| Year |
Citation |
Score |
| 2023 |
Stokes ME, Vasciaveo A, Small JC, Zask A, Reznik E, Smith N, Wang Q, Daniels J, Forouhar F, Rajbhandari P, Califano A, Stockwell BR. Subtype-selective prenylated isoflavonoids disrupt regulatory drivers of MYCN-amplified cancers. Cell Chemical Biology. PMID 38061356 DOI: 10.1016/j.chembiol.2023.11.007 |
0.325 |
|
| 2023 |
Hu LZ, Douglass E, Turunen M, Pampou S, Grunn A, Realubit R, Antolin AA, Wang ALE, Li H, Subramaniam P, Karan C, Alvarez M, Califano A. Elucidating Compound Mechanism of Action and Polypharmacology with a Large-scale Perturbational Profile Compendium. Biorxiv : the Preprint Server For Biology. PMID 37873470 DOI: 10.1101/2023.10.08.561457 |
0.79 |
|
| 2023 |
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, ... ... Califano A, et al. A transcriptome-based precision oncology platform for patient-therapy alignment in a diverse set of treatment resistant malignancies. Cancer Discovery. PMID 37061969 DOI: 10.1158/2159-8290.CD-22-1020 |
0.79 |
|
| 2023 |
Maurer HC, Curiel-Garcia A, Holmstrom S, Laise P, Palermo CF, Sastra SA, Andren A, Li Z, LeLarge T, Sagalovskiy I, Ross DR, Rosario V, Lu K, Ferraiuolo E, Spinosa N, ... ... Califano A, et al. Ras-dependent activation of BMAL2 regulates hypoxic metabolism in pancreatic cancer. Biorxiv : the Preprint Server For Biology. PMID 36993718 DOI: 10.1101/2023.03.19.533333 |
0.308 |
|
| 2023 |
Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis. Biorxiv : the Preprint Server For Biology. PMID 36824919 DOI: 10.1101/2023.02.15.528736 |
0.306 |
|
| 2022 |
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, ... ... Califano A, et al. Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer. Nature Cancer. PMID 36585452 DOI: 10.1038/s43018-022-00489-5 |
0.634 |
|
| 2022 |
Vasciaveo A, Arriaga JM, Nunes de Almeida F, 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, ... ... Califano A, et al. OncoLoop: A network-based precision cancer medicine framework. Cancer Discovery. PMID 36374194 DOI: 10.1158/2159-8290.CD-22-0342 |
0.791 |
|
| 2022 |
Laise P, Bosker G, Califano A, Alvarez MJ. A Patient-to-Model-to-Patient (PMP) Cancer Drug Discovery Protocol for Identifying and Validating Therapeutic Agents Targeting Tumor Regulatory Architecture. Current Protocols. 2: e544. PMID 36083100 DOI: 10.1002/cpz1.544 |
0.32 |
|
| 2022 |
Douglass EF, 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, ... ... Califano A, et al. A community challenge for a pancancer drug mechanism of action inference from perturbational profile data. Cell Reports. Medicine. 3: 100492. PMID 35106508 DOI: 10.1016/j.xcrm.2021.100492 |
0.796 |
|
| 2021 |
Scotto L, Kinahan C, Douglass E, Deng C, Safari M, Casadei B, Marchi E, Lue JK, Montanari F, Falchi L, Qiao C, Renu N, Bates SE, Califano A, O'Connor OA. TARGETING THE T-CELL LYMPHOMA EPIGENOME INDUCES CELL DEATH, CANCER TESTES ANTIGENS, IMMUNE MODULATORY SIGNALING PATHWAYS. Molecular Cancer Therapeutics. PMID 34108263 DOI: 10.1158/1535-7163.MCT-20-0377 |
0.796 |
|
| 2021 |
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. PMID 33434495 DOI: 10.1016/j.cell.2020.11.045 |
0.808 |
|
| 2020 |
Diaz JE, Ahsen ME, Schaffter T, Chen X, Realubit RB, Karan C, Califano A, Losic B, Stolovitzky G. The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies. Elife. 9. PMID 32945258 DOI: 10.7554/Elife.52707 |
0.369 |
|
| 2020 |
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. Nature Biotechnology. PMID 32929263 DOI: 10.1038/S41587-020-0652-7 |
0.431 |
|
| 2020 |
Nguyen AP, Nicoletti P, Arnol D, Califano A, Rodríguez Martínez M. Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN. Frontiers in Bioengineering and Biotechnology. 8: 798. PMID 32850701 DOI: 10.3389/Fbioe.2020.00798 |
0.365 |
|
| 2020 |
Scotto L, Kinahan C, Casadei B, Mangone M, Douglass E, Vundavalli MV, Marchi E, Ma H, George C, Montanari F, Califano A, O'Connor OA. Generation of pralatrexate resistant T-cell lymphoma lines reveals two patterns of acquired drug resistance that is overcome with epigenetic modifiers. Genes, Chromosomes & Cancer. PMID 32614991 DOI: 10.1002/Gcc.22884 |
0.774 |
|
| 2020 |
Stokes ME, Small JC, Vasciaveo A, Shimada K, Hirschhorn T, Califano A, Stockwell BR. Mesenchymal subtype neuroblastomas are addicted to TGF-βR2/HMGCR-driven protein geranylgeranylation. Scientific Reports. 10: 10748. PMID 32612149 DOI: 10.1038/S41598-020-67310-0 |
0.402 |
|
| 2020 |
Laise P, Bosker G, Sun X, Shen Y, Douglass EF, Karan C, Realubit RB, Pampou S, Califano A, Alvarez MJ. The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States. Biorxiv : the Preprint Server For Biology. PMID 32511361 DOI: 10.1101/2020.05.12.091256 |
0.788 |
|
| 2020 |
Ortiz MV, Siddiquee A, You D, Mundi PS, Marks L, Guillan K, Diolaiti D, Aburi M, Califano A, Dela Cruz FS, Kung A. Preclinical evaluation of XPO1 inhibition in Wilms tumors. Journal of Clinical Oncology. 38: 3580-3580. DOI: 10.1200/Jco.2020.38.15_Suppl.3580 |
0.329 |
|
| 2020 |
Walker CJ, Shen Y, Mau-Sørensen M, Wen PY, Bent MJVD, Plotkin SR, Walenkamp AME, Green A, Califano A, Chang H, Henegar L, Shacham S, Alvarez MJ, Landesman Y, Lassman AB. Molecular predictors of response to selinexor in recurrent glioblastoma (GBM). Journal of Clinical Oncology. 38: 2565-2565. DOI: 10.1200/Jco.2020.38.15_Suppl.2565 |
0.321 |
|
| 2020 |
Kalinsky K, Lee S, Tiersten A, Makower DF, Cigler T, Franks L, Mundi P, Chi D, Blumberg L, Sender N, Galazyn M, Hosi K, Goel A, Klein P, Andreopoulou E, ... ... Califano A, et al. Abstract P1-19-32: Phase I/II trial of ruxolitinib in combination with trastuzumab in HER2+ metastatic breast cancer (MBC) Cancer Research. 80. DOI: 10.1158/1538-7445.Sabcs19-P1-19-32 |
0.307 |
|
| 2020 |
Califano A. Abstract IA21: Elucidating and targeting mechanisms of single-cell state maintenance: From N-of-1 to N-of-1-of-1 studies Cancer Research. 80. DOI: 10.1158/1538-7445.Camodels2020-Ia21 |
0.421 |
|
| 2020 |
Antonini C, Rosenberger G, Bianconi F, Tomassoni L, Ludovini V, Baglivo S, Calandrini S, Baldelli E, Pierobon M, Petricoin EF, Califano A. Abstract 4384: Quantitative assessment of drug combination effects in NSCLC cell lines through network-based analysis of functional protein activity Cancer Research. 80: 4384-4384. DOI: 10.1158/1538-7445.Am2020-4384 |
0.439 |
|
| 2019 |
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, ... ... Califano A, et al. Genomic and phenotypic characterization of a broad panel of patient derived xenografts reflects the diversity of glioblastoma. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 31852831 DOI: 10.1158/1078-0432.Ccr-19-0909 |
0.319 |
|
| 2019 |
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, ... ... Califano A, et al. Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts. Cancer Discovery. PMID 31197017 DOI: 10.1158/2159-8290.Cd-19-0094 |
