Journal Clubs

  • Weekly literature review presentations within each Core
  • Presentation opportunity for investigators, students, trainees, & postdocs
Date Presenter Name Talk Title Annotation
9/24/2019 Hongying Cheng Regulation of monoamine transporters by small molecules Lab meeting organized by Core B
9/11/2019 Stephanie Aldrich Evaluating in silico binding predictions with experimental mutagenesis to identify calcium channel residues involved in the activity of a novel agonist Lab meeting organized by Core B
8/23/2019 Jin Cheng Computational System Pharmacology and Computer-Aided Drug Design for Drug Abuse Research Core A/CCGS monthly meeting
8/23/2019 Peihao Fan Identification of Novel Targets for Psychosis in AD with Real World Evidence and Network Analysis Approaches Core A/CCGS monthly meeting
8/14/2019 Yan Zhang Dynamical Inference From Single Cell RNA-Seq Lab meeting organized by Core B
8/7/2019 Hongchun Li Protein ubiquitylation via designed PROTACs or natural protein-protein interactions Lab meeting organized by Core B
7/31/2019 Jiyoung Lee Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations Lab meeting organized by Core B
7/24/2019 Shuhan Liu New Application of In Silico Methods in Identifying Key Components of Anti-Cancer Herbal Formulation YIV-906 Core A/CCGS monthly meeting
7/24/2019 Xiguang Qi Strength and Limitation of Applying GES in Drug Mechanism Studies Core A/CCGS monthly meeting
7/24/2019 She Zhang Differences in the intrinsic spatial dynamics of gene loci contribute to cell differentiation Lab meeting organized by Core B
7/17/2019 Bing Liu Dopamine transporter in lipid rafts Lab meeting organized by Core B
7/10/2019 Luca Ponzoni Rhapsody: algorithm improvements and applications Lab meeting organized by Core B
6/28/2019 Ziheng Hu Application of Machine Learning in the Personalized Medicine of Neuropsychiatric and Cardiovascular Disorders Core A/CCGS monthly meeting
6/19/2019 Chen Fangyuan RET pathway activation and missense mutations in breast cancer & characterizing highly mobile genes from chromatin dynamics Lab meeting organized by Core B
5/29/2019 Fen Pei Predicting large scale protein-protein interactions using symmetric non-negative matrix factorization Lab meeting organized by Core B
5/24/2019 Changrui Xing Cannabinoid Receptor CB2 Structure and CB2/Gi Signaling Mechanisms Core A/CCGS monthly meeting
5/1/2019 James Krieger Updates to CoMD: application to various systems Lab meeting organized by Core B
4/24/2019 Burak Kaynak Protein-ligand complexes as constrained dynamical systems Lab meeting organized by Core B
4/10/2019 Mary Cheng Oligomerization in human dopamine transporter Lab meeting organized by Core B
2/27/2019 Dror Tobi Dynamical comparison as a tool to study proteins: the hemoglobin case Lab meeting organized by Core B
2/22/2019 Xibing He Improve the Simulations of Biological Systems from Two Aspects: Force Field and Sampling Core A/CCGS monthly meeting
2/13/2019 Ana Ligia Scott Self-adaptive collective motions of macromolecules incorporating structural and environmental effects Lab meeting organized by Core B
2/6/2019 Pemra Doruker Conformational dynamics and interactions of CaMKII Lab meeting organized by Core B
1/25/2019 Yankang Jing Analyze protein expression data using causal study to dissect disease regulatory networks Core A/CCGS monthly meeting
1/25/2019 Yuemin Bian Prediction of orthosteric and allosteric regulations on cannabinoid receptors using supervised machine learning classifiers Core A/CCGS monthly meeting
12/11/2018 Hongchun Li Intrinsic dynamics of toroidal proteins and their behaviors in several biomolecular machineries Lab meeting organized by Core B
