The Human Genome and High Performance Computing in Molecular Biology. - Chris Sander; Reinhard Schneider 002; Pieter F. W. Stouten (Supercomputer, 1992)

Exercising Multi-Layered Networks on Protein Secondary Structure. - Burkhard Rost; Chris Sander (Int. J. Neural Syst., 1992)

The prediction and design of protein structures. - Chris Sander (Informatik in den Biowissenschaften, 1993)

The HSSP data base of protein structure-sequence alignments. - Chris Sander; Reinhard Schneider 002 (Nucleic Acids Res., 1993)

Evolution and Neural Networks - Protein Secondary Structure Prediction Above 71% Accuracy. - Burkhard Rost; Chris Sander; Reinhard Schneider 002 (HICSS (5), 1994)

GeneQuiz: A Workbench for Sequence Analysis. - Michael Scharf; Reinhard Schneider 002; Georg Casari; Peer Bork; Alfonso Valencia; Christos A. Ouzounis; Chris Sander (ISMB, 1994)

PHD - an automatic mail server for protein secondary structure prediction. - Burkhard Rost; Chris Sander; Reinhard Schneider 002 (Comput. Appl. Biosci., 1994)

The Functional Composition of Living Machines as a Design Principle for Artificial Organisms. - Christos A. Ouzounis; Alfonso Valencia; Javier Tamames; Peer Bork; Chris Sander (ECAL, 1995)

3-D Lookup: Fast Protein Structure Database Searches at 90% Reliability. - Liisa Holm; Chris Sander (ISMB, 1995)

The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies. - Frank Eisenhaber; Philip Lijnzaad; Patrick Argos; Chris Sander; Michael Scharf (J. Comput. Chem., 1995)

The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. - Rob W. W. Hooft; Chris Sander; Michael Scharf; Gert Vriend (Comput. Appl. Biosci., 1996)

The FSSP database: fold classification based on structure-structure alignment of proteins. - Liisa Holm; Chris Sander (Nucleic Acids Res., 1996)

The HSSP database of protein structure-sequence alignments. - Reinhard Schneider 002; Chris Sander (Nucleic Acids Res., 1996)

Decision Support System for the Evolutionary Classification of Protein Structures. - Liisa Holm; Chris Sander (ISMB, 1997)

Classification of protein families and detection of the determinant residues with an improved self-organizing map. - Miguel A. Andrade; Georg Casari; Chris Sander; Alfonso Valencia (Biol. Cybern., 1997)

Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. - Miguel A. Andrade; Georg Casari; Antoine de Daruvar; Chris Sander; Reinhard Schneider 002; Javier Tamames; Alfonso Valencia; Christos A. Ouzounis (Comput. Appl. Biosci., 1997)

Objectively judging the quality of a protein structure from a Ramachandran plot. - Rob W. W. Hooft; Chris Sander; Gert Vriend (Comput. Appl. Biosci., 1997)

Dali/FSSP classification of three-dimensional protein folds. - Liisa Holm; Chris Sander (Nucleic Acids Res., 1997)

The HSSP database of protein structure-sequence alignments. - Reinhard Schneider 002; Antoine de Daruvar; Chris Sander (Nucleic Acids Res., 1997)

MView: a web-compatible database search or multiple alignment viewer. - Nigel P. Brown; Christophe Leroy; Chris Sander (Bioinform., 1998)

Frame: detection of genomic sequencing errors. - Nigel P. Brown; Chris Sander; Peer Bork (Bioinform., 1998)

Removing near-neighbour redundancy from large protein sequence collections. - Liisa Holm; Chris Sander (Bioinform., 1998)

EUCLID: automatic classification of proteins in functional classes by their database annotations. - Javier Tamames; Christos A. Ouzounis; Georg Casari; Chris Sander; Alfonso Valencia (Bioinform., 1998)

The HSSP database of protein structure-sequence alignments and family profiles. - Chris Dodge; Reinhard Schneider 002; Chris Sander (Nucleic Acids Res., 1998)

