Program

Cancer Data Sciences Program

The HCC Program in Cancer Data Sciences (CDS) fosters a broad range of research in statistical, computational, and mathematical questions that arise in cancer investigations.

Recent, High-Impact Publications

  • PROFET predicts continuous gene expression dynamics from scRNA-seq data to elucidate heterogeneity of cancer treatment responses.

    Cheng YC, Gu H, McDonald TO, Wu W, Tripathi S, Guarducci C, Russo D, Abravanel DL, Bailey M, Wang Y, Zhang Y, Pantazis Y, Levine H, Jeselsohn R, Katsoulakis MA, Michor F

    Cell Systems 2026; 101710.PubMed(opens in new window)
  • Trajectory-informed gene feature selection in single-cell analysis with SEEK-VFI.

    Danning R, Ke ZT, Lin X, Ma R

    Cell Reports Methods 2026; 101539.PubMed(opens in new window)
  • Improved heritability partitioning and enrichment analyses using summary statistics with graphREML.

    Li H, Kamath T, Mazumder R, Lin X, O'Connor LJ

    Nature genetics 2026; 58(7):1573-1582.PubMed(opens in new window)
  • Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed.

    Orchard P, Blackwell TW, Kachuri L, Castaldi PJ, Cho MH, Christenson SA, Durda P, Gabriel S, Hersh CP, Huntsman S, Hwang S, Joehanes R, Johnson M, Li X, Lin H, Liu CT, Liu Y, Mak ACY, Manichaikul AW, Paik DT, Saferali A, Smith JD, Taylor KD, Tracy RP, Wang J, Wang M, Weinstock JS, Weiss J, Wheeler HE, Zhou Y, Zöllner S, Wu JC, Mestroni L, Graw S, Taylor MRG, Ortega VE, Johnson WC, Gan W, Abecasis G, Nickerson DA, Gupta N, Ardlie K, Woodruff PG, Bowler RP, Meyers DA, Reiner A, Kooperberg C, Ziv E, Vasan RS, Larson MG, Cupples LA, Silverman EK, Rich SS, Heard-Costa N, Tang H, Rotter JI, Smith AV, Levy D, , , Aguet F, Scott LJ, Raffield LM, Parker SCJ, Abe N, Almasy L, Ament S, Anugu P, Auer P, Avramopoulos D, Balasubramanian A, Barr RG, Barwick L, Beaty T, Becker D, Becker L, Beitelshees A, Benos T, Bezerra M, Bis J, Brody J, Broeckel U, Broome J, Bunting K, Buth E, Carey V, Carty C, Casaburi R, Chaffin M, Chang C, Chang YC, Chavan S, Chen BJ, Chen WM, Choi SH, Chuang LM, Chung RH, Conomos M, Cornell E, Crandall C, Crapo J, Curtis J, Damcott C, David S, de Las Fuentes L, de Vries P, Deka R, DeMeo D, Devine S, Dinh H, Doddapaneni H, Duan Q, Duggirala R, Eaton C, Ekunwe L, El Boueiz A, Emery L, Farber C, Farek J, Franceschini N, Frazar C, Fu M, Fullerton SM, Fulton L, Gao S, Gao Y, Gass M, Geiger H, Ghosh A, Gignoux C, Glahn D, Gogarten S, Gong DW, Goring H, Grine D, Gu CC, Guan Y, Hall M, Han Y, Harris D, Heavner B, Herrington D, Hobbs B, Hong E, Hoth K, Hsiung CA, Hu J, Hung YJ, Huston H, Hwu CM, Jackson R, Jain D, Johnsen J, Johnston R, Jones K, Kessler M, Khan A, Khan Z, Kim W, Kimoff J, Kinney G, Kramer H, Lange C, Lange E, Laurie C, Laurie C, LeBoff M, Lee S, Lee WJ, Levine D, Lewis J, Li Y, Lin X, Liu S, Liu Y, Make B, Manning A, Manson J, Martin L, Marton M, Mathai S, May S, McArdle P, McDonald ML, McFarland S, McGoldrick D, McHugh C, Mei H, Meigs J, Menon V, Min N, Moll M, Momin Z, Montasser M, Mychaleckyj JC, Naik R, Naseri T, Natarajan P, Nelson SC, Neltner B, Nessner C, Nkechinyere O, O'Connell J, O'Connor T, Ochs-Balcom H, Okwuonu G, Pankow J, Parker C, Peloso G, Peralta JM, Perez M, Perry J, Peters U, Phillips LS, Pollin T, Becker JP, Boorgula MP, Psaty B, Qiao D, Rafaels N, Rajendran M, Rasmussen-Torvik L, Ratan A, Reed R, Regan E, Reupena MS, Robillard R, Roselli C, Ruczinski I, Runnels A, Russell P, Ryan K, Sabino EC, Salimi S, Salvi S, Salzberg S, Sandow K, Santibanez J, Schwander K, Sciurba F, Sériès F, Shetty A, Shetty A, Silver B, Skomro R, Smith T, Smoller S, Snively B, Stilp AM, Storm G, Streeten E, Su JL, Sung YJ, Sylvia J, Szpiro A, Taub M, Taylor S, Thornton TA, Threlkeld M, Tinker L, Tirschwell D, Tiwari H, Tong C, Tsai M, Vaidya D, Walker T, Wallace R, Walts A, Wang FF, Wang H, Watson K, Watt J, Weng LC, Wessel J, Williams K, Wilson C, Wilson J, Winterkorn L, Wong Q, Wu B, Xu H, Yanek L, Yang I, Zekavat SM, Zhao SX, Zhao W, Zhu X

