1. A Comparative Analysis of Genome Rearrangement in Ciliates Feng, Yi 2021 Theses BiologyBioinformaticsEvolution (Biology)Gene rearrangementCiliata--GeneticsEuplotesGenetic code
2. A custom two-photon and second-harmonic microscope Nikolenko, Volodymyr; Nemet, Boaz; Yuste, Rafael 2002 Articles BiologyMedical sciencesGreen fluorescent proteinDiagnostic imaging
3. Adipocytes Secrete Lipid-Laden Exosomes and Influence Local Macrophage Behavior Flaherty, Stephen 2020 Theses BiologyLipaseMacrophagesFat cellsAdipose tissues--Analysis
4. A Genomic Map of the Effects of Linked Selection in Drosophila Elyashiv, Eyal; Sattath, Shmuel; Hu, Tina T.; Strutsovsky, Alon; McVicker, Graham; Andolfatto, Peter; Coop, Graham; Sella, Guy 2016 Articles Evolutionary geneticsBiodiversityNatural selection--Mathematical modelsGeneticsBiology
5. Allosteric Coupling, Nucleotide Binding and ATP Hydrolysis by Hsp70 Chaperones on a Structural Basis Wang, Wei 2018 Theses BiologyBiochemistryBiophysicsAllosteric regulationHeat shock proteins
6. An Aerobic Exercise: Defining the Roles of Pseudomonas aeruginosa Terminal Oxidases Jo, Jeanyoung; Price-Whelan, Alexa; Dietrich, Lars 2014 Articles BiochemistryBiologyMicrobiology
7. Analyzing Genomic Studies and a Screen for Genes that Suppress Information Loss During DNA Damage Repair Pierce, Steven 2013 Theses BiologyCytologyBioinformatics
8. An atlas of Caenorhabditis elegans chemoreceptor expression Iglesias, Berta Vidal; Aghayeva, Ulkar; Sun, Haosheng; Wang, Chen; Glenwinkel, Lori Ann; Bayer, Emily Ann; Hobert, Oliver 2018 Articles Caenorhabditis elegansChemoreceptorsNeurosciencesBiology
9. An orphan cbb3-type cytochrome oxidase subunit supports Pseudomonas aeruginosa biofilm growth and virulence Jo, Jeanyoung; Cortez, Krista Lynn; Cornell, William-Cole; Price-Whelan, Alexa M.; Dietrich, Lars 2017 Articles BiofilmsPathogenic bacteriaPseudomonas aeruginosaCytochrome oxidaseBiology
10. A Novel Platform to Perform Cancer-Relevant Synthetic Dosage Lethality Screens in Saccharomyces cerevisiae Dittmar, John 2013 Theses BioinformaticsBiologyGenetics
11. A population genetic interpretation of GWAS findings for human quantitative traits Simons, Yuval Benjamin; Bullaughey, Kevin; Hudson, Richard R.; Sella, Guy 2018 Articles GeneticsPhenotypeBiologyHuman genome
12. Applying medicinal chemistry principles to the Olfactory Code Tahirova, Narmin Tahir 2019 Theses BiologyNeurosciencesChemistryOlfactory receptorsPharmaceutical chemistry
13. Attenuation of Synaptic Potentials in Dendritic Spines Kwon, Taekyung; Sakamoto, Masayuki; Peterka, Darcy; Yuste, Rafael 2017 Articles DendritesBiophysicsNeuronsBiology
14. Auditory Tuning in Vocal Learning Songbirds Yeh, Yow-Tyng 2022 Theses BiologyNeurosciencesSongbirdsBirds--VocalizationBirdsongsSensorimotor cortex
15. A yeast phenomic model for the gene interaction network modulating CFTR-ΔF508 protein biogenesis Louie, Raymond; Guo, Jingyu; Rodgers, John; White, Rick; Shah, Najaf; Pagant, Silvere; Kim, Peter; Livstone, Michael; Dolinski, Kara; McKinney, Brett; Hong, Jeong; Sorscher, Eric; Bryan, Jennifer; Miller, Elizabeth Ann; Hartman IV, John 2012 Articles Cystic fibrosisCystic fibrosis--Genetic aspectsProteins--SynthesisMembrane proteins--SynthesisMedical geneticsGeneticsBiology
