA, Wan S, Wu G, Yang JJ, Evans WE, Loh M, Easton J, Zhang J, Klco JM, Meshinchi S, Brown PA, Pruett-Miller SM, Ma X. Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication. Nature Communications. 2023 Apr 5;14(1):1739. doi: 10.1038/s41467-023-37438-4. PMID: 37019972.

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  • Narang S, Evensen NA, Saliba J, Pierro J, Loh ML, Brown PA, Kolekar P, Mulder H, Shao Y, Easton J, Ma X, Tsirigos A, Carroll WL. NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization. Genome Biology. 2023 Apr 4;24(1):64. doi: 10.1186/s13059-023-02905-0. PMID: 37016431.

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  • Lamble AJ, Hagiwara K, Gerbing RB, Smith JL, Kolekar P, Ries RE, Kolb EA, Alonzo TA, Ma X, Meshinchi S. CREBBP alterations are associated with a poor prognosis in de novo AML. Blood. 2023 Apr 27;141(17):2156-2159. doi: 10.1182/blood.2022017545. PMID: 36634304.

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  • Umeda M, Ma J, Huang BJ, Hagiwara K, Westover T, Abdelhamed S, Barajas JM, Thomas ME, Walsh MP, Song G, Tian L, Liu Y, Chen X, Kolekar P, Tran Q, Foy SG, Maciaszek JL, Kleist AB, Leonti AR, Ju B, Easton J, Wu H, Valentine V, Valentine MB, Liu YC, Ries RE, Smith JL, Parganas E, Iacobucci I, Hiltenbrand R, Miller J, Myers JR, Rampersaud E, Rahbarinia D, Rusch M, Wu G, Inaba H, Wang YC, Alonzo TA, Downing JR, Mullighan CG, Pounds S, Babu MM, Zhang J, Rubnitz JE, Meshinchi S, Ma X, Klco JM. Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia. Blood Cancer Discovery. 2022 May 5;3(3):194-207. doi: 10.1158/2643-3230.BCD-21-0160. PMID: 35176137.

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  • ​Yang F, Brady SW, Tang C, Sun H, Du L, Barz MJ, Ma X, Chen Y, Fang H, Li X, Kolekar P, Pathak O, Cai J, Ding L, Wang T, von Stackelberg A, Shen S, Eckert C, Klco JM, Chen H, Duan C, Liu Y, Li H, Li B, Kirschner-Schwabe R, Zhang J, Zhou BS. Chemotherapy and mismatch repair deficiency cooperate to fuel TP53 mutagenesis and ALL relapse. Nature Cancer. 2021 Aug;2(8):819-834. doi: 10.1038/s43018-021-00230-8. Epub 2021 Jul 22. PMID: 35122027.​​

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  • Huang BJ, Smith JL, Wang YC, Taghizadeh K, Leonti AR, Ries RE, Liu Y, Kolekar P, Tarlock K, Gerbing R, Crowgey E, Furlan SN, Shaw TI, Hagiwara K, Wei L, Cooper TM, Gamis AS, Aplenc R, Kolb EA, Farrar JE, Triche T, Alonzo TA, Ma X, Meshinchi S. CBFB-MYH11 fusion transcripts distinguish acute myeloid leukemias with distinct molecular landscapes and outcomes. Blood Advances. 2021 Dec 14;5(23):4963-4968. doi: 10.1182/bloodadvances.2021004965. PMID: 34547772.​​​

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  • Davis E*, Sun Y*, Liu Y*, Kolekar P*, Shao Y, Szlachta K, Mulder H, Ren D, Rice S, Wang Z, Nakitandwe J, Gout A, Shaner B, Hall S, Robison L, Pounds S, Klco J, Easton J, Ma X. (2021) SequencErr: measuring and suppressing sequencer errors in next generation sequencing data. Genome Biology, 22(1):37. doi: 10.1186/s13059-020-02254-2. PMID: 33487172 (*: Co-First author)

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  • Balaji SA, Shanmugam A, Chougule A, Sridharan S, Prabhash K, Arya A, Chaubey A, Hariharan A, Kolekar P, Sen M, Ravichandran A, Katragadda S, Sankaran S, Bhargava S, Kulkarni P4, Rao S, Sunkavalli C, Banavali S, Joshi A, Noronha V, Dutt A, Bahadur U, Hariharan R, Veeramachaneni V, Gupta V. (2018) Analysis of solid tumor mutation profiles in liquid biopsy. Cancer Medicine, 00:1–9. https://doi.org/10.1002/cam4.1791 PMID: 30264478

 

  • Jigisha Anupama, Margherita Francescatto, Farzana Rahman, Nazeefa Fatima, Dan Deblasio, Avinash Kumar Shanmugam, Venkata Satagopam, Alberto Santos, Pandurang Kolekar, Magali Michaut, Emre Guney. (2018) The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide. PLoS computational biology, 14(1):e1005802. doi: 10.1371/journal.pcbi.1005802. PMID: 29346365

 

  • Parulekar NN, Kolekar PS, Jenkins A, Kleiven S, Utkilen H, Johansen A, Sawant S, Kulkarni-Kale U, Kale M, Sæbø M. (2017) Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis. PLoS One. 12(3):e0173408. doi: 10.1371/journal.pone.0173408. PMID: 28282404

 

  • Waman VP, Kolekar PS, Ramtirthkar MR, Kale MM, Kulkarni-Kale U. (2016). Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes. PeerJ. 4:e2326. doi: 10.7717/peerj.2326. PMID: 27635316 

 

  • Kolekar PS, Pataskar A, Kulkarni-Kale U, Pal JK, Kulkarni A. (2016). IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES). Scientific Reports, 6:27436. doi: 10.1038/srep27436. PMID: 27264539

 

  • Kolekar PS, Waman VP, Kale MM, Kulkarni-Kale U. (2016). RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach. PLoS ONE, 11(2):e0149350. doi:10.1371/journal.pone.0149350. PMID: 26870949

 

  • Waman VP, Kolekar PS, Kale MM, Kulkarni-Kale U. (2014). Population Structure and Evolution of Rhinoviruses. PLoS ONE, 9(2): e88981. doi:10.1371/journal.pone.0088981 PMID: 24586469

 

  • Kolekar PS, Hake N, Kale MM, Kulkarni-Kale U. (2014). WNV Typer: A server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution. Journal of Virological Methods, 198:41-55. PMID: 24388930

 

  • Kolekar PS, Kale MM, Kulkarni-Kale U. (2012).  Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping. Molecular Phylogenetics and Evolution, 65(2):510-522. PMID: 22820020

 

  • Kolekar PS, Kale MM, Kulkarni-Kale U. (2011). Genotyping of Mumps viruses based on SH gene: Development of a server using alignment-free and alignment-based methods. Immunome Research, 7(3):1-7. Publisher's Full Text

 

  • Pandurang Kolekar, Mohan Kale and Urmila Kulkarni-Kale (2011). Molecular Evolution & Phylogeny: What, When, Why & How?, Computational Biology and Applied Bioinformatics, Heitor Silverio Lopes and Leonardo Magalhães Cruz (Ed.), ISBN: 978-953-307-629-4, InTech, Available from: Publisher's Full Text

 

 

  • Kolekar PS, Kale MM, Kulkarni-Kale U. (2010). 'Inter-Arrival Time' Inspired Algorithm and its Application in Clustering and Molecular Phylogeny. AIP Conference Proceedings, 1298(1): 307-312. Abstract

 

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