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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)
Showing 1 to 100 of 215 items.  Page: 1 3

Keynote Address
Nobel Laureate Phillip Sharp
The 21st Century opened with a revolution in RNA Biology

Phillip A. Sharp

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Martin Karplus: His Nobel Lecture and his thoughts on "What does the Future Hold"?

Martin Karplus

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New Grant Programs Offered by the National Institute of General Medical Sciences

Peter C. Preusch,

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NSF Opportunities: A Program Director's Perspective

Manju Hingorani

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Structural Mechanisms of Nucleosome Recognition by Linker Histones

Bing-Rui Zhou , Jiansheng Jiang, Rui Wang, Hanqiao Feng, Rodolfo Ghirlando , T. Sam Xiao, Yawen Bai

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Combined Influence of Linker DNA and Histone Tails on Nucleosome Dynamics as Revealed by Microsecond Molecular Dynamics Simulations

Alexey K. Shaytan , Grigoriy A. Armeev, Alexander Goncearenco, Victor B. Zhurkin, David Landsman, Anna R. Panchenko

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Implication of transposons distribution on chromatin state and genome architecture in human

Vladimir N. Babenko, Vladimir F. Matvienko , Nataly S. Safronova

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Interplay of nucleosome repositioning, DNA methylation and transcription factor binding during stem cell development

Vladimir B. Teif , Karsten Rippe

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SIN Mutations Alter Structure and Dynamics of Human Mononucleosome

Suma Mohan S , Thomas C. Bishop , Vijayalakshmi Mahadevan

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Topological Polymorphism of Two-start Nucleosome Fibers

Davood Norouzi, Victor B. Zhurkin

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Active chromatin regions are sufficient to define borders of topologically associated domains in D. melanogaster interphase chromosomes

Ekaterina E. Khrameeva , Sergey V. Ulyanov, Alexey A. Gavrilov, Yuri Y. Shevelyov, Mikhail S. Gelfand , Sergey V. Razin

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Checkpoints Controlled by PCNA, DNA and ATP Direct the Timing and Order of Events in the Clamp Loading Mechanism

Juan Liu, Manju M. Hingorani

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Do large Purine repeat sequences play a role in transcriptional regulation of genes associated with neurological disorders?

Himanshu N. Singh, Moganty R. Rajeswari

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Evolving insights on how cytosine methylation affects protein-DNA binding

Satyanarayan Rao , Ana Carolina Dantas Machado, Tianyin Zhou, Chaitanya Rastogi, Harmen J. Bussemaker, Remo Rohs

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Genome-wide and positional homopolymeric tract enrichment at promoter-exon boundaries and exclusion of nucleosomes in Plasmodium spp. and related parasites

Karen Russell , Chia-Ho Cheng, Jeffrey W. Bizzaro, Nadia Ponts, Richard Emes, Kenneth A. Marx, Karine Le Roch, Paul Horrocks

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How is fidelity maintained in nucleic acids? Two tales in DNA repair and DNA transcription from computer simulations

Michael Feig, Beibei Wang, Monika Sharma, Zachary Burton, Kristopher Opron, Robert Cukier, Alexander Predeus, Nicholas Kovacs, Sean Law, Shayantani Mukherjee

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Influence of iron on iron dependent repressor (IdeR) activation and DNA binding

Soma Ghosh , Nagasuma Chandra, Saraswathi Vishveshwara

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Interference of PNA Binding to the Non-Template Strand with Transcription Supports the General Model for Transcription Blockage by R-loop Formation.

Boris P. Belotserkovskii, Philip C. Hanawalt

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Life at the Single Molecule Level: from Single Molecule Enzymology to Single Cell Genomics

Sunney Xie

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New insights on Nucleic Acids - protein interfaces revealed by VLDM, a geometrical approach

A. Elbahnsi , O. Mauffret , D. Perahia , B. Hartmann , C. Oguey

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Oligomerization kinetics of ORF1p is correlated with LINE1 retrotransposition

M. Nabuan Naufer , Anthony V. Furano, Mark C. Williams

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Protein-DNA interactions: Fine balance between high affinity and fast kinetics

Yaakov (Koby) Levy

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Sequence-specific DNA looping by mitochondrial transcription factor A (TFAM)

Divakaran Murugesapillai , Maria F. Lodeiro , L. James Maher III , Craig E. Cameron , Mark C. Williams

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TFBSshape: a motif database for DNA shape features of transcription factor binding sites

