1. A Comparative Analysis of Genome Rearrangement in Ciliates Feng, Yi 2021 Theses BiologyBioinformaticsEvolution (Biology)Gene rearrangementCiliata--GeneticsEuplotesGenetic code
2. Characterizing molecular drivers of clinical outcome in pediatric acute leukemias by systems biology and machine learning Alloy, Alexandre Paul 2021 Theses BioinformaticsLeukemia--Genetic aspectsLeukemia in childrenMachine learningAcute leukemia
3. Systems Genetics of DNA Damage Tolerance – Cisplatin, RAD5 & CRISPR-mediated Nonsense Bryant, Eric Edward 2019 Theses GeneticsBioinformaticsBiology--ClassificationDNA damageCisplatinCRISPR (Genetics)
4. A Single-Cell Immune Map of Normal and Cancerous Breast Reveals an Expansion of Phenotypic States Driven by the Tumor Microenvironment Carr, Ambrose James 2018 Theses BioinformaticsOncologyComputer scienceImmunologyTumors
5. The generation and phenotypic effect of human genetic mutations Chen, Chen 2018 Theses BioinformaticsComputer scienceMutation (Biology)Human genetics--VariationMachine learning
6. Learning cell states from high-dimensional single-cell data Levine, Jacob Harrison 2016 Theses BioinformaticsCells--MeasurementMyeloid leukemiaCells--Computer programsBiologyOncology
7. Systems Biology Approaches to The Study of Neurological Disorders and Somatic Cell Reprogramming Shin, William Kihoon 2016 Theses Cell hybridizationCentral nervous system--DiseasesNervous system--DegenerationGenetic transcriptionBioinformaticsNeurosciencesBiology--Classification
8. Context Sensitive Modeling of Cancer Drug Sensitivity Chen, Bo-Juen; Pe'er, Dana; Litvin, Oren; Ungar, Lyle 2015 Articles Drugs--Dose-response relationshipDrug interactionsMelanoma--TreatmentCancer--Chemotherapy--Mathematical modelsCancer cells--Effect of drugs onOncologyBioinformatics
9. Global Survey of Cell Death Mechanisms Reveals Metabolic Regulation of GPX4-Dependent Ferroptosis Shimada, Kencihi 2015 Theses HomeostasisMetabolismBioinformaticsPharmacologyCell deathMolecular biology
10. Heterogeneity and Context-Specificity in Biological Systems Litvin, Oren 2014 Theses BiologyBioinformaticsGenetics—ResearchBacterial diversity--Genetic aspectsGenetics--Mathematical models
11. viSNE and Wanderlust, two algorithms for the visualization and analysis of high-dimensional single-cell data Amir, El-ad David 2014 Theses ImmunologyBioinformatics
12. Analyzing Genomic Studies and a Screen for Genes that Suppress Information Loss During DNA Damage Repair Pierce, Steven 2013 Theses BiologyCytologyBioinformatics
13. A Novel Platform to Perform Cancer-Relevant Synthetic Dosage Lethality Screens in Saccharomyces cerevisiae Dittmar, John 2013 Theses BioinformaticsBiologyGenetics
14. Dissecting genetic determinants of transcription factor activity Lee, Eunjee 2013 Theses BiologyBioinformatics
15. The COMBREX Project: Design, Methodology, and Initial Results Anton, Brian P.; Chang, Yi-Chien; Brown, Peter; Choi, Han-Pil; Faller, Lina L.; Guleria, Jyotsna; Hu, Zhenjun; Klitgord, Niels; Levy-Moonshine, Ami; Maksad, Almaz; Mazumdar, Varun; McGettrick, Mark; Osmani, Lais; Pokrzywa, Revonda; Rachlin, John; Swaminathan, Rajeswari; Allen, Benjamin; Housman, Genevieve; Monahan, Caitlin; Rochussen, Krista; Tao, Kevin; Bhagwat, Ashok S.; Brenner, Steven E.; Columbus, Linda; de Crécy-Lagard, Valérie; Ferguson, Donald; Fomenkov, Alexey; Gadda, Giovanni; Morgan, Richard D.; Osterman, Andrei L.; Rodionov, Dmitry A.; Rodionova, Irina A.; Rudd, Kenneth E.; Söll, Dieter; Spain, James; Xu, Shuang-yong; Bateman, Alex; Blumenthal, Robert M.; Bollinger, J. Martin; Chang, Woo-Suk; Ferrer, Manuel; Friedberg, Iddo; Galperin, Michael Y.; Gobeill, Julien; Haft, Daniel; Hunt, John F.; Karp, Peter; Klimke, William; Krebs, Carsten; Macelis, Dana; Madupu, Ramana; Martin, Maria J.; Miller, Jeffrey H.; O'Donovan, Claire; Palsson, Bernhard; Ruch, Patrick; Setterdahl, Aaron; Sutton, Granger; Tate, John; Yakunin, Alexander; Tchigvintsev, Dmitri; Plata, German Alonso; Hu, Jie; Greiner, Russell; Horn, David; Sjölander, Kimmen; Salzberg, Steven L.; Vitkup, Dennis; Letovsky, Stanley; Segrè, Daniel; DeLisi, Charles; Roberts, Richard J.; Steffen, Martin; Kasif, Simon 2013 Articles Nucleotide sequenceGenomics--Data processingMicrobial proteinsMolecular biologyMicrobiologyBioinformatics
16. JISTIC: Identification of Significant Targets in Cancer Pe'er, Dana; Mozes, Eyal; Sanchez-Garcia, Felix; Akavia, Uri David 2010 Articles OncologyBioinformatics
17. Correlating measurements across samples improves accuracy of large-scale expression profile experiments Alvarez, Mariano; Sumazin, Pavel; Rajbhandari, Presha; Califano, Andrea 2009 Articles GeneticsBioinformatics
18. Detecting transcriptionally active regions using genomic tiling arrays Halasz, Gabor; van Batenburg, Marinus F.; Perusse, Joelle; Hua, Sujun; Lu, Xiang-Jun; White, Kevin P.; Bussemaker, Harmen J. 2006 Articles Genetic transcriptionDNA probesGenomicsDNA microarraysGeneticsBioinformatics
19. Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference Lehner, Ben; Calixto, Andrea; Crombie, Catriona; Tischler, Julia; Fortunato, Angelo; Chalfie, Martin; Fraser, Andrew 2006 Articles Caenorhabditis elegansGenomicsRNA intereferenceGeneticsBioinformaticsBiology
20. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data Gao, Feng; Foat, Barrett; Bussemaker, Harmen J. 2004 Articles BioinformaticsGenetics