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1. Graph complexity analysis identifies an ETV5 tumor-specific network in human and murine low-grade glioma

Pan, Yuan; Duron, Christina; Bush, Erin C.; Ma, Yu; Sims, Peter A.; Gutmann, David H.; Radunskaya, Ami; Hardin, Johanna
2018
Articles
GliomasGene regulatory networksGene expressionSystem analysisSystems biologyMathematics

2. Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry

Freddolino, Peter L.; Yang, Jamie Siyu; Momen-Roknabadi, Amir; Tavazoie, Saeed
2018
Articles
Gene regulatory networksSystems biologyGene expressionStochastic processesEpigenetics

3. Systematically Mapping the Epigenetic Context Dependence of Transcription Factor Binding

Kribelbauer, Judith Franziska
2018
Theses
BiochemistryBioinformaticsBiophysicsTranscription factorsGene regulatory networksEpigenetics

4. 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

5. 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

6. Reverse engineering gene regulatory networks from measurement with missing values

Ogundijo, Oyetunji Enoch; Elmas, Abdulkadir; Wang, Xiaodong
2017
Articles
Missing observations (Statistics)Gene expressionMathematical statisticsGene regulatory networksReverse engineering

7. Confounding effects in gene expression and their impact on downstream analysis

Lachmann, Alexander
2016
Theses
Genetic regulationGenetic regulation--Data processingGene expressionGene expression--Data processingBioinformaticsGene regulatory networksGenetics

8. Noise Expands the Response Range of the Bacillus subtilis Competence Circuit

Mugler, Andrew; Kittisopikul, Mark; Hayden, Luke; Liu, Jintao; Wiggins, Chris H.; Süel, Gürol M.; Walczak, Aleksandra M.
2016
Articles
Frequency response (Dynamics)Gene regulatory networksBacillus subtilisBiologyBiochemistryMolecular biology

9. 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

10. 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