Selected Publications

Following is a list of selected publications. For a more comprehensive list of recent publications, visit PubMed.

2023

178. Kostyrko K, Román M, Lee AG, Simpson DR, Dinh PT, Leung SG, Marini KD, Kelly MR, Broyde J, Califano A, Jackson PK, Alejandro Sweet-Cordero E. UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma. Nat Commun. 2023 Jul 5;14(1):3966. doi: 10.1038/s41467-023-39591-2. PMID: 37407562

177. Ding J, Lee SJ, Vlahos L, Yuki K, Rada CC, van Unen V, Vuppalapaty M, Chen H, Sura A, McCormick AK, Tomaske M, Alwahabi S, Nguyen H, Nowatzke W, Kim L, Kelly L, Vollrath D, Califano A, Yeh WC, Li Y, Kuo CJ. Therapeutic blood-brain barrier modulation and stroke treatment by a bioengineered FZD4-selective WNT surrogate in mice. Nat Commun. 2023 Jun 2;14(1):2947. doi: 10.1038/s41467-023-37689-1. PMID: 37268690

176. Mundi PS, Dela Cruz FS, Grunn A, Diolaiti D, Mauguen A, Rainey AR, Guillan K, Siddiquee A, You D, Realubit R, Karan C, Ortiz MV, Douglass EF, Accordino M, Mistretta S, Brogan F, Bruce JN, Caescu CI, Carvajal RD, Crew KD, Decastro G, Heaney M, Henick BS, Hershman DL, Hou JY, Iwamoto FM, Jurcic JG, Kiran RP, Kluger MD, Kreisl T, Lamanna N, Lassman AB, Lim EA, Manji GA, McKhann GM, McKiernan JM, Neugut AI, Olive KP, Rosenblat T, Schwartz GK, Shu CA, Sisti MB, Tergas A, Vattakalam RM, Welch M, Wenske S, Wright JD, Canoll P, Hibshoosh H, Kalinsky K, Aburi M, Sims PA, Alvarez MJ, Kung AL, Califano A. A Transcriptome-Based Precision Oncology Platform for Patient-Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies. Cancer Discov. 2023 Jun 2;13(6):1386-1407. doi: 10.1158/2159-8290.CD-22-1020. PMID: 37061969

175. Obradovic A, Ager C, Turunen M, Nirschl T, Khosravi-Maharlooei M, Iuga A, Jackson CM, Yegnasubramanian S, Tomassoni L, Fernandez EC, McCann P, Rogava M, DeMarzo AM, Kochel CM, Allaf M, Bivalacqua T, Lim M, Realubit R, Karan C, Drake CG, Califano A. Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators. Cancer Cell. 2023 May 8;41(5):933-949.e11. doi: 10.1016/j.ccell.2023.04.003. Epub 2023 Apr 27. PMID: 37116491

174. Ravi A, Hellmann MD, Arniella MB, Holton M, Freeman SS, Naranbhai V, Stewart C, Leshchiner I, Kim J, Akiyama Y, Griffin AT, Vokes NI, Sakhi M, Kamesan V, Rizvi H, Ricciuti B, Forde PM, Anagnostou V, Riess JW, Gibbons DL, Pennell NA, Velcheti V, Digumarthy SR, Mino-Kenudson M, Califano A, Heymach JV, Herbst RS, Brahmer JR, Schalper KA, Velculescu VE, Henick BS, Rizvi N, Jänne PA, Awad MM, Chow A, Greenbaum BD, Luksza M, Shaw AT, Wolchok J, Hacohen N, Getz G, Gainor JF. Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nat Genet. 2023 May;55(5):807-819. doi: 10.1038/s41588-023-01355-5. Epub 2023 Apr 6. PMID: 37024582

173. Vasciaveo A, Arriaga JM, de Almeida FN, Zou M, Douglass EF, Picech F, Shibata M, Rodriguez-Calero A, de Brot S, Mitrofanova A, Chua CW, Karan C, Realubit R, Pampou S, Kim JY, Afari SN, Mukhammadov T, Zanella L, Corey E, Alvarez MJ, Rubin MA, Shen MM, Califano A, Abate-Shen C. OncoLoop: A Network-Based Precision Cancer Medicine Framework. Cancer Discov. 2023 Feb 6;13(2):386-409. doi: 10.1158/2159-8290.CD-22-0342. PMID: 36374194

172. Zeleke TZ, Pan Q, Chiuzan C, Onishi M, Li Y, Tan H, Alvarez MJ, Honan E, Yang M, Chia PL, Mukhopadhyay P, Kelly S, Wu R, Fenn K, Trivedi MS, Accordino M, Crew KD, Hershman DL, Maurer M, Jones S, High A, Peng J, Califano A, Kalinsky K, Yu J, Silva J. Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer. Nat Cancer. 2023 Feb;4(2):257-275. doi: 10.1038/s43018-022-00489-5. Epub 2022 Dec 30. PMID: 36585452

2022

171. Coutinho DF, Mundi PS, Marks LJ, Burke C, Ortiz MV, Diolaiti D, Bird L, Vallance KL, Ibáñez G, You D, Long M, Rosales N, Grunn A, Ndengu A, Siddiquee A, Gaviria ES, Rainey AR, Fazlollahi L, Hosoi H, Califano A, Kung AL, Dela Cruz FS. Validation of a non-oncogene encoded vulnerability to exportin 1 inhibition in pediatric renal tumors. Med. 2022 Nov 11;3(11):774-791.e7. doi: 10.1016/j.medj.2022.09.002. Epub 2022 Oct 3. PMID: 36195086

170. Obradovic A, Graves D, Korrer M, Wang Y, Roy S, Naveed A, Xu Y, Luginbuhl A, Curry J, Gibson M, Idrees K, Hurley P, Jiang P, Liu XS, Uppaluri R, Drake CG, Califano A, Kim YJ. Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer. Clin Cancer Res. 2022 May 13;28(10):2094-2109. doi: 10.1158/1078-0432.CCR-21-3570. PMID: 35262677