0.365 |
|
| 2019 |
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, ... ... Califano A, et al. Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state. Science Translational Medicine. 11. PMID 30996079 DOI: 10.1126/Scitranslmed.Aav0936 |
0.354 |
|
| 2019 |
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, ... ... Califano A, et al. Patient-driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion-driven Cancer. Cancer Discovery. PMID 30877085 DOI: 10.1158/2159-8290.Cd-18-0953 |
0.393 |
|
| 2019 |
Maurer HC, 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, et al. Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes. Gut. PMID 30658994 DOI: 10.1136/Gutjnl-2018-317706 |
0.328 |
|
| 2019 |
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. 14: e0208646. PMID 30615629 DOI: 10.1371/Journal.Pone.0208646 |
0.407 |
|
| 2019 |
Chowdhury N, Obradovic A, Aggen D, Wang V, Guo X, DeCastro GJ, Ding H, Califano A, Drake CG. Abstract 1476: Decoding the immunologic landscape of human clear cell renal carcinoma Cancer Research. 79: 1476-1476. DOI: 10.1158/1538-7445.Sabcs18-1476 |
0.367 |
|
| 2019 |
Wang* V, Obradovic A, Chowdhury N, Aggen D, Bush E, Decastro GJ, Anderson CB, McKiernan JM, Ding H, Sims P, Califano A, Drake CG. MP21-01 SINGLE CELL TRANSCRIPTIONAL PROFILING OF IMMUNE POPULATIONS WITHIN RENAL CELL CARCINOMA TUMOR MICROENVIRONMENT Journal of Urology. 201. DOI: 10.1097/01.Ju.0000555529.56881.26 |
0.32 |
|
| 2018 |
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. Nature Communications. 9: 5201. PMID 30518758 DOI: 10.1038/S41467-018-07511-4 |
0.364 |
|
| 2018 |
Khatamian A, Paull EO, Califano A, Yu J. SJARACNe: a scalable software tool for gene network reverse engineering from big data. Bioinformatics (Oxford, England). PMID 30388204 DOI: 10.1093/Bioinformatics/Bty907 |
0.641 |
|
| 2018 |
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 and inflammation in prostate cancer initiation. Disease Models & Mechanisms. PMID 30266798 DOI: 10.1242/Dmm.035139 |
0.325 |
|
| 2018 |
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, et al. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nature Communications. 9: 3815. PMID 30232459 DOI: 10.1038/S41467-018-05729-W |
0.403 |
|
| 2018 |
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, ... ... Califano A, et al. A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors. Nature Genetics. PMID 29915428 DOI: 10.1038/S41588-018-0138-4 |
0.392 |
|
| 2018 |
Boboila S, Lopez G, Yu J, Banerjee D, Kadenhe-Chiweshe A, Connolly EP, Kandel JJ, Rajbhandari P, Silva JM, Califano A, Yamashiro DJ. Transcription factor activating protein 4 is synthetically lethal and a master regulator of MYCN-amplified neuroblastoma. Oncogene. PMID 29880876 DOI: 10.1038/S41388-018-0326-9 |
0.679 |
|
| 2018 |
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 Research. PMID 29684207 DOI: 10.1093/Nar/Gky286 |
0.318 |
|
| 2018 |
Ding H, Douglass 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. Nature Communications. 9: 1471. PMID 29662057 DOI: 10.1038/S41467-018-03843-3 |
0.773 |
|
| 2018 |
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, ... ... Califano A, et al. The Immune Landscape of Cancer. Immunity. PMID 29628290 DOI: 10.1016/J.Immuni.2018.03.023 |
0.384 |
|
| 2018 |
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, ... ... Califano A, et al. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell. 22: 575-588.e7. PMID 29625070 DOI: 10.1016/J.Stem.2018.03.012 |
0.341 |
|
| 2018 |
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, ... ... Califano A, et al. Cross-cohort analysis identifies a TEAD4 ↔ MYCN positive-feedback loop as the core regulatory element of high-risk neuroblastoma. Cancer Discovery. PMID 29510988 DOI: 10.1158/2159-8290.Cd-16-0861 |
0.658 |
|
| 2018 |
Banu MA, Dovas A, Cuervo H, Pereira B, Mahajan A, Ding H, Bansal M, Pampou S, Karan C, Califano A, Sims PA, Kitajewski J, Bruce JN, Canoll P. Abstract 5103: Notch is a master regulator of mesenchymal transformation and therapeutic resistance in glioma Cancer Research. 78: 5103-5103. DOI: 10.1158/1538-7445.Am2018-5103 |
0.399 |
|
| 2018 |
Murray D, Begum KN, Califano A, Honig B. Abstract 3300: Network analysis of the human protein-protein interactome: Tumorigenic signaling mechanisms Cancer Research. 78: 3300-3300. DOI: 10.1158/1538-7445.Am2018-3300 |
0.354 |
|
| 2018 |
Zou M, Vasciaveo A, Califano A, Abate-Shen C. Abstract 3017: Identifying drivers for advanced prostate cancer by a transposon-based genetic screen Cancer Research. 78: 3017-3017. DOI: 10.1158/1538-7445.Am2018-3017 |
0.333 |
|
| 2018 |
Zeleke TZ, Putcha P, Yu J, Califano A, Silva JM. Abstract 2898: Inhibition of HDAC6 as a novel targeted therapy in breast cancer Cancer Research. 78: 2898-2898. DOI: 10.1158/1538-7445.Am2018-2898 |
0.662 |
|
| 2018 |
Echeverria GV, Seth S, Ge Z, Carugo A, Bristow C, Mundi P, Jeter-Jones S, Zhang X, Zhou X, McCoy A, Cai S, Tu Y, Sun Y, Marszalek J, Califano A, et al. Abstract 212: High-resolution barcoding in patient-derived xenografts of triple-negative breast cancer reveals reversible chemoresistance conferred by non-mutational mechanisms Cancer Research. 78: 212-212. DOI: 10.1158/1538-7445.Am2018-212 |
0.36 |
|
| 2018 |
Califano A. Abstract CN03-01: Systematic elucidation and pharmacologic targeting of mechanistic tumor dependencies Molecular Cancer Therapeutics. 17. DOI: 10.1158/1535-7163.Targ-17-Cn03-01 |
0.425 |
|
| 2017 |
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, et al. CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. Database : the Journal of Biological Databases and Curation. 2017. PMID 29220450 DOI: 10.1093/Database/Bax054 |
0.355 |
|
| 2017 |
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 Computational Biology. 13: e1005599. PMID 29023443 DOI: 10.1371/Journal.Pcbi.1005599 |
0.425 |
|
| 2017 |
He J, Zhou Z, Reed M, Califano A. Accelerated parallel algorithm for gene network reverse engineering. Bmc Systems Biology. 11: 83. PMID 28950860 DOI: 10.1186/S12918-017-0458-5 |
0.321 |
|
| 2017 |
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 Reports. 20: 1623-1640. PMID 28813674 DOI: 10.1016/J.Celrep.2017.07.052 |
0.434 |
|
| 2017 |
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. Nature Communications. 8: 105. PMID 28740083 DOI: 10.1038/S41467-017-00136-Z |
0.358 |
|
| 2017 |
Efimenko E, Davé UP, Lebedeva IV, Shen Y, Sanchez-Quintero MJ, Diolaiti D, Kung A, Lannutti BJ, Chen J, Realubit R, Niatsetskiya Z, Ten V, Karan C, Chen X, Califano A, et al. PI3Kγ/δ and NOTCH1 cross-regulate pathways that define the T-cell acute lymphoblastic leukemia disease signature. Molecular Cancer Therapeutics. PMID 28716817 DOI: 10.1158/1535-7163.Mct-17-0141 |
0.375 |
|
| 2017 |
