Publications

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

2016

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

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

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

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

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

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

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

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

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

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

2015

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

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

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

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

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

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

111. Rodriguez-Barrueco R, Yu J, Saucedo-Cuevas LP, Olivan M, Llobet-Navas D, Putcha P, Castro V, Murga-Penas EM, Collazo-Lorduy A, Castillo-Martin M, Alvarez M, Cordon-Cardo C, Kalinsky K, Maurer M, Califano A, Silva JM. Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers. Genes Dev. 2015 Aug 1;29(15):1631-48. 

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

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

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

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

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

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

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

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

2014

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

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

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

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

98. Chen JC, Alvarez MJ, Talos F, Dhruv H, Rieckhof GE, Iyer A, Diefes KL, Aldape K, Berens M, Shen MM, Califano A. Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks. Cell. 2014 Oct 9;159(2):402-14. 

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

96. Aytes A, Mitrofanova A, Lefebvre C, Alvarez MJ, Castillo-Martin M, Zheng T, Eastham JA, Gopalan A, Pienta KJ, Shen MM, Califano A, Abate-Shen C. Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy. Cancer Cell. 2014 May 12;25(5):638-51. 

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

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

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

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

2013

91. Piovan E, Yu J, Tosello V, Herranz D, Ambesi-Impiombato A, Da Silva AC, Sanchez-Martin M, Perez-Garcia A, Rigo I, Castillo M, Indraccolo S, Cross JR, de Stanchina E, Paietta E, Racevskis J, Rowe JM, Tallman MS, Basso G, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA. Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia. Cancer Cell. 2013 Dec 9;24(6):766-76. doi: 10.1016/j.ccr.2013.10.022. Epub 2013 Nov 27.

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

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

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

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

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

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

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

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

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

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

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

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

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

2012

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

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

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

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

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

72. Della Gatta G, Palomero T, Perez-Garcia A, Ambesi-Impiombato A, Bansal M, Carpenter ZW, De Keersmaecker K, Sole X, Xu L, Paietta E, Racevskis J, Wiernik PH, Rowe JM, Meijerink JP, Califano A, Ferrando AA. Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL. Nat Med. 2012 Feb 26;18(3):436-40. 

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

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

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

2011

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

67. Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell. 2011 Oct 14;147(2):370-81. 

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

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

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

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

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

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

2010

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

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

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

57. Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol. 2010 Jun 8;6:377. 

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

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

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

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

52. Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A. The transcriptional network for mesenchymal transformation of brain tumours. Nature. 2010 Jan 21;463(7279):318-25. 

2009

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

50. Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol. 2009 Sep;27(9):829-39. 

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

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

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

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

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

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

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

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

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

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

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

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

2008

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

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

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

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

2007 

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

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

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

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

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

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

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

2006

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

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

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

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

2005 and before

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

21. Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. Reverse engineering of regulatory networks in human B cells. Nat Genet. 2005 Apr;37(4):382-90. 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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