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1

Structure-based prediction of protein–protein interactions on a genome-wide scale

Zhang, Qiangfeng Cliff, Petrey, Donald, Deng, Lei, Qiang, Li, Shi, Yu, Thu, Chan Aye, Bisikirska, Brygida, Lefebvre, Celine, Accili, Domenico, Hunter, Tony, Maniatis, Tom, Califano, Andrea, Honig, Bar

Journal:

Year:

2012

Language:

english

File:

PDF, 559 KB

english, 2012

2

Nonperforming Loans and Competing Rules of Monetary Policy: a Statistical Identification Approach

Brancaccio, Emiliano, Moneta, Alessio, Lopreite, Milena, Califano, Andrea

Journal:

Structural Change and Economic Dynamics

Year:

2020

Language:

english

File:

PDF, 645 KB

english, 2020

3

PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis

Sabrina Iñigo, Mariano J. Alvarez, Bárbara Strasser, Andrea Califano, Pablo D. Cerdán

Journal:

The Plant Journal

Year:

2012

Language:

english

File:

PDF, 359 KB

english, 2012

4

Reverse engineering of regulatory networks in human B cells

Basso, Katia, Margolin, Adam A, Stolovitzky, Gustavo, Klein, Ulf, Dalla-Favera, Riccardo, Califano, Andrea

Journal:

Nature Genetics

Year:

2005

Language:

english

File:

PDF, 828 KB

english, 2005

5

Dialogue on Reverse-Engineering Assessment and Methods : The DREAM of High-Throughput Pathway Inference

GUSTAVO STOLOVITZKY, DON MONROE, ANDREA CALIFANO

Journal:

Annals of the New York Academy of Sciences

Year:

2007

Language:

english

File:

PDF, 171 KB

english, 2007

6

Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks

Chen, James C., Alvarez, Mariano J., Talos, Flaminia, Dhruv, Harshil, Rieckhof, Gabrielle E., Iyer, Archana, Diefes, Kristin L., Aldape, Kenneth, Berens, Michael, Shen, Michael M., Califano, Andrea

Journal:

Year:

2014

Language:

english

File:

PDF, 2.65 MB

english, 2014

7

Architectures and components for high power CW fiber lasers

Braglia, Andrea, Califano, Alessio, Liu, Yu, Perrone, Guido

Journal:

International Journal of Modern Physics B

Year:

2014

Language:

english

File:

PDF, 689 KB

english, 2014

8

Verification of systems biology research in the age of collaborative competition

Meyer, Pablo, Alexopoulos, Leonidas G, Bonk, Thomas, Califano, Andrea, Cho, Carolyn R, de la Fuente, Alberto, de Graaf, David, Hartemink, Alexander J, Hoeng, Julia, Ivanov, Nikolai V, Koeppl, Heinz, L

Journal:

Nature Biotechnology

Year:

2011

Language:

english

File:

PDF, 492 KB

english, 2011

9

Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks

Chen, James C., Alvarez, Mariano J., Talos, Flaminia, Dhruv, Harshil, Rieckhof, Gabrielle E., Iyer, Archana, Diefes, Kristin L., Aldape, Kenneth, Berens, Michael, Shen, Michael M., Califano, Andrea

Journal:

Year:

2016

Language:

english

File:

PDF, 62 KB

english, 2016

10

Corrigendum: Structure-based prediction of protein–protein interactions on a genome-wide scale

Zhang, Qiangfeng Cliff, Petrey, Donald, Deng, Lei, Qiang, Li, Shi, Yu, Thu, Chan Aye, Bisikirska, Brygida, Lefebvre, Celine, Accili, Domenico, Hunter, Tony, Maniatis, Tom, Califano, Andrea, Honig, Bar

Journal:

Year:

2013

Language:

english

File:

PDF, 117 KB

english, 2013

11

Multi-speed Europe is already there: Catching up and falling behind

Califano, Andrea, Gasperin, Simone

Journal:

Structural Change and Economic Dynamics

Year:

2019

Language:

english

File:

PDF, 4.90 MB

english, 2019

12

A multimodal diagnostic approach to inverted papilloma: Proposal of a novel diagnostic flow-chart

