Publications in the scientific and medical literature authored  or co-authored by DarwinHealth principals

MOST RECENT PUBLICATIONS

• Zeleke TZ, Pan Q, Chiuzan C, Onishi M, Li Y, Tan H, Alvarez MJ,  Honan E, Yang M, Chia PL , Mukhopadhyay P, Kelly S, Wu R , Fenn K, Trivedi MS, Accordino  M , Crew KD, Hershman DL, Maurer M, Jones S, High A, Peng J, Califano  A, Kalinsky K, Yu J and Silva J.  Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer. Nat Cancer 2023 Feb;4(2):257-275, Pubmed Article
• Landsburg DL, Barta SK, Radhakrishnan R, Batlevi C, Iyer S, Kevin K, Micallef IN, Smith SM, Stevens DA, Alvarez M, Califano A, Shen Y, Bosker G, Parker J, Soikes R, Martinez E, Roemeling R, Martell RE and Oki Y. Fimepinostat (CUDC-907) in patients with relapsed/refractory diffuse large B cell and high-grade B-cell lymphoma: report of a phase 2 trial and exploratory biomarker analyses. BR J Haematol 2021 Oct;195(2):201-209 Pubmed Article
• Laise P, Bosker G, Califano A, Alvarez MJ.A Patient-to-Model-to-Patient (PMP) Cancer Drug Discovery Protocol for Identifying and Validating Therapeutic Agents Targeting Tumor Regulatory Architecture. Curr Protoc. 2022 Sep;2(9) Pubmed Article
• Laise P, Stanifer ML, Bosker G, Sun X, Triana S, Doldan P, La Manna F, De Menna M, Realubit RB, Pampou S, Karan C, Alexandrov T, Kruithof-de Julio M, Califano A, Boulant S, Alvarez MJ. A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection. Commun Biol. 2022 Jul 19;5(1):714 Pubmed Article
• Laise P, Stanifer ML, Bosker G, Sun X, Triana S, Doldan P, La Manna F, De Menna M, Realubit RB, Pampou S, Karan C, Alexandrov T, Kruithof-de Julio M, Califano A, Boulant S, Alvarez MJ. A Model for Network-Based Identification and Pharmacological Targeting of Aberrant, Replication-Permissive Transcriptional Programs Induced by Viral Infection. Res Sq. 2022 Feb 4:rs.3.rs-1287631. Pubmed Article
• Lassman AB, Wen PY, van den Bent MJ, Plotkin SR, Walenkamp AME, Green AL, Li K, Walker CJ, Chang H, Tamir S, Henegar L, Shen Y, Alvarez MJ, Califano A, Landesman Y, Kauffman MG, Shacham S, Mau-Sørensen M.A Phase II Study of the Efficacy and Safety of Oral Selinexor in Recurrent Glioblastoma. Clin Cancer Res. 2022 Feb 1;28(3):452-460. Pubmed Article
• Landsburg DJ, Barta SK, Ramchandren R, Batlevi C, Iyer S, Kelly K, Micallef IN, Smith SM, Stevens DA, Alvarez M, Califano A, Shen Y, Bosker G, Parker J, Soikes R, Martinez E, von Roemeling R, Martell RE, Oki Y.Fimepinostat (CUDC-907) in patients with relapsed/refractory diffuse large B cell and high-grade B-cell lymphoma: report of a phase 2 trial and exploratory biomarker analyses. Br J Haematol. 2021 Oct;195(2):201-209. Pubmed Article
• Sweet K, Bhatnagar B, Döhner H, Donnellan W, Frankfurt O, Heuser M, Kota V, Liu H, Raffoux E, Roboz GJ, Röllig C, Showel MM, Strickland SA Jr, Vives S, Tang S, Unger TJ, Joshi A, Shen Y, Alvarez MJ, Califano A, Crochiere M, Landesman Y, Kauffman M, Shah J, Shacham S, Savona MR, Montesinos P. A 2:1 randomized, open-label, phase II study of selinexor vs. physician’s choice in older patients with relapsed or refractory acute myeloid leukemia. Leuk Lymphoma. 2021 Dec;62(13):3192-3203. doi: 10.1080/10428194.2021.1950706. Pubmed Article
• Paull EO, Aytes A, Jones SJ, Subramaniam PS, Giorgi FM, Douglass EF, Tagore S, Chu B, Vasciaveo A, Zheng S, Verhaak R, Abate-Shen C, Alvarez MJ, Califano A. A modular master regulator landscape controls cancer transcriptional identity. Cell. 2021 Jan 21;184(2):334-351.e20. doi: 10.1016/j.cell.2020.11.045 Pubmed Article
• Mishra V, Re DB, Le Verche V, Alvarez MJ, Vasciaveo A, Jacquier A, Doulias PT, Greco TM, Nizzardo M, Papadimitriou D, Nagata T, Rinchetti P, Perez-Torres EJ, Politi KA, Ikiz B, Clare K, Than ME, Corti S, Ischiropoulos H, Lotti F, Califano A, Przedborski S. Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow. Nat Commun. 2020 Nov 4;11(1):5579. Pubmed Article
• Laise P, Bosker G, Sun X, Shen Y, Douglass EF, Karan C, Realubit RB, Pampou S, Califano A, Alvarez MJ. The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States. bioRxiv. 2020 May 17:2020.05.12.091256 Pubmed Article
