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1. 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

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. Solving Challenging Structures using Single-Particle Cryogenic Electron Microscopy

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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. Mechanics of Gram-positive bacterial cell adhesion

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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

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

Cosmanescu, Filip
2018
Theses
BiochemistryNeurosciencesBiophysicsDrosophila melanogasterNeurons

21. 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; Mancia, Filippo
2018
Articles
CytologySulfatesExtracellular matrixCell physiologyBiophysics

22. 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

23. 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

24. 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

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

Alcott, Brett Eugene
2017
Theses
BiophysicsBiochemistryVirologyMolecular dynamicsMembrane fusion

26. 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

27. 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

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

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

29. 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

30. 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

31. 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

32. 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

33. 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

34. 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

35. 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

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

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

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

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

38. 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

39. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels

Kilpelainen, Tuomas O.; Martin-Carli, Jayne Frances; Skowronski, Alicja Anna; Sun, Qi; Kriebel, Jennifer; Feitosa, Mary F.; Hedman, Asa K.; Drong, Alexander W.; Hayes, James E.; Zhao, Jinghua; Pers, Tune H.; Schick, Ursula; Grarup, Niels; Kutalik, Zoltán; Trompet, Stella; Mangino, Massimo; Kristiansson, Kati; Beekman, Marian; Lyytikäinen, Leo-Pekka; Eriksson, Joel; Henneman, Peter; Lahti, Jari; Tanaka, Toshiko; Luan, Jian’an; Del Greco M, Fabiola; Pasko, Dorota; Renström, Frida; Willems, Sara M.; Mahajan, Anubha; Rose, Lynda M.; Guo, Xiuqing; Liu, Yongmei; Kleber, Marcus E.; Pérusse, Louis; Gaunt, Tom; Ahluwalia, Tarunveer S.; Sung, Yun Ju; Ramos, Yolande F.; Amin, Najaf; Amuzu, Antoinette; Barroso, Inês; Bellis, Claire; Blangero, John; Buckley, Brendan M.; Böhringer, Stefan; Chen, Yii-Der I.; de Craen, Anton J. N.; Crosslin, David R.; Dale, Caroline E.; Dastani, Zari; Day, Felix R.; Deelen, Joris; Delgado, Graciela E.; Demirkan, Ayse; Finucane, Francis M.; Ford, Ian; Garcia, Melissa E.; Gieger, Christian; Gustafsson, Stefan; Hallmans, Göran; Hankinson, Susan E.; Havulinna, Aki S.; Herder, Christian; Hernandez, Dena; Hicks, Andrew A.; Hunter, David J.; Illig, Thomas; Ingelsson, Erik; Ioan-Facsinay, Andreea; Jansson, John-Olov; Jenny, Nancy S.; Jørgensen, Marit E.; Jørgensen, Torben; Karlsson, Magnus; Koenig, Wolfgang; Kraft, Peter; Kwekkeboom, Joanneke; Laatikainen, Tiina; Ladwig, Karl-Heinz; LeDuc, Charles A.; Lowe, Gordon; Lu, Yingchang; Marques-Vidal, Pedro; Meisinger, Christa; Menni, Cristina; Morris, Andrew P.; Myers, Richard H.; Männistö, Satu; Nalls, Mike A.; Paternoster, Lavinia; Peters, Annette; Pradhan, Aruna D.; Rankinen, Tuomo; Rasmussen-Torvik, Laura J.; Rathmann, Wolfgang; Rice, Treva K.; Richards, J. Brent; Ridker, Paul M.; Sattar, Naveed; Savage, David B.; Söderberg, Stefan; Timpson, Nicholas J.; Vandenput, Liesbeth; van Heemst, Diana; Uh, Hae-Won; Vohl, Marie-Claude; Walker, Mark; Wichmann, Heinz-Erich; Widén, Elisabeth; Wood, Andrew R.; Yao, Jie; Zeller, Tanja; Zhang, Yiying; Meulenbelt, Ingrid; Kloppenburg, Margreet; Astrup, Arne; Sørensen, Thorkild I. A.; Sarzynski, Mark A.; Rao, D. C.; Jousilahti, Pekka; Vartiainen, Erkki; Hofman, Albert; Rivadeneira, Fernando; Uitterlinden, André G.; Kajantie, Eero; Osmond, Clive; Palotie, Aarno; Eriksson, Johan G.; Heliövaara, Markku; Knekt, Paul B.; Koskinen, Seppo; Jula, Antti; Perola, Markus; Huupponen, Risto K.; Viikari, Jorma S.; Kähönen, Mika; Lehtimäki, Terho; Raitakari, Olli T.; Mellström, Dan; Lorentzon, Mattias; Casas, Juan P.; Bandinelli, Stefanie; März, Winfried; Isaacs, Aaron; van Dijk, Ko W.; van Duijn, Cornelia M.; Harris, Tamara B.; Bouchard, Claude; Allison, Matthew A.; Chasman, Daniel I.; Ohlsson, Claes; Lind, Lars; Scott, Robert A.; Langenberg, Claudia; Wareham, Nicholas J.; Ferrucci, Luigi; Frayling, Timothy M.; Pramstaller, Peter P.; Borecki, Ingrid B.; Waterworth, Dawn M.; Bergmann, Sven; Waeber, Gérard; Vollenweider, Peter; Vestergaard, Henrik; Hansen, Torben; Pedersen, Oluf; Hu, Frank B.; Slagboom, P. Eline; Grallert, Harald; Spector, Tim D.; Jukema, J. W.; Klein, Robert J.; Schadt, Erik E.; Franks, Paul W.; Lindgren, Cecilia M.; Leibel, Rudolph L.; Loos, Ruth J. F.
2016
Articles
Meta-analysisLeptinMolecular biologyGenetics

