Chris Sander

Publication Activity (10 Years)

Years Active: 1992-2022
Publications (10 Years): 19

Top Topics

Protein Structure

Sequence Analysis

Top Venues

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

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, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio
The reactome pathway knowledgebase 2022. Nucleic Acids Res. 50 (D1) (2022)
Augustin Luna, Fathi Elloumi, Sudhir Varma, Yanghsin Wang, Vinodh N. Rajapakse, Mirit I. Aladjem, Jacques Robert, Chris Sander, Yves Pommier, William C. Reinhold
CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics. Nucleic Acids Res. 49 (Database-Issue) (2021)
Weiqi Ji, Bo Yuan, Ciyue Shen, Aviv Regev, Chris Sander, Sili Deng
Inference of cell dynamics on perturbation data using adjoint sensitivity. CoRR (2021)
Max Franz, Jeffrey V. Wong, Metin Can Siper, Christian Dallago, John M. Giorgi, Emek Demir, Chris Sander, Gary D. Bader
A flexible search system for high-accuracy identification of biological entities and molecules. J. Open Source Softw. 6 (67) (2021)
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, Chris Sander, Emek Demir
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. Patterns 2 (6) (2021)
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, Yana Bromberg, Tatyana Goldberg, László Kaján, Seán I. O'Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost
PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
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, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo G. Gut, David Haan, Arif O. Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578 (7793) (2020)
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, Jonah Dlin, Qizhi Wen, Caitlin O'Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, Christian Dallago, Ethan Cerami, Benjamin Gross, Ugur Dogrusoz, Emek Demir, Gary D. Bader, Chris Sander
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res. 48 (Database-Issue) (2020)
Elin Nyman, Richard R. Stein, Xiaohong Jing, Weiqing Wang, Benjamin Marks, Ioannis K. Zervantonakis, Anil Korkut, Nicholas Paul Gauthier, Chris Sander
Perturbation biology links temporal protein changes to drug responses in a melanoma cell line. PLoS Comput. Biol. 16 (7) (2020)
Roc Reguant, Yevgeniy Antipin, Robert P. Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, Nicholas Paul Gauthier
AlignmentViewer: Sequence Analysis of Large Protein Families. F1000Research 9 (2020)
John Ingraham, Adam J. Riesselman, Chris Sander, Debora S. Marks
Learning Protein Structure with a Differentiable Simulator. ICLR (2019)
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, Eli J. Draizen, Christian Dallago, Chris Sander, Debora S. Marks
The EVcouplings Python framework for coevolutionary sequence analysis. Bioinform. 35 (9) (2019)
Bülent Arman Aksoy, Vlado Dancík, Kenneth Smith, Jessica N. Mazerik, Zhou Ji, Benjamin E. Gross, Olga Nikolova, Nadia Jaber, Andrea Califano, Stuart L. Schreiber, Daniela S. Gerhard, Leandro Hermida, Subhashini Jagu, Chris Sander, Aris Floratos, Paul A. Clemons
CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. Database J. Biol. Databases Curation 2017 (2017)
Augustin Luna, Vinodh N. Rajapakse, Fabricio G. Sousa, Jianjiong Gao, Nikolaus Schultz, Sudhir Varma, William C. Reinhold, Chris Sander, Yves Pommier
rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. Bioinform. 32 (8) (2016)
Augustin Luna, Özgün Babur, Bülent Arman Aksoy, Emek Demir, Chris Sander
PaxtoolsR: pathway analysis in R using Pathway Commons. Bioinform. 32 (8) (2016)
Nicholas Paul Gauthier, Ed Reznik, Jianjiong Gao, Selçuk Onur Sümer, Nikolaus Schultz, Chris Sander, Martin L. Miller
MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. Nucleic Acids Res. 44 (Database-Issue) (2016)
Yasin Senbabaoglu, Selçuk Onur Sümer, Francisco Sánchez-Vega, Debra Bemis, Giovanni Ciriello, Nikolaus Schultz, Chris Sander
A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. PLoS Comput. Biol. 12 (2) (2016)
Ed Reznik, Chris Sander
Extensive Decoupling of Metabolic Genes in Cancer. PLoS Comput. Biol. 11 (5) (2015)
Richard R. Stein, Debora S. Marks, Chris Sander
Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. PLoS Comput. Biol. 11 (7) (2015)
Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks, Arne Elofsson
PconsFold: improved contact predictions improve protein models. Bioinform. 30 (17) (2014)