    Science (New York, N.Y.) 2026; 393(6808):eadx2989.PubMed(opens in new window)
  • An AI-enabled structural atlas decodes kinase specificity across the human proteome.

    Vanderwall DR, Huttlin EL, Mintseris J, Yaron-Barir TM, Johnson JL, Dong KD, Bott AJ, He Y, Schroeter CB, Frere GA, Uduman M, Lee H, Landry S, Beausoleil SA, Paulo JA, Cantley LC, Gygi SP

    Nature biotechnology 2026.PubMed(opens in new window)
  • A Bayesian framework for longitudinal EHR and genetic discovery.

    Urbut SM, Ding Y, Nakao T, Koyama S, Misra A, Jiang X, Harish A, Gaffney L, Hornsby WE, Smoller JW, Gusev A, Natarajan P, Parmigiani G

  • Long non-coding RNA triplex-dependent regulation of melanoma gene networks.

    Shah K, Anastasakou E, Sejour L, Guseva S, Rauchet C, Wert-Lamas L, Calandrelli R, Distel R, Zhong S, Vlachos I, Novina CD

    Nar Genomics And Bioinformatics 2026; 8(3):lqag067.PubMed(opens in new window)
  • High-resolution metagenome assembly for modern long reads with myloasm.

    Shaw J, Marin MG, Li H

    Nature biotechnology 2026.PubMed(opens in new window)
  • Thymic health consequences in adults.

    Bernatz S, Prudente V, Pai S, Attermann AK, Cao Y, Chen J, Lyass A, Foldyna B, Nürnberg L, Bressem K, Abbosh C, Swanton C, Jamal-Hanjani M, Lu MT, Murabito JM, Lunetta KL, Birkbak NJ, Aerts HJWL

  • Thymic health and immunotherapy outcomes in patients with cancer.

    Bernatz S, Prudente V, Pai S, Attermann AK, Di Federico A, Rowan A, Veeriah S, Dyrskjøt L, Nürnberg L, Alessi JV, Ott PA, Sharon E, Hackshaw A, McGranahan N, Abbosh C, Mak RH, Bitterman D, Awad M, Ricciuti B, Swanton C, Jamal-Hanjani M, Birkbak NJ, Aerts HJWL

  • cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions.

    Van Buren E, Zhang Y, Li X, Selvaraj MS, Li Z, Zhou H, Palmer ND, Arnett DK, Blangero J, Boerwinkle E, Cade BE, Carlson JC, Carson AP, Chen YI, Curran J, Duggirala R, Fornage M, Franceschini N, Graff M, Gu C, Guo X, He J, Heard-Cosa N, Hou L, Hung YJ, Kalyani RR, Kardia SLR, Kenny E, Kooperberg C, Kral BG, Lange L, Levy D, Li C, Liu S, Lloyd-Jones D, Loos RJF, Manichaikul AW, Martin LW, Mathias R, Minster RL, Mitchell BD, Mychaleckyj JC, Naseri T, North K, O'Connell J, Perry JA, Peyser PA, Psaty BM, Raffield LM, Vasan RS, Redline S, Reiner AP, Rich SS, Smith JA, Spitzer B, Tang H, Taylor KD, Tracy R, Viali S, Yanek L, Zhao W, , Rotter JI, Peloso GM, Natarajan P, Lin X

    Nature methods 2026.PubMed(opens in new window)
  • Evaluating Treatment Effects with Patient-Response-Related Outcomes in Comparative Clinical Trials.

    Mao L, Tian L, Huang B, Richardson PG, Ludmir EB, Hughes MD, Wei LJ

    Nejm Evidence 2025; 4(12):EVIDctw2400349.PubMed(opens in new window)

Cancer Data Sciences Program Members

Leaders

Members