Fedele V, Dai F, Masilamani A, Heiland DH, Kling E, Gätjens-Sanchez A, Ferrarese R, Platania L, Doostkam S, Kim H, Nelander S, Weyerbrock A, Prinz M, Califano A, Iavarone A, et al. Epigenetic Regulation of ZBTB18 Promotes Glioblastoma Progression. Molecular Cancer Research : McR. PMID 28512252 DOI: 10.1158/1541-7786.Mcr-16-0494 |
0.38 |
|
| 2017 |
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. Nature Communications. 8: 14662. PMID 28429718 DOI: 10.1038/Ncomms14662 |
0.346 |
|
| 2017 |
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, et al. Erratum to: HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers. Breast Cancer Research : Bcr. 19: 49. PMID 28424080 DOI: 10.1186/S13058-017-0841-6 |
0.611 |
|
| 2017 |
Zou M, Toivanen R, Mitrofanova A, Floc'h 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 Discovery. PMID 28411207 DOI: 10.1158/2159-8290.Cd-16-1174 |
0.368 |
|
| 2017 |
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. Proceedings of the National Academy of Sciences of the United States of America. PMID 28174276 DOI: 10.1073/Pnas.1611831114 |
0.367 |
|
| 2017 |
Sanchez-Martin M, Ambesi-Impiombato A, Qin Y, Herranz D, Bansal M, Girardi T, Paietta E, Tallman MS, Rowe JM, Keersmaecker KD, Califano A, Ferrando A. Abstract 49: Synergistic antileukemic therapies in NOTCH1-induced T-ALL Clinical Cancer Research. 23: 49-49. DOI: 10.1158/1557-3265.Hemmal17-49 |
0.417 |
|
| 2017 |
Yu J, Silva JM, Califano A. Abstract PR10: ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-Pr10 |
0.642 |
|
| 2017 |
Califano A. Abstract IA21: Systematic, network-based elucidation of synthetic lethal proteins and synergistic compounds Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-Ia21 |
0.456 |
|
| 2017 |
Kostyrko K, Simpson D, Broyde J, Kelly M, Califano A, Honig B, Jackson P, Sweet-Cordero A. Abstract A27: Identification of novel KRAS-synthetic lethal targets for treatment of KRAS-dependent Non-Small Cell Lung Cancer Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-A27 |
0.393 |
|
| 2017 |
Broyde J, Simpson D, Murray D, Lachmann A, Giorgi FM, Honig B, Sweet-Cordero AE, Califano A. Abstract LB-289: Computational detection of oncogene‐centric pathway members Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Lb-289 |
0.4 |
|
| 2016 |
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. 5: e1213931. PMID 27999735 DOI: 10.1080/2162402X.2016.1213931 |
0.337 |
|
| 2016 |
Califano A, Alvarez MJ. The recurrent architecture of tumour initiation, progression and drug sensitivity. Nature Reviews. Cancer. PMID 27977008 DOI: 10.1038/Nrc.2016.124 |
0.401 |
|
| 2016 |
Udyavar AR, Wooten DJ, Hoeksema MD, 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 Research. PMID 27932399 DOI: 10.1158/0008-5472.CAN-16-1467 |
0.3 |
|
| 2016 |
Dela Cruz FS, Diolaiti D, Turk AT, Rainey AR, Ambesi-Impiombato A, Andrews SJ, Mansukhani MM, Nagy PL, Alvarez MJ, Califano A, Forouhar F, Modzelewski B, Mitchell CM, Yamashiro DJ, Marks LJ, et al. A case study of an integrative genomic and experimental therapeutic approach for rare tumors: identification of vulnerabilities in a pediatric poorly differentiated carcinoma. Genome Medicine. 8: 116. PMID 27799065 DOI: 10.1186/S13073-016-0366-0 |
0.319 |
|
| 2016 |
Tavana O, Li D, Dai C, Lopez G, Banerjee D, Kon N, Chen C, Califano A, Yamashiro DJ, Sun H, Gu W. HAUSP deubiquitinates and stabilizes N-Myc in neuroblastoma. Nature Medicine. PMID 27618649 DOI: 10.1038/Nm.4180 |
0.333 |
|
| 2016 |
Gerhard DS, Clemons PA, Shamji AF, Hon C, Wagner BK, Schreiber SL, Krasnitz A, Sordella R, Sander C, Lowe SW, Powers S, Smith K, Aburi M, Iavarone A, Lasorella A, ... ... Califano A, et al. Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance. Molecular Cancer Research : McR. PMID 27401613 DOI: 10.1158/1541-7786.Mcr-16-0090 |
0.65 |
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| 2016 |
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 (New York, N.Y.). 352: 1576-80. PMID 27339988 DOI: 10.1126/Science.Aad9512 |
0.307 |
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| 2016 |
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. Nature Genetics. PMID 27322546 DOI: 10.1038/Ng.3593 |
0.385 |
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| 2016 |
Lachmann A, Giorgi FM, Alvarez MJ, Califano A. Detection and removal of spatial bias in multiwell assays. Bioinformatics (Oxford, England). PMID 27153732 DOI: 10.1093/Bioinformatics/Btw092 |
0.331 |
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| 2016 |
Lachmann A, Giorgi FM, Lopez G, Califano A. ARACNe-AP: Gene Network Reverse Engineering through Adaptive Partitioning inference of Mutual Information. Bioinformatics (Oxford, England). PMID 27153652 DOI: 10.1093/Bioinformatics/Btw216 |
0.341 |
|
| 2016 |
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. PMID 27132888 DOI: 10.1016/J.Stemcr.2016.04.002 |
0.404 |
|
| 2016 |
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. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc. PMID 26769141 DOI: 10.1038/Modpathol.2015.144 |
0.325 |
|
| 2016 |
Risom T, Langer E, Rantala J, Alvarez M, Johnson-Camacho K, Pelz C, Wang N, Spellman P, Califano A, Gray J, Sears R. Abstract B52: Overcoming phenotypic heterogeneity and plasticity in basal-like breast cancer through targeting adaptive pathway use Molecular Cancer Research. 14. DOI: 10.1158/1557-3125.Advbc15-B52 |
0.425 |
|
| 2016 |
Yu J, Califano A, silva j. Abstract B36: Inhibition of the autocrine IL-6-JAK2-STAT3-Calprotectin axis as targeted therapy for HR-/HER2+ breast cancers Molecular Cancer Research. 14. DOI: 10.1158/1557-3125.Advbc15-B36 |
0.662 |
|
| 2016 |
Putcha P, Yu J, Rodriguez-Barrueco R, Califano A, silva j. Abstract A71: HDAC6 activity is a non-oncogene addiction hub for in inflammatory breast cancers Molecular Cancer Research. 14. DOI: 10.1158/1557-3125.Advbc15-A71 |
0.669 |
|
| 2016 |
Silva J, Rodriguez-Barrueco R, Yu J, Kalinsky K, Maurer M, Califano A. Abstract PD3-03: Inhibition of the autocrine IL6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers Cancer Research. 76. DOI: 10.1158/1538-7445.Sabcs15-Pd3-03 |
0.394 |
|
| 2016 |
Rajbhandari P, Lopez G, Yu J, Rodriguez-Barrueco R, Alvarez M, Martinez D, Yarmarkovich M, Vandesompele J, Mestdagh P, Silva JM, Lasorella A, Iavarone A, Maris JM, Califano A. Abstract 4384: Selective cross-cohort discovery of transcriptional mechanisms presiding over high-risk neuroblastoma subtype state maintenance Cancer Research. 76: 4384-4384. DOI: 10.1158/1538-7445.Am2016-4384 |
0.689 |
|
| 2016 |
Magnen CL, Dutta A, Mitrofanova A, Califano A, Abate-Shen C. Abstract 2888: Identification of an NKX3.1-G9a-UTY regulatory network that controls proper prostate differentiation Cancer Research. 76: 2888-2888. DOI: 10.1158/1538-7445.Am2016-2888 |
0.318 |
|
| 2015 |
