Andreas Bender

Publication Activity (10 Years)

Years Active: 1989-2023
Publications (10 Years): 12

Top Topics

Gene Expression

Top Venues

J. Cheminformatics

PLoS Comput. Biol.

Publications

Benoit Baillif, Jason C. Cole, Ilenia Giangreco, Patrick McCabe, Andreas Bender
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations. J. Cheminformatics 15 (1) (2023)
Srijit Seal, Hongbin Yang, Maria-Anna Trapotsi, Satvik Singh, Jordi Carreras Puigvert, Ola Spjuth, Andreas Bender
Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data. J. Cheminformatics 15 (1) (2023)
Layla Hosseini-Gerami, Rosa D. Hernansaiz-Ballesteros, Anika Liu, Howard Broughton, David A. Collier, Andreas Bender
MAVEN: compound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny. BMC Bioinform. 24 (1) (2023)
Georgi K. Kanev, Yaran Zhang, Albert J. Kooistra, Andreas Bender, Rob Leurs, David Bailey, Thomas Würdinger, Chris de Graaf, Iwan J. P. de Esch, Bart A. Westerman
Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks. PLoS Comput. Biol. 19 (9) (2023)
Koichi Handa, Morgan C. Thomas, Michiharu Kageyama, Takeshi Iijima, Andreas Bender
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data. J. Cheminformatics 15 (1) (2023)
Martin Justinus Rosenfelder, Myra Spiliopoulou, Burkhard Hoppenstedt, Rüdiger Pryss, Patrick Fissler, Mario della Piedra Walter, Iris-Tatjana Kolassa, Andreas Bender
Stability of mental motor-imagery classification in EEG depends on the choice of classifier model and experiment design, but not on signal preprocessing. Frontiers Comput. Neurosci. 17 (2023)
Peter Hendrix, Ching Chu Sun, Henry Brighton, Andreas Bender
On the Connection Between Language Change and Language Processing. Cogn. Sci. 47 (12) (2023)
Layla Hosseini-Gerami, Ixavier Alonzo Higgins, David A. Collier, Emma Laing, David Evans, Howard Broughton, Andreas Bender
Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis. BMC Bioinform. 24 (1) (2023)
Anika Liu, Namshik Han, Jordi Muñoz-Muriedas, Andreas Bender
Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI). PLoS Comput. Biol. 18 (6) (2022)
Miguel García-Ortegón, Gregor N. C. Simm, Austin J. Tripp, José Miguel Hernández-Lobato, Andreas Bender, Sergio Bacallado
DOCKSTRING: easy molecular docking yields better benchmarks for ligand design. CoRR (2021)
Changge Ji, Fredrik Svensson, Azedine Zoufir, Andreas Bender
eMolTox: prediction of molecular toxicity with confidence. Bioinform. 34 (14) (2018)
Ulf Norinder, Fredrik Svensson, Avid M. Afzal, Andreas Bender
Maximizing Gain in HTS Screening Using Conformal Prediction. COPA (2017)
Andreas Bender, Stefan Bozic, Ivan Kondov
An EMF-based Toolkit for Creation of Domain-specific Data Services. MODELSWARD (2014)
Andreas Bender, Hinrich W. H. Göhlmann, Sepp Hochreiter, Ziv Shkedy
Computational Methods Aiding Early-Stage Drug Design (Dagstuhl Seminar 13212). Dagstuhl Reports 3 (5) (2013)
Andreas Bender, Angela Poschlad, Stefan Bozic, Ivan Kondov
A Service-oriented Framework for Integration of Domain-specific Data Models in Scientific Workflows. ICCS (2013)
Rucha K. Chiddarwar, Andreas Bender, Sebastian Rohrer
In silico target prediction: identification of on- and off-targets for crop protection agents. J. Cheminformatics 5 (S-1) (2013)
Hernando Sanchez-Faddeev, Michael T. M. Emmerich, Fons J. Verbeek, Andrew H. Henry, Simon Grimshaw, Herman P. Spaink, Herman W. T. van Vlijmen, Andreas Bender
Using Multiobjective Optimization and Energy Minimization to Design an Isoform-Selective Ligand of the 14-3-3 Protein. ISoLA (2) (2012)