• Alvarez MJ, Yan P, Alpaugh ML, Bowden M, Sicinska E, Zhou CW, Karan C, Realubit RB, Mundi PS, Grunn A, Jäger D, Chabot JA, Fojo AT, Oberstein PE, Hibshoosh H, Milsom JW, Kulke MH, Loda M, Chiosis G, Reidy-Lagunes DL, Califano A. Reply to ‘H-STS, L-STS and KRJ-I are not authentic GEPNET cell lines’. Nat Genet. 2019 Oct;51(10):1427-1428. Pubmed Article
• Alvarez MJ, Subramaniam PS, Tang LH, Grunn A, Aburi M, Rieckhof G, Komissarova EV, Hagan EA, Bodei L, Clemons PA, Dela Cruz FS, Dhall D, Diolaiti D, Fraker DA, Ghavami A, Kaemmerer D, Karan C, Kidd M, Kim KM, Kim HC, Kunju LP, Langel Ü, Li Z, Lee J, Li H, LiVolsi V, Pfragner R, Rainey AR, Realubit RB, Remotti H, Regberg J, Roses R, Rustgi A, Sepulveda AR, Serra S, Shi C, Yuan X, Barberis M, Bergamaschi R, Chinnaiyan AM, Detre T, Ezzat S, Frilling A, Hommann M, Jaeger D, Kim MK, Knudsen BS, Kung AL, Leahy E, Metz DC, Milsom JW, Park YS, Reidy-Lagunes D, Schreiber S, Washington K, Wiedenmann B, Modlin I, Califano A. A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors. Nat Genet. 2018 Jul;50(7):979-989. Pubmed Article
• Rajbhandari, P., G. Lopez, C. Capdevila, B. Salvatori, J. Yu, R. Rodriguez-Barrueco, D. Martinez, M. Yarmarkovich, N. Weichert-Leahey, B. J. Abraham, M. J. Alvarez, A. Iyer, J. L. Harenza, D. Oldridge, K. De Preter, J. Koster, S. Asgharzadeh, R. C. Seeger, J. Wei, J. Kahn, J. Vandesompele, P. Mestdagh, R. Versteeg, A. T. Look, R. A. Young, A. Iavarone, A. Lasorella, J. M. Silva, J. M. Maris and A. Califano (2018). “Cross-cohort analysis identifies a TEAD4 ↔ MYCN positive-feedback loop as the core regulatory element of high-risk neuroblastoma.” Cancer Discov CD-16-0861.  Pubmed  Article
• Alvarez, M. J., P. Subramaniam, A. Grunn, G. Rieckhof, E. V. Kommissarova, E. A. Hagan, L. Bodei, P. A. Clemons, F. S. Dela Cruz, D. Dhall, D. Diolaiti, D. A. Fraker, A. Ghavami, D. Kaemmerer, M. Kidd, K. M. Kim, H. C. Kim, L. P. Kunju, U. Langel, Z. Li, J. Lee, V. LiVolsi, A. R. Rainey, H. Ramotti, J. Regberg, R. Roses, A. K. Rustgi, A. R. Sepulveda, S. Serra, C. Shi, X. Yuan, M. Barberis, R. Bergamaschi, A. M. Chinnaiyan, T. Detre, S. Ezzat, A. Frilling, M. Hommann, D. Jaeger, M. K. Kim, B. S. Knudsen, A. L. Kung, E. Leahy, D. C. Metz, J. W. Milsom, Y. S. Park, D. Reidy-Lagunes, S. Schreiber, L. H. Tang, K. Washington, B. Wiedenmann, I. Modlin and A. Califano (2017). “A Precision Oncology Approach to the Pharmacological Targeting of Mechanistic Dependencies in Neuroendocrine Tumors.” Nat Genet In Press.
• Ding, H., E. F. Douglass, Jr., A. M. Sonabend, A. Mela, S. Bose, C. Gonzalez, P. D. Canoll, P. A. Sims, M. J. Alvarez and A. Califano (2018). “Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.” Nat Commun 9(1): 1471.  Pubmed  Article
• Walsh LA, Alvarez MJ, et al. An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis. Cell Rep. 2017 Aug 15;20(7):1623-1640. doi: 10.1016/j.celrep.2017.07.052.  Pubmed  Article
• Bush EC, Ray F, Alvarez MJ, et al. PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens. Nat Commun. 2017 Jul 24;8(1):105. doi: 10.1038/s41467-017-00136-z.  Pubmed  Article
• Califano A, Alvarez MJ (2017). The recurrent architecture of tumour initiation, progression and drug-sensitivity. Nature Reviews Cancer 17(2):116-130. Pubmed  Article
• Alvarez, M. J., Shen, Y., Giorgi, F. M., Lachmann, A., Ding, B. B., Ye, B. H., & Califano, A. (2016). Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nature Genetics, 48(8), 838–47. Pubmed  Article
• Dela Cruz FS, Diolaiti D, Turk AT, Rainey A, Forouhar F, Ambesi-Impiombato A, Andrews SJ, Mansukhani MM, Nagy PL, Alvarez MJ, Califano A, Modzelewski B, Mitchell C, Yamashiro DJ, Marks LJ, Glade Bender JL, Kung AL (2016). A case study of an integrative genomic and experimental therapeutic approach for rare tumors: identification of vulnerabilities in a pediatric poorly differentiated carcinoma. Genome Medicine, 8:116. Pubmed  Article

