Andrea Califano

Andrea Califano

Titles

Clyde and Helen Wu Professor of Chemical Systems Biology
Chair, Department of Systems Biology
Director, JP Sulzberger Columbia Genome Center
Associate Director, Herbert Irving Comprehensive Cancer Center

Affiliations

Department of Systems Biology
Center for Computational Biology and Bioinformatics
Center for Multiscale Analysis of Genomic and Cellular Networks (MAGNet)
JP Sulzberger Columbia Genome Center
Department of Biomedical Informatics
Department of Biochemistry and Molecular Biophysics

Executive Assistant:
Carolyn Williams
cw2449@columbia.edu

Scientific Administrative Assistant:
Seema Dhindaw
sd2751@columbia.edu


Andrea Califano is director of the Columbia University Department of Systems Biology, director of the JP Sulzberger Columbia Genome Center, director of the Center for Multiscale Analysis of Genetic Networks (MAGNet), and associate director of bioinformatics at Columbia University’s Irving Cancer Research Center. He also currently serves as a member of the Board of Scientific Advisors of the National Cancer Institute.

After completing a doctoral thesis in physics at the University of Florence on the behavior of high-dimensional dynamical systems, Dr. Califano worked at the IBM TJ Watson Research Center, where he became involved in computational biology in 1990. In 1997 he became program director of the IBM Computational Biology Center. In 2000 he co-founded First Genetic Trust, Inc. to pursue translational genomics research and infrastructure-related activities to support large-scale patient studies with genetic components.

Dr. Califano joined Columbia University in 2003 as Professor of Biomedical Informatics, with appointments in the Department of Biomedical Informatics and the Institute for Cancer Genetics. The Califano Lab uses a combination of in silico reverse engineering methods and high-throughput experimental assays to characterize gene regulatory networks that determine pathophysiological behavior in cells.

His lab has developed algorithms to dissect transcriptional, post-transcriptional, and post-translational regulatory interactions in mammalian cells and to identify master regulators of aberrant cellular events. His lab has also developed methods to elucidate the mechanisms of action of drugs and to identify genetic alterations that contribute to the aberrant activity of master regulators.

In collaboration with colleagues in the Columbia scientific community, the Califano Lab was the first to publish fully context-specific molecular interaction networks (interactomes) for normal and tumor cells in humans, including neoplastic malignancies of lymphoma and glioma subtypes. Ongoing projects in the lab aim to define the regulatory networks for neoplasmic states of the breast, ovary, prostate, germ cell, colon, and lung; for the study of pluripotency and lineage differentiation in stem cells; and for the mechanisms associated with the onset and progression of neurodegenerative diseases.

Dr. Califano is a principal investigator on several major center of excellence grants, including MAGNet, the Library of Integrated Network-Based Cellular Signatures (LINCS), and the Cancer Target Discovery and Development Center (CTD2).

Dr. Califano is very active nationally, serving on numerous editorial and scientific advisory boards, including the Board of Scientific Advisors of St. Jude Children’s Hospital, the Sanford-Burnham Institute, and the MD Anderson Department of Genomic Medicine. He has served as a co-organizer of many conferences and meetings, including the annual RECOMB-ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges; the American Association of Cancer Research Special Conference on Chemical Systems Biology; and the New York Academy of Sciences Systems Biology Discussion Group.


Education History


Selected Publications

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.

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.

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.

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.

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.

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.


Address

Columbia University Department of Systems Biology
Herbert Irving Comprehensive Cancer Center
1130 St. Nicholas Avenue
New York, NY 10032


Lab Staff

Research Staff

Research Staff

Mahalaxmi Aburi

Executive Director and Scientific Operations Manager, Califano Lab

Executive Director and Scientific Operations Manager, Califano Lab

Research Staff

Mariano Alvarez

Associate Research Scientist

Associate Research Scientist

Research Staff

Mukesh Bansal

Associate Research Scientist

Associate Research Scientist

Research Staff

Brygida Bisikirska

Associate Research Scientist

Associate Research Scientist

Research Staff

Elizabeth Evans

Translational Medicine Coordinator

Translational Medicine Coordinator

Research Staff

Manjunath Kustagi

Analyst, Senior Programmer

Analyst, Senior Programmer

Research Staff

Gonzalo Lopez

Associate Research Scientist

Associate Research Scientist

Research Staff

Sergey Pampou

Associate Research Scientist
Head, Functional Genomics, High-Throughput Screening, Columbia Genome Center

