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1. Atf5 Links Olfactory Receptor Induced Stress Response to Proper Neuronal Function

Kahiapo, Jerome Keoki
2020
Theses
CytologyBiochemistryMolecular biologyOlfactory receptor genesSmellSensory neuronsMammals

2. Structural and Biophysical Studies of Hair Cell Mechanotransduction Proteins

Dionne, Gilman
2020
Theses
BiochemistryBiophysicsProteinsCellular signal transduction--Research

3. Biomolecular NMR spectroscopy: Application to the study of the piRNA-pathway protein GTSF1, and backbone and side-chain spin relaxation methods development

O'Brien, Paul
2019
Theses
BiophysicsBiochemistryNuclear magnetic resonance spectroscopyProteins--StructureMolecular dynamics

4. 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

5. Solving Challenging Structures using Single-Particle Cryogenic Electron Microscopy

Tan, Yong Zi
2019
Theses
BiochemistryBiophysicsElectron microscopyMacromolecules--StructureRibosomesMembrane proteinsCytology--Technique

6. Accurate and sensitive quantification of protein-DNA binding affinity

Rastogi, Chaitanya; Rube, Hans Tomas; Kribelbauer, Judith Franziska; Crocker, Justin; Loker, Ryan Edmund; Martini, Gabriella D.; Laptenko, Oleg; Freed-Pastor, William Allen; Prives, Carol L.; Stern, David L.; Mann, Richard S.; Bussemaker, Harmen J.
2018
Articles
Transcription factorsDNA-protein interactionsProtein bindingProbabilities--Mathematical models

7. Balance Control Mediated by Vestibular Circuits Directing Limb Extension or Antagonist Muscle Co-activation

Murray, Andrew; Croce, Katherine; Belton, Timothy; Akay, Turgay; Jessell, Thomas M.
2018
Articles
Motor ability--Physiological aspectsMotor ability--TestingNeurochemistryMolecular biologyVestibular nucleiEquilibrium (Physiology)Neurosciences

8. Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

Yuan, Yuan; Xie, Shirley; Darnell, Jennifer C.; Darnell, Andrew J.; Saito, Yuhki; Phatnani, Hemali P.; Murphy, Elisabeth A.; Zhang, Chaolin; Maniatis, Tom; Darnell, Robert B.
2018
Articles
Motor neuronsCytoskeletonSeptinsRNA splicingBiology

9. 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

10. Developing a molecular dynamics force field for both folded and disordered protein states

Robustelli, Paul; Piana, Stefano; Shaw, David Elliot
2018
Articles
Molecular dynamicsComputer simulationProteinsProtein folding

11. Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES

Pisareva, Vera P.; Pisarev, Andrey V.; Fernández, Israel S.
2018
Articles
VirologyRNAHepatitis C virusBiochemistry

12. Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme

Zhang, Zhening; Liang, Wenguang G.; Bailey, Lucas J.; Tan, Yong Zi; Wei, Hui; Wang, Andrew; Farcasanu, Mara; Woods, Virgil A.; McCord, Lauren A.; Lee, David; Shang, Weifeng; Deprez-Poulain, Rebecca; Deprez, Benoit; Liu, David R.; Koide, Akiko; Koide, Shohei; Kossiakoff, Anthony A.; Li, Sheng; Carragher, Bridget; Potter, Clinton; Tang, Wei-Jen
2018
Articles
Molecular biologyInsulinPeptidesProteolytic enzymesBiophysics

13. 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

14. Integration of EGFR and LIN-12/Notch signaling in Vulval Precursor Cell fate specification in Caenorhabditis elegans

Underwood, Ryan
2018
Theses
BiochemistryMetazoaCell interactionCellular signal transductionBiophysics

15. Mechanics of Gram-positive bacterial cell adhesion

Echelman, Daniel Jay
2018
Theses
BiophysicsNanoscienceMicrobiologyCell adhesion--Molecular aspectsGram-positive bacteriaCells--Mechanical properties