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, et al. HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers. Breast Cancer Research : Bcr. 17: 149. PMID 26643555 DOI: 10.1186/S13058-015-0658-0 |
0.679 |
|
| 2015 |
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 Research. PMID 26589882 DOI: 10.1158/0008-5472.Can-15-0828 |
0.37 |
|
| 2015 |
Yu J, Silva J, Califano A. ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling. Bioinformatics (Oxford, England). PMID 26415723 DOI: 10.1093/Bioinformatics/Btv556 |
0.636 |
|
| 2015 |
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 Reports. PMID 26387954 DOI: 10.1016/J.Celrep.2015.08.051 |
0.392 |
|
| 2015 |
Alvarez MJ, Chen JC, Califano A. DIGGIT: A Bioconductor package to infer genetic variants driving cellular phenotypes. Bioinformatics (Oxford, England). PMID 26338767 DOI: 10.1093/Bioinformatics/Btv499 |
0.334 |
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| 2015 |
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, et al. Toward understanding and exploiting tumor heterogeneity. Nature Medicine. 21: 846-53. PMID 26248267 DOI: 10.1038/Nm.3915 |
0.3 |
|
| 2015 |
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, et al. Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers. Genes & Development. 29: 1631-48. PMID 26227964 DOI: 10.1101/Gad.262642.115 |
0.659 |
|
| 2015 |
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. Nature Neuroscience. PMID 26214373 DOI: 10.1038/Nn.4070 |
0.347 |
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| 2015 |
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. 162: 441-51. PMID 26186195 DOI: 10.1016/J.Cell.2015.05.056 |
0.367 |
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| 2015 |
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 Reports. 12: 335-45. PMID 26146077 DOI: 10.1016/J.Celrep.2015.06.019 |
0.332 |
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| 2015 |
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. 10: e0131038. PMID 26110827 DOI: 10.1371/Journal.Pone.0131038 |
0.37 |
|
| 2015 |
Bansal M, Mendiratta G, Anand S, Kushwaha R, Kim R, Kustagi M, Iyer A, Chaganti RS, Califano A, Sumazin P. Direct ChIP-Seq significance analysis improves target prediction. Bmc Genomics. 16: S4. PMID 26040656 DOI: 10.1186/1471-2164-16-S5-S4 |
0.333 |
|
| 2015 |
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. 10: e0120352. PMID 25781952 DOI: 10.1371/Journal.Pone.0120352 |
0.359 |
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| 2015 |
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, et al. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Research. 25: 257-67. PMID 25378249 DOI: 10.1101/Gr.178194.114 |
0.401 |
|
| 2015 |
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, ... ... Califano A, et al. Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency. Stem Cells (Dayton, Ohio). 33: 367-77. PMID 25336442 DOI: 10.1002/Stem.1870 |
0.434 |
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| 2015 |
Kalac M, Mangone M, Rinderspacher A, Deng S, Scotto L, Vendome J, Bansal M, Califano A, Landry D, O'Connor OA. Targeting NF-κB with First in Class N-Quinoline Benzenesulfonamides (NQBS) Reveals Potent Activity in Models of Diffuse Large B-Cell Lymphoma (DLBCL) Blood. 126: 4435-4435. DOI: 10.1182/Blood.V126.23.4435.4435 |
0.301 |
|
| 2015 |
Sanchez-Martin M, Ambesi-Impiombato A, Xu L, Qin Y, Herranz D, Bansal M, Girardi T, De Keersmaecker K, Califano A, Ferrando AA. Synergistic Targeting of Protein Translation and Inhibition of NOTCH Signaling in T-ALL Blood. 126: 3719-3719. DOI: 10.1182/Blood.V126.23.3719.3719 |
0.421 |
|
| 2015 |
Alvarez MJ, Shen Y, Bisikirska B, Realubit R, Pampou S, Karan C, Califano A. Abstract A24: Network-based inference of resistance mechanisms to estrogen inhibitors in ER+ breast cancer Clinical Cancer Research. 21. DOI: 10.1158/1557-3265.Pms14-A24 |
0.412 |
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| 2015 |
Bisikirska BC, Bansal M, Shen Y, Teruya_Feldstein J, Chaganti R, Califano A. Abstract A16: Master regulators of transformation of follicular lymphoma to diffused large B-cell lymphoma in patients defined by expression and activity of MYC Molecular Cancer Research. 13. DOI: 10.1158/1557-3125.Myc15-A16 |
0.387 |
|
| 2015 |
Broyde J, Simpson D, Wah DA, Giorgi FM, Petrey D, Alvarez MJ, Silkov A, Lachmann A, Hill DE, Vidal M, Jackson P, Honig B, Sweet-Cordero A, Califano A. Abstract PR13: Systems and structural biology approaches to elucidate new effectors in KRAS mutant tumors Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Pr13 |
0.45 |
|
| 2015 |
Lopez G, Alvarez M, Chen J, Rajbhandari P, Cole KA, Attiyeh EF, Diskin S, Mestdagh P, Vandesompele J, Maris JM, Califano A. Abstract PR10: Oncogenic dysregulations in neuroblastoma are associated with distal large chromosomal aberrations Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Pr10 |
0.333 |
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| 2015 |
Chiu H, Yang X, Califano A, Sumazin P. Abstract IA14: Genomic alterations dysregulate cancer genes by modulating microRNA activity Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Ia14 |
0.418 |
|
| 2015 |
Califano A. Abstract IA06: A precision medicine framework for brain tumors Brain. 75. DOI: 10.1158/1538-7445.Brain15-Ia06 |
0.419 |
|
| 2015 |
Udyavar AR, Hoeksema M, Wooten DJ, Bansal M, Califano A, Estrada L, Irish J, Massion P, Quaranta V. Abstract 3761: Distinct transcriptional programs drive phenotypic heterogeneity in small cell lung cancer Cancer Research. 75: 3761-3761. DOI: 10.1158/1538-7445.Am2015-3761 |
0.315 |
|
| 2015 |
Zhang S, Lopez G, Yu J, Silva J, Kadenhe-Chiweshe A, Califano A, Yamashiro D. Abstract 2083: TFAP4 inhibits differentiation of MYCN-amplified neuroblastoma Cancer Research. 75: 2083-2083. DOI: 10.1158/1538-7445.Am2015-2083 |
0.665 |
|
| 2014 |
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, ... ... Califano A, et al. A community computational challenge to predict the activity of pairs of compounds. Nature Biotechnology. 32: 1213-22. PMID 25419740 DOI: 10.1038/Nbt.3052 |
0.32 |
|
| 2014 |
Califano A. Predicting protein networks in cancer. Nature Genetics. 46: 1252-3. PMID 25418743 DOI: 10.1038/Ng.3156 |
0.349 |
|
| 2014 |
Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G. Toward better benchmarking: challenge-based methods assessment in cancer genomics. Genome Biology. 15: 462. PMID 25314947 DOI: 10.1186/S13059-014-0462-7 |
0.615 |
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| 2014 |
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. 9: e109569. PMID 25314274 DOI: 10.1371/Journal.Pone.0109569 |
0.402 |
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| 2014 |
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. 159: 402-14. PMID 25303533 DOI: 10.1016/J.Cell.2014.09.021 |
0.372 |