Lin Yang, Iris Dror, Tianyin Zhou, Anthony Mathelier, Wyeth W. Wasserman, Raluca Gordan, Remo Rohs

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The busy life of nascent chains: Mechanisms of folding of newly synthesized proteins

Guenter Kramer , Bernd Bukau

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Analysis of DNA Deformations in Transcription Factor-DNA Complexes

Jared Sagendorf, Helen M. Berman, Remo Rohs

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GBshape: a genome browser database for DNA shape annotations

Tsu-Pei Chiu, Lin Yang, Tianyin Zhou, Bradley J. Main, Stephen C.J. Parker, Sergey V. Nuzhdin, Thomas D. Tullius, Remo Rohs

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Quantitative Modeling of Transcription Factor Binding Specificities Using DNA Shape

Tianyin Zhou , Ning Shen, Lin Yang, Namiko Abe, John Horton, Richard S. Mann, Harmen J. Bussemaker, Raluca Gordan, Remo Rohs

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Structural and Binding Properties of DNA Response Elements Bound to p53 Proteins and the Role of Spacer Sequences in p53-DNA Interactions

P. Vyas, I. Beno, Z. Xi, N. Kessler, M. Kitayner, D. Crothers, Z. Shakked, T.E. Haran

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Compensatory Evolution in Response to a Novel RNA Polymerase: Electrostatic Properties of Promoters May Lead the Adaptation in T7-T3 bacteriophages

Alexander A. Osypov , Svetlana G. Kamzolova

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Electrostatic Properties of Rho-dependent and Rho-independent Terminators

Gleb G. Krutinin, Eugenia A. Krutinina, Svetlana G. Kamzolova, Alexander A. Osypov

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Electrostatic properties of T7-like phages promoters for host bacterial and native viral RNA polymerases

Alexander A. Osypov, Svetlana G. Kamzolova,

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Electrostatics of E. coli CRP Transcription Factor Match That of Its Binding Sites

Eugenia A. Krutinina, Gleb G. Krutinin, Svetlana G. Kamzolova, Alexander A. Osypov

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Genetic and Electrostatic Maps of Bacteriophage Lambda Genome

Gleb G. Krutinin, Eugenia A. Krutinina, Svetlana G. Kamzolova, Alexander A. Osypov

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Illuminating Obscure States of the Phage T3 DNA Packaging Motor

Philip Serwer , Elena T. Wright , Guimei Yu , Wen Jiang

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Spatial Organization of Electrostatic Interactions Between T7 Specific RNA Polymerase and Its Native Promoters

A.A. Sorokin, E.A. Temlyakova, T.R. Dzhelyadin, S.G. Kamzolova

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The Dependency of Promoter Strength upon the Electrostatic Up-element in E.coli rrnB P1 Promoter Mutants

Gleb G. Krutinin, Eugenia A. Krutinina, Svetlana G. Kamzolova, Alexander A. Osypov

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Multiscale Estimation of Binding Kinetics Using Molecular Dynamics, Brownian Dynamics, and Milestoning

Lane W. Votapka, Rommie E. Amaro

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Expanding the conformational space of structure/function relationship of tyrosine kinases

Bradley Dickson, Chao Feng, He Huang, Mehul Joshi, Carol Beth Post

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Protein folding simulation using temperature based cascade MD

Vinod Jani, Uddhavesh Sonavane , Rajendra Joshi

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A full exploration of the conformational ensembles of nucleic acid structural motifs

Thomas Cheatham III

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Encounter Complexes and Dimensionality Reduction in Protein-Protein Association

Dima Kozakov 1 , Pirooz Vakili, Ioannis Ch. Paschalidis , Sandor Vajda

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Exploring conformational dynamics of biomolecular recognition via hierarchical sampling approach

Ashalatha Sreshty Mamidi , Avadhesha Surolia

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Exploring the possibilities for targeting the existing anti-viral molecules against cancer

Poonam Singh , Ankur Omer

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Inhibition of Aβ aggregation in Alzheimer's disease using the poly-ion short single stranded DNA: In silico Study

Mary Dutta, Mattaparthi Venkata Satish Kumar

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MDTRA: Unified Approach to Molecular Dynamics Data Preparation and Analysis

Alexander V. Popov, Yuri N. Vorobjev, Dmitry O. Zharkov

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Molecular Dynamics Simulation Studies of Protein Sectors: Motional Correlations

Bharat Lakhani, Emily Black, David L. Beveridge

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Studies using molecular dynamics reveal mechanism of interaction of hemocyanin with phenolic substrates