16. Mechanism of calmodulin inactivation of the calcium-selective TRP channel TRPV6

Singh, Appu K.; McGoldrick, Luke Lawrence Reedy; Twomey, Edward Charles; Sobolevsky, Alexander I.; Columbia University. Cellular, Molecular and Biomedical Studies
2018
Articles
CalmodulinTRP channelsMolecular biologyIon channels

17. Precise temporal regulation of alternative splicing during neural development

Weyn-Vanhentenryck, Sabastien Matthieu; Feng, Huijuan; Ustianenko, Dmytro; Duffié, Rachel; Yan, Qinghong; Jacko, Martin; Martinez, Jose C.; Goodwin, Marianne; Zhang, Xuegong; Hengst, Ulrich; Lomvardas, Stavros; Swanson, Maurice S.; Zhang, Chaolin
2018
Articles
Genetic regulationNeurologyRNA splicing

18. RNA force field with accuracy comparable to state-of-the-art protein force fields

Tan, Dazhi; Piana, Stefano; Dirks, Robert M.; Shaw, David Elliot
2018
Articles
BiochemistryBiophysicsRNA-protein interactionsMolecular dynamicsNucleic acids

19. Routine single particle CryoEM sample and grid characterization by tomography

Noble, Alex J.; Dandey, Venkata P.; Wei, Hui; Brasch, Julia; Chase, Jillian; Acharya, Priyamvada; Tan, Yong Zi; Zhang, Zhening; Kim, Laura Y.; Scapin, Giovanna; Rapp, Micah Allen; Eng, Edward T.; Rice, William J.; Cheng, Anchi; Negro, Carl J.; Shapiro, Lawrence S.; Kwong, Peter D.; Jeruzalmi, David; des Georges, Amedee; Potter, Clinton; Carragher, Bridget
2018
Articles
TomographyBiochemistryParticlesBiophysicsElectron microscopy

20. SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing

Yuan, Jinzhou; Sheng, Jenny; Sims, Peter A.
2018
Articles
Imaging systems in biologyNucleotide sequenceMicrofluidicsMolecular biology

21. 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

22. Structural and biophysical studies of the Drosophila melanogaster Dpr and DIP families

Cosmanescu, Filip
2018
Theses
BiochemistryNeurosciencesBiophysicsDrosophila melanogasterNeurons

23. Structure-based analysis of CysZ-mediated cellular uptake of sulfate

Assur, Zahra; Liu, Qun; Clarke, Oliver B.; Belcher Dufrisne, Meagan Leigh; Wiriyasermkul, Pattama; Giesem, M. Hunter; Leal-Pinto, Edgar; Kloss, Brian; Tabuso, Shantelle; Love, James; Punta, Marco; Banerjee, Surajit; Rajashankar, Kanagalaghatta R.; Rost, Burkhard; Logothetis, Diomedes; Quick, Matthias; Hendrickson, Wayne A.; Mancia, Filippo
2018
Articles
CytologySulfatesExtracellular matrixCell physiologyBiophysics

24. Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

Rao, Satyanarayan; Chiu, Tsu-Pei; Kribelbauer, Judith F.; Mann, Richard S.; Bussemaker, Harmen J.; Rohs, Remo
2018
Articles
DNA--MethylationEpigeneticsDNA-binding proteinsSystems biology

25. Systematic reconstruction of autism biology from massive genetic mutation profiles

Luo, Weijun; Zhang, Chaolin; Jiang, Yong-hui; Brouwer, Cory R.
2018
Articles
Mutation (Biology)Developmental geneticsAutism--ResearchAutism spectrum disorders--Genetic aspectsSystems biology

26. Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons

Monahan, Kevin; Schieren, Ira; Cheung, Jonah; Mumbey-Wafula, Alice Mary; Monuki, Edwin S.; Lomvardas, Stavros
2017
Articles
GeneticsOlfactory receptor genesGene expressionOlfactory nerve

27. Nanoscale Electrical and Coarse-grained Molecular Dynamics Studies of Influenza Hemagglutinin-mediated Membrane Fusion Pores