16. Bacterial tail anchors can target to the mitochondrial outer membrane Lutfullahoğlu-Bal, Güleycan; Keskin, Abdurrahman; Seferoğlu, Ayşe B.; Dunn, Cory D. 2017 Articles BiologyBacterial proteinsEndosymbiosisMitochondrial membranesEukaryotic cellsCell organelles--Formation
17. Broadening horizons: holistic viewpoints from the Biology of Genomes Carr, Ambrose James; Pe'er, Dana 2014 Articles Medical transcriptionMutation (Biology)GenomicsBiologyBiomechanics
18. Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elements Murphy, David 2021 Theses GeneticsEvolution (Biology)BiologyHuman genomeBiodiversity
19. Cardiomyopathy at the Intersection of Stem Cells and Tissue Engineering Wang, Bryan Zicheng 2022 Theses BiologyMyocardium--DiseasesStem cellsGene editingTissue engineeringHeart--Diseases--Genetic aspects
21. cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg Newcomb, Susan Elizabeth; Voutev, Roumen; Jory, Aurelie E.; Delker, Rebecca; Slattery, Matthew; Mann, Richard S. 2018 Articles Drosophila melanogaster--GeneticsGrowth factors--ReceptorsCloningBiologyGene expression
22. Complex Regulation of Pax6 Neuronal Progenitors By Rb Family Members During Corticogenesis Naglieri, Benedetta 2012 Theses BiologyCerebral cortexTumor suppressor proteinsRetinoblastomaCarcinogenesis
23. Comprehensive machine learning analysis of Hydra behavior reveals a stable basal behavioral repertoire Han, Shuting; Taralova, Ekaterina; Dupre, Christophe; Yuste, Rafael 2018 Articles NeurosciencesMachine learningAnimal behaviorBehavioral assessmentBiology
24. Computational and Imaging Methods for Studying Neuronal Populations during Behavior Han, Shuting 2019 Theses BiologyNeurosciencesMachine learningBrain--ImagingNeuropsychiatryAnimal behaviorNeurons
25. Connecting Cellular Redox State and Community Behavior in Pseudomonas aeruginosa PA14 Okegbe, Chinweike 2016 Theses MorphologyOxidation-reduction reactionBiofilmsBiology
26. Conserved pathways within bacteria and yeast as revealed by global protein network alignment Kelly, Brian P.; Sharan, Roded; Karp, Richard; Sittler, Taylor; Root, David; Stockwell, Brent R.; Ideker, Trey 2003 Articles Saccharomyces cerevisiaeHelicobacter pyloriMolecular biologyProtein-protein interactionsBiology
27. Context-dependent expression of a conditionally-inducible form of active Akt Park, Soyeon; Burke, Robert E.; Kareva, Tatyana; Kholodilov, Nikolai; Aime, Pascaline; Franke, Thomas F.; Levy, Oren Abraham; Greene, Lloyd A. 2018 Articles Protein kinasesDopaminergic neuronsNeurosciencesBiology
28. Control of Candida albicans Metabolism and Biofilm Formation by Pseudomonas aeruginosa Phenazines Morales, Diana K.; Grahl, Nora; Okegbe, Chinweike; Dietrich, Lars; Jacobs, Nicholas J.; Hogana, Deborah A. 2013 Articles BiologyBiochemistry
29. Cryo-electron microscopy and single particle reconstructions of the Leishmania major ribosome and of the encephalomyocarditis virus internal ribosome entry site bound to the 40S subunit Jobe, Amy Beth 2017 Theses Electron microscopyRibosomesLeishmaniaRNACryoelectronicsBiologyBiochemistryBiophysics
30. Cryo-electron microscopy studies of dynamical features of ribosomes during the translation process Sun, Ming 2016 Theses BiophysicsProteins--StructureRibosomes--StructureRibosomesCryoelectronicsBiologyBiochemistry