REGULATORY NETWORKS

• Califano, A. (2011). Striking a balance between feasible and realistic biological models. Science Translational Medicine, 3(103), 103ps39. Pubmed  Article
• Lefebvre, C., Rieckhof, G., & Califano, A. (2012). Reverse-engineering human regulatory networks. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. Pubmed  Article
• Floratos, a., Honig, B., Pe’er, D., & Califano, a. (2012). Using systems and structure biology tools to dissect cellular phenotypes. Journal of the American Medical Informatics Association, 19(2), 171–175. Pubmed  Article
• Margolin, A. A., & Califano, A. (2007). Theory and limitations of genetic network inference from microarray data. Annals of the New York Academy of Sciences, 1115, 51–72. Pubmed  Article
• Stolovitzky, G., Prill, R. J., & Califano, A. (2009). Lessons from the DREAM2 Challenges. Annals of the New York Academy of Sciences, 1158, 159–95. Pubmed  Article
• Stolovitzky, G., Monroe, D., & Califano, A. (2007). Dialogue on reverse-engineering assessment and methods: The DREAM of high-throughput pathway inference. Annals of the New York Academy of Sciences, 1115(914), 1–22. Pubmed  Article
• Guitart-Pla, O., Kustagi, M., Rügheimer, F., Califano, A., & Schwikowski, B. (2015). The Cyni framework for network inference in Cytoscape. Bioinformatics (Oxford, England), 31(9), 1499–501. Pubmed  Article

