Anders Wallqvist

Publication Activity (10 Years)

Years Active: 1987-2024
Publications (10 Years): 13

Top Topics

Gene Expression

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

Comput. Biol. Medicine

Publications

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
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. PLoS Comput. Biol. 20 (2) (2024)
Ruifeng Liu, Srinivas Laxminarayan, Jaques Reifman, Anders Wallqvist
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning. J. Comput. Aided Mol. Des. 36 (12) (2022)
Daniel R. Ripoll, Sidhartha Chaudhury, Anders Wallqvist
Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification. PLoS Comput. Biol. 17 (3) (2021)
Ruifeng Liu, Anders Wallqvist
Molecular Similarity-Based Domain Applicability Metric Efficiently Identifies Out-of-Domain Compounds. J. Chem. Inf. Model. 59 (1) (2019)
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PLoS Comput. Biol. 15 (1) (2019)
Ruifeng Liu, Hao Wang, Kyle P. Glover, Michael G. Feasel, Anders Wallqvist
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. 59 (1) (2019)
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
A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools. Comput. Biol. Medicine 105 (2019)
Ruifeng Liu, Kyle P. Glover, Michael G. Feasel, Anders Wallqvist
General Approach to Estimate Error Bars for Quantitative Structure-Activity Relationship Predictions of Molecular Activity. J. Chem. Inf. Model. 58 (8) (2018)
Chenggang Yu, Hyung Jun Woo, Xueping Yu, Tatsuya Oyama, Anders Wallqvist, Jaques Reifman
A strategy for evaluating pathway analysis methods. BMC Bioinform. 18 (1) (2017)
Ruifeng Liu, Mohamed Diwan M. AbdulHameed, Anders Wallqvist
Molecular Structure-Based Large-Scale Prediction of Chemical-Induced Gene Expression Changes. J. Chem. Inf. Model. 57 (9) (2017)
Patric Schyman, Ruifeng Liu, Anders Wallqvist
General Purpose 2D and 3D Similarity Approach to Identify hERG Blockers. J. Chem. Inf. Model. 56 (1) (2016)
Anders Wallqvist, Xin Fang, Shivendra G. Tewari, Ping Ye, Jaques Reifman
Metabolic host responses to malarial infection during the intraerythrocytic developmental cycle. BMC Syst. Biol. 10 (2016)
Vesna Memisevic, Kamal Kumar, Nela Zavaljevski, David DeShazer, Anders Wallqvist, Jaques Reifman
secretion systems. BMC Bioinform. 17 (2016)
Vesna Memisevic, Nela Zavaljevski, Seesandra V. Rajagopala, Keehwan Kwon, Rembert Pieper, David DeShazer, Jaques Reifman, Anders Wallqvist
Infectivity Mechanisms. PLoS Comput. Biol. 11 (3) (2015)
Ruifeng Liu, Xueping Yu, Anders Wallqvist
Data-driven identification of structural alerts for mitigating the risk of drug-induced human liver injuries. J. Cheminformatics 7 (2015)
Francisco G. Vital-Lopez, Jaques Reifman, Anders Wallqvist
Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism. PLoS Comput. Biol. 11 (10) (2015)
Ruifeng Liu, Patric Schyman, Anders Wallqvist
Critically Assessing the Predictive Power of QSAR Models for Human Liver Microsomal Stability. J. Chem. Inf. Model. 55 (8) (2015)
Vesna Memievi, Kamal Kumar, Li Cheng, Nela Zavaljevski, David DeShazer, Anders Wallqvist, Jaques Reifman
DBSecSys: a database of Burkholderia mallei secretion systems. BMC Bioinform. 15 (2014)
Bora Sul, Anders Wallqvist, Michael J. Morris, Jaques Reifman, Vineet Rakesh
A computational study of the respiratory airflow characteristics in normal and obstructed human airways. Comput. Biol. Medicine 52 (2014)
Ruifeng Liu, Narender Singh, Gregory J. Tawa, Anders Wallqvist, Jaques Reifman
Exploiting large-scale drug-protein interaction information for computational drug repurposing. BMC Bioinform. 15 (2014)
Ruifeng Liu, Anders Wallqvist
Assessment of Chemical Mutagenicity. J. Chem. Inf. Model. 54 (3) (2014)
Francisco G. Vital-Lopez, Anders Wallqvist, Jaques Reifman
