Dynamics of large proteins through hierarchical levels of coarse-grained structures. - Pemra Doruker; Robert L. Jernigan; Ivet Bahar (J. Comput. Chem., 2002)

Protein Functional Motion Query and Visualization. - Xiong Liu 001; Hassan A. Karimi; Lee-Wei Yang; Ivet Bahar (COMPSAC Workshops, 2004)

Mining frequent patterns in protein structures: a study of protease families. - Shann-Ching Chen; Ivet Bahar (ISMB/ECCB (Supplement of Bioinformatics), 2004)

iGNM: a database of protein functional motions based on Gaussian Network Model. - Lee-Wei Yang; Xiong Liu 001; Christopher Jon Jursa; Mark Holliman; A. J. Rader; Hassan A. Karimi; Ivet Bahar (Bioinform., 2005)

Anisotropic network model: systematic evaluation and a new web interface. - Eran Eyal; Lee-Wei Yang; Ivet Bahar (Bioinform., 2006)

Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. - Illés J. Farkas; Chuang Wu; Chakra Chennubhotla 001; Ivet Bahar; Zoltán N. Oltvai (BMC Bioinform., 2006)

oGNM: online computation of structural dynamics using the Gaussian Network Model. - Lee-Wei Yang; A. J. Rader; Xiong Liu 001; Christopher Jon Jursa; Shann-Ching Chen; Hassan A. Karimi; Ivet Bahar (Nucleic Acids Res., 2006)

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. - Eran Eyal; Chakra Chennubhotla 001; Lee-Wei Yang; Ivet Bahar (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices. - Eran Eyal; Shmuel Pietrokovski; Ivet Bahar (Bioinform., 2007)

Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity? - Dror Tobi; Ivet Bahar (BMC Bioinform., 2007)

Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. - Chakra Chennubhotla 001; Ivet Bahar (J. Comput. Biol., 2007)

Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. - Chakra Chennubhotla 001; Ivet Bahar (PLoS Comput. Biol., 2007)

Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. - Chakra Chennubhotla 001; Ivet Bahar (PLoS Comput. Biol., 2007)

Analysis of correlated mutations in HIV-1 protease using spectral clustering. - Ying Liu; Eran Eyal; Ivet Bahar (Bioinform., 2008)

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)

Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models. - Timothy R. Lezon; Andrej Sali; Ivet Bahar (PLoS Comput. Biol., 2009)

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL. - Zheng Yang; Peter Májek; Ivet Bahar (PLoS Comput. Biol., 2009)

Toward Understanding Allosteric Signaling Mechanisms in the ATPase Domain of Molecular Chaperones. - Ying Liu; Ivet Bahar (Pacific Symposium on Biocomputing, 2010)

Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology. - Timothy R. Lezon; 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)

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)

Computational Generation inhibitor-Bound Conformers of P38 Map Kinase and Comparison with Experiments. - Ahmet Bakan; Ivet Bahar (Pacific Symposium on Biocomputing, 2011)

ProDy: Protein Dynamics Inferred from Theory and Experiments. - Ahmet Bakan; Lidio M. C. Meireles; Ivet Bahar (Bioinform., 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)

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics. - Zeynep Kurkcuoglu; Ahmet Bakan; Duygu Kocaman; Ivet Bahar; Pemra Doruker (PLoS Comput. Biol., 2012)

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)

Evol and ProDy for bridging protein sequence evolution and structural dynamics. - Ahmet Bakan; Anindita Dutta; Wenzhi Mao; Ying Liu; Chakra Chennubhotla 001; Timothy R. Lezon; Ivet Bahar (Bioinform., 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)

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)

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)

BalestraWeb: efficient online evaluation of drug-target interactions. - Murat Can Cobanoglu; Zoltán N. Oltvai; D. Lansing Taylor; Ivet Bahar (Bioinform., 2015)

The anisotropic network model web server at 2015 (ANM 2.0). - Eran Eyal; Gengkon Lum; Ivet Bahar (Bioinform., 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 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 001; Richard Scheines (J. Am. Medical Informatics Assoc., 2015)

iGNM 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)

DynOmics: dynamics of structural proteome and beyond. - Hongchun Li; Yuan-Yu Chang; Ji Young Lee; Ivet Bahar; Lee-Wei Yang (Nucleic Acids Res., 2017)

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)

QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics. - Hongchun Li; Fen Pei; D. Lansing Taylor; Ivet Bahar (Bioinform., 2020)

Rhapsody: predicting the pathogenicity of human missense variants. - Luca Ponzoni; Daniel A. Peñaherrera; Zoltán N. Oltvai; Ivet Bahar (Bioinform., 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)

ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution. - Burak T. Kaynak; She Zhang; Ivet Bahar; Pemra Doruker (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)

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 023; Eric P. Xing (BMC Bioinform., 2021)

Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. - Fen Pei; Qingya Shi; Haotian Zhang; Ivet Bahar (J. Chem. Inf. Model., 2021)

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)

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)