Søren Brunak

Publication Activity (10 Years)

Years Active: 1989-2023
Publications (10 Years): 27

Top Topics

Question Answering

Survival Analysis

Top Venues

Nucleic Acids Res.

npj Digit. Medicine

PLoS Comput. Biol.

Publications

Agnete T. Lundgaard, Frédéric Burdet, Troels Siggaard, David Westergaard, Danai Vagiaki, Lisa Cantwell, Timo Röder, Dorte Vistisen, Thomas Sparsø, Giuseppe N. Giordano, Mark Ibberson, Karina Banasik, Søren Brunak
BALDR: A Web-based platform for informed comparison and prioritization of biomarker candidates for type 2 diabetes mellitus. PLoS Comput. Biol. 19 (8) (2023)
Victorine P. Muse, Alejandro Aguayo-Orozco, Sedrah B. Balaganeshan, Søren Brunak
Population-wide analysis of hospital laboratory tests to assess seasonal variation and temporal reference interval modification. Patterns 4 (8) (2023)
Jessica Xin Hjaltelin, Hannah Currant, Isabella Friis Jørgensen, Søren Brunak
Visualising disease trajectories from population-wide data. Frontiers Bioinform. 3 (2023)
Hans-Christian Thorsen-Meyer, Davide Placido, Benjamin Skov Kaas-Hansen, Anna P. Nielsen, Theis Lange, Annelaura B. Nielsen, Palle Toft, Jens Schierbeck, Thomas Strøm, Piotr Chmura, Marc Heimann, Kirstine Belling, Anders Perner, Søren Brunak
Discrete-time survival analysis in the critically ill: a deep learning approach using heterogeneous data. npj Digit. Medicine 5 (2022)
Laust Hvas Mortensen, Søren Brunak
Reply to: Immortal time bias in the analysis of drug prescription trajectories. npj Digit. Medicine 5 (2022)
Alejandro Aguayo-Orozco, Amalie Dahl Haue, Isabella Friis Jørgensen, David Westergaard, Pope L. Moseley, Laust Hvas Mortensen, Søren Brunak
Optimizing drug selection from a prescription trajectory of one patient. npj Digit. Medicine 4 (2021)
Isabella Friis Jørgensen, Søren Brunak
Time-ordered comorbidity correlations identify patients at risk of mis- and overdiagnosis. npj Digit. Medicine 4 (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)
Søren Brunak, Catherine Bjerre Collin, Katharina Eva Ó Cathaoir, Martin Golebiewski, Marc Kirschner, Ingrid Kockum, Heike Moser, Dagmar Waltemath
Towards standardization guidelines for in silico approaches in personalized medicine. J. Integr. Bioinform. 17 (2-3) (2020)
Dhouha Grissa, Ditlev Nytoft Rasmussen, Aleksander Krag, Søren Brunak, Lars Juhl Jensen
Using National Electronic Health Care Registries to Analyse and Predict Alcoholic Liver Disease. EGC (2020)
Dhouha Grissa, Ditlev Nytoft Rasmussen, Aleksander Krag, Søren Brunak, Lars Juhl Jensen
Alcoholic liver disease: A registry view on comorbidities and disease prediction. PLoS Comput. Biol. 16 (9) (2020)
Nadine Kadi Eskildsen, Robert Eriksson, Sten B. Christensen, Tamilla Stine Aghassipour, Mikael Juul Bygsø, Søren Brunak, Suzanne Lisbet Hansen
Implementation and comparison of two text mining methods with a standard pharmacovigilance method for signal detection of medication errors. BMC Medical Informatics Decis. Mak. 20 (1) (2020)
Emilio Fenoy, José M. G. Izarzugaza, Vanessa Isabell Jurtz, Søren Brunak, Morten Nielsen
A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction. Bioinform. 35 (7) (2019)
Martin Lademann, Mette Lademann, Anders Boeck Jensen, Søren Brunak
Incorporating symptom data in longitudinal disease trajectories for more detailed patient stratification. Int. J. Medical Informatics 129 (2019)
Alejandro Aguayo-Orozco, Karine Audouze, Troels Siggaard, Robert Barouki, Søren Brunak, Olivier Taboureau
sAOP: linking chemical stressors to adverse outcomes pathway networks. Bioinform. 35 (24) (2019)
Maria Luisa Matey-Hernandez, Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, José M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun, Hongzhi Cao, Chen Ye, John van Beusekom, Thomas Espeseth, Esben N. Flindt, Rune M. Friborg, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngreen, Thomas Mailund, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick F. Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon Rasmussen, Søren Besenbacher, Anders D. Børglum, Jun Wang, Hans Eiberg, Karsten Kristiansen, Mikkel Heide Schierup, Søren Brunak
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. BMC Bioinform. 19 (1) (2018)