Alcott, Brett Eugene
2017
Theses
BiophysicsBiochemistryVirologyMolecular dynamicsMembrane fusion

28. Potent and reversible lentiviral vector restriction in murine induced pluripotent stem cells

Geis, Franziska K.; Galla, Melanie; Hofmann, Dirk; Kuehle, Johannes; Zychlinski, Daniela; Maetzig, Tobias; Schott, Juliane W.; Schwarzer, Adrian; Gofnet, Christine; Goff, Stephen P.; Schambach, Axel
2017
Articles
LentivirusesStem cellsPeptidylprolyl isomeraseRetroviruses

29. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

Kribelbauer, Judith F.; Laptenko, Oleg; Chen, Siying; Martini, Gabriella D.; Freed-Pastor, William Allen; Prives, Carol L.; Mann, Richard S.; Bussemaker, Harmen J.
2017
Articles
DNA--MethylationTranscription factorsGenetic regulationDNA-protein interactionsEpigenetics

30. Regulation of Release Factor 2 in Non-canonical Translation Pathways

Huang, Bridget Yih Jiin
2017
Theses
Bacterial proteinsRibosomesBiochemistryProteins--SynthesisBiophysics

31. RPGRIP1L and FTO – genes implicated in the effects of FTO intronic sequence variants on food intake – also affect adipogenesis and adipocyte biology.

Martin-Carli, Jayne Frances
2017
Theses
BiochemistryCytologyMolecular biologyObesity--Genetic aspects

32. Sensing and Processing of DNA Interstrand Crosslinks by the Mismatch Repair Pathway

Kato, Niyo; Kawasoe, Yoshitaka; Williams, Hannah; Coates, Elena Lauren; Roy, Upasana; Shi, Yuqian; Beese, Lorena S.; Scharer, Orlando D.; Yan, Hong; Gottesman, Maxwell E.; Takahashi, Tatsuro S.; Gautier, Jean J.
2017
Articles
Crosslinked polymersDNA repairMolecular biologyDNA

33. 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

34. The T-cell leukemia related rpl10-R98S mutant traps the 60S export adapter Nmd3 in the ribosomal P site in yeast

Patchett, Stephanie; Musalgaonkar, Sharmishtha; Malyutin, Andrey; Johnson, Arlen W.
2017
Articles
T cellsRibosomesGeneticsLymphoblastic leukemiaMolecular biology

35. A computational interactome and functional annotation for the human proteome

Garzon Canas, Jose I.; Deng, Lei; Murray, Diana; Shapira, Sagi; Petrey, Donald S.; Honig, Barry
2016
Articles
Computational biologyProteomicsProtein-protein interactionsSystems biology

36. A High-Throughput Strategy for Dissecting Mammalian Genetic Interactions

Stockman, Victoria B.; Ghamsari, Lila; Lasso Cabrera, Gorka; Honig, Barry; Shapira, Sagi; Wang, Harris H.
2016
Articles
RNAMammals--Molecular geneticsNucleotide sequenceSystems biologyMolecular geneticsCloningGeneticsBiology--Classification

37. ALS-associated mutant FUS induces selective motor neuron degeneration through toxic gain of function

Sharma, Aarti; Lyashchenko, Alexander K.; Lu, Lei; Ebrahimi Nasrabady, Sara; Elmaleh, Margot; Mendelsohn, Monica; Nemes, Adriana; Tapia, Juan Carlos; Mentis, George Z.; Shneider, Neil
2016
Articles
Nervous system--Degeneration--Molecular aspectsAmyotrophic lateral sclerosisNeurologyMedicineMolecular biologyNeurosciences

38. An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq

Yuan, Jinzhou; Sims, Peter A.
2016
Articles
Nucleotide sequenceGene expression

39. A Sixth Modality of Infectious Disease: Contagious Cancer from Devils to Clams and Beyond

Metzger, Michael; Goff, Stephen P.
2016
Articles
Parasites--EvolutionCancerImmunologic diseasesEpidemiology

40. Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8

Soto, Cinque; Ofek, Gilad; Joyce, M. Gordon; Zhang, Baoshan; McKee, Krisha; Longo, Nancy S.; Yang, Yongping; Huang, Jinghe; Parks, Robert; Eudailey, Joshua; Lloyd, Krissey E.; Alam, S. Munir; Haynes, Barton F.; Mullikin, James C.; Connors, Mark; Mascola, John R.; Shapiro, Lawrence S.; Kwong, Peter D.; NISC Comparative Sequencing Program
2016
Articles
Neutralization (Chemistry)ImmunoglobulinsPhylogenyHIV infectionsBiochemistryBiology

41. Molecular basis of sidekick-mediated cell-cell adhesion and specificity

Goodman, Kerry; Yamagata, Masahito; Jin, Xiangshu; Mannepalli, Seetha M.; Katsamba, Phinikoula S.; Ahlsen, Goran; Sergeeva, Alina P.; Honig, Barry; Sanes, Joshua R.; Shapiro, Lawrence S.
2016
Articles
NeurosciencesCell interactionCell adhesionMolecular biology

42. Oxidative Folding in Bacteria: Studies Using Single Molecule Force Spectroscopy

Kahn, Thomas
2016
Theses
Protein foldingOxidoreductasesEscherichia coli--PhysiologyOxidationBiophysicsBiochemistry

43. PLATE-Seq: An Efficient and Scalable Method for Using RNA-Seq as a Primary Output in High Throughput Drug Screens

Ray, Forest
2016
Theses
Drugs--EffectivenessHigh throughput screening (Drug development)Gene expression--Research--MethodologyBiology

44. Restriction of HIV-1-based lentiviral vectors in adult primary marrow-derived and peripheral mobilized human CD34+ hematopoietic stem and progenitor cells occurs prior to viral DNA integration

Griffin, Daniel; Goff, Stephen P.
2016
Articles
Gene therapyLentivirusesStem cellsHIV infectionsMolecular biology

45. Structural basis of suppression of host translation termination by Moloney Murine Leukemia Virus

Tang, Xuhua; Zhu, Yiping; Baker, Stacey L.; Bowler, Matthew W.; Chen, Benjamin Jieming; Chen, Chen; Hogg, J. Robert; Goff, Stephen P.; Song, Haiwei
2016
Articles
Mouse leukemia virusesReverse transcriptaseMolecular biologyVirologyBiophysicsGenetic translation

46. Structural Studies of a Mammalian Epithelial Calcium Channel

Saotome, Kei
2016
Theses
Calcium--Physiological effectBiochemistryTRP channelsCalcium channels

47. Targeted Isolation of Antibodies Directed against Major Sites of SIV Env Vulnerability

Mason, Rosemarie D.; Welles, Hugh C.; Adams, Cameron; Chakrabarti, Bimal K.; Gorman, Jason; Zhou, Tongqing; Nguyen, Richard; O’Dell, Sijy; Lusvarghi, Sabrina; Bewley, Carole A.; Li, Hui; Shaw, George M.; Sheng, Zizhang; Shapiro, Lawrence S.; Wyatt, Richard; Kwong, Peter D.; Mascola, John R.; Roederer, Mario
2016
Articles
HIV infections—PreventionImmunotherapySimian immunodeficiency virusPublic healthVirologyImmunology

48. The Role of the Clustered Protocadherins in the Assembly of Olfactory Neural Circuits

Mountoufaris, George
2016
Theses
Olfactory nerveCadherinsNeural circuitryNeurosciences

49. Understanding complex biomolecular systems through the synergy of molecular dynamics simulations, NMR spectroscopy and X-Ray crystallography

Zeiske, Tim
2016
Theses
Molecular dynamics--Simulation methodsMolecular dynamics--Computer simulationNuclear magnetic resonance spectroscopyBiomolecules--Computer simulationX-ray crystallographyMacromolecules--StructureMolecular dynamicsBiophysicsBiochemistry