Hossein Rahmani, Hendrik Blockeel, Andreas Bender
Predicting Genes Involved in Human Cancer Using Network Contextual Information. J. Integr. Bioinform. 9 (1) (2012)
Austin B. Yongye, Andreas Bender, Karina Martínez-Mayorga
Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble. J. Comput. Aided Mol. Des. 24 (8) (2010)
Hossein Rahmani, Hendrik Blockeel, Andreas Bender
Predicting the functions of proteins in Protein-Protein Interaction networks from global information. MLSB (2010)
Andreas Bender, Jeremy L. Jenkins, Josef Scheiber, Sai Chetan K. Sukuru, Meir Glick, John W. Davies
How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space. J. Chem. Inf. Model. 49 (1) (2009)
José L. Medina-Franco, Karina Martínez-Mayorga, Andreas Bender, Ray M. Marín, Marc A. Giulianotti, Clemencia Pinilla, Richard A. Houghten
. J. Chem. Inf. Model. 49 (2) (2009)
Josef Scheiber, Jeremy L. Jenkins, Andreas Bender, Mariusz Milik, Dmitri Mikhailov, Sai Chetan K. Sukuru, Ben Cornett, Steven Whitebread, Laszlo Urban, John W. Davies, Meir Glick
SPREAD - exploiting chemical features that cause differential activity behavior. Stat. Anal. Data Min. 2 (2) (2009)
Josef Scheiber, Bin Chen, Mariusz Milik, Sai Chetan K. Sukuru, Andreas Bender, Dmitri Mikhailov, Steven Whitebread, Jacques Hamon, Kamal Azzaoui, Laszlo Urban, Meir Glick, John W. Davies, Jeremy L. Jenkins
Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis. J. Chem. Inf. Model. 49 (2) (2009)
J. Anthony Wilson, Andreas Bender, Taner Kaya, Paul A. Clemons
Alpha Shapes Applied to Molecular Shape Characterization Exhibit Novel Properties Compared to Established Shape Descriptors. J. Chem. Inf. Model. 49 (10) (2009)
Muthukumarasamy Karthikeyan, Subramanian Krishnan, Anil Kumar Pandey, Andreas Bender, Alexander Tropsha
Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem. J. Chem. Inf. Model. 48 (4) (2008)
Paras Chopra, Andreas Bender
Requires BglF Conformational Change for Sugar Transport. Trans. Comp. Sys. Biology 9 (2008)
Qingliang Li, Andreas Bender, Jianfeng Pei, Luhua Lai
A Large Descriptor Set and a Probabilistic Kernel-Based Classifier Significantly Improve Druglikeness Classification. J. Chem. Inf. Model. 47 (5) (2007)
Thomas J. Crisman, Christian N. Parker, Jeremy L. Jenkins, Josef Scheiber, Mathis Thoma, Zhao Bin Kang, Richard Kim, Andreas Bender, James H. Nettles, John W. Davies, Meir Glick
Understanding False Positives in Reporter Gene Assays: in Silico Chemogenomics Approaches To Prioritize Cell-Based HTS Data. J. Chem. Inf. Model. 47 (4) (2007)
Paras Chopra, Andreas Bender
Evolved Cellular Automata for Protein Secondary Structure Prediction Imitate the Determinants for Folding Observed in Nature. Silico Biol. 7 (1) (2007)
Muthukumarasamy Karthikeyan, Subramanian Krishnan, Anil Kumar Pandey, Andreas Bender
Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme. J. Chem. Inf. Model. 46 (2) (2006)
Andreas Bender, Jeremy L. Jenkins, Meir Glick, Zhan Deng, James H. Nettles, John W. Davies
"Bayes Affinity Fingerprints" Improve Retrieval Rates in Virtual Screening and Define Orthogonal Bioactivity Space: When Are Multitarget Drugs a Feasible Concept? J. Chem. Inf. Model. 46 (6) (2006)
Muthukumarasamy Karthikeyan, Andreas Bender
Encoding and Decoding Graphical Chemical Structures as Two-Dimensional (PDF417) Barcodes. J. Chem. Inf. Model. 45 (3) (2005)
Andreas Bender, Guy Castagnoli
On the Implementation of Elliptic Curve Cryptosystems. CRYPTO (1989)