169. Ronaldson-Bouchard K, Teles D, Yeager K, Tavakol DN, Zhao Y, Chramiec A, Tagore S, Summers M, Stylianos S, Tamargo M, Lee BM, Halligan SP, Abaci EH, Guo Z, Jacków J, Pappalardo A, Shih J, Soni RK, Sonar S, German C, Christiano AM, Califano A, Hirschi KK, Chen CS, Przekwas A, Vunjak-Novakovic G. A multi-organ chip with matured tissue niches linked by vascular flow. Nat Biomed Eng. 2022 Apr;6(4):351-371. doi: 10.1038/s41551-022-00882-6. Epub 2022 Apr 27. PMID: 35478225

168. Lassman AB, Wen PY, van den Bent MJ, Plotkin SR, Walenkamp AME, Green AL, Li K, Walker CJ, Chang H, Tamir S, Henegar L, Shen Y, Alvarez MJ, Califano A, Landesman Y, Kauffman MG, Shacham S, Mau-Sørensen M. A Phase II Study of the Efficacy and Safety of Oral Selinexor in Recurrent Glioblastoma. Clin Cancer Res. 2022 Feb 1;28(3):452-460. doi: 10.1158/1078-0432.CCR-21-2225. Epub 2021 Nov 2. PMID: 34728525

167. Douglass EF Jr, Allaway RJ, Szalai B, Wang W, Tian T, Fernández-Torras A, Realubit R, Karan C, Zheng S, Pessia A, Tanoli Z, Jafari M, Wan F, Li S, Xiong Y, Duran-Frigola M, Bertoni M, Badia-I-Mompel P, Mateo L, Guitart-Pla O, Chung V; DREAM CTD-squared Pancancer Drug Activity Challenge Consortium; Tang J, Zeng J, Aloy P, Saez-Rodriguez J, Guinney J, Gerhard DS, Califano A. A community challenge for a pancancer drug mechanism of action inference from perturbational profile data. Cell Rep Med. 2022 Jan 18;3(1):100492. doi: 10.1016/j.xcrm.2021.100492. eCollection 2022 Jan 18. PMID: 35106508

2021

166. Son J, Ding H, Farb TB, Efanov AM, Sun J, Gore JL, Syed SK, Lei Z, Wang Q, Accili D, Califano A. J Clin Invest. BACH2 inhibition reverses β cell failure in type 2 diabetes models. 2021 Dec 15;131(24):e153876. doi: 10.1172/JCI153876. PMID: 34907913

165. Gil V, Miranda S, Riisnaes R, Gurel B, D'Ambrosio M, Vasciaveo A, Crespo M, Ferreira A, Brina D, Troiani M, Sharp A, Sheehan B, Christova R, Seed G, Figueiredo I, Lambros M, Dolling D, Rekowski J, Alajati A, Clarke M, Pereira R, Flohr P, Fowler G, Boysen G, Sumanasuriya S, Bianchini D, Rescigno P, Aversa C, Tunariu N, Guo C, Paschalis A, Bertan C, Buroni L, Ning J, Carreira S, Workman P, Swain A, Califano A, Shen MM, Alimonti A, Neeb A, Welti J, Yuan W, de Bono J; PCF/SU2C International Prostate Cancer Dream Team. HER3 Is an Actionable Target in Advanced Prostate Cancer. Cancer Res. 2021 Dec 15;81(24):6207-6218. doi: 10.1158/0008-5472.CAN-21-3360. Epub 2021 Nov 9. PMID: 34753775

164. Sweet K, Bhatnagar B, Döhner H, Donnellan W, Frankfurt O, Heuser M, Kota V, Liu H, Raffoux E, Roboz GJ, Röllig C, Showel MM, Strickland SA Jr, Vives S, Tang S, Unger TJ, Joshi A, Shen Y, Alvarez MJ, Califano A, Crochiere M, Landesman Y, Kauffman M, Shah J, Shacham S, Savona MR, Montesinos P. A 2:1 randomized, open-label, phase II study of selinexor vs. physician's choice in older patients with relapsed or refractory acute myeloid leukemia. Leuk Lymphoma. 2021 Dec;62(13):3192-3203. doi: 10.1080/10428194.2021.1950706. Epub 2021 Jul 29. PMID: 34323164

163. Landsburg DJ, Barta SK, Ramchandren R, Batlevi C, Iyer S, Kelly K, Micallef IN, Smith SM, Stevens DA, Alvarez M, Califano A, Shen Y, Bosker G, Parker J, Soikes R, Martinez E, von Roemeling R, Martell RE, Oki Y. Fimepinostat (CUDC-907) in patients with relapsed/refractory diffuse large B cell and high-grade B-cell lymphoma: report of a phase 2 trial and exploratory biomarker analyses. Br J Haematol. 2021 Oct;195(2):201-209. doi: 10.1111/bjh.17730. Epub 2021 Aug 2. PMID: 34341990

162. Affo S, Nair A, Brundu F, Ravichandra A, Bhattacharjee S, Matsuda M, Chin L, Filliol A, Wen W, Song X, Decker A, Worley J, Caviglia JM, Yu L, Yin D, Saito Y, Savage T, Wells RG, Mack M, Zender L, Arpaia N, Remotti HE, Rabadan R, Sims P, Leblond AL, Weber A, Riener MO, Stockwell BR, Gaublomme J, Llovet JM, Kalluri R, Michalopoulos GK, Seki E, Sia D, Chen X, Califano A, Schwabe RF. Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations. Cancer Cell. 2021 Jun 14;39(6):866-882.e11. doi: 10.1016/j.ccell.2021.03.012. Epub 2021 Apr 29. PMID: 33930309

161. Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC; FANTOM consortium; Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun. 2021 Jun 2;12(1):3297. doi: 10.1038/s41467-021-23143-7. PMID: 34078885

160. Lo YH, Kolahi KS, Du Y, Chang CY, Krokhotin A, Nair A, Sobba WD, Karlsson K, Jones SJ, Longacre TA, Mah AT, Tercan B, Sockell A, Xu H, Seoane JA, Chen J, Shmulevich I, Weissman JS, Curtis C, Califano A, Fu H, Crabtree GR, Kuo CJ. A CRISPR/Cas9-Engineered ARID1A-Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation. Cancer Discov. 2021 Jun;11(6):1562-1581. doi: 10.1158/2159-8290.CD-20-1109. Epub 2021 Jan 15. PMID: 33451982