Head, Functional Genomics, High-Throughput Screening

Research Staff

Yishai Shimoni

Associate Research Scientist

Associate Research Scientist

Research Staff

Prem Subramaniam

Associate Research Scientist

Associate Research Scientist

Research Staff

David Wah

Associate Research Scientist

Associate Research Scientist

Postdoctoral Scientists

Postdoctoral Scientists

James Chi-Ping Chen

Postdoctoral Research Fellow

Postdoctoral Research Fellow

Postdoctoral Scientists

Federico Giorgi

Postdoctoral Research Scientist

Postdoctoral Research Scientist

Postdoctoral Scientists

Archana Iyer

Postdoctoral Research Fellow

Postdoctoral Research Fellow

Postdoctoral Scientists

Antonina Mitrofanova

Postdoctoral Research Scientist

Postdoctoral Research Scientist

Postdoctoral Scientists

Paola Nicoletti

Postdoctoral Research Scientist

Postdoctoral Research Scientist

Postdoctoral Scientists

Beatrice Salvatori

Postdoctoral Research Scientist

Postdoctoral Research Scientist

Postdoctoral Scientists

Yao Shen

Postdoctoral Research Scientist

Postdoctoral Research Scientist

Postdoctoral Scientists

Ruping Sun

Postdoctoral Research Scientist

Postdoctoral Research Scientist

Graduate Students

Graduate Students

Joshua Broyde

Graduate Student

Graduate Student

Graduate Students

Jing He

Graduate Student

Graduate Student

Graduate Students

Forest Ray

Graduate Student

Graduate Student

Graduate Students

William Shin

Graduate Student

Graduate Student

Graduate Students

Jung-Hoon Woo

Graduate Student

Graduate Student

Administration

Administration

Seema Dhindaw

Scientific Administrative Assistant, Califano Lab

Scientific Administrative Assistant, Califano Lab

Administration

Carolyn Williams

Executive Assistant to Andrea Califano

Executive Assistant to Andrea Califano

Former Lab Members

Former Lab Members

Pradeep Bandaru

PhD Student, Kuriyan Lab, UC Berkeley

PhD Student, Kuriyan Lab, UC Berkeley

Former Lab Members

Nike Beaubier

Shelanski Lab, Columbia University

Shelanski Lab, Columbia University

Former Lab Members

Hua-Sheng Chiu

Research Associate, Baylor College of Medicine

Research Associate, Baylor College of Medicine

Former Lab Members

Wei-Jen Chung

Computational Biologist, Genentech

Computational Biologist, Genentech

Former Lab Members

In Sock Jang

Electrical Engineer, SAGE

Electrical Engineer, SAGE

Former Lab Members

Hesed Kim

New York Stem Cell Foundation

New York Stem Cell Foundation

Former Lab Members

Ryan Kim

New York University

New York University

Former Lab Members

Celine Lefebvre

Project Manager, Institut Gustave Roussy, Villejuif, France

Project Manager, Institut Gustave Roussy, Villejuif, France

Former Lab Members

Wei-Keat Lim

Scientist, Therasis

Scientist, Therasis

Former Lab Members

Kartik Mani

Medical Student, Albert Einstein College of Medicine

Medical Student, Albert Einstein College of Medicine

Former Lab Members

Adam Margolin

Director of Systems Biology, SAGE Bionetworks

Director of Systems Biology, SAGE Bionetworks

Former Lab Members

Jose Morales

Research Scientist, Columbia University Division of Laboratory Medicine, Department of Pathology

Research Scientist, Columbia University Division of Laboratory Medicine, Department of Pathology

Former Lab Members

Gabrielle Rieckhof

Executive Director, Institute for Systems Genetics, New York University Langone Medical Center

Executive Director, Institute for Systems Genetics, New York University Langone Medical Center

Former Lab Members

Pavel Sumazin

Assistant Professor, Baylor College of Medicine

Assistant Professor, Baylor College of Medicine

Former Lab Members

Kai Weng

Merck (Rosetta Informatics)

Merck (Rosetta Informatics)

Former Lab Members

Xuerui Yang

Assistant Professor (Principal Investigator), Tsinghua University

Assistant Professor (Principal Investigator), Tsinghua University

Former Lab Members

Jiyang Yu

Senior Scientist, Pfizer, Pearl River, NY

Senior Scientist, Pfizer, Pearl River, NY

Former Lab Members

Xiang Sean Zhou

New York University

New York University


News

Columbia Launches Initiative to Advance Personalized Medicine
The Spring 2014 issue of Columbia Medicine reports on a university-wide project to identify more patient-specific ways to diagnose and treat disease, and the key role the Department of Systems Biology is playing in this effort.
Synergy between Two Genes Drives Aggressive Prostate Cancer
Using a new computational method for comparing regulatory networks in human cancer cells with those in a mouse model, researchers found that FOXM1 and CENPF together drive the most lethal prostate tumors.
Synthetic and Systems Biology: Reinventing the Code of Life
In video of this roundtable discussion at the Helix Center, professors Saeed Tavazoie and Andrea Califano join a panel of experts in discussing the intersection of systems and synthetic biology, and the role these two disciplines will play in the biological sciences.
Target Identified for Reversing Drug Resistance in Acute Lymphoblastic Leukemia
By combining computational modeling with extensive laboratory tests, researchers determined that the protein kinase AKT plays a crucial role in desensitizing tumor cells to an important cancer therapy.
Biomarker Identified for Predicting Prostate Cancer Aggressiveness
Measurements of the expression levels of three genes associated with aging can be used to better assess which patients with indolent prostate cancer require treatment.
High-Throughput Screening and Chemistry Symposium
Learn about the Columbia Genome Center's capabilities in high-throughput screening and synthetic chemistry, and some recent research at Columbia that utilized these tools.
Study Supports Cell-of-Origin Model of Prostate Cancer Heterogeneity
The cell-of-origin model suggests that the aggressiveness of a tumor may result from the type of cell from which it arises. A new study has identified molecular signatures that hold potential as biomarkers of specific prostate cancer subtypes.
Progress in Chemical Systems Biology
Proceedings of the AACR Special Conference on Chemical Systems Biology spotlight new opportunities in cancer research at the interface of chemical biology and systems biology.
Vast Hidden Network Regulates Gene Expression in Cancer
Analysis of gene expression data in glioblastoma in combination with matched microRNA profiles uncovered a posttranscriptional regulation layer of surprising magnitude, comprising more than 248,000 microRNA (miR)-mediated interactions.
Transcriptional Network for Mesenchymal Transformation of Brain Tumors
Antonio Iavarone, Andrea Califano, and colleagues have identified a small transcription factor network that is responsible for the mesenchymal behavior of glioma cells.
Andrea Califano Appointed to the NCI Board of Scientific Advisors
The board provides scientific advice on matters concerning scientific program policy, progress and future direction of the NCI’s extramural research programs, and concept review of extramural program initiatives.