Selected Publications
Pölönen P, Di Giacomo D, Seffernick AE, Elsayed A, Kimura S, Benini F, Montefiori LE, Wood BL, Xu J, Chen C, Cheng Z, Newman H, Myers J, Iacobucci I, Li E, Sussman J, Hedges D, Hui Y, Diorio C, Uppuluri L, Frank D, Fan Y, Chang Y, Meshinchi S, Ries R, Shraim R, Li A, Bernt KM, Devidas M, Winter SS, Dunsmore KP, Inaba H, Carroll WL, Ramirez NC, Phillips AH, Kriwacki RW, Yang JJ, Vincent TL, Zhao Y, Ghate PS, Wang J, Reilly C, Zhou X, Sanders MA, Takita J, Kato M, Takasugi N, Chang BH, Press RD, Loh M, Rampersaud E, Raetz E, Hunger SP, Tan K, Chang TC, Wu G, Pounds SB, Mullighan CG, Teachey DT. The genomic basis of childhood T-lineage acute lymphoblastic leukaemia. Nature 2024 Aug;632(8027):1082-1091. doi: 10.1038/s41586-024-07807-0. Epub 2024 Aug 14. PMID: 39143224; PMCID: PMC11611067.
H Elsayed A, Cao X, Marrero RJ, Nguyen NHK, Wu H, Ni Y, Ribeiro RC, Tobias H, Valk PJ, Béliveau F, Richard-Carpentier G, Hébert J, Zwaan CM, Gamis A, Kolb EA, Aplenc R, Alonzo TA, Meshinchi S, Rubnitz J, Pounds S, Lamba JK. Integrated drug resistance and leukemic stemness gene-expression scores predict outcomes in large cohort of over 3500 AML patients from 10 trials. NPJ Precis Oncol. 2024 Aug 1;8(1):168. doi: 10.1038/s41698-024-00643-5. PMID: 39090192; PMCID: PMC11294346
Lamba JK, Marrero R, Wu H, Cao X, Parcha PK, Karol SE, Inaba H, Kuo DJ, Degar BA, Heym K, Taub JW, Lacayo NJ, Pui CH, Ribeiro RC, Pounds SB, Rubnitz JE. Pharmacogenomics, Race, and Treatment Outcome in Pediatric Acute Myeloid Leukemia. JAMA Netw Open. 2024 May 1;7(5):e2411726. doi: 10.1001/jamanetworkopen.2024.11726. Erratum in: JAMA Netw Open. 2025 Feb 3;8(2):e250502. doi: 10.1001/jamanetworkopen.2025.0502. PMID: 38753328; PMCID: PMC11099689.
Ni Y, Seffernick AE, Onar-Thomas A, Pounds SB. Computing Power and Sample Size for the False Discovery Rate in Multiple Applications. Genes (Basel). 2024 Mar 7;15(3):344. doi: 10.3390/genes15030344. PMID: 38540403; PMCID: PMC10970028.
Umeda M, Ma J, Westover T, Ni Y, Song G, Maciaszek JL, Rusch M, Rahbarinia D, Foy S, Huang BJ, Walsh MP, Kumar P, Liu Y, Yang W, Fan Y, Wu G, Baker SD, Ma X, Wang L, Alonzo TA, Rubnitz JE, Pounds S, Klco JM. A new genomic framework to categorize pediatric acute myeloid leukemia. Nat Genet 2024 Feb;56(2):281-293. doi: 10.1038/s41588-023-01640-3. Epub 2024 Jan 11. PMID: 38212634; PMCID: PMC10864188.
Nguyen NHK, Rafiee R, Tagmount A, Sobh A, Loguinov A, de Jesus Sosa AK, Elsayed AH, Gbadamosi M, Seligson N, Cogle CR, Rubnitz J, Ribeiro R, Downing J, Cao X, Pounds SB, Vulpe CD, Lamba JK. Genome-wide CRISPR/Cas9 screen identifies etoposide response modulators associated with clinical outcomes in pediatric AML. Blood Adv 2023 May 9;7(9):1769-1783. doi: 10.1182/bloodadvances.2022007934. PMID: 36111891; PMCID: PMC10182178.