159. Obradovic A, Chowdhury N, Haake SM, Ager C, Wang V, Vlahos L, Guo XV, Aggen DH, Rathmell WK, Jonasch E, Johnson JE, Roth M, Beckermann KE, Rini BI, McKiernan J, Califano A, Drake CG. Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages. Cell. 2021 May 27;184(11):2988-3005.e16. doi: 10.1016/j.cell.2021.04.038. Epub 2021 May 20. PMID: 34019793

158. Ager CR, Obradovic AZ, Arriaga JM, Chaimowitz MG, Califano A, Abate-Shen C, Drake CG. Longitudinal Immune Profiling Reveals Unique Myeloid and T-cell Phenotypes Associated with Spontaneous Immunoediting in a Prostate Tumor Model. Cancer Immunol Res. 2021 May;9(5):529-541. doi: 10.1158/2326-6066.CIR-20-0637. Epub 2021 Feb 26. PMID: 33637604

157. Hahn WC, Bader JS, Braun TP, Califano A, Clemons PA, Druker BJ, Ewald AJ, Fu H, Jagu S, Kemp CJ, Kim W, Kuo CJ, McManus M, B Mills G, Mo X, Sahni N, Schreiber SL, Talamas JA, Tamayo P, Tyner JW, Wagner BK, Weiss WA, Gerhard DS; Cancer Target Discovery and Development Network. An expanded universe of cancer targets. Cell. 2021 Mar 4;184(5):1142-1155. doi: 10.1016/j.cell.2021.02.020. PMID: 33667368

156. Broyde J, Simpson DR, Murray D, Paull EO, Chu BW, Tagore S, Jones SJ, Griffin AT, Giorgi FM, Lachmann A, Jackson P, Sweet-Cordero EA, Honig B, Califano A. Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. Nat Biotechnol. 2021 Feb;39(2):215-224. doi: 10.1038/s41587-020-0652-7. Epub 2020 Sep 14. PMID: 32929263

155. Paull EO, Aytes A, Jones SJ, Subramaniam PS, Giorgi FM, Douglass EF, Tagore S, Chu B, Vasciaveo A, Zheng S, Verhaak R, Abate-Shen C, Alvarez MJ, Califano A. A modular master regulator landscape controls cancer transcriptional identity. Cell. 2021 Jan 21;184(2):334-351.e20. doi: 10.1016/j.cell.2020.11.045. Epub 2021 Jan 11. PMID: 33434495

2020

154. Rosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Syst. 2020 Dec 16;11(6):589-607.e8. doi: 10.1016/j.cels.2020.11.006. PMID: 33333029

153. Arumugam K, Shin W, Schiavone V, Vlahos L, Tu X, Carnevali D, Kesner J, Paull EO, Romo N, Subramaniam P, Worley J, Tan X, Califano A, Cosma MP. The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State. Cell Rep. 2020 Dec 8;33(10):108474. doi: 10.1016/j.celrep.2020.108474. PMID: 33296649

152. Pan H, Xue C, Auerbach BJ, Fan J, Bashore AC, Cui J, Yang DY, Trignano SB, Liu W, Shi J, Ihuegbu CO, Bush EC, Worley J, Vlahos L, Laise P, Solomon RA, Connolly ES, Califano A, Sims PA, Zhang H, Li M, Reilly MP. Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human. Circulation. 2020 Nov 24;142(21):2060-2075. doi: 10.1161/CIRCULATIONAHA.120.048378. Epub 2020 Sep 23. PMID: 32962412

151. Mishra V, Re DB, Le Verche V, Alvarez MJ, Vasciaveo A, Jacquier A, Doulias PT, Greco TM, Nizzardo M, Papadimitriou D, Nagata T, Rinchetti P, Perez-Torres EJ, Politi KA, Ikiz B, Clare K, Than ME, Corti S, Ischiropoulos H, Lotti F, Califano A, Przedborski S. Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow. Nat Commun. 2020 Nov 4;11(1):5579. doi: 10.1038/s41467-020-19177-y. PMID: 33149111

150. Vaubel RA, Tian S, Remonde D, Schroeder MA, Mladek AC, Kitange GJ, Caron A, Kollmeyer TM, Grove R, Peng S, Carlson BL, Ma DJ, Sarkar G, Evers L, Decker PA, Yan H, Dhruv HD, Berens ME, Wang Q, Marin BM, Klee EW, Califano A, LaChance DH, Eckel-Passow JE, Verhaak RG, Sulman EP, Burns TC, Meyer FB, O'Neill BP, Tran NL, Giannini C, Jenkins RB, Parney IF, Sarkaria JN. Genomic and phenotypic characterization of a broad panel of patient-derived xenografts reflects the diversity of glioblastoma. Clin Cancer Res. 2020 Mar 1;26(5):1094-1104. doi: 10.1158/1078-0432.CCR-19-0909. Epub 2019 Dec 18. PMID: 31852831

149. Öberg K, Califano A, Strosberg JR, Ma S, Pape U, Bodei L, Kaltsas G, Toumpanakis C, Goldenring JR, Frilling A, Paulson S. A meta-analysis of the accuracy of a neuroendocrine tumor mRNA genomic biomarker (NETest) in blood. Ann Oncol. 2020 Feb;31(2):202-212. doi: 10.1016/j.annonc.2019.11.003. Epub 2019 Dec 20. PMID: 31959337

2019

148. 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. Epub 2019 Jun 13. PMID: 31197017

147. Echeverria GV, Ge Z, Seth S, Zhang X, Jeter-Jones S, Zhou X, Cai S, Tu Y, McCoy A, Peoples M, Sun Y, Qiu H, Chang Q, Bristow C, Carugo A, Shao J, Ma X, Harris A, Mundi P, Lau R, Ramamoorthy V, Wu Y, Alvarez MJ, Califano A, Moulder SL, Symmans WF, Marszalek JR, Heffernan TP, Chang JT, Piwnica-Worms H. Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state. Sci Transl Med. 2019 Apr 17;11(488). pii: eaav0936. doi: 10.1126/scitranslmed.aav0936. PMID: 30996079

