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1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. 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

23. 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

24. 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

25. 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

26. 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

27. 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

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

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

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

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

30. 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

31. 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

32. 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

33. 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

34. 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

35. What Is a Genome?

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

36. 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

37. 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

38. 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

39. 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

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

Karlin, Arthur
2015
Articles
Molecular biologyBiochemistryPhysiology

41. 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

42. 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

43. Regulation of Transcription Elongation and Termination

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

44. 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

45. 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

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

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

47. 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

48. 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

49. 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

50. 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

51. Accelerating the Original Profile Kernel

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

52. 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

53. 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

54. 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

55. 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

56. 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

57. 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

58. 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

59. 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

60. 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

61. 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

62. 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

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

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

64. 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

65. Thermal Adaptation of Conformational Dynamics in Ribonuclease H

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

66. 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

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

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

68. 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

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

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

70. Accurate proteome-wide protein quantification from high-resolution 15N mass spectra

Kryglyak, Leonid; Singh, Mona; Perlman, David H.; Tavazoie, Saeed; Caudy, Amy A.; Ruse, Christian; Amini, Sasan; Bloom, Joshua S.; Khan, Zia
2011
Articles
BiochemistryMolecular biology

71. ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

Friedman, Brad; Maniatis, Tom
2011
Articles
StatisticsBioinformatics

72. Large-scale experimental studies show unexpected amino acid effects on protein expression and solubility in vivo in E. coli

Hunt, John F.; Tong, Saichiu; Bracic, Ana; Luff, Jon; Naumov, Victor; Acton, Thomas; Manor, Philip; Xiao, Rong; Rost, Burkhard; Montelione, Gaetano; Everett, John; Price, W. Nicholson; Handelman, Samuel
2011
Articles
Molecular biologyBiochemistry

73. SUMO-Interacting Motifs of Human TRIM5α are Important for Antiviral Activity

Arriagada, Gloria; Muntean, Lucia N.; Goff, Stephen P.
2011
Articles
MicrobiologyVirologyMolecular biology

74. Abl Family Tyrosine Kinases Are Essential for Basement Membrane Integrity and Cortical Lamination in the Cerebellum

Qiu, Zhaozhu; Cang, Yong; Goff, Stephen P.
2010
Articles
Molecular biologyNeurosciencesMicrobiology

75. Developmental control of lateralized neuron size in the nematode Caenorhabditis elegans

Lockery, Shawn; Hobert, Oliver; Goldsmith, Andrew; Sarin, Sumeet
2010
Articles
NeurosciencesMolecular biology

76. Dynamic Instability of Genomic Methylation Patterns in Pluripotent Stem Cells

Ooi, Steen K. T.; Wolf, Daniel; Hartung, Odelya; Agarwal, Suneet; Daley, George Q.; Goff, Stephen P.; Bestor, Timothy H.
2010
Articles
GeneticsMolecular biologyBiochemistry

77. Estimation of the 3D Variance-Covariance Map in Cryo-Electron Microscopy

Liao, Hstau Y.; Hashem, Yaser; Frank, Joachim
2010
Articles
Molecular biology

78. From DNA to proteins via the ribosome: Structural insights into the workings of the translation machinery

Frank, Joachim; Agirrezabala, Xabier
2010
Articles
GeneticsMolecular biology

79. Interactions of Host Proteins with the Murine Leukemia Virus Integrase

Studamire, Barbara; Goff, Stephen P.
2010
Articles
PathologyMolecular biologyBiochemistry

80. The rate of the molecular clock and the cost of gratuitous protein synthesis

Plata, Germán Alonso; Gottesman, Maxwell E.; Vitkup, Dennis
2010
Articles
Molecular biologyBiochemistry

81. Correlating protein function and stability through the analysis of single amino acid substitutions

Bromberg, Yana; Rost, Burkhard
2009
Articles
BioinformaticsBiochemistry

82. Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies

Bushman, Frederic D.; Fernandes, Jason; D'Orso, Ivan; Malani, Nirav; Zhou, Honglin; Hazuda, Daria J.; Espeseth, Amy S.; Konig, Renate; Bandyopadhyay, Sourav; Ideker, Trey; Cagney, Gerard; Diamond, Tracy L.; Goff, Stephen P.; Krogan, Nevan J.; Frankel, Alan D.; Young, John A. T.; Chanda, Sumit K.
2009
Articles
PathologyGeneticsCytology

83. Quelling targets the rDNA locus and functions in rDNA copy number control

Cecere, Germano; Cogoni, Carlo
2009
Articles
MicrobiologyMolecular biology

84. Host Proteins Interacting with the Moloney Murine Leukemia Virus Integrase: Multiple Transcriptional Regulators and Chromatin Binding Factors

Studamire, Barbara; Goff, Stephen P.
2008
Articles
VirologyOncologyBiochemistry

85. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

Kristensen, David; Ward, R Matthew; Lisewski, Andreas; Erdin, Serkan; Chen, Brian Y; Fofanov, Viacheslav; Kimmel, Marek; Kavraki, Lydia; Lichtarge, Olivier
2008
Articles
GenomicsProteins--StructureBiophysicsMolecular biology

