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1. Generation of pralatrexate resistant T-cell lymphoma lines reveals two patterns of acquired drug resistance that is overcome with epigenetic modifiers

Scotto, Luigi; Kinahan, Cristina; Casadei, Beatrice; Mangone, Michael; Douglass Jr, Eugene F.; Vundavalli, Murty V.; Marchi, Enrica; Ma, Helen; Chauncey, George; Montanari, Francesca; Califano, Andrea; O’Connor, Owen Anthony
2020
Articles
LymphomasDrug resistance

2. Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis

Bansal, Mukesh; He, Jing; Peyton, Michael; Kustagi, Manjunath; Iyer, Archana; Comb, Michael; White, Michael; Minna, John D.; Califano, Andrea
2019
Articles
AdenocarcinomaMolecular biologyLungs--Cancer--Molecular aspectsProteomics

3. Accelerated parallel algorithm for gene network reverse engineering

He, Jing; Zhou, Zhou; Reed, Michael K.; Califano, Andrea
2017
Articles
Parallel programming (Computer science)Gene regulatory networksGene expression--Data processingSystems biology

4. A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue

Talos, Flaminia; Mitrofanova, Antonina; Califano, Andrea; Shen, Michael M.
2017
Articles
Gene regulatory networksGenetic regulation--Data processing

5. Systematic, network-based characterization of therapeutic target inhibitors

Shen, Yao; Alvarez, Mariano; Bisikirska, Brygida; Lachmann, Alexander; Realubit, Ronald B.; Pampou, Sergey Yu; Coku, Jorida; Karan Jr., Charles; Califano, Andrea
2017
Articles
TherapeuticsGene expressionComputational biologyBioinformatics

6. ABC Transporters and the Proteasome Complex Are Implicated in Susceptibility to Stevens–Johnson Syndrome and Toxic Epidermal Necrolysis across Multiple Drugs

Nicoletti, Paola; Bansal, Mukesh; Lefebvre, Celine; Guarnieri, Paolo; Shen, Yufeng; Pe’er, Itsik; Califano, Andrea; Floratos, Aristidis
2015
Articles
Drugs--Side effectsATP-binding cassette transportersGene expressionGenetic regulationApoptosisToxic epidermal necrolysisBiology--ClassificationBioinformaticsGenetics

7. Assembly and Interrogation of Alzheimer’s Disease Genetic Networks Reveal Novel Regulators of Progression

Aubry, Soline; Shin, William Kihoon; Crary, John F.; Lefort, Roger; Qureshi, Yasir H.; Lefebvre, Celine; Califano, Andrea; Shelanski, Michael L.
2015
Articles
Systems biologyGene regulatory networksAlzheimer's disease--ResearchNeurosciencesChemical engineeringBiochemistry

8. Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks

Repunte-Canonigo, Vez; Shin, William Kihoon; Vendruscolo, Leandro F.; Lefebvre, Celine; van der Stap, Lena; Kawamura, Tomoya; Schlosburg, Joel E.; Alvarez, Mariano Javier; Koob, George F.; Califano, Andrea; Sanno, Pietro Paolo
2015
Articles
Gene regulatory networksAlcoholismBiology--Classification

9. Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats

Repunte-Canonigo, Vez; Lefebvre, Celine; George, Olivier; Kawamura, Tomoya; Morales, Marisela; Koob, George; Califano, Andrea; Masliah, Eliezer; Sanna, Pietro
2014
Articles
Nervous system--DiseasesHIV (Viruses)Neurosciences

10. Inferring Protein Modulation from Gene Expression Data Using Conditional Mutual Information

Giorgi, Federico M.; Lopez, Gonzalo; Woo, Jung H.; Bisikirska, Brygida; Califano, Andrea; Bansal, Mukesh
2014
Articles
Gene expressionGenetic algorithmsTranscription factorsBioinformaticsGeneticsMolecular biology