Publications

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RECENT PUBLICATIONS

  1. Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RG, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG..ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State., Cell Rep. 2014 PMID:24440720
  2. Sonabend AM, Bansal M, Guarnieri P, Lei L, Amendolara B, Soderquist C, Leung R, Yun J, Kennedy B, Sisti J, Bruce S, Bruce R, Shakya R, Ludwig T, Rosenfeld S, Sims PA, Bruce JN, Califano A, Canoll P.The Transcriptional Regulatory Network of Proneural Glioma Determines the Genetic Alterations Selected During Tumor Progression., Cancer Res. 2014 PMID:24390738
  3. Piovan E, Yu J, Tosello V, Herranz D, Ambesi-Impiombato A, Da Silva AC, Sanchez-Martin M, Perez-Garcia A, Rigo I, Castillo M, Indraccolo S, Cross JR, de Stanchina E, Paietta E, Racevskis J, Rowe JM, Tallman MS, Basso G, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA. Direct Reversal of Glucocorticoid Resistance by AKT Inhibition in Acute Lymphoblastic Leukemia.,Cancer Cell 2013 PMID:24291004
  4. Irshad S, Bansal M, Castillo-Martin M, Zheng T, Aytes A, Wenske S, Le Magnen C, Guarnieri P, Sumazin P, Benson MC, Shen MM, Califano A, Abate-Shen C.A molecular signature predictive of indolent prostate cancer., Sci Transl Med. 2013 PMID:24027026
  5. Ying CY, Dominguez-Sola D, Fabi M, Lorenz IC, Hussein S, Bansal M, Califano A, Pasqualucci L, Basso K, Dalla-Favera R.MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma., Nat Immunol 2013 PMID:23974956
  6. Aytes A, Mitrofanova A, Kinkade CW, Lefebvre C, Lei M, Phelan V, Lekaye HC, Koutcher JA, Cardiff RD, Califano A, Shen MM, Abate-Shen C.ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer.., Proc Natl Acad Sci2013 PMID:23918374
  7. Chen J, Repunte-Canonigo V, Kawamura T, Lefebvre C, Shin W, Howell LL, Hemby SE, Harvey BK, Califano A, Morales M, Koob GF, Sanna PP. Hypothalamic proteoglycan syndecan-3 is a novel cocaine addiction resilience factor., Nat Commun.2013 PMID:23736082
  8. Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA. Improving breast cancer survival analysis through competition-based multidimensional modeling., PLoS Comput Biol. 2013 PMID:23671412
  9. Califano A, Kellis M, Stolovitzky G. Preface: RECOMB systems biology, regulatory genomics, and DREAM 2012 special issue.., J Comput Biol. 2013 PMID:23641866
  10. Keniry M, Pires MM, Mense S, Lefebvre C, Gan B, Justiano K, Lau YK, Hopkins B, Hodakoski C, Koujak S, Toole J, Fenton F, Calahan A, Califano A, DePinho RA, Maurer M, Parsons R. Survival factor NFIL3 restricts FOXO-induced gene expression in cancer., Genes Dev. 2013 PMID: 23630076
  11. Wang ZA, Mitrofanova A, Bergren SK, Abate-Shen C, Cardiff RD, Califano A, Shen MM. Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity., Nat Cell Biol. 2013 PMID: 23434823
  12. Yu J, Putcha P, Califano A, Silva JM. Pooled ShRNA Screenings: Computational Analysis., Methods Mol Biol 2013 PMID: 23359167
  13. 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, PNAS 2013 Jan 7. PMID: 23297232
  14. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale, Nature 2012 Sep 30. PMID: 23023127
  15. 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 Reserch 2012 Sep 15. PMID: 22836754
  16. 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 2012 Jul 27. PMID: 22836096
  17. 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 2012 Sep 1. PMID: 22815528
  18. Della Gatta G, Palomero T, Perez-Garcia A, Ambesi-Impiombato A, Bansal M, Carpenter ZW, De Keersmaecker K, Sole X, Xu L, Paietta E, Racevskis J, Wiernik PH, Rowe JM, Meijerink JP, Califano A, Ferrando AA. Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL, Nat Med 2012 Feb 26. PMID: 22366949