Baggett DW, Medyukhina A, Tripathi S, Shirnekhi HK, Wu H, Pounds SB, Khairy K, Kriwacki R. An Image Analysis Pipeline for Quantifying the Features of Fluorescently-Labeled Biomolecular Condensates in Cells. Front Bioinform 2022 Jun 6;2:897238. doi: 10.3389/fbinf.2022.897238. PMID: 36304323; PMCID: PMC9580871.
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 Discov 2022 May 5;3(3):194-207. doi: 10.1158/2643-3230.BCD-21-0160. PMID: 35176137; PMCID: PMC9780084.
Fornerod M, Ma J, Noort S, Walsh MP, Shi L, Nance S, Liu Y, Wang Y, Song G, Lamprecht T, Easton J, Mulder HL, Yergeau D, Myers J, Kamens JL, Obeng EA, Pigazzi M, Jarosova M, Kelaidi C, Polychronopoulou S, Lamba JK, Baker SD, Rubnitz JE, Reinhardt D, an den Heuvel-Eibrink MM, Locatelli F, Hasle H, Klco JM, Downing JR, Zhang J, Pounds S, Zwaan CM, Gruber, TA. Integrative genomic analysis of pediatric myeloid-related acute leukemias identifies novel subtypes and prognostic indicators. Blood Cancer Discovery October 6, 2021.
Nguyen NHK, Wu H, Tan H, Peng J, Rubnitz JE, Cao X, Pounds S, Lamba JK. Global Proteomic Profiling of Pediatric AML: A Pilot Study. Cancers (Basel) Jun 24;13(13):3161, 2021.
Stockard B, Bhise N, Shin M, Guingab-Cagmat J, Garrett TJ, Pounds S, Lamba JK. Cellular Metabolomics Profiles Associated With Drug Chemosensitivity in AML. Front Oncol Jun 10;11:678008, 2021.
Cao X, Pounds SB. Gene-Set Distance Analysis (GSDA): A Powerful Tool for Gene-Set Association Analysis. BMC Bioinformatics 22:207, 2021.
Davis EM, Sun Y, Liu Y, Kolekar P, Shao Y, Szlachta K, Mulder HL, Ren D, Rice SV, Wang Z, Nkitandwe J, Gout AM, Shaner B, Hall S, Robison LL, Pounds S, Klco JM, Easton J, and Ma X. SequencErr: measuring and suppressing errors in next-generation sequencing data. Genome Biology 22:37, 2021.
Klco J, Schwartz J, Ma J, Kamens J, Westover T, Walsh M, Brady S, Michael J, Chen X, Song G, Wu G, Wu H, Branstetter C, Hiltenbrand R, Walsh M, Nichols K, Maciaszek J, Liu Y, Kumar P, Easton J, Newman S, Rubnitz J, Mullighan C, Pounds S, Zhang J, Gruber T, Ma X, and Montefiori L. The Acquisition of Molecular Drivers in Pediatric Therapy-Related Myeloid Neoplasms. Nature Communications Feb 12;12(1):985, 2021..
Lamba JK, Cao X, Raimondi S, Downing J, Ribeiro R, Gruber TA, Rubnitz J, Pounds S. DNA Methylation Clusters and their Relation to Cytogenetic Features in Pediatric AML. Cancers (Basel) 12(10):3024, 2020.
Autry RJ, Paugh SW, Carter R, Shi L, Liu J, Ferguson DC, Lau CE, Bonten EJ, Yang W, McCorkle JR, Beard JA, Panetta JC, Diedrich JD, Crews KR, Pei D, Coke CJ, Natarajan S, Alireza Khatmian, Karol SE, Lopez-Lopez E, Diouf B, Smith C, Gocho Y, Hagiwara K, Roberts KG, Pounds S, Kornblau SM, Stock W, Paietaa EM, Litzow MR, Inaba H, Mullighan CG, Jeha S, Pui C-H, Cheng C, Savic D, Yu J, Gawad C, Relling MV, Yang JJ, Evans WE. Integrative genomic analyses reveal known and novel mechanisms of glucocorticoid resistance in acute lymphoblastic leukemia. Nature Cancer Mar; 1(3):329-344, 2020.