31. Cryo-EM and time-resolved cryo-EM studies on translation Chen, Bo 2015 Theses RibosomesProteins--SynthesisGenetic translationElectron microscopyBiophysicsBiology
32. Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA Zhang, Yinglu; Rataj, Katarzyna; Simpson, Gordon G.; Tong, Liang 2016 Articles Crystals--StructureProteins--StructurePlants, Flowering of--Flowering timeBiology
33. Deciphering End Resection in Double-Strand Break repair in Saccharomyces cerevisiae Chen, Huan 2015 Theses Saccharomyces cerevisiaeDNA repairDNA damageBiologyMolecular biologyGenetics
34. Depolarizing effect of neocortical chandelier neurons Woodruff, Alan; Xu, Qing; Anderson, Stewart A.; Yuste, Rafael 2009 Articles BiologyMedicineNeurosciences
35. Designer Exons Inform a Biophysical Model for Exon Definition Arias, Mauricio A. 2013 Theses Exons (Genetics)Molecular biologyBiophysicsMessenger RNABiology
36. Determining the Role of Trib3 in Neuronal Apoptosis Zareen, Neela 2012 Theses BiologyNeurosciences
37. Developing New Strategies for Engineering Novel Natural Product Metabolic Pathways Patenode, Caroline Anne 2016 Theses BiocatalysisNatural products--SynthesisBiologyMicrobiologyChemistry
38. Development of genetically intact bioengineered spores of Bacillus subtilis Flores Quijano, Juan Manuel de Jesus 2022 Theses BiologyBacillus subtilis--GeneticsPlasmids--GeneticsBiotechnologyNatural pesticidesProbiotics
39. Discovery and Optimization of Novel Small-Molecule Inhibitors of Glutathione Peroxidase 4 Lin, Annie 2023 Theses BiologyDrug resistance in cancer cellsCell deathGlutathioneCancer cells--Effect of drugs on
40. Disentangling mutation and selection in human genetic variation: promises and pitfalls Agarwal, Ipsita 2021 Theses BiologyGeneticsEvolution (Biology)Mutation (Biology)Human genomeExomes
41. Dissecting complex transcriptional responses using pathway-level scores based on prior information Bussemaker, Harmen J.; Ward, Lucas; Boorsma, Andre 2007 Articles Messenger RNADNA microarraysBiologyGenetics
42. Dissecting genetic determinants of transcription factor activity Lee, Eunjee 2013 Theses BiologyBioinformatics
43. Effect of ethanol on innate antiviral pathways and HCV replication in human liver cells Plumlee, Courtney R.; Lazaro, Catherine; Fausto, Nelson; Polyak, Stephen 2005 Articles Hepatitis C virusCellular signal transductionAlcohol--Psychological aspectsHost-virus relationshipsCytologyBiologyVirology
44. Electromechanical Coupling in Cells and Its Effects on Membrane Tension and Conductance Jones Molina, John Anthony 2021 Theses BiophysicsCytologyBiologyCell membranes
45. Elucidating the abilities of MDM2, MDMX and p21 to regulate ferroptosis Venkatesh, Divya 2020 Theses BiologyGeneticsLipids--PeroxidationCell deathCancer
46. Elucidating the Biological Function of PWWP-Domain Containing Protein Complexes Reddy, Bharat 2013 Theses BiologyGeneticsMolecular biology
47. Elucidating the roles of PARP1 and RBBP6 in the regulation of pre-mRNA 3' end processing Campigli Di Giammartino, Dafne 2014 Theses Biology
48. Environmental Stresses Disrupt Telomere Length Homeostasis Romano, Gal Hagit; Harari, Yaniv; Yehuda, Tal; Podhorzer, Ariel; Rubinstein, Linda; Shamir, Ron; Gottlieb, Assaf; Silberberg, Yael; Pe'er, Dana; Ruppin, Eytan; Sharan, Roded; Kupiec, Martin 2013 Articles HomeostasisTelomereStress (Physiology)GeneticsBiology--ClassificationBiology
