Foundational Publications

Elyada E, Bolisetty M, Laise P, Flynn WF, Courtois ET, Burkhart RA, Teinor JA, Belleau P, Biffi G, Lucito MS, Sivajothi S, Armstrong TD, Engle DD, Yu KH, Hao Y, Wolfgang CL, Park Y, Preall J, Jaffee EM, Califano A, Robson P, Tuveson DA. Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts. Cancer Discov. 2019 Aug;9(8):1102-1123. doi: 10.1158/2159-8290.CD-19-0094. 

Levitin HM, Yuan J, Cheng YL, Ruiz FJ, Bush EC, Bruce JN, Canoll P, Iavarone A, Lasorella A, Blei DM, Sims PA. De novo gene signature identification from single-cell RNA-seq with hierarchical Poisson factorization. Mol Syst Biol. 2019 Feb 22;15(2):e8557. doi: 10.15252/msb.20188557.

Maurer C, Holmstrom SR, He J, Laise P, Su T, Ahmed A, Hibshoosh H, Chabot JA, Oberstein PE, Sepulveda AR, Genkinger JM, Zhang J, Iuga AC, Bansal M, Califano A, Olive KP. Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes. Gut. 2019 Jun;68(6):1034-1043. doi: 10.1136/gutjnl-2018-317706. 

Bansal M, He J, Peyton M, Kustagi M, Iyer A, Comb M, White M, Minna JD, Califano A. Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis. PLoS One. 2019 Jan 7;14(1):e0208646. doi: 10.1371/journal.pone.0208646. 

Yuan J, Sheng J, Sims PA. SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing. Genome Biol. 2018 Dec 24;19(1):227. doi: 10.1186/s13059-018-1607-x.

Wendorff AA, Quinn SA, Rashkovan M, Madubata CJ, Ambesi-Impiombato A, Litzow MR, Tallman MS, Paietta E, Paganin M, Basso G, Gastier-Foster JM, Loh ML, Rabadan R, Van Vlierberghe P, Ferrando AA. Phf6 Loss Enhances HSC Self-Renewal Driving Tumor Initiation and Leukemia Stem Cell Activity in T-ALL. Cancer Discov. 2019 Mar;9(3):436-451. doi: 10.1158/2159-8290.CD-18-1005. 

Aytes A, Giacobbe A, Mitrofanova A, Ruggero K, Cyrta J, Arriaga J, Palomero L, Farran-Matas S, Rubin MA, Shen MM, Califano A, Abate-Shen C. NSD2 is a conserved driver of metastatic prostate cancer progression. Nat Commun. 2018 Dec 5;9(1):5201. doi: 10.1038/s41467-018-07511-4.

Khatamian A, Paull EO, Califano A, Yu J. SJARACNe: a scalable software tool for gene network reverse engineering from big data. Bioinformatics. 2019 Jun 1;35(12):2165-2166. doi: 10.1093/bioinformatics/bty907.

Le Magnen C, Virk RK, Dutta A, Kim JY, Panja S, Lopez-Bujanda ZA, Califano A, Drake CG, Mitrofanova A, Abate-Shen C. Cooperation of loss of NKX3.1 and inflammation in prostate cancer initiation. Dis Model Mech. 2018 Nov 16;11(11). pii: dmm035139. doi: 10.1242/dmm.035139.

Risom T, Langer EM, Chapman MP, Rantala J, Fields AJ, Boniface C, Alvarez MJ, Kendsersky ND, Pelz CR, Johnson-Camacho K, Dobrolecki LE, Chin K, Aswani AJ, Wang NJ, Califano A, Lewis MT, Tomlin CJ, Spellman PT, Adey A, Gray JW, Sears RC. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nat Commun. 2018 Sep 19;9(1):3815. doi: 10.1038/s41467-018-05729-w.

Yuan J, Levitin HM, Frattini V, Bush EC, Boyett DM, Samanamud J, Ceccarelli M, Dovas A, Zanazzi G, Canoll P, Bruce JN, Lasorella A, Iavarone A, Sims PA. Single-cell transcriptome analysis of lineage diversity in high-grade glioma. Genome Med. 2018 Jul 24;10(1):57. doi: 10.1186/s13073-018-0567-9.