Bridging the gap between gene expression and metabolic phenotype via kinetic models. BMC Syst. Biol. 7 (2013)
Vesna Memievi, Anders Wallqvist, Jaques Reifman
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions. BMC Bioinform. 14 (2013)
Narender Singh, Sidhartha Chaudhury, Ruifeng Liu, Mohamed Diwan M. AbdulHameed, Gregory J. Tawa, Anders Wallqvist
QSAR Classification Model for Antibacterial Compounds and Its Use in Virtual Screening. J. Chem. Inf. Model. 52 (10) (2012)
Daniel R. Ripoll, Ilja V. Khavrutskii, Sidhartha Chaudhury, Jin Liu, Robert A. Kuschner, Anders Wallqvist, Jaques Reifman
Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase. PLoS Comput. Biol. 8 (8) (2012)
Mohamed Diwan M. AbdulHameed, Sidhartha Chaudhury, Narender Singh, Hongmao Sun, Anders Wallqvist, Gregory J. Tawa
Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach. J. Chem. Inf. Model. 52 (2) (2012)
Bhaskar Dutta, Anders Wallqvist, Jaques Reifman
PathNet: A tool for pathway analysis using topological information. Source Code Biol. Medicine 7 (2012)
Xueping Yu, Anders Wallqvist, Jaques Reifman
Inferring high-confidence human protein-protein interactions. BMC Bioinform. 13 (2012)
Narender Singh, Hongmao Sun, Sidhartha Chaudhury, Mohamed AbdulHameed, Anders Wallqvist, Gregory J. Tawa
A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space. J. Cheminformatics 4 (2012)
Ruifeng Liu, Jin Liu, Gregory J. Tawa, Anders Wallqvist
2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes. J. Chem. Inf. Model. 52 (6) (2012)
Xin Fang, Anders Wallqvist, Jaques Reifman
H37Rv under Hypoxia. PLoS Comput. Biol. 8 (9) (2012)
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
Accelerating Biomedical Research in Designing Diagnostic Assays, Drugs, and Vaccines. Comput. Sci. Eng. 12 (5) (2010)
Xin Fang, Anders Wallqvist, Jaques Reifman
Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis. BMC Syst. Biol. 4 (2010)
Xin Fang, Anders Wallqvist, Jaques Reifman
A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis. BMC Syst. Biol. 3 (2009)
Xueping Yu, Joseph Ivanic, Anders Wallqvist, Jaques Reifman
A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity. PLoS Comput. Biol. 5 (9) (2009)
Joseph Ivanic, Anders Wallqvist, Jaques Reifman
Probing the Extent of Randomness in Protein Interaction Networks. PLoS Comput. Biol. 4 (7) (2008)
Shuxing Zhang, Kamal Kumar, Xiaohui Jiang, Anders Wallqvist, Jaques Reifman
DOVIS: an implementation for high-throughput virtual screening using AutoDock. BMC Bioinform. 9 (2008)
Joseph Ivanic, Anders Wallqvist, Jaques Reifman
Evidence of probabilistic behaviour in protein interaction networks. BMC Syst. Biol. 2 (2008)
Anders Wallqvist, Ruili Huang, David G. Covell
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. 47 (4) (2007)
Anders Wallqvist, Ruili Huang, Narmada Thanki, David G. Covell
Evaluating Chemical Structure Similarity as an Indicator of Cellular Growth Inhibition. J. Chem. Inf. Model. 46 (1) (2006)
Anders Wallqvist, Alfred A. Rabow, Robert H. Shoemaker, Edward A. Sausville, David G. Covell
Linking the growth inhibition response from the National Cancer Institute's anticancer screen to gene expression levels and other molecular target data. Bioinform. 19 (17) (2003)
Bruno O. Villoutreix, David G. Covell, Anna M. Blom, Anders Wallqvist, Ute Friedrich, Björn Dahlbäck
Screening the molecular surface of human anticoagulant protein C: A search for interaction sites. J. Comput. Aided Mol. Des. 15 (1) (2001)
Anders Wallqvist, Yoshifumi Fukunishi, Lynne Reed Murphy, Addi Fadel, Ronald M. Levy
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. Bioinform. 16 (11) (2000)
Anders Wallqvist, Bruce J. Berne, Chani Pangali
Exploiting Physical Parallelism Using Supercomputers: Two Examples from Chemical Physics. Computer 20 (5) (1987)