50. What Is a Genome?

Goldman, Aaron David; Landweber, Laura
2016
Articles
Genomics--Data processingCell physiologyGenomesGeneticsMolecular biology

51. A Competition Mechanism for a Homeotic Neuron Identity Transformation in Caenorhabditis Elegans

Gordon, Patricia Marie
2015
Theses
Caenorhabditis elegansCaenorhabditis elegans--GeneticsCell divisionCell differentiationHomeobox genes

52. Activation of GTP hydrolysis in mRNA-tRNA translocation by elongation factor G

Li, Wen; Liu, Zheng; Koripella, Ravi Kiran; Langlois, Robert; Sanyal, Suparna; Frank, Joachim
2015
Articles
HydrolysisRibosomesGuanosine triphosphataseMolecular biologyBiochemistry

53. A Kazal-Type Serine Protease Inhibitor from the Defense Gland Secretion of the Subterranean Termite Coptotermes formosanus Shiraki

Negulescu, Horia; Guo, Youzhong; Garner, Thomas P.; Goodwin, Octavia Y.; Henderson, Gregg; Laine, Roger A.; Macnaughtan, Megan A.
2015
Articles
Proteins--StructureProteins--SecretionRhinotermitidaeAmino acid sequenceProtease inhibitorsFormosan subterranean termiteBiochemistryEntomology

54. Efferent Vestibular Neurons Show Homogenous Discharge Output But Heterogeneous Synaptic Input Profile In Vitro

Mathews, Miranda A.; Murray, Andrew; Wijesinghe, Rajiv; Cullen, Karen; Tung, Victoria W. K.; Camp, Aaron J.
2015
Articles
NeuronsAction potentials (Electrophysiology)Neural transmissionMembrane potentials (Electrophysiology)Vestibular nucleiNeurosciences

55. 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

56. Membrane potential and Ca2+ concentration dependence on pressure and vasoactive agents in arterial smooth muscle: A model

Karlin, Arthur
2015
Articles
Molecular biologyBiochemistryPhysiology

57. Molecular Evolution and Genetic Analysis of the Major Capsid Protein VP1 of Duck Hepatitis A Viruses: Implications for Antigenic Stability

Ma, Xiuli; Sheng, Zizhang; Huang, Bing; Qi, Lihong; Li, Yufeng; Yu, Kexiang; Liu, Cunxia; Qin, Zhuoming; Wang, Dan; Song, Minxun; Li, Feng
2015
Articles
Ducks--MortalityViruses--EvolutionEvolutionary geneticsImmune serumsHepatitis A virusEvolution (Biology)GeneticsAnimals--Diseases

58. Nuclear matrix protein Matrin 3 is a regulator of ZAP-mediated retroviral restriction

Erazo, Angela; Goff, Stephen P.
2015
Articles
Gene expressionNuclear matrixRetrovirusesAntiretroviral agentsMolecular biologyBiochemistry

59. Regulation of Transcription Elongation and Termination

Washburn, Robert; Gottesman, Max E.
2015
Articles
Genetic transcriptionBiomoleculesBiomolecules--StructureMicrobiology

60. The CUL4-DDB1 ubiquitin ligase complex controls adult and embryonic stem cell differentiation and homeostasis

Gao, Jie; Buckley, Shannon M.; Cimmino, Luisa; Guillamot, Maria; Strikoudis, Alexandros; Cang, Yong; Goff, Stephen P.; Aifantis, Iannis
2015
Articles
UbiquitinMolecular biologyStem cellsCell differentiationHematopoiesisRegenerative medicine

61. Allele-Specific Knockdown of ALS-Associated Mutant TDP-43 in Neural Stem Cells Derived from Induced Pluripotent Stem Cells

Nishimura, Agnes L.; Scotter, Emma L.; Abdelgany, Amr; Shum, Carole; Sardone, Valentina; Wright, Jamie; Lee, Youn-Bok; Chen, Han-Jou; Bilican, Bilada; Carrasco, Monica; Maniatis, Tom; Chandran, Siddharthan; Gallo, Jean-Marc; Rogelj, Boris; Shaw, Christopher E.
2014
Articles
Neural stem cellsCell differentiationSmall interfering RNAMorphology