Alvarez MJ, Subramaniam PS, Tang LH, Grunn A, Aburi M, Rieckhof G, Komissarova EV, Hagan EA, Bodei L, Clemons PA, Dela Cruz FS, Dhall D, Diolaiti D, Fraker DA, Ghavami A, Kaemmerer D, Karan C, Kidd M, Kim KM, Kim HC, Kunju LP, Langel Ü, Li Z, Lee J, Li H, LiVolsi V, Pfragner R, Rainey AR, Realubit RB, Remotti H, Regberg J, Roses R, Rustgi A, Sepulveda AR, Serra S, Shi C, Yuan X, Barberis M, Bergamaschi R, Chinnaiyan AM, Detre T, Ezzat S, Frilling A, Hommann M, Jaeger D, Kim MK, Knudsen BS, Kung AL, Leahy E, Metz DC, Milsom JW, Park YS, Reidy-Lagunes D, Schreiber S, Washington K, Wiedenmann B, Modlin I, Califano A. A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors. Nat Genet. 2018 Jul;50(7):979-989. doi: 10.1038/s41588-018-0138-4.

Chiu HS, Martínez MR, Komissarova EV, Llobet-Navas D, Bansal M, Paull EO, Silva J, Yang X, Sumazin P, Califano A. The number of titrated microRNA species dictates ceRNA regulation. Nucleic Acids Res. 2018 May 18;46(9):4354-4369. doi: 10.1093/nar/gky286.

Ding H, Douglass EF Jr, Sonabend AM, Mela A, Bose S, Gonzalez C, Canoll PD, Sims PA, Alvarez MJ, Califano A. Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm. Nat Commun. 2018 Apr 16;9(1):1471. doi: 10.1038/s41467-018-03843-3.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. The Immune Landscape of Cancer. Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5.

Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell. 2018 Apr 5;22(4):575-588.e7. doi: 10.1016/j.stem.2018.03.012.

Ding H, Wang W, Califano A. iterClust: a statistical framework for iterative clustering analysis. Bioinformatics. 2018 Aug 15;34(16):2865-2866. doi: 10.1093/bioinformatics/bty176.

Rajbhandari P, Lopez G, Capdevila C, Salvatori B, Yu J, Rodriguez-Barrueco R, Martinez D, Yarmarkovich M, Weichert-Leahey N, Abraham BJ, Alvarez MJ, Iyer A, Harenza JL, Oldridge D, De Preter K, Koster J, Asgharzadeh S, Seeger RC, Wei JS, Khan J, Vandesompele J, Mestdagh P, Versteeg R, Look AT, Young RA, Iavarone A, Lasorella A, Silva JM, Maris JM, Califano A. Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma. Cancer Discov. 2018 May;8(5):582-599. doi: 10.1158/2159-8290.CD-16-0861.

Arnes L, Liu Z, Wang J, Maurer C, Sagalovskiy I, Sanchez-Martin M, Bommakanti N, Garofalo DC, Balderes DA, Sussel L, Olive KP, Rabadan R. Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma. Gut. 2018 Feb 10. pii: gutjnl-2017-314353. doi: 10.1136/gutjnl-2017-314353.

Tzoneva G, Dieck CL, Oshima K, Ambesi-Impiombato A, Sánchez-Martín M, Madubata CJ, Khiabanian H, Yu J, Waanders E, Iacobucci I, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Gastier-Foster JM, Loh ML, Kirschner-Schwabe R, Mullighan CG, Rabadan R, Ferrando AA. Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia. Nature. 2018 Jan 25;553(7689):511-514. doi: 10.1038/nature25186. 

Shen Y, Alvarez MJ, Bisikirska B, Lachmann A, Realubit R, Pampou S, Coku J, Karan C, Califano A. Systematic, network-based characterization of therapeutic target inhibitors. PLoS Comput Biol. 2017 Oct 12;13(10):e1005599. doi: 10.1371/journal.pcbi.1005599.

He J, Zhou Z, Reed M, Califano A. Accelerated parallel algorithm for gene network reverse engineering. BMC Syst Biol. 2017 Sep 21;11(Suppl 4):83. doi: 10.1186/s12918-017-0458-5.

Giudice ID, Rigolin GM, Raponi S, Cafforio L, Ilari C, Wang J, Bordyuh M, Piciocchi A, Marinelli M, Nanni M, Tavolaro S, Filetti M, Bardi A, Tammiso E, Volta E, Negrini M, Saccenti E, Mauro FR, Rossi D, Gaidano G, Guarini A, Rabadan R, Cuneo A, Foà R. Refined karyotype-based prognostic stratification of chronic lymphocytic leukemia with a low- and very-low-risk genetic profile. Leukemia. 2018 Feb;32(2):543-546. doi: 10.1038/leu.2017.292.

Chiu HS, Martínez MR, Bansal M, Subramanian A, Golub TR, Yang X, Sumazin P, Califano A. High-throughput validation of ceRNA regulatory networks. BMC Genomics. 2017 May 30;18(1):418. doi: 10.1186/s12864-017-3790-7.

