Foundational Publications

 

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.