62. Asynchronous Transcriptional Silencing of Individual Retroviral Genomes in Embryonic Cells

Schlesinger, Sharon; Meshorer, Eran; Goff, Stephen P.
2014
Articles
CytologyGeneticsVirology

63. Concentration-Dependent Exchange of Replication Protein A on Single-Stranded DNA Revealed by Single-Molecule Imaging

Gibb, Bryan; Ye, Ling Feng; Gergoudis, Stephanie C.; Kwon, YoungHo; Niu, Hengyao; Sung, Patrick; Greene, Eric C.
2014
Articles
Protein bindingDNA--MetabolismSaccharomyces cerevisiae--GeneticsGenetics

64. Kinematic Responses to Changes in Walking Orientation and Gravitational Load in Drosophila melanogaster

Mendes, Cesar; Rajendren, Soumya V.; Bartos, Imre; Marka, Szabolcs; Mann, Richard S.
2014
Articles
WalkingInsects--LocomotionDrosophila melanogasterEntomologyNeurosciencesKinesiology

65. Learning from cadherin structures and sequences: affinity determinants and protein architecture

Felsovalyi, Klara
2014
Theses
Protein bindingCadherinsBiochemistryBioinformaticsBiophysics

66. Mechanisms for Taste Sensation of Carbonation

Yarmolinsky, David
2014
Theses
BiologyNeurosciences

67. Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor

Arkhipov, Anton; Shan, Yibing; Kim, Eric T.; Shaw, David Elliot
2014
Articles
Cell membranesCrystals--StructureDimersBiochemistry

68. Single-Cell Identity Generated by Combinatorial Homophilic Interactions between α, β, and γ Protocadherins

Thu, Chan Aye; Chen, Weisheng; Rubinstein, Rotem; Chevee, Maxime; Wolcott, Holly N.; Felsovalyi, Klara O.; Tapia, Juan Carlos; Shapiro, Lawrence S.; Honig, Barry; Maniatis, Tom
2014
Articles
Cellular recognitionNeuronsCytologyCadherinsNeurosciences

69. Structural and biophysical characterization of protocadherin extracellular regions

Wolcott, Holly Noelle
2014
Theses
BiochemistryBiophysics

70. Accelerating the Original Profile Kernel

Hamp, Tobias; Goldberg, Tatyana; Rost, Burkhard
2013
Articles
Pattern recognition systemsKernel functionsProteins--Analysis--MethodologyMolecular biology

71. Astrocyte pathology and the absence of non-cell autonomy in an induced pluripotent stem cell model of TDP-43 proteinopathy

Serio, Andrea; Bilican, Bilada; Barmada, Sami J.; Ando, Dale Michael; Zhao, Chen; Siller, Rick; Burr, Karen; Haghi, Ghazal; Story, David; Nishimura, Agnes Lumi; Carrasco, Monica A.; Phatnani, Hemali P.; Shum, Carole; Wilmut, Ian; Maniatis, Tom; Shaw, Christopher E.; Finkbeiner, Steven; Chandran, Siddharthan
2013
Articles
NeurosciencesBiochemistry

72. Bacterial Adaptation through Loss of Function

Hottes, Alison K.; Freddolino, Peter L.; Khare, Anupama; Donnell, Zachary N.; Liu, Julia C.; Tavazoie, Saeed
2013
Articles
Microbial mutationNonsense mutationBacteriaGeneticsMicrobiologyBiology--Classification

73. CysZ: Structural and Functional Studies of a Novel Sulfate Transport Protein

Assur, Zahra
2013
Theses
CytologyCarrier proteinsBiochemistryBiophysics

74. Differential effects of natural rewards and pain on vesicular glutamate transporter expression in the nucleus accumbens

Manders, Toby R.; Ziff, Edward B.; Wang, Jing; Turkey, David S.; Lee, Michelle; Xu, Duo; Eberle, Sarah E.; Goffer, Yossef
2013
Articles
BiochemistryNeurosciences