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| 2014 |
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. 25: 638-51. PMID 24823640 DOI: 10.1016/J.Ccr.2014.03.017 |
0.4 |
|
| 2014 |
Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, ... ... Califano A, et al. A promoter-level mammalian expression atlas. Nature. 507: 462-70. PMID 24670764 DOI: 10.1038/Nature13182 |
0.4 |
|
| 2014 |
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, et al. Convection-enhanced delivery of etoposide is effective against murine proneural glioblastoma. Neuro-Oncology. 16: 1210-9. PMID 24637229 DOI: 10.1093/Neuonc/Nou026 |
0.329 |
|
| 2014 |
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, ... ... Califano A, et al. ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Reports. 6: 313-24. PMID 24440720 DOI: 10.1016/J.Celrep.2013.12.032 |
0.416 |
|
| 2014 |
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, ... ... Califano A, et al. The transcriptional regulatory network of proneural glioma determines the genetic alterations selected during tumor progression. Cancer Research. 74: 1440-51. PMID 24390738 DOI: 10.1158/0008-5472.Can-13-2150 |
0.374 |
|
| 2014 |
Kalinsky K, Chi D, Lee SM, Adelson KB, Crew KD, Chuang E, Makower D, Hershman DL, Califano A, Silva J, Maurer MA. Phase I/II trial of ruxolitinib in combination with trastuzumab in metastatic HER2-positive breast cancer. Journal of Clinical Oncology. 32: TPS666-TPS666. DOI: 10.1200/Jco.2014.32.15_Suppl.Tps666 |
0.333 |
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| 2014 |
Wah DA, Giorgi FM, Petrey D, Alvarez MJ, Silkov T, Broyde J, Rieckhof GE, Honig B, Califano A. Abstract PR09: A systems biology approach to elucidate novel drug targets in KRAS mutant tumors Molecular Cancer Research. 12. DOI: 10.1158/1557-3125.Rasonc14-Pr09 |
0.357 |
|
| 2014 |
Mitrofanova A, Floch N, Aytes A, Shen M, Abate-Shen C, Califano A. Abstract A29: Interrogating therapeutic response for advanced prostate cancer in vivo using cross-species regulatory models Molecular Cancer Research. 12. DOI: 10.1158/1557-3125.Modorg-A29 |
0.369 |
|
| 2014 |
Putcha P, Yu J, Califano A, Silva J. Abstract 4623: HDAC6 inhibition is a novel strategy to selectively impact inflammatory breast cancer cell survival Cancer Research. 74: 4623-4623. DOI: 10.1158/1538-7445.Am2014-4623 |
0.66 |
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| 2014 |
Irshad S, Bansal M, Magnen CL, Dillon R, Castillo-Martin M, Zheng T, Aytes A, Wenske S, Guarnieri P, Sumazin P, Benson M, Shen MM, Califano A, Abate-Shen C. Abstract 2873: A molecular signature predictive of indolent prostate cancer Cancer Research. 74: 2873-2873. DOI: 10.1158/1538-7445.Am2014-2873 |
0.371 |
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| 2014 |
Barrueco RR, Yu J, Alvarez M, Castro V, Marshall N, Su R, Castro L, Maurer M, Califano A, Silva JM. Abstract 2761: Characterizing the mechanism and the clinical relevance of the synthetic lethal interaction between STAT3 inhibition and HER2 overexpression in breast cancers Cancer Research. 74: 2761-2761. DOI: 10.1158/1538-7445.Am2014-2761 |
0.685 |
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| 2014 |
Sonabend AM, Carminucci AS, Amendolara B, Bansal M, Praver M, Realubit R, Li H, Karan C, Banu M, Lei L, Califano A, Canoll P, Bruce J. ET-57 * TOPOISOMERASE II IN PRONEURAL GLIOMAS, A MODULATOR OF TRANSCRIPTION AND A THERAPEUTIC TARGET Neuro-Oncology. 16: v91-v91. DOI: 10.1093/Neuonc/Nou255.54 |
0.369 |
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| 2013 |
Jang IS, Margolin A, Califano A. hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests. Interface Focus. 3: 20130011. PMID 24511376 DOI: 10.1098/Rsfs.2013.0011 |
0.734 |
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| 2013 |
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, ... ... Califano A, et al. Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia. Cancer Cell. 24: 766-76. PMID 24291004 DOI: 10.1016/J.Ccr.2013.10.022 |
0.619 |
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| 2013 |
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. Science Translational Medicine. 5: 202ra122. PMID 24027026 DOI: 10.1126/Scitranslmed.3006408 |
0.36 |
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| 2013 |
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. Nature Immunology. 14: 1084-92. PMID 23974956 DOI: 10.1038/Ni.2688 |
0.332 |
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| 2013 |
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. Proceedings of the National Academy of Sciences of the United States of America. 110: E3506-15. PMID 23918374 DOI: 10.1073/Pnas.1303558110 |
0.333 |
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| 2013 |
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, ... ... Califano A, et al. Improving breast cancer survival analysis through competition-based multidimensional modeling. Plos Computational Biology. 9: e1003047. PMID 23671412 DOI: 10.1371/Journal.Pcbi.1003047 |
0.706 |
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| 2013 |
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, et al. Survival factor NFIL3 restricts FOXO-induced gene expression in cancer. Genes & Development. 27: 916-27. PMID 23630076 DOI: 10.1101/Gad.214049.113 |
0.415 |
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| 2013 |
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. Nature Cell Biology. 15: 274-83. PMID 23434823 DOI: 10.1038/Ncb2697 |
0.341 |
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| 2013 |
Yu J, Putcha P, Califano A, Silva JM. Pooled shRNA screenings: computational analysis. Methods in Molecular Biology (Clifton, N.J.). 980: 371-84. PMID 23359167 DOI: 10.1007/978-1-62703-287-2_22 |
0.62 |
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| 2013 |
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. Proceedings of the National Academy of Sciences of the United States of America. 110: 1404-9. PMID 23297232 DOI: 10.1073/Pnas.1206761110 |
0.342 |
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| 2013 |
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. 32: 5283-91. PMID 23178486 DOI: 10.1038/Onc.2012.543 |
0.404 |
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| 2013 |
Kalinsky K, Chi D, Lee S, Tiersten A, Makower D, Chuang E, Crew KD, Hershman DL, Silva J, Califano A, Maurer M. Abstract OT1-1-09: Phase I/II trial of ruxolitinib in combination with trastuzumab in metastatic HER2 positive breast cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Sabcs14-Ot1-1-09 |
0.331 |
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| 2013 |
Chiu H, Yang X, Martínez MR, Iyer A, Sumazin P, Califano A. Abstract 5231: Highly conserved ceRNA regulatory interactions cooperate with genomic variability to modulate drivers of tumorigenesis. Cancer Research. 73: 5231-5231. DOI: 10.1158/1538-7445.Am2013-5231 |