49. Exploring a non-canonical mode of gene regulation mediated by mRNA transcript isoform switching in the context of mammalian development Keskin, Abdurrahman 2023 Theses BiologyEmbryonic stem cellsGene expressionMammals--GeneticsMammals--Development
50. Expression and Functional Analyses of the Entire Cadherin Gene Family in C. elegans Majeed, Maryam 2022 Theses BiologyNeurosciencesCaenorhabditis elegans--GeneticsGene expressionCadherins
51. Framework for Mapping Gene Regulation via Single-cell Genetic Screens Tan, Xiangtian 2021 Theses BiologyCytologyGenetic transcription--RegulationCancer cellsProteins--Analysis
52. Functional odor classification through a medicinal chemistry approach Poivet, Erwan E.; Tahirova, Narmin Tahir; Peterlin, Zita; Xu, Lu; Zou, Dong-Jing; Acree, Terry; Firestein, Stuart J. 2018 Articles BiochemistryPharmaceutical chemistryOdorsBiology
53. Function and Regulation of ALS/FTD-associated RNA Binding Protein FUS Tsai, Yueh-Lin 2021 Theses BiologyCytologyMolecular biologyRNA-protein interactionsAmyotrophic lateral sclerosisDementia
54. Gain-of-Function Effects of Mutant p53 Explored Using a Three-Dimensional Culture Model of Breast Cancer Freed-Pastor, William Allen 2012 Theses Biology
55. Gates and Latches: the mechanochemistry of ATP binding in kinesin 1 and Eg5 Behnke-Parks, William M. 2011 Theses BiologyBiophysicsBiochemistryKinesinMechanical chemistryCell division
56. Gene regulatory factors that control the identities of specific neuron types in Caenorhabditis elegans Zhang, Feifan 2014 Theses GeneticsBiology
57. Genetic Variant Effects on Transcription Factor Regulation Li, Xiaoting 2023 Theses BiologyHuman genetics--VariationDiseases--Risk factorsHuman genomeGenomicsGenetic transcriptionGene expression
58. HDAC6 activity is required for efficient polarization and intracellular transport of organelles in directionally migrating cells Salam, Ambar Asghar 2013 Theses Biology
59. Heterogeneity and Context-Specificity in Biological Systems Litvin, Oren 2014 Theses BiologyBioinformaticsGenetics—ResearchBacterial diversity--Genetic aspectsGenetics--Mathematical models
60. Hierarchical Modularity in the Reassembly of Hydra’s Nervous System Lovas, Jonathan Roek 2020 Theses NeurosciencesDevelopmental biologyBiologyHydraNeural circuitry
61. Human Germline Mutation and the Erratic Evolutionary Clock Moorjani, Priya Gian; Gao, Ziyue; Przeworski, Molly F. 2016 Articles Mutation (Biology)Evolution (Biology)Germ cellsBiology
62. Hydra Behavior Dataset Han, Shuting 2018 Data (Information) HydraAnimal behaviorAnimals--FoodBiology
63. Identification and Biophysical Characterization of Small Molecules Modulating Protein Disulfide Isomerase in Neurodegenerative Diseases Kaplan, Anna 2015 Theses Nervous system--DegenerationNeuroprotective agentsProtein disulfide isomeraseBiophysicsBiochemistryBiology
64. Impact of adult hippocampal neurogenesis on behavior Denny, Christine 2012 Theses BiologyNeurosciencesPsychologyDevelopmental neurobiologyHippocampus (Brain)--Growth
65. Integrin-Linked Kinase, ECM Composition, and Substrate Rigidity Regulate Focal Adhesion - Actin Coupling, Modulating Survival, Proliferation and Migration: Towards a Biophysical Cancer Biomarker Chander, Ashok Coil 2012 Theses BiologyCytologyBiophysics
