Ivet Bahar

Publication Activity (10 Years)

Years Active: 2002-2022
Publications (10 Years): 16

Top Topics

Causal Discovery

Comparative Study

Protein Backbone

Top Venues

PLoS Comput. Biol.

J. Chem. Inf. Model.

Nucleic Acids Res.

Publications

Iris N. Smith, Jennifer E. Dawson, James Krieger, Stetson Thacker, Ivet Bahar, Charis Eng
Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation. J. Chem. Inf. Model. 62 (17) (2022)
Omer Acar, She Zhang, Ivet Bahar, Anne-Ruxandra Carvunis
Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow. PLoS Comput. Biol. 18 (5) (2022)
Haohan Wang, Fen Pei, Michael M. Vanyukov, Ivet Bahar, Wei Wu, Eric P. Xing
Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets. BMC Bioinform. 22 (1) (2021)
Fen Pei, Qingya Shi, Haotian Zhang, Ivet Bahar
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. J. Chem. Inf. Model. 61 (4) (2021)
Burak T. Kaynak, She Zhang, Ivet Bahar, Pemra Doruker
ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution. Bioinform. 37 (21) (2021)
She Zhang, James Krieger, Yan Zhang, Cihan Kaya, Burak T. Kaynak, Karolina Mikulska-Ruminska, Pemra Doruker, Hongchun Li, Ivet Bahar
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python. Bioinform. 37 (20) (2021)
Luca Ponzoni, Nga H. Nguyen, Ivet Bahar, Jeffrey L. Brodsky
Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel. PLoS Comput. Biol. 16 (4) (2020)
Luca Ponzoni, Daniel A. Peñaherrera, Zoltán N. Oltvai, Ivet Bahar
Rhapsody: predicting the pathogenicity of human missense variants. Bioinform. 36 (10) (2020)
Hongchun Li, Fen Pei, D. Lansing Taylor, Ivet Bahar
QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics. Bioinform. 36 (12) (2020)
Karolina Mikulska-Ruminska, Indira Shrivastava, James Krieger, She Zhang, Hongchun Li, Hülya Bayir, Sally E. Wenzel, Andrew P. Vandemark, Valerian E. Kagan, Ivet Bahar
Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. J. Chem. Inf. Model. 59 (5) (2019)
Hongchun Li, Yuan-Yu Chang, Ji Young Lee, Ivet Bahar, Lee-Wei Yang
DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Hongchun Li, Yuan-Yu Chang, Lee-Wei Yang, Ivet Bahar
GNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res. 44 (Database-Issue) (2016)
Eran Eyal, Gengkon Lum, Ivet Bahar
The anisotropic network model web server at 2015 (ANM 2.0). Bioinform. 31 (9) (2015)
Wenzhi Mao, Cihan Kaya, Anindita Dutta, Amnon Horovitz, Ivet Bahar
Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. Bioinform. 31 (12) (2015)
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
The center for causal discovery of biomedical knowledge from big data. J. Am. Medical Informatics Assoc. 22 (6) (2015)
Murat Can Cobanoglu, Zoltán N. Oltvai, D. Lansing Taylor, Ivet Bahar
BalestraWeb: efficient online evaluation of drug-target interactions. Bioinform. 31 (1) (2015)
Mary Hongying Cheng, Ivet Bahar
Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle. PLoS Comput. Biol. 10 (10) (2014)
Ignacio J. General, Ying Liu, Mandy E. Blackburn, Wenzhi Mao, Lila M. Gierasch, Ivet Bahar
ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones. PLoS Comput. Biol. 10 (5) (2014)
Ahmet Bakan, Anindita Dutta, Wenzhi Mao, Ying Liu, Chakra Chennubhotla, Timothy R. Lezon, Ivet Bahar
for bridging protein sequence evolution and structural dynamics. Bioinform. 30 (18) (2014)
Avisek Das, Mert Gur, Mary Hongying Cheng, Sunhwan Jo, Ivet Bahar, Benoît Roux
Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model. PLoS Comput. Biol. 10 (4) (2014)
Murat Can Cobanoglu, Chang Liu, Feizhuo Hu, Zoltán N. Oltvai, Ivet Bahar