0.429 |
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| 2013 |
Rodriguez-Barrueco R, Yu J, Alvarez M, Castro V, Villagrasa P, Marshall N, Sun R, Castro L, Califano A. Abstract PR11: Characterizing the mechanism and the clinical relevance of the synthetic lethal interaction between STAT3 inhibition and HER2 overexpression in breast cancers Molecular Cancer Therapeutics. 12. DOI: 10.1158/1535-7163.Pms-Pr11 |
0.698 |
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| 2013 |
Alvarez MJ, Shen Y, Karan C, Bansal M, Mattioli M, Pampou S, Califano A. Abstract PR04: A network-based approach for drug synergy prediction from gene expression data Molecular Cancer Therapeutics. 12. DOI: 10.1158/1535-7163.Pms-Pr04 |
0.425 |
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| 2013 |
Mitrofanova A, Aytes A, Lefebvre C, Shen M, Abate-Shen C, Califano A. Abstract A26: Cross-species analysis of genome-wide regulatory models elucidates master regulators of prostate cancer progression and treatment response Molecular Cancer Therapeutics. 12. DOI: 10.1158/1535-7163.Pms-A26 |
0.408 |
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| 2013 |
Dinkelspiel H, Iyer A, Lefebvre C, Wright J, Lewin S, Herzog T, Kitajewski J, Califano A. Identification of master regulators of cisplatin resistance in ovarian cancer Gynecologic Oncology. 130: e4-e5. DOI: 10.1016/J.Ygyno.2013.04.067 |
0.32 |
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| 2012 |
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. 490: 556-60. PMID 23023127 DOI: 10.1038/Nature11503 |
0.352 |
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| 2012 |
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 Research. 72: 4765-76. PMID 22836754 DOI: 10.1158/0008-5472.Can-12-0820 |
0.342 |
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| 2012 |
Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nature Genetics. 44: 841-7. PMID 22836096 DOI: 10.1038/Ng.2355 |
0.345 |
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| 2012 |
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 Research. 72: 4483-93. PMID 22815528 DOI: 10.1158/0008-5472.Can-12-0283 |
0.375 |
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| 2012 |
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, et al. Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL. Nature Medicine. 18: 436-40. PMID 22366949 DOI: 10.1038/Nm.2610 |
0.375 |
|
| 2012 |
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. Proceedings of the National Academy of Sciences of the United States of America. 109: 2672-7. PMID 22308355 DOI: 10.1073/Pnas.1113019109 |
0.371 |
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| 2012 |
Lefebvre C, Rieckhof G, Califano A. Reverse-engineering human regulatory networks. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 4: 311-25. PMID 22246697 DOI: 10.1002/Wsbm.1159 |
0.405 |
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| 2012 |
Floratos A, Honig B, Pe'er D, Califano A. Using systems and structure biology tools to dissect cellular phenotypes. Journal of the American Medical Informatics Association : Jamia. 19: 171-5. PMID 22081223 DOI: 10.1136/Amiajnl-2011-000490 |
0.337 |
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| 2012 |
Bansal M, Califano A. Genome-wide dissection of posttranscriptional and posttranslational interactions. Methods in Molecular Biology (Clifton, N.J.). 786: 131-49. PMID 21938624 DOI: 10.1007/978-1-61779-292-2_8 |
0.404 |
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| 2012 |
Ying CY, Dominguez-Sola D, Fabi M, Lorenz IC, Bansal M, Califano A, Pasqualucci L, Basso K, Dalla-Favera R. MEF2B Mutations Lead to De-Regulated Expression of the BCL6 Oncogene in Diffuse Large B-Cell Lymphoma and Follicular Lymphoma Blood. 120: 1284-1284. DOI: 10.1182/Blood.V120.21.1284.1284 |
0.376 |
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| 2012 |
Aytes A, Mitrofanova A, Lefebvre C, Shen MM, Califano A, Abate-Shen C. Abstract A36: Identification of master regulators driving advanced prostate cancer and treatment response through the assembly of mouse and human prostate cancer interactomes Cancer Research. 72: A36-A36. DOI: 10.1158/1538-7445.Prca2012-A36 |
0.376 |
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| 2012 |
Sumazin P, Chiu H, Califano A. Abstract A14: microRNA-mediated interactions regulate established oncongenic pathways in cancer Cancer Research. 72: A14-A14. DOI: 10.1158/1538-7445.Nonrna12-A14 |
0.437 |
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| 2012 |
Califano A. Abstract IA10: Interrogating gene regulatory networks to explore the boundary between chemistry and biology in cancer Cancer Research. 72. DOI: 10.1158/1538-7445.Csb12-Ia10 |
0.356 |
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| 2012 |
Shen Y, Alvarez M, Pampou S, Coku J, Califano A. Abstract A35: Predicting drugs effect on transcription factor activity by regulatory network analysis of drug perturbed cellular states Cancer Research. 72. DOI: 10.1158/1538-7445.Csb12-A36 |
0.464 |
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| 2012 |
Yu J, Piovan E, Flaherty MS, Silva J, Ferrando A, Califano A. Abstract A35: Discovery of driver-type therapeutic targets to reverse glucocorticoid resistance in T-ALL Cancer Research. 72. DOI: 10.1158/1538-7445.Csb12-A35 |
0.655 |
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| 2012 |
Chung W, Sumazin P, Yang X, Bansal M, Califano A. Abstract 2946: Post-transcriptional regulators of microRNA biogenesis regulate pathogenesis of cancer Cancer Research. 72: 2946-2946. DOI: 10.1158/1538-7445.Am2012-2946 |
0.306 |
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| 2011 |
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. 147: 370-81. PMID 22000015 DOI: 10.1016/J.Cell.2011.09.041 |
0.351 |
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| 2011 |
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. 50: 1063-75. PMID 21987448 DOI: 10.1002/Gcc.20924 |
0.335 |
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| 2011 |
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 (Cambridge, England). 138: 3885-95. PMID 21862554 DOI: 10.1242/dev.065656 |
0.345 |
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| 2011 |
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, ... ... Califano A, et al. Gene expression analysis uncovers similarity and differences among Burkitt lymphoma subtypes. Blood. 117: 3596-608. PMID 21245480 DOI: 10.1182/Blood-2010-08-301556 |
0.381 |
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| 2011 |
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. Journal of Cellular and Molecular Medicine. 15: 949-56. PMID 20497491 DOI: 10.1111/J.1582-4934.2010.01092.X |