Chiu TP, Rao S, Mann RS, Honig B, Rohs R. Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding . Nucleic Acids Res. 2017 Dec 1;45(21):12565-12576.

Zou M, Toivanen R, Mitrofanova A, Floch N, Hayati S, Sun Y, Le Magnen C, Chester D, Mostaghel EA, Califano A, Rubin MA, Shen MM, Abate-Shen C. Transdifferentation as a mechanism of treatment resistance in a mouse model of castration-resistant prostate cancer . Cancer Discov. 2017 Jul;7(7):736-749.

Bush EC, Ray F, Alvarez MJ, Realubit R, Li H, Karan C, Califano A, Sims PA. PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens . Nat Commun. 2017 Jul24;8(1):105.

Talos F, Mitrofanova A, Bergren SK, Califano A, Shen MM. A computatioal systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue . Nat Commun. 2017 Apr 21;8:14662.

Udyavar AR, Wooten DJ, Hoeksema M, Bansal M, Califano A, Estrada L, Schnell S, Irish JM, Massion PP, Quaranta V. Novel hybrid phentoype revealed in small cell lung cancer by a transcription factor network model that can explain tumor heterogeneity . Cancer Research. 2017 Mar 1;77(5):1063-1074.

Olive KP. Fanning the flames of cancer chemoresistance: Inflammation and anticancer therapy . J Oncol Pract. 2017 Mar;13(3):181-183.

Zhang X, Maity T, Kashyap MK, Bansal M, Venugopalan A, Singh S, Awasthi S, Marimuthu A, Charles Jacob HK, Belkina N, Pitts S, Cultraro CM, Gao S, Kirkali G, Biswas R, Chaerkady R, Califano A, Pandey A, Guha U. Quantitative tyrosine phosphoproteomics of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor-treated lung adenocarcinoma cells reveals potential novel biomarkers of therapeutic response . Mol Cell Proteomics. 2017 May;16(5):891-910.

Califano A, Alvarez MJ. The recurrent architecture of tumour initiation, progression and drug sensitivity . Nature Reviews Cancer. 2017 Feb;17(2):116-130.

Sanchez-Martin M, Ambesi-Impiombato A, Qin Y, Herranz D, Bansal M, Girardi T, Paietta E, Tallman MS, Rowe JM, De Keersmaecker K, Califano A, Ferrando AA. Synergistic antileukemic therapies in NOTCH1-induced T-ALL . PNAS 2017 Feb21;114(8):2006-2011.

Stockman VB, Ghamsari L, Lasso G, Honig B, Shapira SD, Wang HH. A high-throughput strategy for dissecting mammalian genetic interactions . PLoS One.2016 Dec9;11(12):e0167617.

Hwang H, Petrey D, Honig B. A hybrid method for protein-protein interface prediction . Protein Sci. 2016 Jan; 25(1):159-65.

Yuan J, Sims PA. An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq . Scientific Reports. 2016 Sep 27; 6:33883.

Koşaloğlu Z, Zörnig I, Halama N, Kaiser I, Buchhalter I, Grabe N, Eils R, Schlesner M, Califano A, Jäger D. Identification of immunotherapeutic targets by genomic profiling of rectal NET metastases . Oncoimmunology. 2016 Jul22;5(11):e1213931.

Aytes A, Mitrofanova A, Lefebvre C, Alvarez MJ, Castillo-Martin M, Zheng T, Eastham JA, Gopalan A, Pienta KJ, Shen MM, Califano A, Abate-Shen C. Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy . Cancer Cell. 2014; 25(5):638-51. 

Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. Reverse engineering of regulatory networks in human B cells . Nat Genet. 2005; 37(4):382-90. 

Bisikirska B, Bansal A, Shen Y, Teruya-Feldstein J, Chaganti RS, Califano A. Systematic Elucidation and Pharmacological Targeting of Follicular Lymphoma Progression Drivers: A New Spin on Precision Cancer Medicine. Cancer Res. 2015; In press.

Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, Sims PA. Scalable microfluidics for single-cell RNA printing and sequencing . Genome Biol. 2015; 16:120. 

Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A. The transcriptional network for mesenchymal transformation of brain tumours . Nature. 2010; 463(7279):318-25.

Chen JC, Alvarez MJ, Talos F, Dhruv H, Rieckhof GE, Iyer A, Diefes KL, Aldape K, Berens M, Shen MM, Califano A. Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks . Cell. 2014; 159(2):402-14.

Della Gatta G, Palomero T, Perez-Garcia A, Ambesi-Impiombato A, Bansal M, Carpenter ZW, De Keersmaecker K, Sole X, Xu L, Paietta E, Racevskis J, Wiernik PH, Rowe JM, Meijerink JP, Califano A, Ferrando AA. Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL . Nat Med. 2012; 18(3):436-40. 

