Andrea Califano - Publications

Affiliations: 
Biochemistry & Molecular Biophysics Columbia University, New York, NY 
Area:
gene regulatory models
Website:
http://wiki.c2b2.columbia.edu/califanolab/index.php/Califano_Info

121 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 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. 51: 411-412. PMID 31433971 DOI: 10.1016/j.immuni.2019.08.004  0.68
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  0.48
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  0.44
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  0.44
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  0.68
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  0.4
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  0.68
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  0.68
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  0.68
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  0.68
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  0.4
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  0.44
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  0.68
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  0.48
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  0.6
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  0.48
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  0.48
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  0.4
2016 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. PMID 26735018 DOI: 10.1038/nature16475  0.48
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  0.48
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  0.48
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  0.68
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  0.48
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  0.68
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  0.48
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  0.4
2015 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 Biology. 16: 68. PMID 25886852 DOI: 10.1186/s13059-015-0593-5  0.48
2015 Califano A, Kellis M, Stolovitzky G. Preface: RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2014 Special Issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 251-2. PMID 25844665 DOI: 10.1089/cmb.2015.020P  0.48
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  0.48
2015 Shelanski M, Shin W, Aubry S, Sims P, Alvarez MJ, Califano A. A systems approach to drug discovery in Alzheimer's disease. Neurotherapeutics : the Journal of the American Society For Experimental Neurotherapeutics. 12: 126-31. PMID 25608936 DOI: 10.1007/s13311-014-0335-5  0.48
2015 Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B. The Cyni framework for network inference in Cytoscape. Bioinformatics (Oxford, England). 31: 1499-501. PMID 25527096 DOI: 10.1093/bioinformatics/btu812  0.4
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  0.48
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  0.48
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  0.48
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  0.44
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  0.48
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  0.48
2014 Repunte-Canonigo V, Lefebvre C, George O, Kawamura T, Morales M, Koob GF, Califano A, Masliah E, Sanna PP. Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats. Molecular Neurodegeneration. 9: 26. PMID 24980976 DOI: 10.1186/1750-1326-9-26  0.48
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  0.48
2014 Califano A, Kellis M, Stolovitzky G. RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 21: 371-2. PMID 24784777 DOI: 10.1089/cmb.2014.009p  0.48
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  0.48
2014 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, ... ... Califano A, et al. The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes & Development. 28: 765-82. PMID 24636986 DOI: 10.1101/gad.237404.114  0.48
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  0.48
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  0.48
2014 Ikiz B, Alvarez MJ, Ré DB, LeVerche 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 InVitro Models of Amyotrophic Lateral Sclerosis Cell Reports. DOI: 10.1016/j.celrep.2015.06.019  0.48
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  0.48
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  0.48
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  0.48
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  0.32
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  0.48
2013 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. Nature Communications. 4: 1955. PMID 23736082 DOI: 10.1038/ncomms2955  0.48
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  0.48
2013 Califano A, Kellis M, Stolovitzky G. Preface: RECOMB systems biology, regulatory genomics, and DREAM 2012 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 373-4. PMID 23641866 DOI: 10.1089/cmb.2013.008p  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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 (2013) 5, (203er9)) Science Translational Medicine. 5. DOI: 10.1126/scitranslmed.3007585  0.48
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 (2013) 5, (203er9)) Science Translational Medicine. 5. DOI: 10.1126/scitranslmed.3007585  0.4
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2012 Califano A, Kellis M, Stolovitzky G. Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 101. PMID 22300312 DOI: 10.1089/cmb.2012.010p  0.48
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  0.48
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  0.4
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  0.48
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  0.48
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  0.4
2011 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, et al. Verification of systems biology research in the age of collaborative competition. Nature Biotechnology. 29: 811-5. PMID 21904331 DOI: 10.1038/nbt.1968  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.4
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  0.48
2010 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. 17: 28-40. PMID 20060366 DOI: 10.1016/j.ccr.2009.11.019  0.32
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  0.48
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  0.48
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  0.48
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  0.48
2009 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. Developmental Cell. 17: 210-21. PMID 19686682 DOI: 10.1016/j.devcel.2009.07.009  0.48
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  0.32
2009 Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J, Chen CZ, Califano A, Dalla-Favera R. Identification of the human mature B cell miRNome. Immunity. 30: 744-52. PMID 19446474 DOI: 10.1016/j.immuni.2009.03.017  0.48
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  0.4
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  0.48
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  0.48
2009 Stolovitzky G, Kahlem P, Califano A. The challenges of systems biology. Preface. Annals of the New York Academy of Sciences. 1158: ix-xii. PMID 19348626 DOI: 10.1111/j.1749-6632.2009.04470.x  0.48
2009 Shortliffe EH, Califano A, Hunter L. New JBI emphasis on translational bioinformatics. Journal of Biomedical Informatics. 42: 199-200. PMID 19298948 DOI: 10.1016/j.jbi.2009.03.001  0.48
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  0.4
2009 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. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 264-75. PMID 19209707  0.48
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  0.48
2008 Cadeiras M, Bayern M, Burke E, Dedrick R, Gangadin A, Latif F, Latif F, Shahzad K, Shazad K, Sinha A, Tabak EG, Marboe CC, Califano AC, Deng MC. Gene expression profiles of patients with antibody-mediated rejection after cardiac transplantation. The Journal of Heart and Lung Transplantation : the Official Publication of the International Society For Heart Transplantation. 27: 932-4. PMID 18656812 DOI: 10.1016/j.healun.2008.05.001  0.48
2008 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, et al. iTools: a framework for classification, categorization and integration of computational biology resources. Plos One. 3: e2265. PMID 18509477 DOI: 10.1371/journal.pone.0002265  0.48
2008 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. 93: 1033-8. PMID 18492688 DOI: 10.3324/haematol.12754  0.48
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  0.48
2007 Li Z, Zheng T, Califano A, Floratos A. Pattern-based mining strategy to detect multi-locus association and gene x environment interaction. Bmc Proceedings. 1: S16. PMID 18466505  0.4
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  0.48
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  0.48
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  0.48
2007 Lim WK, Wang K, Lefebvre C, Califano A. Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics (Oxford, England). 23: i282-8. PMID 17646307 DOI: 10.1093/bioinformatics/btm201  0.44
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2004 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. 104: 4088-96. PMID 15331443 DOI: 10.1182/blood-2003-12-4291  0.48
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  0.32
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  0.48
2003 Liu AH, Zhang X, Stolovitzky GA, Califano A, Firestein SJ. Motif-based construction of a functional map for mammalian olfactory receptors. Genomics. 81: 443-56. PMID 12706103 DOI: 10.1016/S0888-7543(03)00022-3  0.48
2003 Liu AH, Califano A. CASTOR: clustering algorithm for sequence taxonomical organization and relationships. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 21-45. PMID 12676049 DOI: 10.1089/106652703763255651  0.48
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  0.48
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  0.48
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  0.48
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