0.41 |
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| 2011 |
Abate-Shen C, Meneses AA, Kinkade CW, Mitrofanova A, Lefebvre C, Chua CW, Castillo-Martin M, Gelmann E, Shen MM, Califano A. Abstract SY22-01: Interrogating gene expression programs from preclinical analyses of genetically engineered mouse models Cancer Research. 71. DOI: 10.1158/1538-7445.Am2011-Sy22-01 |
0.385 |
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| 2011 |
Califano A. Abstract PL02-01: A systems biology approach to integrative cancer genomics Cancer Research. 71. DOI: 10.1158/1538-7445.Am2011-Pl02-01 |
0.436 |
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| 2011 |
Sumazin P, Yang X, Chung W, Bansal M, Califano A. Abstract LB-339: MicroRNA modulators regulate oncogenes and tumor suppressors in glioblastoma Cancer Research. 71. DOI: 10.1158/1538-7445.Am2011-Lb-339 |
0.359 |
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| 2011 |
Chung W, Sumazin P, Yang X, Bansal M, Califano A. Abstract LB-337: Post-transcriptional regulators of microRNA biogenesis drive glioblastoma-specific expression Cellular and Molecular Biology. 71. DOI: 10.1158/1538-7445.Am2011-Lb-337 |
0.33 |
|
| 2011 |
Jagadish N, Kustagi M, Mendiratta G, Kushwaha R, Bansal M, Hyunjae KR, Sumazin P, Alvarez M, Lefebvre C, Viale A, Korkola JE, Houldsworth J, Bosl GJ, Califano A, Chaganti RS. Abstract 3410: Regulation of pluripotency and lineage differentiation in human male germ cell tumors Cancer Research. 71: 3410-3410. DOI: 10.1158/1538-7445.Am2011-3410 |
0.445 |
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| 2011 |
Califano A, Butte A, Friend S, Ideker T, Schadt EE. Integrative Network-based Association Studies: Leveraging cell regulatory models in the post-GWAS era Nature Precedings. DOI: 10.1038/Npre.2011.5732.1 |
0.453 |
|
| 2010 |
Margolin AA, Wang K, Califano A, Nemenman I. Multivariate dependence and genetic networks inference. Iet Systems Biology. 4: 428-40. PMID 21073241 DOI: 10.1049/Iet-Syb.2010.0009 |
0.751 |
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| 2010 |
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, ... ... Califano A, et al. The TLX1 oncogene drives aneuploidy in T cell transformation. Nature Medicine. 16: 1321-7. PMID 20972433 DOI: 10.1038/Nm.2246 |
0.355 |
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| 2010 |
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, ... ... Califano A, et al. Towards patient-based cancer therapeutics. Nature Biotechnology. 28: 904-6. PMID 20829823 DOI: 10.1038/Nbt0910-904 |
0.4 |
|
| 2010 |
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, et al. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Molecular Systems Biology. 6: 377. PMID 20531406 DOI: 10.1038/Msb.2010.31 |
0.402 |
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| 2010 |
Floratos A, Smith K, Ji Z, Watkinson J, Califano A. geWorkbench: an open source platform for integrative genomics. Bioinformatics (Oxford, England). 26: 1779-80. PMID 20511363 DOI: 10.1093/Bioinformatics/Btq282 |
0.344 |
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| 2010 |
Zhou X, Sumazin P, Rajbhandari P, Califano A. A systems biology approach to transcription factor binding site prediction. Plos One. 5: e9878. PMID 20360861 DOI: 10.1371/Journal.Pone.0009878 |
0.34 |
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| 2010 |
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. 463: 318-25. PMID 20032975 DOI: 10.1038/Nature08712 |
0.412 |
|
| 2010 |
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. 115: 975-84. PMID 19965633 DOI: 10.1182/Blood-2009-06-227017 |
0.654 |
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| 2010 |
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 P, Kelliher M, Kee BL, ... ... Califano A, et al. BCL11B Mutations In T-Cell Acute Lymphoblastic Leukemia Blood. 116: 471-471. DOI: 10.1182/Blood.V116.21.471.471 |
0.35 |
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| 2010 |
Gatta GD, Impiombato AA, Palomero T, Tosello V, Sumazin P, Califano A, Ferrando A. Identification of NOTCH1-Controlled Transcriptional Programs In Human T-Cell Development Blood. 116: 2495-2495. DOI: 10.1182/Blood.V116.21.2495.2495 |
0.395 |
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| 2010 |
Piovan E, Yu J, Real P, Ann GM, Califano A, Ferrando A. Oncogenic AKT Signaling Negatively Regulates Glucocorticoid Receptor Function to Promote Glucocorticoid Resistance In T Cell Acute Lymphoblastic Leukemia Blood. 116: 11-11. DOI: 10.1182/Blood.V116.21.11.11 |
0.65 |
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| 2010 |
Jagadish N, Kustagi M, Mendiratta G, Kushwaha R, Korkola JE, Houldsworth J, Viale A, Hyunjae KR, Sumazin P, Bosl GJ, Califano A, Chaganti RSK. Abstract 4240: Transcription factor networks that regulate pluripotency and lineage differentiation in adult human male germ cell tumors Cancer Research. 70: 4240-4240. DOI: 10.1158/1538-7445.Am10-4240 |
0.445 |
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| 2009 |
Alvarez MJ, Sumazin P, Rajbhandari P, Califano A. Correlating measurements across samples improves accuracy of large-scale expression profile experiments. Genome Biology. 10: R143. PMID 20042104 DOI: 10.1186/Gb-2009-10-12-R143 |
0.306 |
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| 2009 |
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. Nature Biotechnology. 27: 829-39. PMID 19741643 DOI: 10.1038/Nbt.1563 |
0.764 |
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| 2009 |
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. Proceedings of the National Academy of Sciences of the United States of America. 106: 11294-9. PMID 19549844 DOI: 10.1073/Pnas.0903854106 |
0.357 |
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| 2009 |
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. 459: 717-21. PMID 19412164 DOI: 10.1038/Nature07968 |
0.336 |
|
| 2009 |
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, et al. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Molecular Oncology. 3: 9-17. PMID 19383362 DOI: 10.1016/J.Molonc.2008.11.003 |
0.383 |
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| 2009 |
Stolovitzky G, Prill RJ, Califano A. Lessons from the DREAM2 Challenges. Annals of the New York Academy of Sciences. 1158: 159-95. PMID 19348640 DOI: 10.1111/J.1749-6632.2009.04497.X |
0.308 |
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| 2009 |
Lim WK, Lyashenko E, Califano A. Master regulators used as breast cancer metastasis classifier. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 504-15. PMID 19209726 |
0.302 |
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| 2009 |
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. Proceedings of the National Academy of Sciences of the United States of America. 106: 244-9. PMID 19118200 DOI: 10.1073/Pnas.0806445106 |