12/4/2018 Indira Myers Bahar, Kagan and Bayir lab collaborative efforts Lab meeting organized by Core B
11/30/2018 Jin Cheng Computational System Pharmacology (CSP)-Targeting Mapping for Cocaine and Fentanyl Overdose Core A/CCGS monthly meeting
11/30/2018 Viet Man Oligomerization of Alzheimer’s Amyloid-β peptides: Mechanism and Inhibition Core A/CCGS monthly meeting
11/27/2018 Balint Dudas The activation mechanism of auto-inhibited RalF Lab meeting organized by Core B
11/20/2018 Yan Zhang/She Zhang An improvement to the system-environment framework when the environment is a lattice Lab meeting organized by Core B
10/26/2018 Carlo Iasella Comparative Effectiveness and Safety Analysis of Dual Antiplatelet Therapies after Percutaneous Coronary Intervention Core A/CCGS monthly meeting
10/26/2018 Ying Xue Cilostazol as an alternative to aspirin after PCI – Clinical study and computational system pharmacology analysis Core A/CCGS monthly meeting
10/16/2018 Ji Young Lee A mechanism of channel pore opening in AMPA receptor related with external domains dynamics Lab meeting organized by Core B
10/9/2018 Ana Ligia Scott Structural analysis and searching for allosteric modulators of dengue virus protease (NS2B / NS3) Lab meeting organized by Core B
10/2/2018 Luca Ponzoni Classification of Single Amino acid Variants (SAVs) Lab meeting organized by Core B
9/25/2018 Bing Liu Computational Modeling Reveals Polypharmacological Strategies for Regulating alpha1-antitrypsin Z Mutant Protein Disposal Lab meeting organized by Core B
8/14/2018 Yan Zhang CCT Conformational Space Elucidated by Elastic Network Model Analysis of Cryo-EM Data Lab meeting organized by Core B
8/7/2018 Burak Kaynak Towards to rigid body motions in MCell Lab meeting organized by Core B
7/24/2018 Stephanie Aldrich Voltage-gated sodium channel Lab meeting organized by Core B
7/17/2018 She Zhang Signature dynamics of protein families: conserved vs specific mechanisms of conformational motions Lab meeting organized by Core B
6/19/2018 Hongchun Li BalestraWeb 20 Lab meeting organized by Core B
6/12/2018 Various Presenters Progress report Lab meeting organized by Core B
5/25/2018 Ziheng Hu Machine-learning based prediction of substance abuse trajectory using behavioral traits at early adolescence Core A/CCGS monthly meeting
5/15/2018 Various Presenters ProDy workshop rehearsal Lab meeting organized by Core B
5/7/2018 Peihao Fan Computational Approach for Autophagy and Apoptosis Specific Knowledgebase-guided System Pharmacology Drug Research Core A/CCGS monthly meeting
4/24/2018 Jiyoung Lee Channel pore in AMPA receptor Lab meeting organized by Core B
4/17/2018 Karolina Mikulska-Ruminska In search of cardiolipin binding site motif Lab meeting organized by Core B
4/10/2018 Burak Kaynak Chapters Lab meeting organized by Core B
4/9/2018 Yankang Jing DAKB-GPCRs: An Integrated Computational Platform for Drug Abuse Core A/CCGS monthly meeting
4/3/2018 Luca Ponzoni State-of-the-art sequence-based methods for pathogenicity predictions Lab meeting organized by Core B
3/20/2018 Mary Cheng Protein complex network of VCP, PINK1, and P47 Lab meeting organized by Core B
3/13/2018 Bing Liu PEBP1-15LO1-LC3 orchestrate autophagic activity to limit ferroptosis Lab meeting organized by Core B
3/6/2018 Ana Ligia Scott Some Studies of Conformational Changes and Functional Movements studies using Full-Atom combined with Coarse-Grained model Lab meeting organized by Core B
2/5/2018 Xibing He Calculating the protein-ligand binding affinities for systems of Cathepsin S and cannabinoid type 1 receptor using the model of extended linear interaction energies Core A/CCGS monthly meeting