TRANSCRIPTIONAL LAYER

• Basso, K., Margolin, A. a, Stolovitzky, G., Klein, U., Dalla-Favera, R., & Califano, A. (2005). Reverse engineering of regulatory networks in human B cells. Nature Genetics, 37(4), 382–90. Pubmed  Article
• Margolin, A. A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Dalla Favera, R., & Califano, A. (2006). ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7 Suppl 1, S7. Pubmed  Article
• Margolin, A. a, Wang, K., Lim, W. K., Kustagi, M., Nemenman, I., & Califano, A. (2006). Reverse engineering cellular networks. Nature Protocols, 1(2), 662–71. Pubmed  Article
• Zhou, X., Sumazin, P., Rajbhandari, P., & Califano, A. (2010). A systems biology approach to transcription factor binding site prediction. PloS One, 5(3), e9878. Pubmed  Article
• Saito, M., Novak, U., Piovan, E., Basso, K., Sumazin, P., Schneider, C., … Dalla-Favera, R. (2009). 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(27), 11294–9. Pubmed  Article
• Basso, K., Saito, M., Sumazin, P., Margolin, A. A., Wang, K., Lim, W.-K., … Dalla-Favera, R. (2010). Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood, 115(5), 975–84. Pubmed  Article
• FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., de Hoon, M. J. L., … Hayashizaki, Y. (2014). A promoter-level mammalian expression atlas. Nature, 507(7493), 462–70. Pubmed  Article

POST-TRANSCRIPTIONAL LAYER

• Sumazin, P., Yang, X., Chiu, H., Chung, W., Iyer, A., Llobet-Navas, D., … Califano, A. (2011). An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell, 147(2), 370–81. Pubmed  Article
• Chiu, H.-S., Llobet-Navas, D., Yang, X., Chung, W.-J., Ambesi-Impiombato, A., Iyer, A., … Sumazin, P. (2015). Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Research, 25(2), 257–67. Pubmed  Article
• Basso, K., Sumazin, P., Morozov, P., Schneider, C., Maute, R. L., Kitagawa, Y., … Dalla-Favera, R. (2009). Identification of the human mature B cell miRNome. Immunity, 30(5), 744–52. Pubmed  Article
• Klein, U., Lia, M., Crespo, M., Siegel, R., Shen, Q., Mo, T., … Dalla-Favera, R. (2010). The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell, 17(1), 28–40. Pubmed  Article
• Maute, R. L., Schneider, C., Sumazin, P., Holmes, A., Califano, A., Basso, K., & Dalla-Favera, R. (2013). 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, 110(4), 1404–1409. Pubmed  Article
• Llobet-Navas, D., Rodríguez-Barrueco, R., Castro, V., Ugalde, A. P., Sumazin, P., Jacob-Sendler, D., … Silva, J. M. (2014). The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes and Development, 28(7), 765–782. Pubmed  Article

POST-TRANSLATIONAL LAYER

• Wang, K., Saito, M., Bisikirska, B. C., Alvarez, M. J., Lim, W. K., Rajbhandari, P., … Califano, A. (2009). Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nature Biotechnology, 27(9), 829–39. Pubmed  Article
• Zhang, Q. C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C. A., … Honig, B. (2012). Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature, 490(7421), 556–60. Pubmed  Article
• Bisikirska, B. C., Adam, S. J., Alvarez, M. J., Rajbhandari, P., Cox, R., Lefebvre, C., … Califano, A. (2013). STK38 is a critical upstream regulator of MYC’s oncogenic activity in human B-cell lymphoma. Oncogene, 32(45), 5283–91. Pubmed  Article
• Wang, K., Alvarez, M. J., Bisikirska, B. C., Linding, R., Basso, K., Dalla Favera, R., & Califano, A. (2009). Dissecting the interface between signaling and transcriptional regulation in human B cells. Pacific Symposium on Biocomputing, 275, 264–75. Pubmed  Article
• Giorgi, F. M., Lopez, G., Woo, J. H., Bisikirska, B., Califano, A., & Bansal, M. (2014). Inferring protein modulation from gene expression data using conditional mutual information. PloS One, 9(10), e109569. Pubmed  Article