David Westergaard, Hans Henrik Stærfeldt, Christian Tønsberg, Lars Juhl Jensen, Søren Brunak
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. PLoS Comput. Biol. 14 (2) (2018)
Francesco Russo, Sebastiano Di Bella, Federica Vannini, Gabriele Berti, Flavia Scoyni, Helen Cook, Alberto Santos, Giovanni Nigita, Vincenzo Bonnici, Alessandro Laganà, Filippo Geraci, Alfredo Pulvirenti, Rosalba Giugno, Federico De Masi, Kirstine Belling, Lars Juhl Jensen, Søren Brunak, Marco Pellegrini, Alfredo Ferro
miRandola 2017: a curated knowledge base of non-invasive biomarkers. Nucleic Acids Res. 46 (Database-Issue) (2018)
Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, José M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun, Hongzhi Cao, Chen Ye, John van Beusekom, Thomas Espeseth, Esben N. Flindt, Rune M. Friborg, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngreen, Thomas Mailund, Maria Luisa Matey-Hernandez, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick F. Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon Rasmussen, Søren Besenbacher, Anders D. Børglum, Jun Wang, Hans Eiberg, Karsten Kristiansen, Søren Brunak, Mikkel Heide Schierup
assembly of 150 genomes from Denmark as a population reference. Nat. 548 (7665) (2017)
Mette Beck, David Westergaard, Leif Groop, Søren Brunak
Temporal Order of Disease Pairs Affects Subsequent Disease Trajectories: The Case of Diabetes and Sleep Apnea. PSB (2017)
Dac-Trung Nguyen, Stephen L. Mathias, Cristian Bologa, Søren Brunak, Nicolas F. Fernandez, Anna Gaulton, Anne Hersey, Jayme Holmes, Lars Juhl Jensen, Anneli Karlsson, Guixia Liu, Avi Ma'ayan, Geetha Mandava, Subramani Mani, Saurabh Mehta, John P. Overington, Juhee Patel, Andrew D. Rouillard, Stephan C. Schürer, Timothy Sheils, Anton Simeonov, Larry A. Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy J. Yang, Ajit Jadhav, Tudor I. Oprea, Rajarshi Guha
Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 45 (Database-Issue) (2017)
Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jimenez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44 (Database-Issue) (2016)
Anna-Sapfo Malaspinas, Michael C. Westaway, Craig Muller, Vitor C. Sousa, Oscar Lao, Isabel Alves, Anders Bergström, Georgios Athanasiadis, Jade Yu Cheng, Jacob E. Crawford, Tim H. Heupink, Enrico Macholdt, Stephan Peischl, Simon Rasmussen, Stephan Schiffels, Sankar Subramanian, Joanne L. Wright, Anders Albrechtsen, Chiara Barbieri, Isabelle Dupanloup, Anders Eriksson, Ashot Margaryan, Ida Moltke, Irina Pugach, Thorfinn Sand Korneliussen, Ivan P. Levkivskyi, José Víctor Moreno-Mayar, Shengyu Ni, Fernando Racimo, Martin Sikora, Yali Xue, Farhang A. Aghakhanian, Nicolas Brucato, Søren Brunak, Paula F. Campos, Warren Clark, Sturla Ellingvåg, Gudjugudju Fourmile, Pascale Gerbault, Darren Injie, George Koki, Matthew Leavesley, Betty Logan, Aubrey Lynch, Elizabeth A. Matisoo-Smith, Peter J. McAllister, Alexander J. Mentzer, Mait Metspalu, Andrea B. Migliano, Les Murgha, Maude E. Phipps, William Pomat, Doc Reynolds, Francois-Xavier Ricaut, Peter Siba, Mark G. Thomas, Thomas Wales, Colleen Ma'run Wall, Stephen J. Oppenheimer, Chris Tyler-Smith, Richard Durbin, Joe Dortch, Andrea Manica, Mikkel H. Schierup, Robert A. Foley, Marta Mirazón Lahr, Claire Bowern, Jeffrey D. Wall, Thomas Mailund, Mark Stoneking, Rasmus Nielsen, Manjinder S. Sandhu, Laurent Excoffier, David M. Lambert, Eske Willerslev
A genomic history of Aboriginal Australia. Nat. 538 (7624) (2016)
Jens Kringelum, Sonny Kim Kjærulff, Søren Brunak, Ole Lund, Tudor I. Oprea, Olivier Taboureau
ChemProt-3.0: a global chemical biology diseases mapping. Database J. Biol. Databases Curation 2016 (2016)
Kristoffer Forslund, Falk Hildebrand, Trine Rask Nielsen, Gwen Falony, Emmanuelle Le Chatelier, Shinichi Sunagawa, Edi Prifti, Sara Vieira-Silva, Valborg Gudmundsdottir, Helle Krogh Pedersen, Manimozhiyan Arumugam, Karsten Kristiansen, Anita Yvonne Voigt, Henrik Vestergaard, Rajna Hercog, Paul I. Costea, Jens Roat Kultima, Junhua Li, Torben Jørgensen, Florence Levenez, Joël Dore, Henrik Bjørn Nielsen, Søren Brunak, Jeroen Raes, Torben Hansen, Jun Wang, S. Dusko Ehrlich, Peer Bork, Oluf Pedersen
