Anders Wallqvist

44 papers Journal 44
YearRankTypeTitle / Venue / Authors
2024 J jnl
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism.
PLoS Comput. Biol.
Bonnie V. Dougherty, Connor J. Moore, Kristopher D. Rawls, Matthew L. Jenior, Bryan Chun, Sarbajeet Nagdas, Jeffrey J. Saucerman, Glynis L. Kolling, Anders Wallqvist, Jason A. Papin
2022 J jnl
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning.
J. Comput. Aided Mol. Des.
Ruifeng Liu, Srinivas Laxminarayan, Jaques Reifman, Anders Wallqvist
2021 J jnl
Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification.
PLoS Comput. Biol.
Daniel R. Ripoll, Sidhartha Chaudhury, Anders Wallqvist
2019 J jnl
A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools.
Comput. Biol. Medicine
Kristopher D. Rawls, Bonnie V. Dougherty, Edik M. Blais, Ethan Stancliffe, Glynis L. Kolling, Kalyan C. Vinnakota, Venkat R. Pannala, Anders Wallqvist, Jason A. Papin
2019 J jnl
Dissecting Machine-Learning Prediction of Molecular Activity: Is an Applicability Domain Needed for Quantitative Structure-Activity Relationship Models Based on Deep Neural Networks?
J. Chem. Inf. Model.
Ruifeng Liu, Hao Wang, Kyle P. Glover, Michael G. Feasel, Anders Wallqvist
2019 J jnl
Molecular Similarity-Based Domain Applicability Metric Efficiently Identifies Out-of-Domain Compounds.
J. Chem. Inf. Model.
Ruifeng Liu, Anders Wallqvist
2019 J jnl
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems.
PLoS Comput. Biol.
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
2018 J jnl
General Approach to Estimate Error Bars for Quantitative Structure-Activity Relationship Predictions of Molecular Activity.
J. Chem. Inf. Model.
Ruifeng Liu, Kyle P. Glover, Michael G. Feasel, Anders Wallqvist
2017 J jnl
A strategy for evaluating pathway analysis methods.
BMC Bioinform.
Chenggang Yu, Hyung Jun Woo, Xueping Yu, Tatsuya Oyama, Anders Wallqvist, Jaques Reifman
2017 J jnl
Molecular Structure-Based Large-Scale Prediction of Chemical-Induced Gene Expression Changes.
J. Chem. Inf. Model.
Ruifeng Liu, Mohamed Diwan M. AbdulHameed, Anders Wallqvist
2016 J jnl
DBSecSys 2.0: a database of
BMC Bioinform.
Vesna Memisevic, Kamal Kumar, Nela Zavaljevski, David DeShazer, Anders Wallqvist, Jaques Reifman
2016 J jnl
General Purpose 2D and 3D Similarity Approach to Identify hERG Blockers.
J. Chem. Inf. Model.
Patric Schyman, Ruifeng Liu, Anders Wallqvist
2016 J jnl
Metabolic host responses to malarial infection during the intraerythrocytic developmental cycle.
BMC Syst. Biol.
Anders Wallqvist, Xin Fang, Shivendra G. Tewari, Ping Ye, Jaques Reifman
2015 J jnl
Biofilm Formation Mechanisms of
PLoS Comput. Biol.
Francisco G. Vital-Lopez, Jaques Reifman, Anders Wallqvist
2015 J jnl
Critically Assessing the Predictive Power of QSAR Models for Human Liver Microsomal Stability.
J. Chem. Inf. Model.
Ruifeng Liu, Patric Schyman, Anders Wallqvist
2015 J jnl
Data-driven identification of structural alerts for mitigating the risk of drug-induced human liver injuries.
J. Cheminformatics
Ruifeng Liu, Xueping Yu, Anders Wallqvist
2015 J jnl
Mining Host-Pathogen Protein Interactions to Characterize
PLoS Comput. Biol.
Vesna Memisevic, Nela Zavaljevski, Seesandra V. Rajagopala, Keehwan Kwon, Rembert Pieper, David DeShazer, Jaques Reifman, Anders Wallqvist
2014 J jnl
A computational study of the respiratory airflow characteristics in normal and obstructed human airways.
Comput. Biol. Medicine
Bora Sul, Anders Wallqvist, Michael J. Morris, Jaques Reifman, Vineet Rakesh
2014 J jnl
DBSecSys: a database of Burkholderia mallei secretion systems.
BMC Bioinform.
Vesna Memievi, Kamal Kumar, Li Cheng, Nela Zavaljevski, David DeShazer, Anders Wallqvist, Jaques Reifman
2014 J jnl
Exploiting large-scale drug-protein interaction information for computational drug repurposing.
BMC Bioinform.
Ruifeng Liu, Narender Singh, Gregory J. Tawa, Anders Wallqvist, Jaques Reifman
2014 J jnl
Merging Applicability Domains for
J. Chem. Inf. Model.
Ruifeng Liu, Anders Wallqvist
2013 J jnl
Bridging the gap between gene expression and metabolic phenotype via kinetic models.