CELL-STATE CHECKPOINTS

• Chen, J. C., Alvarez, M. J., Talos, F., Dhruv, H., Rieckhof, G. E., Iyer, A., … Califano, A. (2014). Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks. Cell, 159(2), 402–14. Pubmed  Article
• Califano, A., Butte, A. J., Friend, S., Ideker, T., & Schadt, E. (2012). Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nature Genetics, 44(8), 841–7. Pubmed  Article
• Alvarez, M. J., Chen, J. C., & Califano, A. (2015). DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. Bioinformatics (Oxford, England), 31(24), 4032–4. Pubmed  Article
• Floratos, A., Honig, B., Pe’er, D., & Califano, A. (2012). Using systems and structure biology tools to dissect cellular phenotypes. Journal of the American Medical Informatics Association : JAMIA, 19(2), 171–5. Pubmed  Article
• Alizadeh, A. A., Aranda, V., Bardelli, A., Blanpain, C., Bock, C., Borowski, C., … Zucman-Rossi, J. (2015). Toward understanding and exploiting tumor heterogeneity. Nature Medicine, 21(8), 846–53. Pubmed  Article

TUMOR CHECKPOINTS

• Califano, A. (2011). Striking a balance between feasible and realistic biological models. Science Translational Medicine, 3(103), 103ps39. Pubmed  Article
• Cancer Target Discovery and Development Network, Schreiber, S. L., Shamji, A. F., Clemons, P. A., Hon, C., Koehler, A. N., … Posner, B. A. (2010). Towards patient-based cancer therapeutics. Nature Biotechnology, 28(9), 904–6. Pubmed  Article
• Carro, M. S., Lim, W. K., Alvarez, M. J., Bollo, R. J., Zhao, X., Snyder, E. Y., … Iavarone, A. (2010). The transcriptional network for mesenchymal transformation of brain tumours. Nature, 463(7279), 318–25. Pubmed  Article
• Aytes, A., Mitrofanova, A., Lefebvre, C., Alvarez, M. J., Castillo-Martin, M., Zheng, T., … Abate-Shen, C. (2014). Cross-Species Regulatory Network Analysis Identifies a Synergistic Interaction between FOXM1 and CENPF that Drives Prostate Cancer Malignancy. Cancer Cell, 25(5), 638–51. Pubmed  Article
• Rodriguez-Barrueco, R., Yu, J., Saucedo-Cuevas, L. P., Olivan, M., Llobet-Navas, D., Putcha, P., … Silva, J. M. (2015). Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers. Genes & Development, 29(15), 1631–48. Pubmed  Article
• Palomero, T., Lim, W. K., Odom, D. T., Sulis, M. L., Real, P. J., Margolin, A., … Ferrando, A. a. (2006). NOTCh3 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(48), 18261–18266. Pubmed  Article
• Della Gatta, G., Palomero, T., Perez-Garcia, A., Ambesi-Impiombato, A., Bansal, M., Carpenter, Z. W., … Ferrando, A. a. (2012). Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL. Nature Medicine, 18(3), 436–40. Pubmed  Article
• Compagno, M., Lim, W. K., Grunn, A., Nandula, S. V, Brahmachary, M., Shen, Q., … Pasqualucci, L. (2009). Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature, 459(7247), 717–21. Pubmed  Article
• Floc’h, N., Kinkade, C. W., Kobayashi, T., Aytes, A., Lefebvre, C., Mitrofanova, A., … Abate-Shen, C. (2012). Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model. Cancer Research, 72(17), 4483–93. Pubmed  Article
• Bisikirska, B., Bansal, M., Shen, Y., Teruya-Feldstein, J., Chaganti, R., & Califano, A. (2016). Elucidation and Pharmacological Targeting of Novel Molecular Drivers of Follicular Lymphoma Progression. Cancer Research, 76(3), 664–74. Pubmed Article
• Lim, W. K., Lyashenko, E., & Califano, A. (2009). Master regulators used as breast cancer metastasis classifier. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 504–15. Pubmed  Article
• De Keersmaecker, K., Real, P. J., Gatta, G. Della, Palomero, T., Sulis, M. L., Tosello, V., … Ferrando, A. a. (2010). The TLX1 oncogene drives aneuploidy in T cell transformation. Nature Medicine, 16(11), 1321–1327. Pubmed  Article
• Bilal, E., Dutkowski, J., Guinney, J., Jang, I. S., Logsdon, B. a., Pandey, G., … Margolin, A. a. (2013). Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Computational Biology, 9(5), e1003047. Pubmed  Article
• Ying, C. Y., Dominguez-Sola, D., Fabi, M., Lorenz, I. C., Hussein, S., Bansal, M., … Dalla-Favera, R. (2013). MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma. Nature Immunology, 14(10), 1084–92. Pubmed  Article
• Aytes, A., Mitrofanova, A., Kinkade, C. W., Lefebvre, C., Lei, M., Phelan, V., … Abate-Shen, C. (2013). 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(37), E3506–15. Pubmed  Article
• Sonabend, A. M., Bansal, M., Guarnieri, P., Lei, L., Amendolara, B., Soderquist, C., … Canoll, P. (2014). The transcriptional regulatory network of proneural glioma determines the genetic alterations selected during tumor progression. Cancer Research, 74(5), 1440–51. Pubmed  Article
• Chudnovsky, Y., Kim, D., Zheng, S., Whyte, W. A., Bansal, M., Bray, M. A., … Chheda, M. G. (2014). ZFHX4 Interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Reports, 6(2), 313–324. Pubmed  Article
• Putcha, P., Yu, J., Rodriguez-Barrueco, R., Saucedo-Cuevas, L., Villagrasa, P., Murga-Penas, E., … Silva, J. (2015). HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers. Breast Cancer Research, 17(1), 149. Pubmed  Article
• Lee, S. B., Frattini, V., Bansal, M., Castano, A. M., Sherman, D., Hutchinson, K., … Lasorella, A. (2016). An ID2-dependent mechanism for VHL inactivation in cancer. Nature, 529(7585), 172–7. Pubmed  Article