66. Interpreting the Dependence of Mutation Rates on Age and Time Gao, Ziyue; Wyman, Minyoung J.; Sella, Guy; Przeworski, Molly F. 2016 Articles DNA replicationCell divisionCells--Growth--Mathematical modelsDNA repairMutation (Biology)GeneticsBiologyCytology
67. Investigating neurodegenerative diseases with small molecule modulators Letso, Reka Rebecca 2011 Theses BiologyChemistryNervous system--DegenerationCell deathMotor neurons--DiseasesSpinal muscular atrophy
68. Investigating The Role Of Signaling Pathways In Adult Stem Cells Governed By Population Asymmetry Melamed, David Eric 2018 Theses BiologyCellular signal transductionAdult stem cells
69. Landscape of the p53 transcriptome and clinical implications Regunath, Kausik 2020 Theses BiologyGenomesCancer--Genetic aspectsTumors
70. Learning cell states from high-dimensional single-cell data Levine, Jacob Harrison 2016 Theses BioinformaticsCells--MeasurementMyeloid leukemiaCells--Computer programsBiologyOncology
71. Life history effects on neutral polymorphism and divergence rates, in autosomes and sex chromosomes Amster, Guy 2019 Theses BiologySex chromosomesGenetic polymorphismsPopulation geneticsChromosomesBiodiversity
72. Light and Temperature Cues Elicit Metabolic Reprogramming in the Non-phototrophic Bacterium Pseudomonas aeruginosa Kahl, Lisa Juliane 2020 Theses BiologyMicrobiologyMetabolismBiological rhythmsPhotobiologyBacteria--PhysiologyRespiration
73. Light sheet theta microscopy for rapid high-resolution imaging of large biological samples Migliori, Bianca; Datta, Malika S.; Dupre, Christophe; Apak, Mehmet C.; Asano, Shoh; Gao, Ruixuan; Boyden, Edward S.; Hermanson, Ola; Yuste, Rafael; Tomer, Raju 2018 Articles BiologyMicroscopyBrain--ImagingHigh resolution imagingNeurosciences
74. 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
75. Mapping the whole-body muscle activity of Hydra vulgaris Szymanski, John Robert; Yuste, Rafael 2019 Data (Information) BiologyHydraMusclesEvolution (Biology)
76. Markers and Mechanisms of β-cell Dedifferentiation Fan, Jason Chen 2018 Theses MedicineBiologyCytologyPancreatic beta cells
77. Mechanical perturbation of filamin A immunoglobulin repeats 20-21 reveals potential non-equilibrium mechanochemical partner binding function Chen, Hu; Chandrasekar, Saranya; Sheetz, Michael P.; Stossel, Thomas P.; Nakamura, Fumihiko; Yan, Jie 2013 Articles Biology
78. Mechanochemical Methods for Single Molecule Biochemistry and Studies of Thiol-Disulfide Exchange in Proteins Kosuri, Pallav 2012 Theses BiophysicsBiochemistryBiology
79. Metabolic Strategies to Cope with Overcrowding in a Pseudomonas aeruginosa Biofilm Jo, Jeanyoung 2018 Theses BiologyMicrobiologyPseudomonas aeruginosaBiofilmsMicrobial respiration
80. Microtubules, Acetylation, and MEC-3 Regulated Genes in C. Elegans Mechanosensations Keller, Charles Clifford 2011 Theses BiologyNeurosciencesCaenorhabditis elegans--GeneticsMicrotubulesAcetylationTouchEukaryotic cellsGene expression
81. Mid-channel proteolysis of the L-type voltage gated calcium channel and the potential role of amyloid-β precursor protein Henckels, Kathryn 2014 Theses BiologyNeurosciences
82. Modular assembly of yeast cytochrome oxidase McStay, Gavin Peter; Su, Chen-Hsien; Tzagoloff, Alexander A. 2012 Articles Molecular biologyBiologyEvolution (Biology)