  19. Califano A, Kellis M, Stolovitzky G. Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue, J Comput Biol. 2012 Feb 19. PMID: 22300312
  20. Martínez MR, Corradin A, Klein U, Álvareza MJ, Toffolo GM, di Camillo B, Califano A, Stolovitzky GA. Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis, Proc Natl Acad Sci U S A 2012 Feb 14. PMID: 22308355
  21. Lefebvre C, Rieckhof G, Califano A. Reverse-engineering human regulatory networks, Wiley Interdiscip Rev Syst Biol Med. 2012 July. PMID: 22246697
  22. Floratos A, Honig B, Pe'er D, Califano A.Using systems and structure biology tools to dissect cellular phenotypes, J Am Med Inform Assoc. 2012 Mar-Apr. PMID: 22081223
  23. Bansal M, Califano A.Genome-wide dissection of posttranscriptional and posttranslational interactions, Methods Mol Biol. 2012 PMID: 21938624
  24. Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A.An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma, Cell 2011 Oct 14. PMID: 22000015
  25. Basso K, Mussolin L, Lettieri A, Brahmachary M, Lim WK, Califano A, Basso G, Biondi A, Cazzaniga G, Rosolen A.T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses, Genes Chromosomes Cancer. 2011 Dec. PMID: 21987448
  26. Califano A.Striking a balance between feasible and realistic biological models, Sci Transl Med. 2011 Oct 5. PMID: 21974934
  27. Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G.Verification of systems biology research in the age of collaborative competition, Nat Biotechnol. 2011 Sep 8. PMID: 21904331
  28. Kruithof-de Julio M, Alvarez MJ, Galli A, Chu J, Price SM, Califano A, Shen MM.Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling, Development. 2011 Sep. PMID: 21862554
  29. Piccaluga PP, De Falco G, Kustagi M, Gazzola A, Agostinelli C, Tripodo C, Leucci E, Onnis A, Astolfi A, Sapienza MR, Bellan C, Lazzi S, Tumwine L, Mawanda M, Ogwang M, Calbi V, Formica S, Califano A, Pileri SA, Leoncini L.Gene expression analysis uncovers similarity and differences among Burkitt lymphoma subtypes, Blood. 2011 Mar 31. PMID: 21245480
  30. Kellis M, Califano A, Bar-Joseph Z.Preface: RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 special issue, J Comput Biol. 2011 Feb. PMID: 21314452
  31. Califano A.Rewiring Makes The Difference, Mol Syst Biol. 2011 Jan 18. PMID: 21245848

SELECTED PUBLICATIONS (Past 15 years)

  1. De Keersmaecker K, Real PJ, Gatta GD, Palomero T, Sulis ML, Tosello V, Van Vlierberghe P, Barnes K, Castillo M, Sole X, Hadler M, Lenz J, Aplan PD, Kelliher M, Kee BL, Pandolfi PP, Kappes D, Gounari F, Petrie H, Van der Meulen J, Speleman F, Paietta E, Racevskis J, Wiernik PH, Rowe JM, Soulier J, Avran D, Cavé H, Dastugue N, Raimondi S, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA. The TLX1 oncogene drives aneuploidy in T cell transformation, Nat Med. 2010 Oct 24. PMID: 20972433
  2. Cancer Target Discovery and Development Network, Schreiber SL, Shamji AF, Clemons PA, Hon C, Koehler AN, Munoz B, Palmer M, Stern AM, Wagner BK, Powers S, Lowe SW, Guo X, Krasnitz A, Sawey ET, Sordella R, Stein L, Trotman LC, Califano A, Dalla-Favera R, Ferrando A, Iavarone A, Pasqualucci L, Silva J, Stockwell BR, Hahn WC, Chin L, DePinho RA, Boehm JS, Gopal S, Huang A, Root DE, Weir BA, Gerhard DS, Zenklusen JC, Roth MG, White MA, Minna JD, MacMillan JB, Posner BA. Towards patient-based cancer therapeutics, Nat Biotechnol. 2010 Sep;28(9):904-6. PMID: 20829823
  3. Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers, Mol Syst Biol. 2010 Jun 8;6:377. PMID: 20531406
  4. Floratos A, Smith K, Ji Z, Watkinson J, Califano A. geWorkbench: an open source platform for integrative genomics, Bioinformatics 2010 Jul 15;26(14):1779-80. Epub 2010 May 28. PMID: 20511363