86. Role of Gas6 in Erythropoiesis and Anemia in Mice

Angelillo-Scherrer, Anne; Burnier, Laurent; Lambrechts, Diether; Fish, Richard J.; Tjwa, Marc; Plaisance, Stéphane; Sugamele, Rocco; DeMol, Maria; Martinez-Soria, Eduardo; Maxwell, Patrick H.; Lemke, Greg; Goff, Stephen P.; Matsushima, Glenn K.; Earp, H. Shelton; Chanson, Marc; Collen, Désiré; Izui, Shozo; Schapira, Marc; Conway, Edward M.; Carmeliet, Peter
2008
Articles
CytologyMedicine

87. DWARF – a data warehouse system for analyzing protein families

Fischer, Markus; Thai, Quan; Grieb, Melanie; Pleiss, Jürgen
2006
Articles
Proteins--Data processingProtein engineeringBioengineering--Data processingData warehousingBioinformatics

88. ERK Phosphorylates p66shcA on Ser36 and Subsequently Regulates p27^kip1 Expression via the Akt-FOXO3a Pathway: Implication of p27^kip1 in Cell Response to Oxidative Stress

Hu, Yuanyu; Wang, Xueying; Zeng, Li; Cai, De-Yu; Sabapathy, Kanaga; Goff, Stephen P.; Firpo, Eduardo J.; Li, Baojie
2005
Articles
Molecular biologyCytology

89. Overexpression of Fasciculation and Elongation Protein ζ-1 (FEZ1) Induces a Post-entry Block to Retroviruses in Cultured Cells

Naghavi, Mojgan H.; Hatziioannou, Theodora; Gao, Guangxia; Goff, Stephen P.
2005
Articles
Molecular biologyVirologyGenetics

90. Role of Gas6 Receptors in Platelet Signaling during Thrombus Stabilization and Implications for Antithrombotic Therapy

Angelillo-Scherrer, Anne; Burnier, Laurent; Flores, Nathalie; Savi, Pierre; DeMol, Maria; Schaeffer, Paul; Herbert, Jean-Marc; Lemke, Greg; Goff, Stephen P.; Matsushima, Glenn K.; Earp, H. Shelton; Vesin, Christian; Hoylaerts, Marc F.; Plaisance, Stéphane; Collen, Désiré; Conway, Edward M.; Wehrle-Haller, Bernhard; Carmeliet, Peter
2005
Articles
CytologyMedicine

91. Determination of the Critical Concentration of Neutrophils Required to Block Bacterial Growth in Tissues

Li, Yongmei; Karlin, Arthur; Loike, John D.; Silverstein, Samuel C.
2004
Articles
Bacterial growthBiophysics--ResearchNeutrophilsMedicineMicrobiologyMolecular biology

92. Distinct Roles of c-Abl and Atm in Oxidative Stress Response Are Mediated by Protein Kinase C δ

Goff, Stephen P.; Nakayama, Keiko; Nakayama, Keiichi I.; Boast, Sharon; Ishii, Tetsuro; Hu, Yuanyu; Rasheed, Naslin; Wang, Xueying; Li, Baojie
2004
Articles
Molecular biologyGenetics

93. Isolation of Suppressor Genes that Restore Retrovirus Susceptibility to a Virus-resistant Cell Line

Gao, Guangxia; Goff, Stephen P.
2004
Articles
CytologyGeneticsVirology

94. Endophilins interact with Moloney murine leukemia virus Gag and modulate virion production

Wang, Margaret; Kim, Wankee; Gao, Guangxia; Torrey, Ted; Morse, Herbert; De Camilli, Pietro; Goff, Stephen P.
2003
Articles
Molecular biologyVirology

95. Endophilins Interact with Moloney Murine Leukemia Virus Gag and Modulate Virion Production.

Wang, Margaret Q.; Kim, Wankee; Gao, Guangxia; Morse, Herbert C.; De Camilli, Pietro; Goff, Stephen P.; Torrey, Ted A.
2003
Articles
Molecular biologyOncologyVirology

96. C-Abl Is Required for the Development of Hyperoxia-Induced Retinopathy

Nunes, Irene; Zanetta, Lucia; Higgins, Rosemary D.; Shamamian, Peter; Goff, Stephen P.
2001
Articles
BiochemistryOphthalmologyMedicine

97. Somatic Cell Mutants Resistant to Retrovirus Replication: Intracellular Blocks during the Early Stages of Infection

Gao, Guangxia; Goff, Stephen P.
1999
Articles
Molecular biologyVirologyCytology

98. The Thrombopoietin Receptor Can Mediate Proliferation Without Activation of the Jak-STAT Pathway

Dorsch, Marion; Fan, Pang-Dian; Danial, Nika N.; Rothman, Paul B.; Goff, Stephen P.
1997
Articles
Molecular biologyBiochemistryMedicine

99. Abl-interactor-1, A Novel SH3 Protein Binding to the Carboxy-terminal Portion of the Abl Protein, Suppresses v-abl Transforming Activity

Shi, Yanggu; Alin, Kimona; Goff, Stephen P.
1995
Articles
CytologyGeneticsVirology

100. The Drosophila snr1 and brm Proteins are Related to Yeast SWI/SNF Proteins and are Components of a Large Protein Complex

Dingwall, A. K.; Beek, S. J.; McCallum, C. M.; Tamkun, J. W.; Kalpana, G. V.; Goff, Stephen P.; Scott, M. P.
1995
Articles
Genetic transcription--RegulationMolecular biologyCytology