75. Distinctive Genes Determine Different Intramuscular Fat and Muscle Fiber Ratios of the longissimus dorsi Muscles in Jinhua and Landrace Pigs

Wu, Ting; Zhang, Zhenhai; Yuan, Zhanqin; Lo, Li Jan; Chen, Jun; Wang, Yizhen; Peng, Jinrong
2013
Articles
Swine--GeneticsMeat--QualityGene expressionGenetic regulationSwine--AnatomyGeneticsVeterinary medicine

76. Divergent Transcriptional Regulatory Logic at the Intersection of Tissue Growth and Developmental Patterning

Slattery, Matthew; Voutev, Roumen; Ma, Lijia; Nègre, Nicolas; White, Kevin P.; Mann, Richard S.
2013
Articles
Genetic transcription--RegulationDevelopmental biologyDevelopmental geneticsTissues--GrowthGeneticsMolecular biology

77. Genetic analysis of novel regulators of neuronal migration in Caenorhabditis elegans: the insulin/IGF-1 signaling pathway, a chromatin-binding factor ZFP-1 (AF10) and endogenous RNAi

Kennedy, Lisa Michelle
2013
Theses
Genetics

78. Genetic and Functional Modularity of Hox Activities in the Specification of Limb-Innervating Motor Neurons

Lacombe, Julie; Hanley, Olivia; Jung, Heekyung; Philippidou, Polyxeni; Surmeli, Gulsen; Dasen, Jeremy S.; Grinstein, Jonathan
2013
Articles
Motor neuronsNeuronsNeural circuitryNeurogeneticsHomeobox genesGenetics

79. Homology-based inference sets the bar high for protein function prediction

Rost, Burkhard; Roos, Manfred; Mahlich, Yannick; Landerer, Cedric; Krompass, Denis; Kiening, Michael; Kaufman, Stefanie; Hönigschmid, Peter; Hopf, Thomas A.; Hamp, Tobias; Kassner, Rebecca; Seemayer, Sefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Boehm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark
2013
Articles
Bioinformatics

80. Orientations and Proximities of the Extracellular Ends of Transmembrane Helices S0 and S4 in Open and Closed BK Potassium Channels

Niu, Xiaowei; Liu, Guoxia; Wu, Roland; Chudasama, Neelesh; Zakharov, Sergey; Karlin, Arthur; Marx, Steven O.
2013
Articles
BiochemistryMolecular biologyBiophysicsMedicine

81. Players in the silencing of retroviral DNAs in embryonic stem cells

Schlesinger, Sharon; Wang, Gary Zhe; Lee, Andreia H.; Goff, Stephen P.
2013
Presentations (Communicative Events)
Retrovirus infectionsGene silencingEmbryonic stem cellsVirologyMolecular biology

82. Proviral Silencing in Embryonic Cells is Regulated by Yin Yang 1

Schlesinger, Sharon; Lee, Andreia H.; Wang, Gary Zhe; Green, Lisa; Goff, Stephen P.
2013
Articles
CytologyVirologyGenetics

83. Quantification of gait parameters in freely walking wild type and sensory deprived Drosophila melanogaster

Mendes, Cesar; Bartos, Imre; Akay, Turgay; Marka, Szabolcs; Mann, Richard S.
2013
Articles
BiochemistryBiophysicsNeurosciences

84. Role of SUMO-1 and SUMO Interacting Motifs in Rhesus TRIM5α-mediated Restriction

Lukic, Zana; Arriagada, Gloria; Goff, Stephen P.; Campbell, Edward M.
2013
Articles
Molecular biologyVirology

85. Synaptic State Matching: A Dynamical Architecture for Predictive Internal Representation and Feature Detection

Tavazoie, Saeed
2013
Articles
Neural networks (Neurobiology)SynapsesPerceptual-motor processesMolecular biologyBiophysicsNeurosciences