146. Slotkin EK, Diolaiti D, Shukla NN, Dela Cruz FS, Clark JJ, Gundem G, Yellapantula VD, Levine MF, You D, Ma P, Pachhal S, Ibanez Sanchez G, Benayed R, Jungbluth AA, Smyth LM, Mauguen A, Gushterova I, Ding H, Spraggon L, Darnell R, Califano A, Ladanyi M, Papaemmanuil E, Kung AL, Hyman DM, Roberts SS. Patient-Driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion-Driven Cancer. Cancer Discov. 2019 May;9(5):605-616. doi: 10.1158/2159-8290.CD-18-0953. Epub 2019 Mar 15. PMID: 30877085

145. 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. Epub 2019 Jan 18. PMID: 30658994

2018

144. 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. PMID: 30518758

143. 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. PMID: 30232459

142. 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. Epub 2018 Jun 18. PMID: 29915428

141. 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. 29684207

140. 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, 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 CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L. 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. PMID: 29628290

139. 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 J, Kahn 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. Epub 2018 Mar 6. PMID: 29510988

138. Ding H, Douglass Jr. EF, 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. PMID: 29662057

137. 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. PMID: 29625070

2017

136. Chen X, Deng H, Churchill MJ, Luchsinger LL, Du X, Chu TH, Friedman RA, Middelhoff M, Ding H, Tailor YH, Wang ALE, Liu H, Niu Z, Wang H, Jiang Z, Renders S, Ho SH, Shah SV, Tishchenko P, Chang W, Swayne TC, Munteanu L, Califano A, Takahashi R, Nagar KK, Renz BW, Worthley DL, Westphalen CB, Hayakawa Y, Asfaha S, Borot F, Lin CS, Snoeck HW, Mukherjee S, Wang TC. Bone Marrow Myeloid Cells Regulate Myeloid-Biased Hematopoietic Stem Cells via a Histamine-Dependent Feedback Loop. Cell Stem Cell. 2017 Dec 7;21(6):747-760.e7. doi: 10.1016/j.stem.2017.11.003. Epub 2017 Nov 30. PMID: 29198940

135. Walsh LA, Alvarez MJ, Sabio EY, Reyngold M, Makarov V, Mukherjee S, Lee KW, Desrichard A, Turcan Ş, Dalin MG, Rajasekhar VK, Chen S, Vahdat LT, Califano A, Chan TA. An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis. Cell Rep. 2017 Aug 15;20(7):1623-1640. doi: 10.1016/j.celrep.2017.07.052. PMID: 28813674

134. 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. Bush EC, Ray F, Alvarez MJ, Realubit R, Li H, Karan C, Califano A, Sims PA. Nat Commun. 2017 Jul 24;8(1):105. doi: 10.1038/s41467-017-00136-z. PMID: 28740083

133. 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. Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer. Cancer Discov. 2017 Jul;7(7):736-749. doi: 10.1158/2159-8290.CD-16-1174. Epub 2017 Apr 14. PMID: 28411207

132. Talos F, Mitrofanova A, Bergren SK, Califano A, Shen MM. A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue. Nat Commun. 2017 Apr 21;8:14662. doi: 10.1038/ncomms14662. PMID: 28429718

131. Udyavar AR, Wooten DJ, Hoeksema M, Bansal M, Califano A, Estrada L, Schnell S, Irish JM, Massion PP, Quaranta V. Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity. Cancer Res. 2017 Mar 1;77(5):1063-1074. doi: 10.1158/0008-5472.CAN-16-1467. Epub 2016 Dec 8. PMID: 27932399

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. Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):2006-2011. doi: 10.1073/pnas.1611831114. Epub 2017 Feb 7. PMID: 28174276

129. Califano A, Alvarez MJ. The recurrent architecture of tumour initiation, progression and drug sensitivity. Nat Rev Cancer. 2017 Feb;17(2):116-130. doi: 10.1038/nrc.2016.124. Epub 2016 Dec 15. PMID: 27977008

128. Aksoy BA, Dancík V, Smith K, Mazerik JN, Ji Z, Gross B, Nikolova O, Jaber N, Califano A, Schreiber SL, Gerhard DS, Hermida LC, Jagu S, Sander C, Floratos A, Clemons PA. CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. Database (Oxford). 2017 Jan 1;2017:bax054.doi: 10.1093/database/bax054. PMID: 29220450

2016

127. Califano A, Alvarez, MJ. The recurrent architecture of tumour initiation, progression and drug sensitivity. Nature Reviews Cancer. 2016 Dec 15. doi:10.1038/nrc.2016.124. 

126. Dutta A, Le Magnen C, Mitrofanova A, Ouyang X, Califano A, Abate-Shen C. Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation. Science. 2016 Jun 24;352(6293):1576-80. 

125. Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat Genet. 2016 Jun 20.

124. Lachmann A, Giorgi FM, Alvarez MJ, Califano A. Detection and removal of spatial bias in multiwell assays. Bioinformatics. 2016 Jul 1;32(13):1959-65. 

123. Lachmann A, Giorgi FM, Lopez G, Califano A. ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information. Bioinformatics. 2016 Jul 15;32(14):2233-5. 

122. Kushwaha R, Jagadish N, Kustagi M, Mendiratta G, Seandel M, Soni R, Korkola JE, Thodima V, Califano A, Bosl GJ, Chaganti RS. Mechanism and Role of SOX2 Repression in Seminoma: Relevance to Human Germline Specification. Stem Cell Reports. 2016 May 10;6(5):772-83.

121. Westphalen CB, Takemoto Y, Tanaka T, Macchini M, Jiang Z, Renz BW, Chen X, Ormanns S, Nagar K, Tailor Y, May R, Cho Y, Asfaha S, Worthley DL, Hayakawa Y, Urbanska AM, Quante M, Reichert M, Broyde J, Subramaniam PS, Remotti H, Su GH, Rustgi AK, Friedman RA, Honig B, Califano A, Houchen CW, Olive KP, Wang TC. Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis. Cell Stem Cell. 2016 Apr 7;18(4):441-55.

120. Sepulveda JL, Gutierrez-Pajares JL, Luna A, Yao Y, Tobias JW, Thomas S, Woo Y, Giorgi F, Komissarova EV, Califano A, Wang TC, Sepulveda AR. High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing. Mod Pathol. 2016 Feb;29(2):182-93. 

119. Yu J, Silva J, Califano A. ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. Bioinformatics. 2016 Jan 15;32(2):260-7. 