NEURODEGENERATION CHECKPOINTS

• Ikiz, B., Alvarez, M. J., Ré, D. B., Le Verche, V., Politi, K., Lotti, F., … Przedborski, S. (2015). The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis. Cell Reports, 12(2), 335–45. Pubmed  Article
• Aubry, S., Shin, W., Crary, J. F., Lefort, R., Qureshi, Y. H., Lefebvre, C., … Shelanski, M. L. (2015). Assembly and interrogation of Alzheimer’s disease genetic networks reveal novel regulators of progression. PloS One, 10(3), e0120352. Pubmed  Article
• Brichta, L., Shin, W., Jackson-Lewis, V., Blesa, J., Yap, E.-L., Walker, Z., … Greengard, P. (2015). Identification of neurodegenerative factors using translatome-regulatory network analysis. Nature Neuroscience, 18(9), 1325–33. Pubmed  Article
• Shelanski, M., Shin, W., Aubry, S., Sims, P., Alvarez, M. J., & Califano, A. (2015). A systems approach to drug discovery in Alzheimer’s disease. Neurotherapeutics : The Journal of the American Society for Experimental NeuroTherapeutics, 12(1), 126–31. Pubmed  Article

BEHAVIOR CHECKPOINTS

• Repunte-Canonigo, V., Shin, W., Vendruscolo, L. F., Lefebvre, C., van der Stap, L., Kawamura, T., … Sanna, P. P. (2015). Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks. Genome Biology, 16(1), 68. Pubmed  Article
• Chen, J., Repunte-Canonigo, V., Kawamura, T., Lefebvre, C., Shin, W., Howell, L. L., … Sanna, P. P. (2013). Hypothalamic proteoglycan syndecan-3 is a novel cocaine addiction resilience factor. Nat Commun, 4, 1955. Pubmed  Article