Touring protein fold space with Dali/FSSP. - Liisa Holm; Chris Sander (Nucleic Acids Res., 1998)

Automated genome sequence analysis and annotation. - Miguel A. Andrade; Nigel P. Brown; Christophe Leroy; S. Hörsch; Antoine de Daruvar; C. Reich; Angelo Franchini; Javier Tamames; Alfonso Valencia; Christos A. Ouzounis; Chris Sander (Bioinform., 1999)

Protein folds and families: sequence and structure alignments. - Liisa Holm; Chris Sander (Nucleic Acids Res., 1999)

CAST: an iterative algorithm for the complexity analysis of sequence tracts. - Vasilis J. Promponas; Anton J. Enright; Sophia Tsoka; David P. Kreil; Christophe Leroy; Stavros J. Hamodrakas; Chris Sander; Christos A. Ouzounis (Bioinform., 2000)

Bioinformatics - Challenges in 2001. - Chris Sander (Bioinform., 2001)

The Journal Bioinformatics, key medium for computational biology. - Chris Sander (Bioinform., 2002)

Characterizing gene sets with FuncAssociate. - Gabriel F. Berriz; Oliver D. King; Barbara Bryant; Chris Sander; Frederick P. Roth (Bioinform., 2003)

Evaluation of annotation strategies using an entire genome sequence. - Ioannis Iliopoulos; Sophia Tsoka; Miguel A. Andrade; Anton J. Enright; Mark Carroll; Patrick Poullet; Vasilis J. Promponas; Theodore Liakopoulos; Giorgos Palaios; Claude Pasquier; Stavros J. Hamodrakas; Javier Tamames; et al. (Bioinform., 2003)

Growth in Bioinformatics. - Chris Sander (Bioinform., 2003)

cPath: open source software for collecting, storing, and querying biological pathways. - Ethan G. Cerami; Gary D. Bader; Benjamin E. Gross; Chris Sander (BMC Bioinform., 2006)

Pathguide: a Pathway Resource List. - Gary D. Bader; Michael P. Cary; Chris Sander (Nucleic Acids Res., 2006)

Signal Processing in the TGF-β Superfamily Ligand-Receptor Network. - Jose M. G. Vilar; Ronald Jansen; Chris Sander (PLoS Comput. Biol., 2006)

CancerGenes: a gene selection resource for cancer genome projects. - Maureen E. Higgins; Martine Claremont; John E. Major; Chris Sander; Alex E. Lash (Nucleic Acids Res., 2007)

Computational Analysis of Mouse piRNA Sequence and Biogenesis. - Doron Betel; Robert P. Sheridan; Debora S. Marks; Chris Sander (PLoS Comput. Biol., 2007)

From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. - Jomol P. Mathew; Barry S. Taylor; Gary D. Bader; Saiju Pyarajan; Marco Antoniotti; Arul M. Chinnaiyan; Chris Sander; Steven J. Burakoff; Bud Mishra (PLoS Comput. Biol., 2007)

Predicting cancer involvement of genes from heterogeneous data. - Ramon Aragues; Chris Sander; Baldo Oliva (BMC Bioinform., 2008)

The microRNA.org resource: targets and expression. - Doron Betel; Manda Wilson; Aaron Gabow; Debora S. Marks; Chris Sander (Nucleic Acids Res., 2008)

ChiBE: interactive visualization and manipulation of BioPAX pathway models. - Ozgun Babur; Ugur Dogrusöz; Emek Demir; Chris Sander (Bioinform., 2010)

3D Protein Structure Predicted from Sequence - Debora S. Marks; Lucy J. Colwell; Robert P. Sheridan; Thomas A. Hopf; Andrea Pagnani; Riccardo Zecchina; Chris Sander (CoRR, 2011)

Pathway Commons, a web resource for biological pathway data. - Ethan G. Cerami; Benjamin E. Gross; Emek Demir; Igor V. Rodchenkov; Özgün Babur; Nadia Anwar; Nikolaus Schultz; Gary D. Bader; Chris Sander (Nucleic Acids Res., 2011)