40. 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

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

Kahn, Thomas
2016
Theses
Protein foldingOxidoreductasesEscherichia coli--PhysiologyOxidationBiophysicsBiochemistry

42. 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

43. 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

44. 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

45. Structural Studies of a Mammalian Epithelial Calcium Channel

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

46. 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

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

Mountoufaris, George
2016
Theses
Olfactory nerveCadherinsNeural circuitryNeurosciences

48. 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

49. What Is a Genome?

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

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

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

51. 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

52. 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

53. 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

54. 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

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

Karlin, Arthur
2015
Articles
Molecular biologyBiochemistryPhysiology

56. 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

57. 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

58. Regulation of Transcription Elongation and Termination

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

59. 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

60. 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

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

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

62. 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

63. 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

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

Felsovalyi, Klara
2014
Theses
Protein bindingCadherinsBiochemistryBioinformaticsBiophysics

65. Mechanisms for Taste Sensation of Carbonation

Yarmolinsky, David
2014
Theses
BiologyNeurosciences

66. 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

67. 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

68. Structural and biophysical characterization of protocadherin extracellular regions

Wolcott, Holly Noelle
2014
Theses
BiochemistryBiophysics

69. Accelerating the Original Profile Kernel

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

70. 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

71. 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

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

Assur, Zahra
2013
Theses
CytologyCarrier proteinsBiochemistryBiophysics

73. 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

74. 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

75. 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 geneticsTissues--GrowthGeneticsMolecular biology

76. 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

77. 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

78. 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

79. 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

80. 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

81. 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

82. 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

83. 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

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

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

85. 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

86. Thermal Adaptation of Conformational Dynamics in Ribonuclease H

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

87. Thermal adaptation of conformational dynamics in ribonuclease H

Stafford, Kate
2013
Theses
Biochemistry

88. 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

89. 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
BiochemistryBiophysics

90. 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

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

Pires, Maira Moura
2012
Theses
BiologyOncology

92. 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

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

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

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

Kosuri, Pallav
2012
Theses
BiophysicsBiochemistryBiology

95. 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

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

Liu, Peng
2012
Theses
BiophysicsBioinformatics

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

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

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

Lelli, Katherine Marie
2012
Theses
Genetics

99. 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

100. Towards the integration of structural and systems biology: structure-based studies of protein-protein interactions on a genome-wide scale

Zhang, Qiangfeng Cliff
2012
Theses
BioinformaticsBiophysicsSystems biologyProtein-protein interactionsGenomes
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