PHYSIOLOGIC STATES CHECKPOINTS

• Dutta, A., Le Magnen, C., Mitrofanova, A., Ouyang, X., Califano, A., & Abate-Shen, C. (2016). Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation. Science (New York, N.Y.), 352(6293), 1576–80.  Pubmed  Article
• Lefebvre, C., Rajbhandari, P., Alvarez, M. J., Bandaru, P., Lim, W. K., Sato, M., … Califano, A. (2010). A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Molecular Systems Biology, 6(377), 377. Pubmed  Article
• Kushwaha, R., Jagadish, N., Kustagi, M., Tomishima, M. J., Mendiratta, G., Bansal, M., … Chaganti, R. S. K. (2015). Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency. Stem Cells, 33(2), 367–77. Pubmed  Article
• Martínez, M. R., Corradin, A., Klein, U., Álvareza, M. J., Toffolo, G. M., di Camillo, B., … Stolovitzky, G. A. (2012). 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(7), 2672–7. Pubmed  Article
• Zhao, X., D’Arca, D., Lim, W. K., Brahmachary, M., Carro, M. S., Ludwig, T., … Lasorella, A. (2009). 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(2), 210–21. Pubmed  Article
• Cadeiras, M., von Bayern, M., Sinha, A., Shahzad, K., Latif, F., Lim, W. K., … Deng, M. C. (2011). Drawing networks of rejection – a systems biological approach to the identification of candidate genes in heart transplantation. Journal of Cellular and Molecular Medicine, 15(4), 949–56. Pubmed  Article
• Kruithof-de Julio, M., Alvarez, M. J., Galli, A., Chu, J., Price, S. M., Califano, A., & Shen, M. M. (2011). Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling. Development (Cambridge, England), 138(18), 3885–95. Pubmed  Article
• Wang, J., Kobayashi, T., Floc’h, N., Kinkade, C. W., Aytes, A., Dankort, D., … Abate-Shen, C. (2012). B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer. Cancer Research, 72(18), 4765–76. Pubmed  Article

SYSTEMS PHARMACOLOGY

• Woo, J. H., Shimoni, Y., Yang, W. S., Subramaniam, P., Iyer, A., Nicoletti, P., … Califano, A. (2015). Elucidating Compound Mechanism of Action by Network Perturbation Analysis. Cell, 162(2), 441–51. Pubmed  Article
• Bansal, M., Yang, J., Karan, C., Menden, M. P., Costello, J. C., Tang, H., … Califano, A. (2014). A community computational challenge to predict the activity of pairs of compounds. Nature Biotechnology, 32(12), 1213–1222. Pubmed  Article
• Mani, K. M., Lefebvre, C., Wang, K., Lim, W. K., Basso, K., Dalla-Favera, R., & Califano, A. (2008). A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Molecular Systems Biology, 4(169), 169. Pubmed  Article
• Piovan, E., Yu, J., Tosello, V., Herranz, D., Ambesi-Impiombato, A., Da Silva, A. C., … Ferrando, A. a. (2013). Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia. Cancer Cell, 24(6), 766–76. Pubmed  Article
• Mitrofanova, A., Aytes, A., Zou, M., Shen, M. M., Abate-Shen, C., & Califano, A. (2015). Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models. Cell Reports, 12(12), 2060–2071. Pubmed  Article
• Sonabend, A. M., Carminucci, A. S., Amendolara, B., Bansal, M., Leung, R., Lei, L., … Bruce, J. N. (2014). Convection-enhanced delivery of etoposide is effective against murine proneural glioblastoma. Neuro-Oncology, 16(9), 1210–1219. Pubmed  Article
• Nicoletti, P., Bansal, M., Lefebvre, C., Guarnieri, P., Shen, Y., Pe’er, I., … Floratos, A. (2015). ABC transporters and the proteasome complex are implicated in susceptibility to Stevens-Johnson syndrome and Toxic Epidermal Necrolysis across multiple drugs. PLoS ONE, 10(6), 1–15. Pubmed  Article