  5. Cadeiras M, von Bayern M, Sinha A, Shahzad K, Lim WK, Grenett H, Tabak E, Klingler T, Califano A, Deng MC. Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation, J Cell Mol Med. 2010 May 24. PMID: 20497491
  6. Zhou X, Sumazin P, Rajbhandari P, Califano A. A systems biology approach to transcription factor binding site prediction, PLoS One. 2010 Mar 26;5(3):e9878. PMID: 20360861
  7. Klein U, Lia M, Crespo M, Siegel R, Shen Q, Mo T, Ambesi-Impiombato A, Califano A, Migliazza A, Bhagat G, Dalla-Favera R. The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia, Cancer Cell. 2010 Jan 19;17(1):28-40. PMID: 20060366
  8. Alvarez MJ, Sumazin P, Rajbhandari P, Califano A. Correlating measurements across samples improves accuracy of large-scale expression profile experiments, Genome Biol. 2009;10(12):R143. PMID: 20042104
  9. Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A. The transcriptional network for mesenchymal transformation of brain tumours, Nature. 2010 Jan 21;463(7279):318-25. PMID: 20032975
  10. Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim WK, Kitagawa Y, Schneider C, Alvarez MJ, Califano A, Dalla-Favera R. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood. 2010 Feb 4;115(5):975-84.
  11. Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol. 2009 Sep;27(9):829-39.
  12. Zhao X, D' Arca D, Lim WK, Brahmachary M, Carro MS, Ludwig T, Cardo CC, Guillemot F, Aldape K, Califano A, Iavarone A, Lasorella A. The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell. 2009 Aug;17(2):210-21.
  13. Saito M, Novak U, Piovan E, Basso K, Sumazin P, Schneider C, Crespo M, Shen Q, Bhagat G, Califano A, Chadburn A, Pasqualucci L, Dalla-Favera R. BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11294-9
  14. Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J Jr, Chen CZ, Califano A, Dalla-Favera R. Identification of the human mature B cell miRNome. Immunity. 2009 May;30(5):744-52.
  15. 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. [http://www.ncbi.nlm.nih.gov/pubmed/19412164 Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature. 2009 Jun 4;459(7247):717-21.
  16. Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan [Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008)]. B. Mol Oncol. 2009 Feb;3(1):9-17
  17. Stolovitzky G, Prill RJ, Califano A. Lessons from the DREAM2 Challenges, Ann NY Acad Sci. 2009 Mar;1158:159-95.
  18. Stolovitzky G, Kahlem P, Califano A. The challenges of systems biology. Preface. Ann N Y Acad Sci. 2009 Mar;1158:ix-xii.
  19. Shortliffe EH, Califano A, Hunter L. New JBI emphasis on translational Bioinformatics J Biomed Inform. 2009 Apr;42(2):199-200.
  20. Lim WK, Lyashenko E, Califano A. Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput. 2009:504-15.
  21. Wang K, Alvarez MJ, Bisikirska BC, Linding R, Basso K, Dalla Favera R, Califano A. Dissecting the interface between signaling and transcriptional regulation in human B cells. Pac Symp Biocomput. 2009:264-75.
  22. Strasser B, Alvarez MJ, Califano A, Cerdán PD. A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature. Plant J. 2009 May;58(4):629-40.
  23. Margolin AA*, Palomero T, Sumazin P, Califano A*, Ferrando A*, Stolovitzky G*, ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes, Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):244-9.
  24. Cadeiras M, Burke E, Dedrick R, Gangadin A, Latif F, Shahzad K, Sinha A, Tabak EG, Marboe CC, Califano AC, Deng MC. Gene expression profiles of patients with antibody-mediated rejection after cardiac transplantation. J Heart Lung Transplant. 2008 Aug;27(8):932-4.
  25. Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW. iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One. 2008 May 28;3(5):e2265.