Frattini V, Trifonov V, Chan JM, Castano A, Lia M, Abate F, Keir ST, Ji AX, Zoppoli P, Niola F, Danussi C, Dolgalev I, Porrati P, Pellegatta S, Heguy A, Gupta G, Pisapia DJ, Canoll P, Bruce JN, McLendon RE, Yan H, Aldape K, Finocchiaro G, Mikkelsen T, Prive GG, Bigner DD, Lasorella A, Rabadan R, Iavarone A. The integrated landscape of driver genomic alterations in glioblastoma . Nat Genet. 2013; 45(10):1141-9.

Hsiao TL, Revelles O, Chen L, Sauer U, Vitkup D. Automatic policing of biochemical annotations using genomic correlations . Nat Chem Biol. 2010; 6(1):34-40.

Hu J, Locasale JW, Bielas JH, O'Sullivan J, Sheahan K, Cantley LC, Vander Heiden MG, Vitkup D. Heterogeneity of tumor-induced gene expression changes in the human metabolic network . Nat Biotechnol. 2013; 31(6):522-9.

Kushwaha R, Jagadish N, Kustagi M, Tomishima MJ, Mendiratta G, Bansal M, Kim HR, Sumazin P, Alvarez MJ, Lefebvre C, Villagrasa-Gonzalez P, Viale A, Korkola JE, Houldsworth J, Feldman DR, Bosl GJ, Califano A, Chaganti RS. Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency . Stem Cells. 2015; 33(2):367-77.

Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers . Mol Syst Biol. 2010; 6:377.

Mitrofanova A, Aytes A, Zou M, Shen MM, Abate-Shen C, Califano A.   A systems biology approach to predict drug response for human prostate cancer based on in vivo preclinical analyses of mouse models . Cell Rep. 2015 Sep 29;12(12):2060-71.

Piovan E, Yu J, Tosello V, Herranz D, Ambesi-Impiombato A, Da Silva AC, Sanchez-Martin M, Perez-Garcia A, Rigo I, Castillo M, Indraccolo S, Cross JR, de Stanchina E, Paietta E, Racevskis J, Rowe JM, Tallman MS, Basso G, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA. Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia . Cancer Cell. 2013; 24(6):766-76. Epub 2013/12/03.

Plata G, Fuhrer T, Hsiao TL, Sauer U, Vitkup D. Global probabilistic annotation of metabolic networks enables enzyme discovery . Nat Chem Biol. 2012; 8(10):848-54.

Rodriguez-Barrueco R, Yu J, Saucedo-Cuevas LP, Olivan M, Llobet-Navas D, Putcha P, Castro V, Murga-Penas EM, Collazo-Lorduy A, Castillo-Martin M, Alvarez M, Cordon-Cardo C, Kalinsky K, Maurer M, Califano A, Silva JM. Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers . Genes Dev. 2015; 29(15):1631-48. 

Rossi D, Khiabanian H, Spina V, Ciardullo C, Bruscaggin A, Fama R, Rasi S, Monti S, Deambrogi C, De Paoli L, Wang J, Gattei V, Guarini A, Foa R, Rabadan R, Gaidano G. Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia . Blood. 2014; 123(14):2139-47.

Singh D, Chan JM, Zoppoli P, Niola F, Sullivan R, Castano A, Liu EM, Reichel J, Porrati P, Pellegatta S, Qiu K, Gao Z, Ceccarelli M, Riccardi R, Brat DJ, Guha A, Aldape K, Golfinos JG, Zagzag D, Mikkelsen T, Finocchiaro G, Lasorella A, Rabadan R, Iavarone A. Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma . Science. 2012. Epub 2012/07/28.

Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma . Cell. 2011; 147(2):370-81.

Tzoneva G, Perez-Garcia A, Carpenter Z, Khiabanian H, Tosello V, Allegretta M, Paietta E, Racevskis J, Rowe JM, Tallman MS, Paganin M, Basso G, Hof J, Kirschner-Schwabe R, Palomero T, Rabadan R, Ferrando A. Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL . Nat Med. 2013; 19(3):368-71.

Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells . Nat Biotechnol. 2009; 27(9):829-39.

Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodriguez Martinez M, Lopez G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A. Elucidating Compound Mechanism of Action by Network Dysregulation Analysis in Pertubed Cells . Cell. 2015; 162(2):441-51.

Zhang QC, Petrey D, Garzon JI, Deng L, Honig B. PrePPI: a structure-informed database of protein-protein interactions . Nucleic Acids Res. 2013; 41(Database issue):D828-33.