Ivet Bahar

According to our database, Ivet Bahar authored at least 46 papers between 2002 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow.

Omer Acar, She Zhang, Ivet Bahar, Anne-Ruxandra Carvunis

PLoS Comput. Biol., 2022

Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation.

Iris N. Smith, Jennifer E. Dawson, James Krieger, Stetson Thacker, Ivet Bahar, Charis Eng

J. Chem. Inf. Model., 2022

2021

Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization.

Fen Pei, Qingya Shi, Haotian Zhang, Ivet Bahar

J. Chem. Inf. Model., 2021

Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets.

Haohan Wang, Fen Pei, Michael M. Vanyukov, Ivet Bahar, Wei Wu, Eric P. Xing

BMC Bioinform., 2021

ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python.

She Zhang, James Krieger, Yan Zhang, Cihan Kaya, Burak T. Kaynak, Karolina Mikulska-Ruminska, Pemra Doruker, Hongchun Li, Ivet Bahar

Bioinform., 2021

ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution.

Burak T. Kaynak, She Zhang, Ivet Bahar, Pemra Doruker

Bioinform., 2021

2020

Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel.

Luca Ponzoni, Nga H. Nguyen, Ivet Bahar, Jeffrey L. Brodsky

PLoS Comput. Biol., 2020

Rhapsody: predicting the pathogenicity of human missense variants.

Luca Ponzoni, Daniel A. Peñaherrera, Zoltán N. Oltvai, Ivet Bahar

Bioinform., 2020

QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics.

Hongchun Li, Fen Pei, D. Lansing Taylor, Ivet Bahar

Bioinform., 2020

2019

Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members.

Karolina Mikulska-Ruminska, Indira Shrivastava, James Krieger, She Zhang, Hongchun Li, Hülya Bayir, Sally E. Wenzel, Andrew P. Vandemark, Valerian E. Kagan, Ivet Bahar

J. Chem. Inf. Model., 2019

2017

DynOmics: dynamics of structural proteome and beyond.

Hongchun Li, Yuan-Yu Chang, Ji Young Lee, Ivet Bahar, Lee-Wei Yang

Nucleic Acids Res., 2017

2016

<i>i</i>GNM 2.0: the Gaussian network model database for biomolecular structural dynamics.

Hongchun Li, Yuan-Yu Chang, Lee-Wei Yang, Ivet Bahar

Nucleic Acids Res., 2016

2015

The center for causal discovery of biomedical knowledge from big data.

Gregory F. Cooper, Ivet Bahar, Michael J. Becich, Panayiotis V. Benos, Jeremy M. Berg, Jeremy U. Espino, Clark Glymour, Rebecca Crowley Jacobson, Michelle Kienholz, Adrian V. Lee, Xinghua Lu, Richard Scheines

J. Am. Medical Informatics Assoc., 2015

Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution.

Wenzhi Mao, Cihan Kaya, Anindita Dutta, Amnon Horovitz, Ivet Bahar

Bioinform., 2015

The anisotropic network model web server at 2015 (ANM 2.0).

Eran Eyal, Gengkon Lum, Ivet Bahar

Bioinform., 2015

BalestraWeb: efficient online evaluation of drug-target interactions.

Murat Can Cobanoglu, Zoltán N. Oltvai, D. Lansing Taylor, Ivet Bahar

Bioinform., 2015

2014

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones.

Ignacio J. General, Ying Liu, Mandy E. Blackburn, Wenzhi Mao, Lila M. Gierasch, Ivet Bahar

PLoS Comput. Biol., 2014

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model.

Avisek Das, Mert Gur, Mary Hongying Cheng, Sunhwan Jo, Ivet Bahar, Benoît Roux

PLoS Comput. Biol., 2014

Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle.

Mary Hongying Cheng, Ivet Bahar

PLoS Comput. Biol., 2014

<i>Evol</i> and <i>ProDy</i> for bridging protein sequence evolution and structural dynamics.

Ahmet Bakan, Anindita Dutta, Wenzhi Mao, Ying Liu, Chakra Chennubhotla, Timothy R. Lezon, Ivet Bahar

Bioinform., 2014

2013

Predicting Drug-Target Interactions Using Probabilistic Matrix Factorization.