1/16/2018 James Krieger Collective MD for sampling conformational landscapes Lab meeting organized by Core B
1/9/2018 She Zhang 3D structures of individual mammalian genomes studied by single-cell Hi-C (paper discussion) Lab meeting organized by Core B
1/2/2018 Cihan Kaya Projects and Future Ideas Lab meeting organized by Core B
12/19/2017 Ivet Bahar General discussion Lab meeting organized by Core B
12/12/2017 She Zhang Studying Chromatin Dynamics Using the Gaussian Network Model Lab meeting organized by Core B
11/29/2017 Hongchun Li Druggability analysis for Trypsin Lab meeting organized by Core B
11/20/2017 Hongjuan Bao GBMPlatform: A Glioblastoma  Chemogenomics Knowledgebase for System Pharmacology Research Core A/CCGS monthly meeting
11/7/2017 Ivet Bahar Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions (paper discussion) Lab meeting organized by Core B
10/4/2017 Jiyoung Lee ANM/GNM Druggability MD simulations Pharmacophore modeling of Trypsin Lab meeting organized by Core B
9/26/2017 Yan Zhang DNA Condensation Lab meeting organized by Core B
9/22/2017 Junmei Wang, PhD Physics-based scoring function development and their applications on modeling protein-ligand interactions Group meeting organized by Core A
9/22/2017 Yuemin Bian Computational chemogenomics-based targets identification and protein binding modes analysis for cannabidiol Group meeting organized by Core A
9/5/2017 Bing Liu Deciphering the Dynamics of Cannabinoid Receptor Type 2 Lab meeting organized by Core B
8/22/2017 Stephaine Aldrich Modeling voltage sensor movement in the Cav21 calcium channel Lab meeting organized by Core B
8/15/2017 Various Presenters Research Summaries Lab meeting organized by Core B
7/18/2017 Ivet Bahar Biomolecular Systems Dynamics using Elastic Network Models: From Proteins to Chromosomes Lab meeting organized by Core B
7/5/2017 Ivet Bahar Biomolecular Systems Dynamics using Elastic Network Models: From Proteins to Chromosomes Lab meeting organized by Core B
6/30/2017 Mary Cheng Allosteric Modulation of Human Dopamine Transporter Activity under Conditions Promoting its Dimerization Lab meeting organized by Core B
6/5/2017 Luca Ponzoni Impact of dynamical features on the classification of missense variants Lab meeting organized by Core B
5/5/2017 Haohan Wang Spectral Linear Mixed Model, accounting for complicated population structures in association studies Group meeting organized by Core C
5/5/2017 Haohan Wang Discovering Weaker Genetic Associations with Validated Association, with Studies of Alzheimer’s Disease and Drug Abuse Disorder Group meeting organized by Core C
5/2/2017 James Krieger Dynamics of ionotropic glutamate receptors and allosteric potential of their N-terminal domains (continued) Lab meeting organized by Core B
4/25/2017 James Krieger Dynamics of ionotropic glutamate receptors and allosteric potential of their N-terminal domains Lab meeting organized by Core B
4/19/2017 Fen Pei Inferring protein-protein interaction mechanism for HD model based on drug combination data Lab meeting organized by Core B
4/13/2017 Jiyoung Lee, PhD Anisotropic network modeling (ANM) analysis of b-arrestin-1 Group meeting organized by Core B
3/21/2017 She Zhang Chromosomal Dynamics using the GNM Lab meeting organized by Core B
3/15/2017 Cihan Kaya Activation triggered subunit exchange in CaMKII Lab meeting organized by Core B
3/3/2017 Nanyi Wang ProSelection: A novel program to pick optimal protein structure subsets for in silico target identification and drug discovery research Group meeting organized by Core A
2/28/2017 Luca Ponzoni Prediction of functional effects of human nsSNPs Lab meeting organized by Core B