A series of PDB related databases for everyday needs. - Robbie P. Joosten; Tim A. H. te Beek; Elmar Krieger; Maarten L. Hekkelman; Rob W. W. Hooft; Reinhard Schneider 002; Chris Sander; Gert Vriend (Nucleic Acids Res., 2011)

PiHelper: an open source framework for drug-target and antibody-target data. - Bülent Arman Aksoy; Jianjiong Gao; Gideon Dresdner; Weiqing Wang; Alex Root; Xiaohong Jing; Ethan G. Cerami; Chris Sander (Bioinform., 2013)

The BioPAX Validator. - Igor V. Rodchenkov; Emek Demir; Chris Sander; Gary D. Bader (Bioinform., 2013)

Using Biological Pathway Data with Paxtools. - Emek Demir; Özgün Babur; Igor V. Rodchenkov; Bülent Arman Aksoy; Ken I. Fukuda; Benjamin E. Gross; Selçuk Onur Sümer; Gary D. Bader; Chris Sander (PLoS Comput. Biol., 2013)

Perturbation Biology: Inferring Signaling Networks in Cellular Systems. - Evan J. Molinelli; Anil Korkut; Weiqing Wang; Martin L. Miller; Nicholas Paul Gauthier; Xiaohong Jing; Poorvi Kaushik; Qin He; Gordon B. Mills; David B. Solit; Christine A. Pratilas; Martin Weigt; et al. (PLoS Comput. Biol., 2013)

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota. - Richard R. Stein; Vanni Bucci; Nora C. Toussaint; Charlie G. Buffie; Gunnar Rätsch; Eric G. Pamer; Chris Sander; João B. Xavier (PLoS Comput. Biol., 2013)

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. - Bülent Arman Aksoy; Emek Demir; Özgün Babur; Weiqing Wang; Xiaohong Jing; Nikolaus Schultz; Chris Sander (Bioinform., 2014)

Pattern search in BioPAX models. - Özgün Babur; Bülent Arman Aksoy; Igor V. Rodchenkov; Selçuk Onur Sümer; Chris Sander; Emek Demir (Bioinform., 2014)

PconsFold: improved contact predictions improve protein models. - Mirco Michel; Sikander Hayat; Marcin J. Skwark; Chris Sander; Debora S. Marks; Arne Elofsson (Bioinform., 2014)

PredictProtein - an open resource for online prediction of protein structural and functional features. - Guy Yachdav; Edda Kloppmann; László Kaján; Maximilian Hecht; Tatyana Goldberg; Tobias Hamp; Peter Hönigschmid; Andrea Schafferhans; Manfred Roos; Michael Bernhofer; Lothar Richter; Haim Ashkenazy; et al. (Nucleic Acids Res., 2014)

Extensive Decoupling of Metabolic Genes in Cancer. - Ed Reznik; Chris Sander (PLoS Comput. Biol., 2015)

Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. - Richard R. Stein; Debora S. Marks; Chris Sander (PLoS Comput. Biol., 2015)

PaxtoolsR: pathway analysis in R using Pathway Commons. - Augustin Luna; Özgün Babur; Bülent Arman Aksoy; Emek Demir; Chris Sander (Bioinform., 2016)

rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. - Augustin Luna; Vinodh N. Rajapakse; Fabricio G. Sousa; Jianjiong Gao; Nikolaus Schultz; Sudhir Varma; William C. Reinhold; Chris Sander; Yves Pommier (Bioinform., 2016)

MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. - Nicholas Paul Gauthier; Ed Reznik; Jianjiong Gao; Selçuk Onur Sümer; Nikolaus Schultz; Chris Sander; Martin L. Miller (Nucleic Acids Res., 2016)

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. - Yasin Senbabaoglu; Selçuk Onur Sümer; Francisco Sánchez-Vega; Debra Bemis; Giovanni Ciriello; Nikolaus Schultz; Chris Sander (PLoS Comput. Biol., 2016)

CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. - Bülent Arman Aksoy; Vlado Dancík; Kenneth Smith 001; Jessica N. Mazerik; Zhou Ji; Benjamin E. Gross; Olga Nikolova; Nadia Jaber; Andrea Califano; Stuart L. Schreiber; Daniela S. Gerhard; Leandro Hermida; et al. (Database J. Biol. Databases Curation, 2017)

Learning Protein Structure with a Differentiable Simulator. - John Ingraham; Adam J. Riesselman; Chris Sander; Debora S. Marks (ICLR, 2019)

The EVcouplings Python framework for coevolutionary sequence analysis. - Thomas A. Hopf; Anna G. Green; Benjamin Schubert; Sophia Mersmann; Charlotta Schärfe; John Ingraham; Ágnes Tóth-Petróczy; Kelly Brock; Adam J. Riesselman; Perry Palmedo; Chan Kang; Robert P. Sheridan; et al. (Bioinform., 2019)

AlignmentViewer: Sequence Analysis of Large Protein Families. - Roc Reguant; Yevgeniy Antipin; Robert P. Sheridan; Christian Dallago; Drew Diamantoukos; Augustin Luna; Chris Sander; Nicholas Paul Gauthier (F1000Research, 2020)

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. - Igor V. Rodchenkov; Ozgun Babur; Augustin Luna; Bülent Arman Aksoy; Jeffrey V. Wong; Dylan Fong; Max Franz; Metin Can Siper; Manfred Cheung; Michael Wrana; Harsh Mistry; Logan Mosier; et al. (Nucleic Acids Res., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Perturbation biology links temporal protein changes to drug responses in a melanoma cell line. - Elin Nyman; Richard R. Stein; Xiaohong Jing; Weiqing Wang; Benjamin Marks; Ioannis K. Zervantonakis; Anil Korkut; Nicholas Paul Gauthier; Chris Sander (PLoS Comput. Biol., 2020)

Inference of cell dynamics on perturbation data using adjoint sensitivity. - Weiqi Ji; Bo Yuan; Ciyue Shen; Aviv Regev; Chris Sander; Sili Deng (CoRR, 2021)

A flexible search system for high-accuracy identification of biological entities and molecules. - Max Franz; Jeffrey V. Wong; Metin Can Siper; Christian Dallago; John M. Giorgi; Emek Demir; Chris Sander; Gary D. Bader (J. Open Source Softw., 2021)

PredictProtein - Predicting Protein Structure and Function for 29 Years. - Michael Bernhofer; Christian Dallago; Timothy Karl; Venkata P. Satagopam; Michael Heinzinger; Maria Littmann; Tobias Olenyi; Jiajun Qiu; Konstantin Schütze; Guy Yachdav; Haim Ashkenazy; Nir Ben-Tal; et al. (Nucleic Acids Res., 2021)

CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics. - Augustin Luna; Fathi Elloumi; Sudhir Varma; Yanghsin Wang; Vinodh N. Rajapakse; Mirit I. Aladjem; Jacques Robert; Chris Sander; Yves Pommier; William C. Reinhold (Nucleic Acids Res., 2021)

Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. - Özgün Babur; Augustin Luna; Anil Korkut; Funda Durupinar; Metin Can Siper; Ugur Dogrusoz; Alvaro Sebastian Vaca Jacome; Ryan Peckner; Karen E. Christianson; Jacob D. Jaffe; Paul T. Spellman; Joseph E. Aslan; et al. (Patterns, 2021)

The reactome pathway knowledgebase 2022. - Marc Gillespie; Bijay Jassal; Ralf Stephan; Marija Milacic; Karen Rothfels; Andrea Senff-Ribeiro; Johannes Griss; Cristoffer Sevilla; Lisa Matthews; Chuqiao Gong; Chuan Deng; Thawfeek M. Varusai; et al. (Nucleic Acids Res., 2022)

TCGA Kidney Cancers. - John N. Weinstein; Eric A. Collisson; Gordon B. Mills; Kenna R. Mills Shaw; Brad A. Ozenberger; Kyle Ellrott; Ilya Shmulevich; Chris Sander; Joshua M. Stuart (UCI Machine Learning Repository, 2023)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)