118. Lee SB, Frattini V, Bansal M, Castano AM, Sherman D, Hutchinson K, Bruce JN, Califano A, Liu G, Cardozo T, Iavarone A, Lasorella A. An ID2-dependent mechanism for VHL inactivation in cancer. Nature. 2016 Jan 14;529(7585):172-7. 

2015

117. Alvarez MJ, Chen JC, Califano A. DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. Bioinformatics. 2015 Dec 15;31(24):4032-4. 

116. Putcha P, Yu J, Rodriguez-Barrueco R, Saucedo-Cuevas L, Villagrasa P, Murga-Penas E, Quayle SN, Yang M, Castro V, Llobet-Navas D, Birnbaum D, Finetti P, Woodward WA, Bertucci F, Alpaugh ML, Califano A, Silva J. HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers. Breast Cancer Res. 2015 Dec 8;17(1):149. 

115. Bisikirska B, Bansal M, Shen Y, Teruya-Feldstein J, Chaganti R, Califano A. Elucidation and Pharmacological Targeting of Novel Molecular Drivers of Follicular Lymphoma Progression. Cancer Res. 2015 Nov 20. [Epub ahead of print]

114. Mitrofanova A, Aytes A, Zou M, Shen MM, Abate-Shen C, Califano A. Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models. Cell Rep. 2015 Sep 29;12(12):2060-71. 

113. Brichta L, Shin W, Jackson-Lewis V, Blesa J, Yap EL, Walker Z, Zhang J, Roussarie JP, Alvarez MJ, Califano A, Przedborski S, Greengard P. Identification of neurodegenerative factors using translatome-regulatory network analysis. Nat Neurosci. 2015 Sep;18(9):1325-33. 

112. Alizadeh AA, Aranda V, Bardelli A, Blanpain C, Bock C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M, Esteller M, Fitzgerald R, Korbel JO, Lichter P, Mason CE, Navin N, Pe'er D, Polyak K, Roberts CW, Siu L, Snyder A, Stower H, Swanton C, Verhaak RG, Zenklusen JC, Zuber J, Zucman-Rossi J. Toward understanding and exploiting tumor heterogeneity. Nat Med. 2015 Aug;21(8):846-53. 

111. 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 Aug 1;29(15):1631-48. 

110. Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A. Elucidating Compound Mechanism of Action by Network Perturbation Analysis. Cell. 2015 Jul 16;162(2):441-51. 

109. Ikiz B, Alvarez MJ, Ré DB, Le Verche V, Politi K, Lotti F, Phani S, Pradhan R, Yu C, Croft GF, Jacquier A, Henderson CE, Califano A, Przedborski S. The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis. Cell Rep. 2015 Jul 14;12(2):335-45. 

108 Nicoletti P, Bansal M, Lefebvre C, Guarnieri P, Shen Y, Pe'er I, Califano A, Floratos A. ABC transporters and the proteasome complex are implicated in susceptibility to Stevens-Johnson syndrome and toxic epidermal necrolysis across multiple drugs. PLoS One. 2015 Jun 25;10(6):e0131038. 

107. Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B. The Cyni framework for network inference in Cytoscape. Bioinformatics. 2015 May 1;31(9):1499-501. 

106. Aubry S, Shin W, Crary JF, Lefort R, Qureshi YH, Lefebvre C, Califano A, Shelanski ML. Assembly and interrogation of Alzheimer's disease genetic networks reveal novel regulators of progression. PLoS One. 2015 Mar 17;10(3):e0120352. 

105. Chiu HS, Llobet-Navas D, Yang X, Chung WJ, Ambesi-Impiombato A, Iyer A, Kim HR, Seviour EG, Luo Z, Sehgal V, Moss T, Lu Y, Ram P, Silva J, Mills GB, Califano A, Sumazin P. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Res. 2015 Feb;25(2):257-67. 

104. Repunte-Canonigo V, Shin W, Vendruscolo LF, Lefebvre C, van der Stap L, Kawamura T, Schlosburg JE, Alvarez M, Koob GF, Califano A, Sanna PP. Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks. Genome Biol. 2015 Feb 2;16:68. 

103. Shelanski M, Shin W, Aubry S, Sims P, Alvarez MJ, Califano A. A systems approach to drug discovery in Alzheimer's disease. Neurotherapeutics. 2015 Jan;12(1):126-31. 

2014

102. Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y; NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A; NCI-DREAM Community. A community computational challenge to predict the activity of pairs of compounds. Nat Biotechnol. 2014 Dec;32(12):1213-22. 

101. Califano A. Predicting protein networks in cancer. Nat Genet. 2014 Dec;46(12):1252-3. 

100. Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. A community effort to assess and improve drug sensitivity prediction algorithms. Nat Biotechnol. 2014 Dec;32(12):1202-12. 

99. Giorgi FM, Lopez G, Woo JH, Bisikirska B, Califano A, Bansal M. Inferring protein modulation from gene expression data using conditional mutual information. PLoS One. 2014 Oct 14;9(10):e109569. 

98. 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 Oct 9;159(2):402-14. 

97. Sonabend AM, Carminucci AS, Amendolara B, Bansal M, Leung R, Lei L, Realubit R, Li H, Karan C, Yun J, Showers C, Rothcock R, O J, Califano A, Canoll P, Bruce JN. Convection-enhanced delivery of etoposide is effective against murine proneural glioblastoma. Neuro Oncol. 2014 Sep;16(9):1210-9. 

96. 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 May 12;25(5):638-51. 

95. Califano A, Kellis M, Stolovitzky G. RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue. J Comput Biol. 2014 May;21(5):371-2. 

94. Llobet-Navas D, Rodríguez-Barrueco R, Castro V, Ugalde AP, Sumazin P, Jacob-Sendler D, Demircan B, Castillo-Martín M, Putcha P, Marshall N, Villagrasa P, Chan J, Sanchez-Garcia F, Pe'er D, Rabadán R, Iavarone A, Cordón-Cardó C, Califano A, López-Otín C, Ezhkova E, Silva JM. The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes Dev. 2014 Apr 1;28(7):765-82. 

93. Sonabend AM, Bansal M, Guarnieri P, Lei L, Amendolara B, Soderquist C, Leung R, Yun J, Kennedy B, Sisti J, Bruce S, Bruce R, Shakya R, Ludwig T, Rosenfeld S, Sims PA, Bruce JN, Califano A, Canoll P. The transcriptional regulatory network of proneural glioma determines the genetic alterations selected during tumor progression. Cancer Res. 2014 Mar 1;74(5):1440-51. 

92. Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RG, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG. ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Rep. 2014 Jan 30;6(2):313-24. 

2013

91. 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 Dec 9;24(6):766-76. doi: 10.1016/j.ccr.2013.10.022. Epub 2013 Nov 27.

90. Bisikirska BC, Adam SJ, Alvarez MJ, Rajbhandari P, Cox R, Lefebvre C, Wang K, Rieckhof GE, Felsher DW, Califano A. STK38 is a critical upstream regulator of MYC's oncogenic activity in human B-cell lymphoma. Oncogene. 2013 Nov 7;32(45):5283-91.

89. Ying CY, Dominguez-Sola D, Fabi M, Lorenz IC, Hussein S, Bansal M, Califano A, Pasqualucci L, Basso K, Dalla-Favera R. MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma. Nat Immunol. 2013 Oct;14(10):1084-92. 

88. Irshad S, Bansal M, Castillo-Martin M, Zheng T, Aytes A, Wenske S, Le Magnen C, Guarnieri P, Sumazin P, Benson MC, Shen MM, Califano A, Abate-Shen C. A molecular signature predictive of indolent prostate cancer. Sci Transl Med. 2013 Sep 11;5(202):202ra122. 

87. Aytes A, Mitrofanova A, Kinkade CW, Lefebvre C, Lei M, Phelan V, LeKaye HC, Koutcher JA, Cardiff RD, Califano A, Shen MM, Abate-Shen C. ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer. Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):E3506-15. 

86. Jang IS, Margolin A, Califano A. hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests. Interface Focus. 2013 Aug 6;3(4):20130011. 

85. Chen J, Repunte-Canonigo V, Kawamura T, Lefebvre C, Shin W, Howell LL, Hemby SE, Harvey BK, Califano A, Morales M, Koob GF, Sanna PP. Hypothalamic proteoglycan syndecan-3 is a novel cocaine addiction resilience factor. Nat Commun. 2013;4:1955. 

84. Califano A, Kellis M, Stolovitzky G. Preface: RECOMB systems biology, regulatory genomics, and DREAM 2012 special issue. J Comput Biol. 2013 May;20(5):373-4. 

83. Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA. Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol. 2013;9(5):e1003047. 

82. Keniry M, Pires MM, Mense S, Lefebvre C, Gan B, Justiano K, Lau YK, Hopkins B, Hodakoski C, Koujak S, Toole J, Fenton F, Calahan A, Califano A, DePinho RA, Maurer M, Parsons R. Survival factor NFIL3 restricts FOXO-induced gene expression in cancer. Genes Dev. 2013 Apr 15;27(8):916-27. 

81. Wang ZA, Mitrofanova A, Bergren SK, Abate-Shen C, Cardiff RD, Califano A, Shen MM. Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity. Nat Cell Biol. 2013 Mar;15(3):274-83. 

80. Yu J, Putcha P, Califano A, Silva JM. Pooled shRNA screenings: computational analysis. Methods Mol Biol. 2013;980:371-84. 

79. Maute RL, Schneider C, Sumazin P, Holmes A, Califano A, Basso K, Dalla-Favera R. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1404-9.

78. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. 2012 Oct 25;490(7421):556-60. Erratum in: Nature. 2013 Mar 7;495(7439):127.

2012

77. Wang J, Kobayashi T, Floc'h N, Kinkade CW, Aytes A, Dankort D, Lefebvre C, Mitrofanova A, Cardiff RD, McMahon M, Califano A, Shen MM, Abate-Shen C. B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer. Cancer Res. 2012 Sep 15;72(18):4765-76. 

76. Floc'h N, Kinkade CW, Kobayashi T, Aytes A, Lefebvre C, Mitrofanova A, Cardiff RD, Califano A, Shen MM, Abate-Shen C. Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model. Cancer Res. 2012 Sep 1;72(17):4483-93. 

75. Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet. 2012 Jul 27;44(8):841-7. 

74. Lefebvre C, Rieckhof G, Califano A. Reverse-engineering human regulatory networks. Wiley Interdiscip Rev Syst Biol Med. 2012 Jul-Aug;4(4):311-25. 

73. Floratos A, Honig B, Pe'er D, Califano A. Using systems and structure biology tools to dissect cellular phenotypes. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):171-5. 

72. 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 Feb 26;18(3):436-40. 

71. Martínez MR, Corradin A, Klein U, Álvarez MJ, Toffolo GM, di Camillo B, Califano A, Stolovitzky GA. Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis. Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2672-7. 

70. Califano A, Kellis M, Stolovitzky G. Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue. J Comput Biol. 2012 Feb;19(2):101. 

69. Bansal M, Califano A. Genome-wide dissection of posttranscriptional and posttranslational interactions. Methods Mol Biol. 2012;786:131-49. 

2011

68. Basso K, Mussolin L, Lettieri A, Brahmachary M, Lim WK, Califano A, Basso G, Biondi A, Cazzaniga G, Rosolen A. T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses. Genes Chromosomes Cancer. 2011 Dec;50(12):1063-75. 

67. 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 Oct 14;147(2):370-81. 

66. Califano A. Striking a balance between feasible and realistic biological models. Sci Transl Med. 2011 Oct 5;3(103):103ps39. 

65. Kruithof-de Julio M, Alvarez MJ, Galli A, Chu J, Price SM, Califano A, Shen MM. Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling. Development. 2011 Sep;138(18):3885-95. 

64. Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G. Verification of systems biology research in the age of collaborative competition. Nat Biotechnol. 2011 Sep 8;29(9):811-5.

63. Piccaluga PP, De Falco G, Kustagi M, Gazzola A, Agostinelli C, Tripodo C, Leucci E, Onnis A, Astolfi A, Sapienza MR, Bellan C, Lazzi S, Tumwine L, Mawanda M, Ogwang M, Calbi V, Formica S, Califano A, Pileri SA, Leoncini L. Gene expression analysis uncovers similarity and differences among Burkitt lymphoma subtypes. Blood. 2011 Mar 31;117(13):3596-608.

62. Kellis M, Califano A, Bar-Joseph Z. Preface: RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 special issue. J Comput Biol. 2011 Feb;18(2):131.