2/21/2017 Karolina Mikulska-Ruminska MechStiff: A New Tool for Evaluating Stress-Induced Dynamics Lab meeting organized by Core B
2/17/2017 Ben Lengerich Improving the Accuracy of Genome-Wide Association Studies Group meeting organized by Core C
2/17/2017 Haohan Wang Genomic Research with Validated Association Group meeting organized by Core C
2/7/2017 Hongchun Li Updates on the theory of Perturbation Response Scanning (PRS) Lab meeting organized by Core B
1/31/2017 Guangya Hu Differences between thermophilic and mesophilic homologous proteins are mainly from residues with high interaction degrees Lab meeting organized by Core B
1/19/2017 Bing Liu, PhD Systems-level insights into cellular regulation from quantitative modeling and analysis Group meeting organized by Core B
1/19/2017 Mary Hongying Cheng, PhD Molecular-level mechanisms of transporters and ion channels Group meeting organized by Core B
12/8/2016 LiRong Wang, PhD Pharmacogenomics study of synthetic cannabinoid intoxication Group meeting organized by Core A
11/4/2016 Bryon Aragam, PhD Reconstructing Biological Networks with Structural Equations – A New Machine Learning Approach to Better Understanding Drug Abuse Group meeting organized by Core C
10/31/2016 Bing Liu Lab meeting organized by Core B
10/26/2016 Cihan Kaya, Hongchun Li Lab meeting paper discussion Lab meeting organized by Core B
10/26/2016 Hongchun Li Lab meeting paper discussion Lab meeting organized by Core B
10/26/2016 She Zhang Adaptability of protein structures to enable functional interactions and evolutionary implications (paper discussion) Lab meeting organized by Core B
10/10/2016 Hongchun Li Dynamic Modulation of Binding Affinity as a Mechanism to Regulate Interferon Signaling Lab meeting organized by Core B
10/10/2016 Yan Zhang Normal Mode Analysis of TRiC/CCT Based on Cryo-EM Density Map Lab meeting organized by Core B
10/5/2016 Cihan Kaya Dynamics of Dopamine Transporters: Bridging Molecular and Cellular Simulations Group meeting organized by Core B
10/5/2016 Jiyoung Lee, PhD Update on Gamma-Secretase Project Group meeting organized by Core B
9/14/2016 Bing Liu Tetrad tutorial Lab meeting organized by Core B
9/7/2016 Raman Venkataramanan, PhD, Prof., Pharm. Sci. and Pathology, Hongfei Zhang, Rujuta Joshi Modeling of PK and PD data in clinical pharmacology Group meeting organized by Core A
9/7/2016 Yuemin Bian Computational Fragment-based Approach for the Discovery of Allosteric Modulators on Metabotropic Glutamate Receptor 5 Group meeting organized by Core A
7/21/2016 Karolina Mikulska-Ruminska Lab meeting organized by Core B
7/21/2016 Kliment Ziko A new paradigm of protein allostery: insight through the gaussian network model Lab meeting organized by Core B
7/14/2016 Bing Liu Computational Modeling of Redox Asthmasome Lab meeting organized by Core B
7/14/2016 Hongchun Li Dynamic Modulation of affinity as a Mechanism to regulate signaling Lab meeting organized by Core B
6/23/2016 Amit Srivastava Lab meeting organized by Core B
6/23/2016 JiYoung Lee ANM analysis of beta-arrestin-1 Lab meeting organized by Core B
6/16/2016 Pei Fen Huntington Disease Project Lab meeting organized by Core B
6/16/2016 She Zhang Revealing Chromatin Dynamics by Gaussian Network Model Lab meeting organized by Core B
6/16/2016 Zuhal Ozcan G-protein-coupled receptors Lab meeting organized by Core B
4/1/2016 Bing Liu, PhD Computational Modeling of the Amphetamine-induced Regulation of Dopamine Transporters Group meeting organized by Core B
4/1/2016 Filippo Pullara, PhD Combined computational and experimental study of CamKII Group meeting organized by Core B