Russo, Camilla, Elefante, Andrea, Romano, Antonio, Cama, Antonia, Erra, Maurizio, Ugga, Lorenzo, Brunetti, Lisa, Motta, Gaetano, Califano, Luigi, Iengo, Maurizio, Cantone, Elena

Journal:

Current Problems in Diagnostic Radiology

Year:

2020

File:

PDF, 1.23 MB

2020

13

T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses

Katia Basso, Lara Mussolin, Antonella Lettieri, Manisha Brahmachary, Wei Keat Lim, Andrea Califano, Giuseppe Basso, Andrea Biondi, Giovanni Cazzaniga, Angelo Rosolen

Journal:

Genes, Chromosomes and Cancer

Year:

2011

Language:

english

File:

PDF, 1.94 MB

english, 2011

14

Identification of the Human Mature B Cell miRNome

Katia Basso, Pavel Sumazin, Pavel Morozov, Christof Schneider, Roy L. Maute, Yukiko Kitagawa, Jonathan Mandelbaum, Joseph Haddad Jr., Chang-Zheng Chen, Andrea Califano, Riccardo Dalla-Favera

Journal:

Year:

2009

Language:

english

File:

PDF, 902 KB

english, 2009

15

Low section of the rectum using the Contour™ device: An alternative technique

Marco Maria Lirici, Andrea Domenico Califano

Journal:

Surgical Endoscopy

Year:

2008

Language:

english

File:

PDF, 277 KB

english, 2008

16

A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature

Bárbara Strasser, Mariano J. Alvarez, Andrea Califano, Pablo D. Cerdán

Journal:

The Plant Journal

Year:

2009

Language:

english

File:

PDF, 330 KB

english, 2009

17

Gene Expression Dynamics during Germinal Center Transit in B Cells

ULF KLEIN, YUHAI TU, GUSTAVO A. STOLOVITZKY, JEFFREY L. KELLER, JOSEPH HADDAD JR., VLADAN MILJKOVIC, GIORGIO CATTORETTI, ANDREA CALIFANO, RICCARDO DALLA-FAVERA

Journal:

Annals of the New York Academy of Sciences

Year:

2003

Language:

english

File:

PDF, 1.36 MB

english, 2003

18

Tracking CD40 Signaling during Normal Germinal Center Development by Gene Expression Profiling

KATIA BASSO, ULF KLEIN, HUIFENG NIU, GUSTAVO A. STOLOVITZKY, YUHAI TU, ANDREA CALIFANO, GIORGIO CATTORETTI, RICCARDO DALLA-FAVERA

Journal:

Annals of the New York Academy of Sciences

Year:

2003

Language:

english

File:

PDF, 162 KB

english, 2003

19

Preface

Gustavo Stolovitzky, Pascal Kahlem, Andrea Califano

Journal:

Annals of the New York Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 49 KB

english, 2009

20

Lessons from the DREAM2 Challenges : A Community Effort to Assess Biological Network Inference

Gustavo Stolovitzky, Robert J. Prill, Andrea Califano

Journal:

Annals of the New York Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 1.02 MB

english, 2009

21

Mutations of multiple genes cause deregulation of NF-κB in diffuse large B-cell lymphoma

Compagno, Mara, Lim, Wei Keat, Grunn, Adina, Nandula, Subhadra V., Brahmachary, Manisha, Shen, Qiong, Bertoni, Francesco, Ponzoni, Maurilio, Scandurra, Marta, Califano, Andrea

Journal:

Year:

2009

Language:

english

File:

PDF, 552 KB

english, 2009

22

Reverse engineering cellular networks

Margolin, Adam A, Wang, Kai, Lim, Wei Keat, Kustagi, Manjunath, Nemenman, Ilya, Califano, Andrea

Journal:

Nature Protocols

Year:

2006

Language:

english

File:

PDF, 562 KB

english, 2006

23

Preface

Gustavo Stolovitzky, Andrea Califano

Journal:

Annals of the New York Academy of Sciences

Year:

2007

Language:

english

File:

PDF, 39 KB

english, 2007

24

Theory and Limitations of Genetic Network Inference from Microarray Data

ADAM A. MARGOLIN, ANDREA CALIFANO

Journal:

Annals of the New York Academy of Sciences

Year:

2007

Language:

english

File:

PDF, 173 KB

english, 2007

25

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas

Mani, Kartik M, Lefebvre, Celine, Wang, Kai, Lim, Wei Keat, Basso, Katia, Dalla-Favera, Riccardo, Califano, Andrea

Journal:

Molecular Systems Biology

Year:

2008

Language:

english

File:

PDF, 2.61 MB

english, 2008

26

Reverse-engineering human regulatory networks

Celine Lefebvre, Gabrielle Rieckhof, Andrea Califano

Journal:

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Year:

2012

Language:

english

File:

PDF, 710 KB

english, 2012

27

Data- and Model-Driven Multiresolution Processing

Andrea Califano, Rick Kjeldsen, Ruud M. Bolle

Journal:

Computer Vision and Image Understanding

Year:

1996

Language:

english

File:

PDF, 3.00 MB

english, 1996

28

The DLEU2/miR-15a/16-1 Cluster Controls B Cell Proliferation and Its Deletion Leads to Chronic Lymphocytic Leukemia

Ulf Klein, Marie Lia, Marta Crespo, Rachael Siegel, Qiong Shen, Tongwei Mo, Alberto Ambesi-Impiombato, Andrea Califano, Anna Migliazza, Govind Bhagat, Riccardo Dalla-Favera

Journal:

Year:

2010

Language:

english

File:

PDF, 1.57 MB

english, 2010

29

Hui-Huang Hsu, Advanced Data Mining Technologies in Bioinformatics, Editors: Idea Group Publishing, pp 239

Andrea Califano

Journal:

Journal of Biomedical Informatics

Year:

2007

Language:

english

File:

PDF, 75 KB

english, 2007

30

New JBI emphasis on translational bioinformatics

Edward H. Shortliffe, Andrea Califano, Lawrence Hunter

Journal:

Journal of Biomedical Informatics

Year:

2009

Language:

english

File:

PDF, 110 KB

english, 2009

31

Advances in sequence analysis

Andrea Califano

Journal:

Current Opinion in Structural Biology

Year:

2001

Language:

english

File:

PDF, 47 KB

english, 2001

32

Drawing networks of rejection – a systems biological approach to the identification of candidate genes in heart transplantation

Martin Cadeiras, Manuel von Bayern, Anshu Sinha, Khurram Shahzad, Farhana Latif, Wei Keat Lim, Hernan Grenett, Esteban Tabak, Tod Klingler, Andrea Califano, Mario C. Deng

Journal:

Journal of Cellular and Molecular Medicine

Year:

2011

Language:

english

File:

PDF, 597 KB

english, 2011

33

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

Adam A Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla Favera, Andrea Califano

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 797 KB

english, 2006

34

ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding

Adam A Margolin, Teresa Palomero, Adolfo A Ferrando, Andrea Califano, Gustavo Stolovitzky

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 186 KB

english, 2007

35

Laparo-endoscopic single site cholecystectomy versus standard laparoscopic cholecystectomy: results of a pilot randomized trial

Marco Maria Lirici, Andrea Domenico Califano, Pierluigi Angelini, Francesco Corcione

Journal:

The American Journal of Surgery

Year:

2011

Language:

english

File:

PDF, 479 KB

english, 2011

36

An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

Pavel Sumazin, Xuerui Yang, Hua-Sheng Chiu, Wei-Jen Chung, Archana Iyer, David Llobet-Navas, Presha Rajbhandari, Mukesh Bansal, Paolo Guarnieri, Jose Silva, Andrea Califano

Journal:

Year:

2011

Language:

english

File:

PDF, 2.37 MB

english, 2011

37

The N-Myc-DLL3 Cascade Is Suppressed by the Ubiquitin Ligase Huwe1 to Inhibit Proliferation and Promote Neurogenesis in the Developing Brain

Xudong Zhao, Domenico D' Arca, Wei Keat Lim, Manisha Brahmachary, Maria Stella Carro, Thomas Ludwig, Carlos Cordon Cardo, Francois Guillemot, Ken Aldape, Andrea Califano, Antonio Iavarone, Anna Lasore

Journal:

Developmental Cell

Year:

2009

Language:

english

File:

PDF, 2.18 MB

english, 2009

38

Gene Expression Profiles of Patients With Antibody-Mediated Rejection After Cardiac Transplantation

Martin Cadeiras, Manuel Bayern, Elizabeth Burke, Russell Dedrick, Anatasia Gangadin, Farhana Latif, Khurram Shazad, Anshu Sinha, Esteban G. Tabak, Charles C. Marboe, Andrea C. Califano, Mario C. Deng

Journal:

The Journal of Heart and Lung Transplantation

Year:

2008

Language:

english

File:

PDF, 422 KB

english, 2008

39

Motif-based construction of a functional map for mammalian olfactory receptors

Agatha H. Liu, Xinmin Zhang, Gustavo A. Stolovitzky, Andrea Califano, Stuart J. Firestein

Journal:

Year:

2003

Language:

english

File:

PDF, 531 KB

english, 2003

40

Report on EU–USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008)

Ruedi Aebersold, Charles Auffray, Erin Baney, Emmanuel Barillot, Alvis Brazma, Catherine Brett, Søren Brunak, Atul Butte, Andrea Califano, Julio Celis, Tanja Čufer, James Ferrell, David Galas, Daniel

Journal:

Molecular Oncology

Year:

2009

Language:

english

File:

PDF, 277 KB

english, 2009

41

Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity

Wang, Zhu A., Mitrofanova, Antonina, Bergren, Sarah K., Abate-Shen, Cory, Cardiff, Robert D., Califano, Andrea, Shen, Michael M.

Journal:

Nature Cell Biology

Year:

2013

Language:

english

File:

PDF, 1.91 MB

english, 2013

42

Simulated structure, dynamics, and vibrational spectra of liquid benzene

Chelli, Riccardo, Cardini, Gianni, Procacci, Piero, Righini, Roberto, Califano, Salvatore, Albrecht, Andreas

Journal:

The Journal of Chemical Physics

Year:

2000

Language:

english

File:

PDF, 605 KB

english, 2000

43

MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma

Ying, Carol Y, Dominguez-Sola, David, Fabi, Melissa, Lorenz, Ivo C, Hussein, Shafinaz, Bansal, Mukesh, Califano, Andrea, Pasqualucci, Laura, Basso, Katia, Dalla-Favera, Riccardo

Journal:

Nature Immunology

Year:

2013

Language:

english

File:

PDF, 1.63 MB

english, 2013

44

Exploring the Thermodynamic Limit of Hamiltonian Models: Convergence to the Vlasov Equation

Antoniazzi, Andrea, Califano, Francesco, Fanelli, Duccio, Ruffo, Stefano

Journal:

Physical Review Letters

Year:

2007

Language:

english

File:

PDF, 370 KB

english, 2007

45

Systematic and Fully Automated Identification of Protein Sequence Patterns

Hart, Reece K., Royyuru, Ajay K., Stolovitzky, Gustavo, Califano, Andrea

Journal:

Journal of Computational Biology

Year:

2000

Language:

english

File:

PDF, 1.11 MB

english, 2000

46

[IEEE 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Orlando, FL, USA (2011.02.3-2011.02.5)] 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Keynote: A systems biology approach to integrative cancer genomics

Califano, Andrea

Year:

2011

Language:

english

File:

PDF, 90 KB

english, 2011

47

RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue

Califano, Andrea, Kellis, Manolis, Stolovitzky, Gustavo

Journal:

Journal of Computational Biology

Year:

2014

Language:

english

File:

PDF, 36 KB

english, 2014

48

Toward better benchmarking: challenge-based methods assessment in cancer genomics

Boutros, Paul C, Margolin, Adam A, Stuart, Joshua M, Califano, Andrea, Stolovitzky, Gustavo

Journal:

Year:

2014

Language:

english

File:

PDF, 543 KB

english, 2014

49

Predicting protein networks in cancer

Califano, Andrea

Journal:

Nature Genetics

Year:

2014

Language:

english

File:

PDF, 659 KB

english, 2014

50

Preface

Kellis, Manolis, Califano, Andrea, Bar-Joseph, Ziv

Journal:

Journal of Computational Biology

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011