61. Califano A. Rewiring makes the difference. Mol Syst Biol. 2011 Jan 18;7:463.

2010

60. De Keersmaecker K, Real PJ, Gatta GD, Palomero T, Sulis ML, Tosello V, Van Vlierberghe P, Barnes K, Castillo M, Sole X, Hadler M, Lenz J, Aplan PD, Kelliher M, Kee BL, Pandolfi PP, Kappes D, Gounari F, Petrie H, Van der Meulen J, Speleman F, Paietta E, Racevskis J, Wiernik PH, Rowe JM, Soulier J, Avran D, Cavé H, Dastugue N, Raimondi S, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA. The TLX1 oncogene drives aneuploidy in T cell transformation. Nat Med. 2010 Nov;16(11):1321-7. 

59. Cancer Target Discovery and Development Network, Schreiber SL, Shamji AF, Clemons PA, Hon C, Koehler AN, Munoz B, Palmer M, Stern AM, Wagner BK, Powers S, Lowe SW, Guo X, Krasnitz A, Sawey ET, Sordella R, Stein L, Trotman LC, Califano A, Dalla-Favera R, Ferrando A, Iavarone A, Pasqualucci L, Silva J, Stockwell BR, Hahn WC, Chin L, DePinho RA, Boehm JS, Gopal S, Huang A, Root DE, Weir BA, Gerhard DS, Zenklusen JC, Roth MG, White MA, Minna JD, MacMillan JB, Posner BA. Towards patient-based cancer therapeutics. Nat Biotechnol. 2010 Sep;28(9):904-6. 

58. Floratos A, Smith K, Ji Z, Watkinson J, Califano A. geWorkbench: an open source platform for integrative genomics. Bioinformatics. 2010 Jul 15;26(14):1779-80. 

57. 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 Jun 8;6:377. 

56. Cadeiras M, von Bayern M, Sinha A, Shahzad K, Latif F, Lim WK, Grenett H, Tabak E, Klingler T, Califano A, Deng MC. Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation. J Cell Mol Med. 2011 Apr;15(4):949-56. 

55. Zhou X, Sumazin P, Rajbhandari P, Califano A. A systems biology approach to transcription factor binding site prediction. PLoS One. 2010 Mar 26;5(3):e9878. 

54. Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim WK, Kitagawa Y, Schneider C, Alvarez MJ, Califano A, Dalla-Favera R. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood. 2010 Feb 4;115(5):975-84. 

53. Klein U, Lia M, Crespo M, Siegel R, Shen Q, Mo T, Ambesi-Impiombato A, Califano A, Migliazza A, Bhagat G, Dalla-Favera R. The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell. 2010 Jan 19;17(1):28-40. 

52. 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 Jan 21;463(7279):318-25. 

2009

51. Alvarez MJ, Sumazin P, Rajbhandari P, Califano A. Correlating measurements across samples improves accuracy of large-scale expression profile experiments. Genome Biol. 2009;10(12):R143. 

50. 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 Sep;27(9):829-39. 

49. Zhao X, D' Arca D, Lim WK, Brahmachary M, Carro MS, Ludwig T, Cardo CC, Guillemot F, Aldape K, Califano A, Iavarone A, Lasorella A. The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell. 2009 Aug;17(2):210-21. 

48. Saito M, Novak U, Piovan E, Basso K, Sumazin P, Schneider C, Crespo M, Shen Q, Bhagat G, Califano A, Chadburn A, Pasqualucci L, Dalla-Favera R. BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11294-9. 

47. Compagno M, Lim WK, Grunn A, Nandula SV, Brahmachary M, Shen Q, Bertoni F, Ponzoni M, Scandurra M, Califano A, Bhagat G, Chadburn A, Dalla-Favera R, Pasqualucci L. Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature. 2009 Jun 4;459(7247):717-21. 

46. Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J Jr, Chen CZ, Califano A, Dalla-Favera R. Identification of the human mature B cell miRNome. Immunity. 2009 May;30(5):744-52. 

45. Strasser B, Alvarez MJ, Califano A, Cerdán PD. A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature. Plant J. 2009 May;58(4):629-40.

44. Lim WK, Lyashenko E, Califano A. Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput. 2009:504-15.

43. Wang K, Alvarez MJ, Bisikirska BC, Linding R, Basso K, Dalla Favera R, Califano A. Dissecting the interface between signaling and transcriptional regulation in human B cells. Pac Symp Biocomput. 2009:264-75.

42. Shortliffe EH, Califano A, Hunter L. New JBI emphasis on translational bioinformatics. J Biomed Inform. 2009 Apr;42(2):199-200.

41. Stolovitzky G, Prill RJ, Califano A. Lessons from the DREAM2 Challenges. Ann N Y Acad Sci. 2009 Mar;1158:159-95.

40. Stolovitzky G, Kahlem P, Califano A. The challenges of systems biology. Preface. Ann N Y Acad Sci. 2009 Mar;1158:ix-xii. 

39. Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol. 2009 Feb;3(1):9-17.

38. Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G. ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):244-9. 

2008

37. Cadeiras M, Burke E, Dedrick R, Gangadin A, Latif F, Shahzad K, Sinha A, Tabak EG, Marboe CC, Califano AC, Deng MC. Gene expression profiles of patients with antibody-mediated rejection after cardiac transplantation. J Heart Lung Transplant. 2008 Aug;27(8):932-4. 

36. Piccaluga PP, Califano A, Klein U, Agostinelli C, Bellosillo B, Gimeno E, Serrano S, Solè F, Zang Y, Falini B, Zinzani PL, Pileri SA. Gene expression analysis provides a potential rationale for revising the histological grading of follicular lymphomas. Haematologica. 2008 Jul;93(7):1033-8. 

35. Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW. iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One. 2008 May 28;3(5):e2265.

34. Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A. A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol. 2008;4:169.

2007 

33. Li Z, Zheng T, Califano A, Floratos A. Pattern-based mining strategy to detect multi-locus association and gene x environment interaction. BMC Proc. 2007;1 Suppl 1:S16.

32. Margolin AA, Califano A. Theory and limitations of genetic network inference from microarray data. Ann N Y Acad Sci. 2007 Dec;1115:51-72.