Predicting Drug-Target Interactions Using Probabilistic Matrix Factorization. J. Chem. Inf. Model. 53 (12) (2013)
Zeynep Kurkcuoglu, Ahmet Bakan, Duygu Kocaman, Ivet Bahar, Pemra Doruker
Coupling between Catalytic Loop Motions and Enzyme Global Dynamics. PLoS Comput. Biol. 8 (9) (2012)
Ahmet Bakan, Ivet Bahar
Computational Generation inhibitor-Bound Conformers of P38 Map Kinase and Comparison with Experiments. Pacific Symposium on Biocomputing (2011)
Enrique Marcos, Ramon Crehuet, Ivet Bahar
Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members. PLoS Comput. Biol. 7 (9) (2011)
Ahmet Bakan, Lidio M. Meireles, Ivet Bahar
: Protein Dynamics Inferred from Theory and Experiments. Bioinform. 27 (11) (2011)
Timothy R. Lezon, Ivet Bahar
Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology. PLoS Comput. Biol. 6 (6) (2010)
Ying Liu, Lila M. Gierasch, Ivet Bahar
Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs. PLoS Comput. Biol. 6 (9) (2010)
Ying Liu, Ivet Bahar
Toward Understanding Allosteric Signaling Mechanisms in the ATPase Domain of Molecular Chaperones. Pacific Symposium on Biocomputing (2010)
Enrique Marcos, Ramon Crehuet, Ivet Bahar
On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm. PLoS Comput. Biol. 6 (4) (2010)
Lee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinform. 25 (16) (2009)
Timothy R. Lezon, Andrej Sali, Ivet Bahar
Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models. PLoS Comput. Biol. 5 (9) (2009)
Lee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinform. 25 (5) (2009)
Zheng Yang, Peter Májek, Ivet Bahar
Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL. PLoS Comput. Biol. 5 (4) (2009)
Ying Liu, Eran Eyal, Ivet Bahar
Analysis of correlated mutations in HIV-1 protease using spectral clustering. Bioinform. 24 (10) (2008)
Chakra Chennubhotla, Ivet Bahar
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. J. Comput. Biol. 14 (6) (2007)
Eran Eyal, Shmuel Pietrokovski, Ivet Bahar
Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices. Bioinform. 23 (14) (2007)
Chakra Chennubhotla, Ivet Bahar
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput. Biol. 3 (9) (2007)
Eran Eyal, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar
Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Chakra Chennubhotla, Ivet Bahar
Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput. Biol. 3 (10) (2007)
Dror Tobi, Ivet Bahar
-grams at functional sites: Is this a mechanism for increasing enzyme specificity? BMC Bioinform. 8 (2007)
Lee-Wei Yang, A. J. Rader, Xiong Liu, Christopher Jon Jursa, Shann-Ching Chen, Hassan A. Karimi, Ivet Bahar
GNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Illés J. Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltán N. Oltvai
. BMC Bioinform. 7 (2006)
Chakra Chennubhotla, Ivet Bahar
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. RECOMB (2006)
Eran Eyal, Lee-Wei Yang, Ivet Bahar
Anisotropic network model: systematic evaluation and a new web interface. Bioinform. 22 (21) (2006)
Lee-Wei Yang, Xiong Liu, Christopher Jon Jursa, Mark Holliman, A. J. Rader, Hassan A. Karimi, Ivet Bahar
GNM: a database of protein functional motions based on Gaussian Network Model. Bioinform. 21 (13) (2005)
Xiong Liu, Hassan A. Karimi, Lee-Wei Yang, Ivet Bahar
Protein Functional Motion Query and Visualization. COMPSAC Workshops (2004)
Shann-Ching Chen, Ivet Bahar
Mining frequent patterns in protein structures: a study of protease families. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Pemra Doruker, Robert L. Jernigan, Ivet Bahar
Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23 (1) (2002)