0.66 |
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| 2009 |
Gatta GD, Palomero T, Sulis ML, Solé X, Lim WK, De Keersmaecker K, Luna PJR, Tosello V, Gounari F, Kee B, Lenz J, Kelliher M, Aplan PD, Meijerink JP, Califano A, et al. Oncogenic Transcriptional Programs Controlled by TLX1/HOX11 and TLX3/HOX11L2 in T-ALL. Blood. 114: 676-676. DOI: 10.1182/Blood.V114.22.676.676 |
0.4 |
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| 2009 |
Mussolin L, Basso K, Lettieri A, Brahmachary M, Cazzaniga G, Califano A, Lim W, Basso G, Biondi A, Rosolen A. Genomic and Transcriptomic Analyses Revealed Differences and Similarities Between T-Lbl and T-ALL . Blood. 114: 2943-2943. DOI: 10.1182/Blood.V114.22.2943.2943 |
0.314 |
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| 2008 |
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. Molecular Systems Biology. 4: 169. PMID 18277385 DOI: 10.1038/Msb.2008.2 |
0.411 |
|
| 2007 |
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 Research. 67: 10703-10. PMID 18006812 DOI: 10.1158/0008-5472.Can-07-1708 |
0.344 |
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| 2007 |
Stolovitzky G, Monroe D, Califano A. Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference. Annals of the New York Academy of Sciences. 1115: 1-22. PMID 17925349 DOI: 10.1196/Annals.1407.021 |
0.358 |
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| 2007 |
Margolin AA, Califano A. Theory and limitations of genetic network inference from microarray data. Annals of the New York Academy of Sciences. 1115: 51-72. PMID 17925348 DOI: 10.1196/Annals.1407.019 |
0.643 |
|
| 2007 |
Sosinsky A, Honig B, Mann RS, Califano A. Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proceedings of the National Academy of Sciences of the United States of America. 104: 6305-10. PMID 17395715 DOI: 10.1073/Pnas.0701614104 |
0.349 |
|
| 2007 |
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. The Journal of Clinical Investigation. 117: 823-34. PMID 17304354 DOI: 10.1172/Jci26833 |
0.332 |
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| 2007 |
Margolin AA, Palomero T, Ferrando AA, Califano A, Stolovitzky G. ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding Bmc Bioinformatics. 8. DOI: 10.1186/1471-2105-8-S8-S2 |
0.635 |
|
| 2007 |
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 of Follicular Lymphoma Provides a Potential Rationale for Histological Grading Revision. Blood. 110: 186-186. DOI: 10.1182/Blood.V110.11.186.186 |
0.327 |
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| 2007 |
Palomero T, Wei KL, 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, et al. Erratum: NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth (Proceedings of the National Academy of Sciences of the United States of America (2006) 103, 48, (18261-18266) DOI: 10.1073/pnas.0606108103) Proceedings of the National Academy of Sciences of the United States of America. 104. DOI: 10.1073/Pnas.0700840104 |
0.608 |
|
| 2006 |
Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A. Reverse engineering cellular networks. Nature Protocols. 1: 662-71. PMID 17406294 DOI: 10.1038/Nprot.2006.106 |
0.761 |
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| 2006 |
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, et al. NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proceedings of the National Academy of Sciences of the United States of America. 103: 18261-6. PMID 17114293 DOI: 10.1073/Pnas.0606108103 |
0.651 |
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| 2006 |
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. 7: S7. PMID 16723010 DOI: 10.1186/1471-2105-7-S1-S7 |
0.751 |
|
| 2006 |
Wang K, Nemenman I, Banerjee N, Margolin AA, Califano A. Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 348-362. |
0.568 |
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| 2005 |
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, ... ... Califano A, et al. Report: workshop on mediastinal grey zone lymphoma. European Journal of Haematology. Supplementum. 45-52. PMID 16007868 DOI: 10.1111/J.1600-0609.2005.00454.X |
0.353 |
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| 2005 |
Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. Reverse engineering of regulatory networks in human B cells. Nature Genetics. 37: 382-90. PMID 15778709 DOI: 10.1038/Ng1532 |
0.648 |
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| 2005 |
Piccaluga P, Agostinelli C, Zupo S, Califano A, Went P, Ascani S, Basso K, Facchetti F, Falini B, Ferrarini M, Gallamini A, Klein U, Novero D, Paulli M, Tura S, et al. Gene Expression Analysis of Peripheral T-Cell Lymphoma Not Otherwise Specified Reveals the Existance of Two Subgroups Related to Different Cellular Counterparts and Recurrent PDGFRA Deregulation. Blood. 106: 1217-1217. DOI: 10.1182/Blood.V106.11.1217.1217 |
0.347 |
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| 2004 |
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. The Journal of Experimental Medicine. 199: 59-68. PMID 14707115 DOI: 10.1084/Jem.20031175 |
0.346 |
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| 2003 |
Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad J, Miljkovic V, Cattoretti G, Califano A, Dalla-Favera R. Gene expression dynamics during germinal center transit in B cells. Annals of the New York Academy of Sciences. 987: 166-72. PMID 12727636 DOI: 10.1111/J.1749-6632.2003.Tb06045.X |
0.344 |
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| 2003 |
Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad J, Miljkovic V, Cattoretti G, Califano A, Dalla-Favera R. Transcriptional analysis of the B cell germinal center reaction. Proceedings of the National Academy of Sciences of the United States of America. 100: 2639-44. PMID 12604779 DOI: 10.1073/Pnas.0437996100 |
0.333 |
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| 2003 |
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. The Journal of Clinical Investigation. 111: 529-37. PMID 12588891 DOI: 10.1172/Jci16624 |
0.369 |
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| 2002 |
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, ... ... Califano A, et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. 415: 436-42. PMID 11807556 DOI: 10.1038/415436A |
0.319 |
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| 2001 |
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 Journal of Experimental Medicine. 194: 1625-1638. PMID 11733577 DOI: 10.1084/Jem.194.11.1625 |
0.35 |
|
| 2001 |
Califano A. Advances in sequence analysis. Current Opinion in Structural Biology. 11: 330-333. PMID 11406383 DOI: 10.1016/S0959-440X(00)00210-4 |
0.327 |
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