K.N.Naresh , Arun Sreekumar , S.S. Rajan

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Design principles governing the motility of myosin motors

Dave Thirumalai,

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The Energy Landscape for Protein Folding and Biomolecular Machines

José Nelson Onuchic

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Activation Mechanism of R776H mutation in Epidermal Growth Factor Receptor (EGFR)

Zheng Ruan, Natarajan Kannan

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A region in the middle domain of E. coli Hsp90 is important for collaboration with DnaK

Andrea N. Kravats, Olivier Genest, Joel R. Hoskins, Shannon M. Doyle, Sue Wickner

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Interaction and collaboration between DnaK and ClpB during protein disaggregation

Shannon M. Doyle , Andrea N. Kravats , Joel R. Hoskins, Yu-Hsuan Shih , George Stan , Sue Wickner

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Multi-drug Resistance Efflux Pumps in Bacteria: how they work?

Melinda S Wren , Kumkum Ganguly , Paige E Paridington , Mira Dimitrijevic , Benjamin H McMahon , Herbert Schweizer , Goutam Gupta

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Structure and energetics of the pumping mechanism of membrane ATPase

BenoƮt Roux, Huan Rui, Avisek Das

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Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico

Olga Kononova , Yaroslav Kholodov, Kelly E. Theisen, Kenneth A. Marx, Ruxandra I. Dima, Fazly I. Ataullakhanov , Ekaterina L. Grishchuk , Valeri Barsegov

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De-Aggregation Mediated Monitoring of Protein Aggregation through Controlled Aggregation of Cyanine Dyes

Prathap Reddy Patlolla, Bhaskar Datta

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Forensic bioaffinity-based assay to determine blood sample age

Juliana Agudelo , Crystal Huynh , Jan Halámek

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Ion Channels: From Structure Refinement and Remodeling to Functional Mechanisms

Huan-Xiang Zhou

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Ion Selectivity in Some Cation Channels

Andrew Das Arulsamy

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Visualization of αC regions in fibrin network formation by high-resolution AFM

Anna D. Protopopova, Nikolay A. Barinov, Dmitry V. Klinov

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Design of Light-sensitive Molecules for Time-resolved Crystallography and Optogenetics

Keith Moffat

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Technologies for Analyzing Neural Circuits of Brain Disorders

Xue Han

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Tools for Mapping and Fixing the Brain

Edward S. Boyden

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A novel role for astrocytes in regulating glutamate clearance during stroke

Amanda Sweeney, Marvin F. Rodriguez, Annalisa Scimemi

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Atomistic Understanding and Design of Microbial Opsin-based Optogenetics Tools

Shigehiko Hayashi

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Let's Get Twisted: The Crystal Structure of Torsionally Stressed DNA

Carina Hernandez, Jens J. Birktoft, Arun Richard , Chandrasekaran , Yoel P. Ohayon, Ruojie Sha, Chengde Mao, Nadrian C. Seeman

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A Nanomechanical Device that Operates in a 3D Crystal

Yudong Hao , Jens J. Birktoft, , Martin Kristiansen , Ruojie Sha, Chengde Mao , Nadrian C. Seeman

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Creating combinatorial patterns with DNA origami arrays

Grigory Tikhomirov , Philip Petersen , Lulu Qian

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DNA nanotech and super-resolution imaging

Peng Yin

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Dynamic DNA devices and assemblies formed by shape-complementary, non-basepairing 3D components(*)

Thomas Gerling, Klaus F. Wagenbauer, Andrea Neuner, Hendrik Dietz

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Programmable Crystal Contacts Used to Improve the Resolution of Self-Assembled 3D DNA Crystals

Yoel P. Ohayon , Arun Richard Chandrasekaran , Carina Hernandez , Jens J. Birktoft , Ruojie Sha, , Steve Ginell , Phil Lukeman , Chengde Mao , Paul M. Chaikin , Nadrian C. Seeman

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Dynamic Self-Assembly of DNA Nanotubes

Leopold N. Green, Hari K. K. Subramanian , Vahid Mardanlou , Jongmin Kim , Rizal F. Hariadi , Elisa Franco

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Smart polymer Functionalized Graphene Nano-Devices for Thermo-Switch Controlled Biodetection

Mustafa Balcioglu , Burak Zafer Buyukbekar , Mustafa Selman Yavuz , Mehmet V. Yigit

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Two dimensional nanomaterials for microRNA analysis

Muhit Rana, Mustafa Hizir, Mustafa Balcioglu, Neil Robertson , Mehmet Yigit

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Cristina GutierrezCryo-EM studies of the naked mole-rat ribosome