  26. Piccaluga PP, Califano A, Klein U, Agostinelli C, Bellosillo B, Gimeno E, Serrano S, Solè F, Zang Y, Falini B, Zinzani PL, Pileri SA. Gene expression analysis provides a potential rationale for revising the histological grading of follicular lymphomas. Haematologica. 2008 Jul;93(7):1033-8
  27. Li Z, Zheng T, Califano A, Floratos A. Pattern-based mining strategy to detect multi-locus association and gene x environment interaction. BMC Proc. 2007;1 Suppl 1:S16
  28. Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A. A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol. 2008;4:169
  29. Piccaluga PP, Agostinelli C, Califano A, Carbone A, Fantoni L, Ferrari S, Gazzola A, Gloghini A, Righi S, Rossi M, Tagliafico E, Zinzani PL, Zupo S, Baccarani M, Pileri SA. Gene expression analysis of angioimmunoblastic lymphoma indicates derivation from T follicular helper cells and vascular endothelial growth factor deregulation. Cancer Res. 2007 Nov 15;67(22):10703-10.
  30. Stolovitzky GA, Monroe D, Califano A, Dialogue on Reverse Engineering Assessment and Methods: the DREAM of high throughput pathway inference Ann N Y Acad Sci. 2007 Oct 9.
  31. Margolin A and Califano A, Theory and Limitations of Genetic Network Inference from Microarray Data Ann N Y Acad Sci. 2007 Oct 9.
  32. Lim WK, Wang K, Lefebvre C, and Califano A Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks Bioinformatics. 2007 Jul 1;23(13):i282-8.
  33. Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A. Reverse engineering cellular networks Nature Protocols. 2006. 1(2):662-671.
  34. Sosinsky A, Honig B, Mann RS, Califano A. Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6305-10.
  35. Piccaluga PP, Agostinelli C, Califano A, Rossi M, Basso K, Zupo S, Went P, Klein U, Zinzani PL, Baccarani M, Dalla Favera R, and Pileri SA Gene Expression Analysis Of Peripheral T-Cell Lymphoma/Unspecified Reveals Distinct Profiles And New Potential Therapeutic Targets Journal of Clinical Investigation 2007, Volume 117, Number 3, Pages 823 - 834
  36. Banerjee N. and Califano A. Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment- Independent Conservation Maps 1996 RECOMB Comparative Genomics Satellite Worshop, Montreal (CA). .
  37. Palomero T, Lim WK, Odom DT, Sulis ML, Real PJ, O'Neal J, Neuberg D, Margolin AA, Weng A, Aster JC, Sigaux F, Soulier J, Look AT, Young R, Califano A and Ferrando A NOTCH1 directly regulates MYC expression and controls oncogenic cell growth Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18261-6. Epub 2006 Nov 17. Erratum in: Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):4240.
  38. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7.
  39. Basso Katia, Margolin Adam A, Stolovitzky Gustavo, Klein Ulf, Dalla-Favera Riccardo, & Califano Andrea Reverse engineering of regulatory networks in human B cells Nature Genetics 2005 37, 382 - 390
  40. Poppema Sibrand, L Kluiver Joost, Atayar Cigdem, Berg Anke van den, Rosenwald Andreas, Hummel Michael, Lenze Dido, Lammert Hetty, Stein Harald, Joos Stephan, Barth Thomas, Dyer Martin, Lichter Peter, Klein Uwe, Cattoretti Giorgio, Gloghini Annunziata, Tu Yuhai, Stolovitzky Gustavo A, Califano Andrea, Carbone Antonino, Dalla-Favera Ricardo, Melzner Ingo, Bucur Alexandra J, Brüderlein Silke, Dorsch Karola, Hasel Cornelia, Barth Thomas FE, Leithäuser Frank, Möller Peter Report: workshop on mediastinal grey zone lymphoma' European Journal Of Haematology 2005 Volume 75:s66 Page 45 - July 2005
  41. Katia Basso, Ulf Klein, Huifeng Niu, Gustavo A. Stolovitzky, Yuhai Tu, Andrea Califano, Giorgio Cattoretti, and Riccardo Dalla-FaveraTracking CD40 signaling during germinal center development Blood 2004 , 15 December 2004, Vol. 104, No. 13, pp. 4088-4096.