4/1/2016 Jiyoung Lee, PhD ANM analysis of intact gamma-secretase with membrane Group meeting organized by Core B
3/21/2016 LiRong Wang, PhD Utilizing transcriptional data for brain disease and drug research Group meeting organized by Core A
3/21/2016 Yan Zhang Mathematical Model of Cannabinoid Receptor Type 2 Endocytosis and Trafficking Group meeting organized by Core A
3/21/2016 Ziheng Hu Big data type data mining effect of anti-hypertensive and anti-diabetic drugs on cognitive decline in Alzheimer’s disease patients Group meeting organized by Core A
2/15/2016 Micol Marchetti-Bowick A Penalized Regression Model for the Joint Estimation of eQTL Associations and Gene Network Structure Group meeting organized by Core C
2/15/2016 Siwei Xie Analysis of Gene Expression Patterns induced by Drugs of Abuse in Mouse Striatum Group meeting organized by Core C
1/8/2016 Jiyoung Lee, PhD ANM analysis of gamma-secretase Group meeting organized by Core A
1/8/2016 Bing Liu, PhD Integrative Analysis of Lipoxygenase Pathways in Asthma Group meeting organized by Core B
1/8/2016 HongChun, Li BalestraWeb server Group meeting organized by Core B
12/4/2015 Peng Yang, PhD Cannabinoid CB2 ligand Design Group meeting organized by Core A
12/4/2015 Yan Zhang Modeling Simulation on Cannabinoid Receptor CB2 Signaling Pathway via Desensitization and Resensitization Group meeting organized by Core A
12/4/2015 Zhiwei Feng, PhD Computer Modeling of 3D Structures of Cannabinoid Receptor Subtype CB2 activated through G-protein Coupling Process Group meeting organized by Core A
11/6/2015 Georg Schoenherr, Min Kyung Lee How to use the GenAMap software system Group meeting organized by Core C
10/2/2015 Jiyoung Lee, PhD Tutorial for Anisotropic Network Model Web Server: Global Motion of Protein Group meeting organized by Core B
9/11/2015 Zhiwei Feng, PhD Diarylurea Small Molecule Inhibitors of TRPV1 as Potential Therapeutics for Neuroinflammation Group meeting organized by Core A
9/11/2015 Ziheng Hu Unraveling the intricate role of anti-hypertensive and anti-diabetic medications in Alzheimer’s disease (Collaboration with Dr. Oscar Lopez, ADCR Center) Group meeting organized by Core A
9/11/2015 Filippo Pullara, PhD CaMKII/Calmodulin binding under oxidative stress conditions: Synergy of Experiments and Computer Simulations approaches Group meeting organized by Core B
9/11/2015 Mustafa Tekpinar, PhD Investigating dynamics of CamKII by elastic network models Group meeting organized by Core B
4/8/2015 Indira Srivastava Mitochondrial Dynamics: Fission and Fusion Lab meeting organized by Core B
4/1/2015 Hongchun Li Mechanisms of insertion of tryptophan rich AMPs on membranes Lab meeting organized by Core B
3/25/2015 Guang Hu Protein rings and cages Lab meeting organized by Core B
3/18/2015 Ivet Bahar Projects in the lab Lab meeting organized by Core B
12/17/2014 Bing Liu Autophagy-Apoptosis Crosstalk Lab meeting organized by Core B
11/5/2014 Murat Can Cobanoglu Prestwick Library Screen Analysis Lab meeting organized by Core B
10/22/2014 Ivet Bahar Learning from Computational Models and Pharmacology Methods Lab meeting organized by Core B
10/7/2014 Filippo Pullara Emerging regulation and functions of autophagy Lab meeting organized by Core B
9/30/2014 JiYoung Lee Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open and Desensitized States Lab meeting organized by Core B
9/23/2014 Mary Cheng A Coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations Lab meeting organized by Core B
9/18/2014 Kirubakaran Palani Computational identification and in vitro validation of novel lead molecules against TOPK and Tankyrase proteins Lab meeting organized by Core B