MOLECULAR CHARACTERIZATION OF CELL STATE

• Klein, U., Tu, Y., Stolovitzky, G. A., Keller, J. L., Haddad  Jr., J., Miljkovic, V., … Dalla-Favera, R. (2003). Gene expression dynamics during germinal center transit in B cells. Ann N Y Acad Sci, 987, 166–172. Pubmed  Article
• Irshad, S., Bansal, M., Castillo-Martin, M., Zheng, T., Aytes, A., Wenske, S., … Abate-Shen, C. (2013). A molecular signature predictive of indolent prostate cancer. Science Translational Medicine, 5(202), 202ra122. Pubmed  Article
• Klein, U., Tu, Y., Stolovitzky, G. A., Keller, J. L., Haddad, J., Miljkovic, V., … Dalla-Favera, R. (2003). Transcriptional analysis of the B cell germinal center reaction. Proceedings of the National Academy of Sciences of the United States of America, 100(5), 2639–44. Pubmed  Article
• Basso, K., Klein, U., Niu, H., Stolovitzky, G. A., Tu, Y., Califano, A., … Dalla-Favera, R. (2004). Tracking CD40 signaling during germinal center development. Blood, 104(13), 4088–96. Pubmed  Article
• Basso, K., Liso, A., Tiacci, E., Benedetti, R., Pulsoni, A., Foa, R., … Falini, B. (2004). 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(1), 59–68. Pubmed  Article
• Davies, S. M., Ruggieri, L., DeFor, T., Wagner, J. E., Weisdorf, D. J., Miller, J. S., … Blazar, B. R. (2002). Evaluation of KIR ligand incompatibility in mismatched unrelated donor hematopoietic transplants. Killer immunoglobulin-like receptor. Blood, 100(10), 3825–7. Pubmed  Article
• Piccaluga, P. P., Agostinelli, C., Califano, A., Carbone, A., Fantoni, L., Ferrari, S., … Pileri, S. A. (2007). Gene expression analysis of angioimmunoblastic lymphoma indicates derivation from T follicular helper cells and vascular endothelial growth factor deregulation. Cancer Research, 67(22), 10703–10710. Pubmed  Article
• Wang, Z. a, Mitrofanova, A., Bergren, S. K., Abate-Shen, C., Cardiff, R. D., Califano, A., & Shen, M. M. (2013). 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(3), 274–83. Pubmed  Article
• Sepulveda, J. L., Gutierrez-Pajares, J. L., Luna, A., Yao, Y., Tobias, J. W., Thomas, S., … Sepulveda, A. R. (2016). High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc, 29(2), 182–93. Pubmed  Article

SYSTEMS BIOLOGY METHODS

• Alvarez, M. J., Sumazin, P., Rajbhandari, P., & Califano, A. (2009). Correlating measurements across samples improves accuracy of large-scale expression profile experiments. Genome Biology, 10(12), R143. Pubmed  Article
• Margolin, A. a, Palomero, T., Sumazin, P., Califano, A., Ferrando, A. a, & Stolovitzky, G. (2009). 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(1), 244–9. Pubmed  Article
• Bansal, M., Mendiratta, G., Anand, S., Kushwaha, R., Kim, R., Kustagi, M., … Sumazin, P. (2015). Direct ChIP-Seq significance analysis improves target prediction. BMC Genomics, 16 Suppl 5(Suppl 5), S4. Pubmed  Article
• Margolin, A., & Califano, A. (2013). hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests. Interface Focus, 3(4), 20130011. Pubmed Article
• Meyer, P., Alexopoulos, L. G., Bonk, T., Califano, A., Cho, C. R., de la Fuente, A., … Stolovitzky, G. (2011). Verification of systems biology research in the age of collaborative competition. Nature Biotechnology, 29(9), 811–5. Pubmed  Article
• Boutros, P. C., Margolin, A. A., Stuart, J. M., Califano, A., & Stolovitzky, G. (2014). Toward better benchmarking: challenge-based methods assessment in cancer genomics. Genome Biology, 15(9), 462. Pubmed  Article
• Yu, J., Silva, J., & Califano, A. (2016). ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. Bioinformatics (Oxford, England), 32(2), 260–7. Pubmed  Article
• Califano, A. (2000). SPLASH: structural pattern localization analysis by sequential histograms. Bioinformatics (Oxford, England), 16(4), 341–57. Pubmed  Article
• Li, Z., Zheng, T., Califano, A., & Floratos, A. (2007). Pattern-based mining strategy to detect multi-locus association and gene x environment interaction. BMC Proceedings, 1 Suppl 1(Suppl 1), S16. Pubmed  Article
• Sosinsky, A., Honig, B., Mann, R. S., & Califano, A. (2007). 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(15), 6305–10. Pubmed  Article
• Lim, W. K., Wang, K., Lefebvre, C., & Califano, A. (2007). Comparative analysis of microarray normalization procedures: Effects on reverse engineering gene networks. Bioinformatics, 23(13), 282–288. Pubmed  Article
• Floratos, A., Smith, K., Ji, Z., Watkinson, J., & Califano, A. (2010). geWorkbench: An open source platform for integrative genomics. Bioinformatics, 26(14), 1779–1780. Pubmed  Article