  42. Basso Katia, Liso Arcangelo, Tiacci Enrico, Benedetti Roberta, Pulsoni Alessandro, Foa Robin, Di Raimondo Francesco, Ambrosetti Achille, Califano Andrea, Klein Ulf, Dalla Favera Riccardo, and Falini Brunangelo Gene Expression Profiling of Hairy Cell Leukemia Reveals a Phenotype Related to Memory B Cells with Altered Expression of Chemokine and Adhesion Receptors J. Exp. Med. 2004, Volume 199, Number 1, 59-68
  43. Wang K, Banerjee N, Margolin AA, Nemenman I, Califano A, Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes, RECOMB 2005.
  44. Califano Andrea, and Liu Agatha H. CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationships Journal of Computational Biology 2003, Vol. 10, No. 1: 21-45
  45. Liu A, Zhang X., Stolovitzky G, Califano A, and Firestein S, Motif-Based Construction of a Functional Map for Mammalian Olfactory Receptors, Genomics. 2003 May;81(5):443-56.
  46. Klein Ulf, Tu Yuhai, Stolovitzky Gustavo A., Keller Jeffrey L., Haddad Jr. Joseph, Miljkovic Vladan, Cattoretti Giorgio, Califano Andrea, and Dalla-Favera Riccardo Transcriptional analysis of the B cell germinal center reaction Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2639-44.
  47. Küppers Ralf, Klein Ulf, Schwering Ines, Distler Verena, Bräuninger Andreas, Cattoretti Giorgio, Tu Yuhai, Stolovitzky Gustavo A., Califano Andrea, Hansmann Martin-Leo, and Dalla-Favera Riccardo Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling J Clin Invest. 2003 February 15; 111(4): 529–537.
  48. Buchanan A, Califano A, Kahn J, McPherson E, Robertson J, Brody B. Pharmacogenetics: ethical issues and policy options. Kennedy Inst Ethics J. 2002 Mar;12(1):1-15.
  49. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, Biegel JA, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G, Louis DN, Mesirov JP, Lander ES, Golub TR. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 2002, Jan 24;415(6870):436-42.
  50. Klein U, Tu Y, Stolovitzky GA, Mattioli M, Cattoretti G, Husson H, Freedman A, Inghirami G, Cro L, Baldini L, Neri A, Califano A, Dalla-Favera R. Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells. J Exp Med. 2001 Dec 3;19(11):1625-38.
  51. Califano A Advances in Sequence Analysis Current Opinion in Structural Biology 2001. 11(3):330-3.
  52. Liu A and Califano A, Functional Classification of Proteins by pattern discovery and top-down clustering of primary sequences, IBM Systems Journal, special issue on Deep Computing for the Life Sciences, Volume 40, Number 2, 2001 40(2):379-393
  53. Hart R, Royyuru AK, Stolovitzky G, and Califano A, Systematic and Automated Discovery of Protein Sequence Patterns, in 'J Comput. Biol. 2000 and ISMB 2000;7(3-4):585-600.
  54. Califano A, Stolovitzky S and Tu Y, Analysis of Gene Expression Microarrays for Phenotype Classification, Proc Int Conf Intell Syst Mol Biol. 2000
  55. Califano A Splash, Structural Pattern Localization Analysis by Sequential Histograms Bioinformatics 2000. Apr;16(4):341-57.
  56. Califano A, Germain B, and Colville S A High-Dimensional Indexing Scheme for Scalable Fingerprint-Based Identification Lecture Notes in Computer Science. 1997 1351:32-39.
  57. Germain RS, Califano A, and Colville S Fingerprint Matching Using Transformation Parameter Clustering IEEE Journal of Computational Science and Engineering. 1997 4(4):42-49.
  58. Califano A, Kjeldsen R, and Bolle RM Data- and model-driven multiresolution processing Journal of Computer Vision and Image Understanding 1996. 63(1):27-49.
  59. Califano A, Rigoutsos I. [FLASH: a fast look-up algorithm for string homology]. Proc Int Conf Intell Syst Mol Biol. 1993;1:56-64.
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