BMC Syst. Biol.
Francisco G. Vital-Lopez, Anders Wallqvist, Jaques Reifman
2013 J jnl
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions.
BMC Bioinform.
Vesna Memievi, Anders Wallqvist, Jaques Reifman
2012 J jnl
2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes.
J. Chem. Inf. Model.
Ruifeng Liu, Jin Liu, Gregory J. Tawa, Anders Wallqvist
2012 J jnl
A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space.
J. Cheminformatics
Narender Singh, Hongmao Sun, Sidhartha Chaudhury, Mohamed AbdulHameed, Anders Wallqvist, Gregory J. Tawa
2012 J jnl
Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach.
J. Chem. Inf. Model.
Mohamed Diwan M. AbdulHameed, Sidhartha Chaudhury, Narender Singh, Hongmao Sun, Anders Wallqvist, Gregory J. Tawa
2012 J jnl
Inferring high-confidence human protein-protein interactions.
BMC Bioinform.
Xueping Yu, Anders Wallqvist, Jaques Reifman
2012 J jnl
Modeling Phenotypic Metabolic Adaptations of
PLoS Comput. Biol.
Xin Fang, Anders Wallqvist, Jaques Reifman
2012 J jnl
PathNet: A tool for pathway analysis using topological information.
Source Code Biol. Medicine
Bhaskar Dutta, Anders Wallqvist, Jaques Reifman
2012 J jnl
QSAR Classification Model for Antibacterial Compounds and Its Use in Virtual Screening.
J. Chem. Inf. Model.
Narender Singh, Sidhartha Chaudhury, Ruifeng Liu, Mohamed Diwan M. AbdulHameed, Gregory J. Tawa, Anders Wallqvist
2012 J jnl
Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase.
PLoS Comput. Biol.
Daniel R. Ripoll, Ilja V. Khavrutskii, Sidhartha Chaudhury, Jin Liu, Robert A. Kuschner, Anders Wallqvist, Jaques Reifman
2010 J jnl
Accelerating Biomedical Research in Designing Diagnostic Assays, Drugs, and Vaccines.
Comput. Sci. Eng.
Anders Wallqvist, Nela Zavaljevski, Ravi Vijaya Satya, Rajkumar Bondugula, Valmik Desai, Xin Hu, Kamal Kumar, Michael S. Lee, In-Chul Yeh, Chenggang Yu, Jaques Reifman
2010 J jnl
Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis.
BMC Syst. Biol.
Xin Fang, Anders Wallqvist, Jaques Reifman
2009 J jnl
A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity.
PLoS Comput. Biol.
Xueping Yu, Joseph Ivanic, Anders Wallqvist, Jaques Reifman
2009 J jnl
A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis.
BMC Syst. Biol.
Xin Fang, Anders Wallqvist, Jaques Reifman
2008 J jnl
DOVIS: an implementation for high-throughput virtual screening using AutoDock.
BMC Bioinform.
Shuxing Zhang, Kamal Kumar, Xiaohui Jiang, Anders Wallqvist, Jaques Reifman
2008 J jnl
Evidence of probabilistic behaviour in protein interaction networks.
BMC Syst. Biol.
Joseph Ivanic, Anders Wallqvist, Jaques Reifman
2008 J jnl
Probing the Extent of Randomness in Protein Interaction Networks.
PLoS Comput. Biol.
Joseph Ivanic, Anders Wallqvist, Jaques Reifman
2007 J jnl
Chemoinformatic Analysis of NCI Preclinical Tumor Data: Evaluating Compound Efficacy from Mouse Xenograft Data, NCI-60 Screening Data, and Compound Descriptors.
J. Chem. Inf. Model.
Anders Wallqvist, Ruili Huang, David G. Covell
2006 J jnl
Evaluating Chemical Structure Similarity as an Indicator of Cellular Growth Inhibition.
J. Chem. Inf. Model.
Anders Wallqvist, Ruili Huang, Narmada Thanki, David G. Covell
2003 J jnl
Linking the growth inhibition response from the National Cancer Institute's anticancer screen to gene expression levels and other molecular target data.
Bioinform.
Anders Wallqvist, Alfred A. Rabow, Robert H. Shoemaker, Edward A. Sausville, David G. Covell
2001 J jnl
Screening the molecular surface of human anticoagulant protein C: A search for interaction sites.
J. Comput. Aided Mol. Des.
Bruno O. Villoutreix, David G. Covell, Anna M. Blom, Anders Wallqvist, Ute Friedrich, Björn Dahlbäck
2000 J jnl
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases.
Bioinform.
Anders Wallqvist, Yoshifumi Fukunishi, Lynne Reed Murphy, Addi Fadel, Ronald M. Levy
1987 J jnl
Exploiting Physical Parallelism Using Supercomputers: Two Examples from Chemical Physics.
Computer
Anders Wallqvist, Bruce J. Berne, Chani Pangali