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ORCIDIvet Bahar
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2020 – today
- 2022
[j42]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): 4175-4190 (2022)- [j41]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) - 2021
- [j40]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): 3657-3659 (2021) - [j39]Burak T. Kaynak, She Zhang, Ivet Bahar, Pemra Doruker:
ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution. Bioinform. 37(21): 3956-3958 (2021) - [j38]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): 50 (2021) - [j37]Fen Pei, Qingya Shi, Haotian Zhang, Ivet Bahar:
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. J. Chem. Inf. Model. 61(4): 1670-1682 (2021) - 2020
- [j36]Luca Ponzoni, Daniel A. Peñaherrera, Zoltán N. Oltvai, Ivet Bahar:
Rhapsody: predicting the pathogenicity of human missense variants. Bioinform. 36(10): 3084-3092 (2020) - [j35]Hongchun Li, Fen Pei, D. Lansing Taylor, Ivet Bahar:
QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics. Bioinform. 36(12): 3935-3937 (2020) - [j34]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)
2010 – 2019
- 2019
- [j33]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): 2496-2508 (2019) - 2017
- [j32]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): W374-W380 (2017) - 2016
- [j31]Hongchun Li, Yuan-Yu Chang, Lee-Wei Yang, Ivet Bahar:
iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res. 44(Database-Issue): 415-422 (2016) - 2015
- [j30]Murat Can Cobanoglu, Zoltán N. Oltvai, D. Lansing Taylor, Ivet Bahar:
BalestraWeb: efficient online evaluation of drug-target interactions. Bioinform. 31(1): 131-133 (2015) - [j29]Eran Eyal, Gengkon Lum, Ivet Bahar:
The anisotropic network model web server at 2015 (ANM 2.0). Bioinform. 31(9): 1487-1489 (2015) - [j28]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): 1929-1937 (2015) - [j27]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): 1132-1136 (2015) - 2014
- [j26]Ahmet Bakan, Anindita Dutta, Wenzhi Mao, Ying Liu, Chakra Chennubhotla, Timothy R. Lezon, Ivet Bahar:
Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinform. 30(18): 2681-2683 (2014) - [j25]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) - [j24]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) - [j23]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) - 2013
- [j22]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): 3399-3409 (2013) - 2012
- [j21]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) - 2011
- [j20]Ahmet Bakan, Lidio M. C. Meireles, Ivet Bahar:
ProDy: Protein Dynamics Inferred from Theory and Experiments. Bioinform. 27(11): 1575-1577 (2011) - [j19]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) - [c6]Ahmet Bakan, Ivet Bahar:
Computational Generation inhibitor-Bound Conformers of P38 Map Kinase and Comparison with Experiments. Pacific Symposium on Biocomputing 2011: 181-192 - 2010
- [j18]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) - [j17]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) - [j16]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) - [c5]Ying Liu, Ivet Bahar:
Toward Understanding Allosteric Signaling Mechanisms in the ATPase Domain of Molecular Chaperones. Pacific Symposium on Biocomputing 2010: 269-280
2000 – 2009
- 2009
- [j15]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): 606-614 (2009) - [j14]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): 2147 (2009) - [j13]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) - [j12]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) - 2008
- [j11]Ying Liu, Eran Eyal, Ivet Bahar:
Analysis of correlated mutations in HIV-1 protease using spectral clustering. Bioinform. 24(10): 1243-1250 (2008) - 2007
- [j10]Eran Eyal, Shmuel Pietrokovski, Ivet Bahar:
Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices. Bioinform. 23(14): 1837-1839 (2007) - [j9]Dror Tobi, Ivet Bahar:
Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity? BMC Bioinform. 8 (2007) - [j8]Chakra Chennubhotla, Ivet Bahar:
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. J. Comput. Biol. 14(6): 765-776 (2007) - [j7]Chakra Chennubhotla, Ivet Bahar:
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput. Biol. 3(9) (2007) - [j6]Chakra Chennubhotla, Ivet Bahar:
Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput. Biol. 3(10) (2007) - [c4]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: 175-184 - 2006
- [j5]Eran Eyal, Lee-Wei Yang, Ivet Bahar:
Anisotropic network model: systematic evaluation and a new web interface. Bioinform. 22(21): 2619-2627 (2006) - [j4]Illés J. Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltán N. Oltvai:
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinform. 7: 478 (2006) - [j3]Lee-Wei Yang, A. J. Rader, Xiong Liu, Christopher Jon Jursa, Shann-Ching Chen, Hassan A. Karimi, Ivet Bahar:
oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res. 34(Web-Server-Issue): 24-31 (2006) - [c3]Chakra Chennubhotla, Ivet Bahar:
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. RECOMB 2006: 379-393 - 2005
- [j2]Lee-Wei Yang, Xiong Liu, Christopher Jon Jursa, Mark Holliman, A. J. Rader, Hassan A. Karimi, Ivet Bahar:
iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinform. 21(13): 2978-2987 (2005) - 2004
- [c2]Xiong Liu, Hassan A. Karimi, Lee-Wei Yang, Ivet Bahar:
Protein Functional Motion Query and Visualization. COMPSAC Workshops 2004: 86-89 - [c1]Shann-Ching Chen, Ivet Bahar:
Mining frequent patterns in protein structures: a study of protease families. ISMB/ECCB (Supplement of Bioinformatics) 2004: 77-85 - 2002
- [j1]Pemra Doruker, Robert L. Jernigan, Ivet Bahar:
Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23(1): 119-127 (2002)
Coauthor Index
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