Bülent Arman Aksoy, Emek Demir, Özgün Babur, Weiqing Wang, Xiaohong Jing, Nikolaus Schultz, Chris Sander
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. Bioinform. 30 (14) (2014)
Guy Yachdav, Edda Kloppmann, László Kaján, Maximilian Hecht, Tatyana Goldberg, Tobias Hamp, Peter Hönigschmid, Andrea Schafferhans, Manfred Roos, Michael Bernhofer, Lothar Richter, Haim Ashkenazy, Marco Punta, Avner Schlessinger, Yana Bromberg, Reinhard Schneider, Gerrit Vriend, Chris Sander, Nir Ben-Tal, Burkhard Rost
PredictProtein - an open resource for online prediction of protein structural and functional features. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Özgün Babur, Bülent Arman Aksoy, Igor V. Rodchenkov, Selçuk Onur Sümer, Chris Sander, Emek Demir
Pattern search in BioPAX models. Bioinform. 30 (1) (2014)
Igor V. Rodchenkov, Emek Demir, Chris Sander, Gary D. Bader
The BioPAX Validator. Bioinform. 29 (20) (2013)
Emek Demir, Özgün Babur, Igor V. Rodchenkov, Bülent Arman Aksoy, Ken I. Fukuda, Benjamin E. Gross, Selçuk Onur Sümer, Gary D. Bader, Chris Sander
Using Biological Pathway Data with Paxtools. PLoS Comput. Biol. 9 (9) (2013)
Bülent Arman Aksoy, Jianjiong Gao, Gideon Dresdner, Weiqing Wang, Alex Root, Xiaohong Jing, Ethan G. Cerami, Chris Sander
PiHelper: an open source framework for drug-target and antibody-target data. Bioinform. 29 (16) (2013)
Evan J. Molinelli, Anil Korkut, Weiqing Wang, Martin L. Miller, Nicholas Paul Gauthier, Xiaohong Jing, Poorvi Kaushik, Qin He, Gordon Mills, David B. Solit, Christine A. Pratilas, Martin Weigt, Alfredo Braunstein, Andrea Pagnani, Riccardo Zecchina, Chris Sander
Perturbation Biology: Inferring Signaling Networks in Cellular Systems. PLoS Comput. Biol. 9 (12) (2013)
Richard R. Stein, Vanni Bucci, Nora C. Toussaint, Charlie G. Buffie, Gunnar Rätsch, Eric G. Pamer, Chris Sander, João B. Xavier
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota. PLoS Comput. Biol. 9 (12) (2013)
Robbie P. Joosten, Tim A. H. te Beek, Elmar Krieger, Maarten L. Hekkelman, Rob W. W. Hooft, Reinhard Schneider, Chris Sander, Gert Vriend
A series of PDB related databases for everyday needs. Nucleic Acids Res. 39 (Database-Issue) (2011)
Ethan G. Cerami, Benjamin E. Gross, Emek Demir, Igor V. Rodchenkov, Özgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, Chris Sander
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 39 (Database-Issue) (2011)
Debora S. Marks, Lucy J. Colwell, Robert P. Sheridan, Thomas A. Hopf, Andrea Pagnani, Riccardo Zecchina, Chris Sander
3D Protein Structure Predicted from Sequence CoRR (2011)
Ozgun Babur, Ugur Dogrusöz, Emek Demir, Chris Sander
ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinform. 26 (3) (2010)
Ramon Aragues, Chris Sander, Baldo Oliva
Predicting cancer involvement of genes from heterogeneous data. BMC Bioinform. 9 (2008)
Doron Betel, Manda Wilson, Aaron Gabow, Debora S. Marks, Chris Sander
The microRNA.org resource: targets and expression. Nucleic Acids Res. 36 (Database-Issue) (2008)
Doron Betel, Robert P. Sheridan, Debora S. Marks, Chris Sander
Computational Analysis of Mouse piRNA Sequence and Biogenesis. PLoS Comput. Biol. 3 (11) (2007)
Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, Chris Sander, Steven J. Burakoff, Bud Mishra
From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. PLoS Comput. Biol. 3 (2) (2007)
Maureen E. Higgins, Martine Claremont, John E. Major, Chris Sander, Alex E. Lash
CancerGenes: a gene selection resource for cancer genome projects. Nucleic Acids Res. 35 (Database-Issue) (2007)
Jose M. G. Vilar, Ronald Jansen, Chris Sander
Signal Processing in the TGF-β Superfamily Ligand-Receptor Network. PLoS Comput. Biol. 2 (1) (2006)
Ethan G. Cerami, Gary D. Bader, Benjamin E. Gross, Chris Sander
cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinform. 7 (2006)
Gary D. Bader, Michael P. Cary, Chris Sander
Pathguide: a Pathway Resource List. Nucleic Acids Res. 34 (Database-Issue) (2006)
Chris Sander
Growth in Bioinformatics. Bioinform. 19 (1) (2003)
Gabriel F. Berriz, Oliver D. King, Barbara Bryant, Chris Sander, Frederick P. Roth
Characterizing gene sets with FuncAssociate. Bioinform. 19 (18) (2003)
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, Asutosh T. Yagnik, Anna Tramontano, Damien Devos, Christian Blaschke, Alfonso Valencia, David Brett, David M. A. Martin, Christophe Leroy, Isidore Rigoutsos, Chris Sander, Christos A. Ouzounis