Murphy A, Chen X, Pinto EM, Williams JS, Clay MR, Pounds SB, Cao X, Shi L, Neale G, Morton CL, Wollard MA, Mulder HL, Gil HJ, Rehg JE, Billups CA, Harlow ML, Dome JS, Houghton PJ, Easton J, Zhang J, George RE, Zambetti GP, Davidoff AM. Forty-five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor. Nature Communications Dec 20;10(1):5806, 2019.
Alexander TB, Gu Z, Choi JK, Iacobucci I, Dickerson K, Loh ML, Horan J, Buldini B, Basso G, Elitzur S, de Haas V, Zwaan CM, Yeoh A, Reinhardt D, Tomizawa D, Kiyokawa N, Lammens T, De Moerloose B, Zhou L, Hori H, Moorman A, Moore AS, Hrusak O, Meschinchi S, Orgel E, Devidas M, Borowitz M, Wood B, Heerema NA, Carrol A, Yang Y-L, Smith MA, Davidsen TM, Hermida LC, Gesuwan P, Marra MA, Ma Y, Mungall AJ, Moore RA, Jones SJM, Dang L, Newman S, Liu Y, Zhang J, Nichols KE, Downing JR, Cao X, Shi L, Pounds S, Pei D, Auvil JMG, Gerhard DS, Hunger SP, Inaba H, Mullighan CG (2018). The genetic basis and cell of origin of mixed phenotype acute leukaemia. Nature Sep 12, 2018. PMID: 30209392.
Rubnitz JE, Lacayo NJ, Inaba H, Heym K, Ribeiro RC, Taub J, McNeer J, Degar B, Schiff D, Yeoh AE, Coustan-Smith E, Wang L, Triplett B, Raimondi SC, Klco J, Choi J, Pounds S, Pui CH. Clofarabine Can Replace Anthracyclines and Etoposide in Remission Induction Therapy for Childhood Acute Myeloid Leukemia: The AML08 Multicenter, Randomized Phase III Trial. Journal of Clinical Oncology Aug 10;37(23):2072-2081, 2019.
Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, Zhou X, Li Y, Rusch MC, Easton J, Huether R, Gonzalez-Pena V, Wilkinson MR, Hermida LC, Davis S, Sioson E, Pounds S, Cao X, Ries RE, Wang Z, Chen X, Dong L, Diskin SJ, Smith MA, Guidry Auvil JM, Meltzer PS, Lau CC, Perlman EJ, Maris JM, Meshinchi S, Hunger SP, Gerhard DS, Zhang J. Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. Nature Mar 15;555(7696):371-376, 2018. doi: 10.1038/nature25795. Epub 2018 Feb 28. PubMed PMID: 29489755.
Liu Y, Easton J, Shao Y, Maciaszek J, Wang Z, Wilkinson MR, Mccastlain K, Edmonson M, Pounds SB, Shi L, Zhou X, Ma Xi, Sioson E, Li Y, Rusch M, Gupta P, Pei D, Cheng C, Smith MA, Auvil JG, Gerhard DS, Relling MV, Winick NJ, Carroll AJ, Heerema NA, Raetz E, Devidas M, Wilman CL, Harvey RC, Carroll WL, Dunsmore KP, Winter SS, Wood BL, Sorrentino BP, Downing JR, Lo ML, Hunger SP, Zhang J, Mullighan CG. The Genomic Landscape of Pediatric and Young Adult T-Lineage Acute Lymphoblastic Leukemia. Nature Genetics 49:1211-1218, 2017.
Zhu L, Poppleton H, Finkelstein D, Gao CL, Shi L, Wang Y-D, Terrada LT, Wang K, Utley S, Pounds S, Neale G, Ellison DW, Onar-Thomas A, Gilbertson RJ. Multi-organ mapping of cancer risk. Cancer Cell 166:1132-1146, 2016.
Cao X, Crews KR, Downing J, Lamba J, Pounds SB. CC-PROMISE Effectively Integrates Two Forms of Molecular Data with Multiple Biologically Related Endpoints. BMC Bioinformatics 17:382, 2016.
Pounds S, Cheng C, Li S, Liu Z, Zhang J, Mullighan C. A Genomic Random Interval Model for Statistical Analysis of Genomic Lesion Data. Bioinformatics 29:2088-95, 2013.
Last update: April 2025