Cristina Gutierrez-Vargas , Zheng Liu, Zhonge Ke, Vera Gorbunova, Joachim Frank

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Quantifying the energy landscapes of ribosome function through simulation

Paul C. Whitford

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Simulating mRNA-tRNA Translocation through the Ribosome

Kien Nguyen , Paul Charles Whitford

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Structures of Plasmodium falciparum ribosomes reveal critical dynamics during translation

Ming Sun, , Wen Li, Karin Blomqvist, Sanchaita Das, Yaser Hashem, Jeffrey D. Dvorin , Joachim Frank,

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Three-dimensional arrangements of ribosomes inside fast growing E. coli cells

Thomas Hoffmann , Julio O. Ortiz, F. Ulrich Hartl , Wolfgang Baumeister

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Benchmark of Amber ff12SB force field by comparison of estimated hairpin loop folding stabilities to experiments

Zhen Tan, Aleksandar Spasic, David H. Mathews

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Constructing Free Energy Landscapes of RNAs at Atomic Resolution and Characterisation of their Excited States

Aditi N. Borkar , Pramodh Vallurupalli, Carlo Camilloni, Lewis E. Kay , Michele Vendruscolo

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Developing a new generation of peptidyl-oligonucleotide conjugates with desired biocatalytic properties against biologically relevant RNA

Aled Williams, Yaroslav Staroseletz, Marina A. Zenkova , Elena V. Bichenkova

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Exact probability calculation of RNA loop formation identifies folding motifs in secondary structures

Michael F. Sloma , David H. Mathews

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Fast Click-Slow Release Strategy Towards HPLC-Free Synthesis of RNA Strands

Papa Nii Asare Okai, Edgar Agustin, Michael R. Miller, Jia Sheng , Maksim Royzen

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Focus on a clear message: Conserved RNA binding proteins function in mRNA control in eye lens development and their deficiency causes cataract

Archana D. Siddam, Carole Gautier-Courteille, Atul Kakrana, Vincent Legagneux, Christine A. Dang, Linette Perez-Campos, Agnes Mereau, David Scheiblin, Justine Viet, David C. Beebe, Jeffery M. Gross, Luc Paillard, Salil A. Lachke

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Improving nucleic acid design using biased sequence initialization

Mohammad Kayedkhordeh, Stanislav Bellaousov, David H. Mathews

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Improving the Amber RNA force field

Asaminew H. Aytenfisu, Aleksandar Spasic, Alan Grossfield, Harry Stern, David H. Mathews

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A New Approach to Model and Directly Control "Co-transcriptional" RNA Folding

Aruni Karunanayake Mudiyanselage, Spencer Moore, Yasaman Gholamalipour, Elvan Cavac, Craig T Martin

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Force and temperature dependent folding of a 2-base-pair RNA kissing complex

William Stephenson , Ashely Colvin, Alan A. Chen , Pan T.X. Li

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Interplay of Water molecules and Mg2+ ions in stability of RNA containing non-Watson-Crick base pairs

Sudhanshu Shanker , Pradipta Bandyopadhyay

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Structural polymorphism of CAG RNA repeats investigated by single-molecule mechanical unfolding

William Stephenson, Botros Toro, Pan T.X. Li

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The crystal structure and catalytic mechanism of the twister ribozyme

David M. J. Lilley , Yijin Liu , Timothy J. Wilson

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RNA labeling and dynamics in live bacterial cells

Irina Smolina , Natalia Broude

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Examining the Unusual Conformation of GAGU Internal Loop Using Molecular Dynamics

Aleksandar Spasic , Laura Needham , David H. Mathews

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Recent progress in determining RNA 3D structure and dynamics using all-atom molecular dynamics simulations

Alan A. Chen

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Exploring the architecture of lncRNA RepA, a key player in X-chromosome inactivation

Fei Liu , Anna Marie Pyle

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Predicting and exploring complex RNA architectures through a coarse-grained model

T. Cragnolini, S. Doutreligne, M. Baaden, P. Derreumaux, S. Pasquali

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Nonenzymatic Recombination of RNA: Detection of Novel Sequences by Next-generation Sequencing

Yaroslav Y. Staroselets , Evgeney V. Brenner, Valentin V. Vlassov, Marina A. Zenkova

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Structural aspects of non-enzymatic recombination in viral RNA

Catherine Watson, Yaroslav Staroseletz, Marina A. Zenkova, Richard Bryce, Elena V. Bichenkova

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