Evaluation of annotation strategies using an entire genome sequence. Bioinform. 19 (6) (2003)
Chris Sander
The Journal Bioinformatics, key medium for computational biology. Bioinform. 18 (1) (2002)
Chris Sander
Bioinformatics - Challenges in 2001. Bioinform. 17 (1) (2001)
Vasilis J. Promponas, Anton J. Enright, Sophia Tsoka, David P. Kreil, Christophe Leroy, Stavros J. Hamodrakas, Chris Sander, Christos A. Ouzounis
CAST: an iterative algorithm for the complexity analysis of sequence tracts. Bioinform. 16 (10) (2000)
Liisa Holm, Chris Sander
Protein folds and families: sequence and structure alignments. Nucleic Acids Res. 27 (1) (1999)
Miguel A. Andrade, N. P. Brown, Christophe Leroy, S. Hörsch, Antoine de Daruvar, C. Reich, Angelo Franchini, Javier Tamames, Alfonso Valencia, Christos A. Ouzounis, Chris Sander
Automated genome sequence analysis and annotation. Bioinform. 15 (5) (1999)
N. P. Brown, Chris Sander, Peer Bork
Frame: detection of genomic sequencing errors. Bioinform. 14 (4) (1998)
Javier Tamames, Christos A. Ouzounis, Georg Casari, Chris Sander, Alfonso Valencia
EUCLID: automatic classification of proteins in functional classes by their database annotations. Bioinform. 14 (6) (1998)
Liisa Holm, Chris Sander
Removing near-neighbour redundancy from large protein sequence collections. Bioinform. 14 (5) (1998)
Liisa Holm, Chris Sander
Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26 (1) (1998)
Chris Dodge, Reinhard Schneider, Chris Sander
The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res. 26 (1) (1998)
N. P. Brown, Christophe Leroy, Chris Sander
MView: a web-compatible database search or multiple alignment viewer. Bioinform. 14 (4) (1998)
Miguel A. Andrade, Georg Casari, Antoine de Daruvar, Chris Sander, Reinhard Schneider, Javier Tamames, Alfonso Valencia, Christos A. Ouzounis
Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. Comput. Appl. Biosci. 13 (4) (1997)
Liisa Holm, Chris Sander
Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res. 25 (1) (1997)
Liisa Holm, Chris Sander
Decision Support System for the Evolutionary Classification of Protein Structures. ISMB (1997)
Reinhard Schneider, Antoine de Daruvar, Chris Sander
The HSSP database of protein structure-sequence alignments. Nucleic Acids Res. 25 (1) (1997)
Rob W. W. Hooft, Chris Sander, Gert Vriend
Objectively judging the quality of a protein structure from a Ramachandran plot. Comput. Appl. Biosci. 13 (4) (1997)
Miguel A. Andrade, Georg Casari, Chris Sander, Alfonso Valencia
Classification of protein families and detection of the determinant residues with an improved self-organizing map. Biol. Cybern. 76 (6) (1997)
Liisa Holm, Chris Sander
The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res. 24 (1) (1996)
Rob W. W. Hooft, Chris Sander, Michael Scharf, Gert Vriend
The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. Comput. Appl. Biosci. 12 (6) (1996)
Reinhard Schneider, Chris Sander
The HSSP database of protein structure-sequence alignments. Nucleic Acids Res. 24 (1) (1996)
Christos A. Ouzounis, Alfonso Valencia, Javier Tamames, Peer Bork, Chris Sander
The Functional Composition of Living Machines as a Design Principle for Artificial Organisms. ECAL (1995)
Liisa Holm, Chris Sander
3-D Lookup: Fast Protein Structure Database Searches at 90% Reliability. ISMB (1995)
Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf
The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies. J. Comput. Chem. 16 (3) (1995)
Burkhard Rost, Chris Sander, Reinhard Schneider
Evolution and Neural Networks - Protein Secondary Structure Prediction Above 71% Accuracy. HICSS (5) (1994)
Burkhard Rost, Chris Sander, Reinhard Schneider
PHD - an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10 (1) (1994)
Michael Scharf, Reinhard Schneider, Georg Casari, Peer Bork, Alfonso Valencia, Christos A. Ouzounis, Chris Sander
GeneQuiz: A Workbench for Sequence Analysis. ISMB (1994)
Chris Sander
The prediction and design of protein structures. Informatik in den Biowissenschaften (1993)
Chris Sander, Reinhard Schneider
The HSSP data base of protein structure-sequence alignments. Nucleic Acids Res. 21 (13) (1993)
Chris Sander, Reinhard Schneider, Pieter F. W. Stouten
The Human Genome and High Performance Computing in Molecular Biology. Supercomputer (1992)
Burkhard Rost, Chris Sander
Exercising Multi-Layered Networks on Protein Secondary Structure. Int. J. Neural Syst. 3 (Supplement) (1992)