Murat Can Cobanoglu, Chang Liu, Feizhuo Hu, Zoltán N. Oltvai, Ivet Bahar

J. Chem. Inf. Model., 2013

2012

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics.

Zeynep Kurkcuoglu, Ahmet Bakan, Duygu Kocaman, Ivet Bahar, Pemra Doruker

PLoS Comput. Biol., 2012

2011

Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members.

Enrique Marcos, Ramon Crehuet, Ivet Bahar

PLoS Comput. Biol., 2011

<i>ProDy</i>: Protein Dynamics Inferred from Theory and Experiments.

Ahmet Bakan, Lidio M. C. Meireles, Ivet Bahar

Bioinform., 2011

Computational Generation inhibitor-Bound Conformers of P38 Map Kinase and Comparison with Experiments.

Ahmet Bakan, Ivet Bahar

Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011

2010

On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm.

Enrique Marcos, Ramon Crehuet, Ivet Bahar

PLoS Comput. Biol., 2010

Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs.

Ying Liu, Lila M. Gierasch, Ivet Bahar

PLoS Comput. Biol., 2010

Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology.

Timothy R. Lezon, Ivet Bahar

PLoS Comput. Biol., 2010

Toward Understanding Allosteric Signaling Mechanisms in the ATPase Domain of Molecular Chaperones.

Ying Liu, Ivet Bahar

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL.

Zheng Yang, Peter Májek, Ivet Bahar

PLoS Comput. Biol., 2009

Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models.

Timothy R. Lezon, Andrej Sali, Ivet Bahar

PLoS Comput. Biol., 2009

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics.

Lee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao

Bioinform., 2009

2008

Analysis of correlated mutations in HIV-1 protease using spectral clustering.

Ying Liu, Eran Eyal, Ivet Bahar

Bioinform., 2008

2007

Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations.

Chakra Chennubhotla, Ivet Bahar

PLoS Comput. Biol., 2007

Signal Propagation in Proteins and Relation to Equilibrium Fluctuations.

Chakra Chennubhotla, Ivet Bahar

PLoS Comput. Biol., 2007

Recruitment of rare <i>3</i>-grams at functional sites: Is this a mechanism for increasing enzyme specificity?

Dror Tobi, Ivet Bahar

BMC Bioinform., 2007

Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices.

Eran Eyal, Shmuel Pietrokovski, Ivet Bahar

Bioinform., 2007

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.

Eran Eyal, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

<i>o</i>GNM: online computation of structural dynamics using the Gaussian Network Model.

Lee-Wei Yang, A. J. Rader, Xiong Liu, Christopher Jon Jursa, Shann-Ching Chen, Hassan A. Karimi, Ivet Bahar

Nucleic Acids Res., 2006

Topological basis of signal integration in the transcriptional-regulatory network of the yeast, <i>Saccharomyces cerevisiae</i>.

Illés J. Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltán N. Oltvai

BMC Bioinform., 2006

Anisotropic network model: systematic evaluation and a new web interface.

Eran Eyal, Lee-Wei Yang, Ivet Bahar

Bioinform., 2006

Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics.

Chakra Chennubhotla, Ivet Bahar

Proceedings of the Research in Computational Molecular Biology, 2006

2005

<i>i</i>GNM: a database of protein functional motions based on Gaussian Network Model.

Lee-Wei Yang, Xiong Liu, Christopher Jon Jursa, Mark Holliman, A. J. Rader, Hassan A. Karimi, Ivet Bahar

Bioinform., 2005

2004

Mining frequent patterns in protein structures: a study of protease families.

Shann-Ching Chen, Ivet Bahar

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Protein Functional Motion Query and Visualization.

Xiong Liu, Hassan A. Karimi, Lee-Wei Yang, Ivet Bahar

Proceedings of the 28th International Computer Software and Applications Conference (COMPSAC 2004), 2004

2002

Dynamics of large proteins through hierarchical levels of coarse-grained structures.

Pemra Doruker, Robert L. Jernigan, Ivet Bahar

J. Comput. Chem., 2002