83. Modulation of touch sensitivity in Caenorhabditis elegans Chen, Xiaoyin 2013 Theses NeurosciencesGeneticsBiology
84. Molecular Basis for the Recognition of the Regulatory Stem-loop Structures in Eukaryotic Messenger RNAs Tan, Dazhi 2014 Theses Messenger RNARNA-protein interactionsEukaryotic cellsBiologyBiochemistryMolecular biology
85. Multi-level analysis of regulation of EGFR signalling during Drosophila melanogaster leg proximal-distal axis patterning Newcomb, Susan Elizabeth 2018 Theses BiologyGeneticsGrowth factors--ReceptorsEpidermal growth factorDrosophila melanogaster
86. Mutagenic Repair Outcomes of DNA Double-Strand Breaks Al-Zain, Amr M. 2021 Theses BiologyMolecular biologyDouble-stranded RNACancer--EtiologyCancer--Genetic aspectsGenomesMutagenesis
87. Mutant p53 succumbs to starvation Moon, Sung-Hwan; Prives, Carol L. 2013 Articles BiologyCytologyOncology
88. Negative regulation of gene expression by the tumor suppressor p53 Barsotti, Anthony M. 2011 Theses BiologyGene expressionAntioncogenesApoptosis
89. Novel Functions for Dynein Adaptor RILP in Neuronal Autophagy Khobrekar, Noopur V. 2021 Theses BiologyBiochemistryDyneinAutophagic vacuolesCell organelles
90. Novel functions of C9ORF72, a gene involved in ALS/FTD Fomin, Vitalay 2019 Theses BiologyBiochemistryGeneticsCytologyAmyotrophic lateral sclerosisFrontotemporal dementiaGene expression
91. Novel Regulatory Mechanisms of Cytoplasmic Dynein: A Role for the Complex Base Weil, Sarah J. 2013 Theses BiologyBiochemistry
92. On the Role of Sensory Cancellation and Corollary Discharge in Neural Coding and Behavior Enikolopov, Armen 2018 Theses NeurosciencesBiologySensory stimulationCochlear nucleus
93. Overproduction of Neurons Is Correlated with Enhanced Cortical Ensembles and Increased Perceptual Discrimination Fang, Weiqun; Yuste, Rafael 2017 Articles NeuronsVisual perceptionVisual cortexDevelopmental neurobiologyBiology
95. Photorelease of GABA with visible light using an inorganic caging group Rial Verde, Emiliano M.; Zayat, Leonardo; Etchenique, Roberto; Yuste, Rafael 2008 Articles BiologyMedicineNeurosciences
96. Physiology of Pseudomonas Aeruginosa Phenazine Production and Transport Sakhtah, Hassan 2016 Theses PhenazineMetabolitesBiofilmsPseudomonas aeruginosaBiology
97. Population genetic models of mutation rate evolution and adaptation and the impact of essential workers in the context of social distancing for epidemic control Milligan, William Robert 2023 Theses BiologyEvolution (Biology)MutagenesisGerm cellsSocial distancing (Public health)Epidemics--PreventionEpidemiologyAllelomorphismIndustrial hygiene
98. Population Genetics of Mutation Load and Quantitative Traits in Humans Simons, Yuval Benjamin 2019 Theses GeneticsBiologyHuman population geneticsMutation (Biology)
99. Portable Scanless Microscope: Two- and One-photon Imaging and Photostimulation with Spatial Light Modulators Nikolenko, Volodymyr; Peterka, Darcy; Yuste, Rafael 2009 Presentations (Communicative Events) BiologyDiagnostic imaging
100. Predicting Autonomous Promoter Activity Based on Genome-wide Modeling of Massively Parallel Reporter Data FitzPatrick, Vincent Drury 2020 Theses BiologyStatisticsPromoters (Genetics)Genomics--Statistical methodsGenetic polymorphisms