31. Stolovitzky G, Monroe D, Califano A. Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference. Ann N Y Acad Sci. 2007 Dec;1115:1-22.

30. Piccaluga PP, Agostinelli C, Califano A, Carbone A, Fantoni L, Ferrari S, Gazzola A, Gloghini A, Righi S, Rossi M, Tagliafico E, Zinzani PL, Zupo S, Baccarani M, Pileri SA. Gene expression analysis of angioimmunoblastic lymphoma indicates derivation from T follicular helper cells and vascular endothelial growth factor deregulation. Cancer Res. 2007 Nov 15;67(22):10703-10. 

29. Lim WK, Wang K, Lefebvre C, Califano A. Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics. 2007 Jul 1;23(13):i282-8.

28. Sosinsky A, Honig B, Mann RS, Califano A. Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6305-10. 

27. Piccaluga PP, Agostinelli C, Califano A, Rossi M, Basso K, Zupo S, Went P, Klein U, Zinzani PL, Baccarani M, Dalla Favera R, Pileri SA. Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets. J Clin Invest. 2007 Mar;117(3):823-34.

2006

26. Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A. Reverse engineering cellular networks. Nat Protoc. 2006;1(2):662-71.

25. Palomero T, Lim WK, Odom DT, Sulis ML, Real PJ, Margolin A, Barnes KC, O'Neil J, Neuberg D, Weng AP, Aster JC, Sigaux F, Soulier J, Look AT, Young RA, Califano A, Ferrando AA. NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18261-6. 

24. Banerjee N. and Califano A. Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps. 2006. 4th RECOMB Comparative Genomics Satellite Worshop, Montreal (CA).

23. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7.

2005 and before

22. Poppema S, Kluiver JL, Atayar C, van den Berg A, Rosenwald A, Hummel M, Lenze D, Lammert H, Stein H, Joos S, Barth T, Dyer M, Lichter P, Klein U, Cattoretti G, Gloghini A, Tu Y, Stolovitzky GA, Califano A, Carbone A, Dalla-Favera R, Melzner I, Bucur AJ, Brüderlein S, Dorsch K, Hasel C, Barth TF, Leithäuser F, Möller P. Report: workshop on mediastinal grey zone lymphoma. Eur J Haematol Suppl. 2005 Jul;(66):45-52.

21. 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 Apr;37(4):382-90. 

20. Wang K, Banerjee N, Margolin AA, Nemenman I, Califano A. Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes. In: Research in Computational Molecular Biology. Lecture Notes in Computer Science 2005;3909;348-362.

19. Basso K, Klein U, Niu H, Stolovitzky GA, Tu Y, Califano A, Cattoretti G, Dalla-Favera R. Tracking CD40 signaling during germinal center development. Blood. 2004 Dec 15;104(13):4088-96. 

18. Basso K, Liso A, Tiacci E, Benedetti R, Pulsoni A, Foa R, Di Raimondo F, Ambrosetti A, Califano A, Klein U, Dalla Favera R, Falini B. Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of chemokine and adhesion receptors. J Exp Med. 2004 Jan 5;199(1):59-68.

17. Liu AH, Califano A. CASTOR: clustering algorithm for sequence taxonomical organization and relationships. J Comput Biol. 2003;10(1):21-45.

16. Liu AH, Zhang X, Stolovitzky GA, Califano A, Firestein SJ. Motif-based construction of a functional map for mammalian olfactory receptors. Genomics. 2003 May;81(5):443-56.

15. Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad J Jr, Miljkovic V, Cattoretti G, Califano A, Dalla-Favera R. Gene expression dynamics during germinal center transit in B cells. Ann N Y Acad Sci. 2003 Apr;987:166-72. 

14. Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad J Jr, Miljkovic V, Cattoretti G, Califano A, Dalla-Favera R. Transcriptional analysis of the B cell germinal center reaction. Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2639-44. 

13. Küppers R, Klein U, Schwering I, Distler V, Bräuninger A, Cattoretti G, Tu Y, Stolovitzky GA, Califano A, Hansmann ML, Dalla-Favera R. Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling. J Clin Invest. 2003 Feb;111(4):529-37.

12. Buchanan A, Califano A, Kahn J, McPherson E, Robertson J, Brody B. Pharmacogenetics: ethical issues and policy options. Kennedy Inst Ethics J. 2002 Mar;12(1):1-15.

11. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, Biegel JA, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G, Louis DN, Mesirov JP, Lander ES, Golub TR. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. 2002 Jan 24;415(6870):436-42.

10. Klein U, Tu Y, Stolovitzky GA, Mattioli M, Cattoretti G, Husson H, Freedman A, Inghirami G, Cro L, Baldini L, Neri A, Califano A, Dalla-Favera R. Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells. J Exp Med. 2001 Dec 3;194(11):1625-38.

9. Califano A. Advances in sequence analysis. Curr Opin Struct Biol. 2001 Jun;11(3):330-3.

8. Liu A, Califano A. Functional classification of Proteins by pattern discovery and top-down clustering of primary sequences. IBM Systems Journal, special issue on Deep Computing for the Life Sciences. 2001;40(2):379-393.

7. Hart RK, Royyuru AK, Stolovitzky G, Califano A. Systematic and fully automated identification of protein sequence patterns. J Comput Biol. 2000;7(3-4):585-600.

6. Califano A, Stolovitzky G, Tu Y. Analysis of gene expression microarrays for phenotype classification. Proc Int Conf Intell Syst Mol Biol. 2000;8:75-85.

5. Califano A. SPLASH: structural pattern localization analysis by sequential histograms.  Bioinformatics. 2000 Apr;16(4):341-57.

4. Califano A, Germain B, Colville S. A High-Dimensional Indexing Scheme for Scalable Fingerprint-Based Identification. Lecture Notes in Computer Science. 1997;1351:32-39.

3. Germain RS, Califano A, Colville S. Fingerprint Matching Using Transformation Parameter Clustering. IEEE J Comp Sci Eng. 1997 4(4):42-49.

2. Califano A, Kjeldsen R, Bolle RM. Data- and model-driven multiresolution processing. Comp Vision Image Und. 1996;63(1):27-49.

1. Califano A, Rigoutsos I. FLASH: a fast look-up algorithm for string homology. Proc Int Conf Intell Syst Mol Biol. 1993;1:56-64.