86. Synonymous site conservation in the HIV-1 genome

Mayrose, Itay; Stern, Adi; Burdelova, Ela; Sabo, Yosef; Laham-Karam, Nihay; Zamostiano, Rachel; Bacharach, Eran; Pupko, Tal
2013
Articles
HIV (Viruses)GenomicsGeneticsBiology

87. Thermal adaptation of conformational dynamics in ribonuclease H

Stafford, Kate
2013
Theses
Biochemistry

88. Thermal Adaptation of Conformational Dynamics in Ribonuclease H

Stafford, Kate A.; Robustelli, Paul; Palmer III, Arthur G,
2013
Articles
BiothermodynamicsProteins--StabilityRibonucleasesMolecular biology

89. Tumor-associated T cell receptor repertoires in low- and high-grade gliomas

Sims, Jennifer S.; Grinshpun, Boris; Amendolara, Benjamin; Shen, Yufeng; Canoll, Peter D.; Sims, Peter A.; Bruce, Jeffrey N.
2013
Presentations (Communicative Events)
AstrocytomasGliomasT cells--ReceptorsExcision (Surgery)Cancer--SurgeryGlioblastoma multiformeOncologySurgeryMedicine

90. An Analysis of the Essential Chromatin Factor Zinc Finger Protein 1 (ZFP-1), and a Study of the Involvement of RNAi factors in Histone Processing in Caenorabditis Elegans

Anastasiades Avgousti, Daphne Christina
2012
Theses
BiochemistryBiophysicsCaenorhabditis elegansChromatinHistonesRNANucleosomes

91. A Survey of 6,300 Genomic Fragments for cis-Regulatory Activity in the Imaginal Discs of Drosophila melanogaster

Jory, Aurelie E.; Estella, Carlos; Giorgianni, Matt W.; Slattery, Matthew; Laverty, Todd R.; Rubin, Gerald M.; Mann, Richard S.
2012
Articles
Genetics

92. Basal-like breast cancer: modeling its initiation and characterizing novel EGFR variants

Pires, Maira Moura
2012
Theses
BiologyOncologyBreast--CancerTumor suppressor proteinsCarcinogenesis

93. Deep sequencing with longitudinal sampling of a VRC01-like-antibody response in a chronically infected individual

Mascola, J. R.; Kwong, P. D.; Mullikin, J. C.; Wu, L.; Nabel, G. J.; Connors, M.; NISC, C.; Zhang, Z.; Zhang, B.; Zhu, J.; Longo, N.; Wu, X.; Shapiro, Lawrence S.
2012
Presentations (Communicative Events)
Nucleotide sequenceLongitudinal methodHIV antibodiesVirologyMolecular biology

94. Developmental Regulation of Chromatin Conformation by Hox Proteins in Drosophila

Angelopoulos, Marios; McKay, Daniel J.; Mann, Richard S.
2012
Articles
BiochemistryBiophysics

95. Mechanochemical Methods for Single Molecule Biochemistry and Studies of Thiol-Disulfide Exchange in Proteins

Kosuri, Pallav
2012
Theses
BiophysicsBiochemistryBiology

96. PrePPI: a structure-informed database of protein–protein interactions

Zhang, Qiangfeng Cliff; Petrey, Donald S.; Garzon Canas, Jose I.; Deng, Lei; Honig, Barry
2012
Articles
BiochemistryMolecular biologyBiomedical engineering

97. Structural Determinants of DNA-binding Specificity for Hox Proteins

Liu, Peng
2012
Theses
BiophysicsBioinformatics

98. Structural Plasticity and Conformational Transitions of HIV Envelope Glycoprotein gp120

Korkut, Anil; Hendrickson, Wayne A.
2012
Articles
HIV infectionsGlycoproteinsProteins--StructureBiochemistry

99. Structure-Function Analysis of Hox-cofactor Interactions during Drosophila melanogaster Embryonic Development.

Lelli, Katherine Marie
2012
Theses
Genetics

100. Studies of a Site-Specific Recombination System and Analysis of New Modulators of Notch Signaling in C. elegans

Vargas, Marcus L.
2012
Theses
GeneticsMolecular biology