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nat. 528 (7582) (2015)
Rebecka Weegar, Maria Kvist, Karin Sundström, Søren Brunak, Hercules Dalianis
Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx. AMIA (2015)
Søren Brunak, Francisco M. de la Vega, Adam A. Margolin, Benjamin J. Raphael, Gunnar Rätsch, Joshua M. Stuart
Session Introduction. Pacific Symposium on Biocomputing (2015)
Irene Kouskoumvekaki, Nour Shublaq, Søren Brunak
Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. Briefings Bioinform. 15 (6) (2014)
Konrad Krysiak-Baltyn, Thomas Nordahl Petersen, Karine Audouze, Niels Jørgensen, Lars Ängquist, Søren Brunak
Compass: A hybrid method for clinical and biobank data mining. J. Biomed. Informatics 47 (2014)
Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap, Thomas Brüls, Jean-Michel Batto, Marcelo Bertalan, Natalia Borruel, Francesc Casellas, Leyden Fernández, Laurent Gautier, Torben Hansen, Masahira Hattori, Tetsuya Hayashi, Michiel Kleerebezem, Ken Kurokawa, Marion Leclerc, Florence Levenez, Chaysavanh Manichanh, Henrik Bjørn Nielsen, Trine Rask Nielsen, Nicolas Pons, Julie Poulain, Junjie Qin, Thomas Sicheritz-Pontén, Sebastian Tims, David Torrents, Edgardo Ugarte, Erwin G. Zoetendal, Jun Wang, Francisco Guarner, Oluf Pedersen, Willem M. de Vos, Søren Brunak, Joël Dore, MetaHIT consortium, Jean Weissenbach, S. Dusko Ehrlich, Peer Bork
Addendum: Enterotypes of the human gut microbiome. Nat. 506 (7489) (2014)
Søren Brunak, Francisco M. de la Vega, Gunnar Rätsch, Joshua M. Stuart
Session Introduction. Pacific Symposium on Biocomputing (2014)
Cecilia Engel Thomas, Peter Bjødstrup Jensen, Thomas Werge, Søren Brunak
Negation scope and spelling variation for text-mining of Danish electronic patient records. Louhi@EACL (2014)
Robert Eriksson, Peter Bjødstrup Jensen, Sune Frankild, Lars Juhl Jensen, Søren Brunak
Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. J. Am. Medical Informatics Assoc. 20 (5) (2013)
Sonny Kim Kjærulff, Louis Wich, Jens Kringelum, Ulrik Plesner Jacobsen, Irene Kouskoumvekaki, Karine Audouze, Ole Lund, Søren Brunak, Tudor I. Oprea, Olivier Taboureau
ChemProt-2.0: visual navigation in a disease chemical biology database. Nucleic Acids Res. 41 (Database-Issue) (2013)
Bente Maegaard, Udo Hahn, Søren Brunak, Stefan Schulz, Ulrich Andersen, Sebastian Welter
Question Answering for Health Professionals and Laypersons. MedInfo (2013)
Tune H. Pers, Piotr Dworzynski, Cecilia Engel Thomas, Kasper Lage, Søren Brunak
MetaRanker 2.0: a web server for prioritization of genetic variation data. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Francisco S. Roque, Peter Bjødstrup Jensen, Henriette Schmock, Marlene Dalgaard, Massimo Andreatta, Thomas F. Hansen, Karen Søeby, Søren Bredkjær, Anders Juul, Thomas Werge, Lars Juhl Jensen, Søren Brunak
Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts. PLoS Comput. Biol. 7 (8) (2011)
Qiyuan Li, Aron C. Eklund, Nicolai J. Birkbak, Christine Desmedt, Benjamin Haibe-Kains, Christos P. Sotiriou, W. Fraser Symmans, Lajos Pusztai, Søren Brunak, Andrea L. Richardson, Zoltan Szallasi
Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. BMC Bioinform. 12 (2011)
Kai Wang, Rasmus Wernersson, Søren Brunak
The strength of intron donor splice sites in human genes displays a bell-shaped pattern. Bioinform. 27 (22) (2011)
Olivier Taboureau, Sonny Kim Nielsen, Karine Audouze, Nils Weinhold, Daniel Edsgärd, Francisco S. Roque, Irene Kouskoumvekaki, Alina Bora, Ramona Curpan, Thomas Skøt Jensen, Søren Brunak, Tudor I. Oprea
ChemProt: a disease chemical biology database. Nucleic Acids Res. 39 (Database-Issue) (2011)
Karine Audouze, Agnieszka Sierakowska Juncker, Francisco S. Roque, Konrad Krysiak-Baltyn, Nils Weinhold, Olivier Taboureau, Thomas Skøt Jensen, Søren Brunak
Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks. PLoS Comput. Biol. 6 (5) (2010)
Nicholas Paul Gauthier, Lars Juhl Jensen, Rasmus Wernersson, Søren Brunak, Thomas Skøt Jensen
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Res. 38 (Database-Issue) (2010)
Francesco Pappalardo, Mark D. Halling-Brown, Nicolas Rapin, Ping Zhang, Davide Alemani, Andrew Emerson, Paola Paci, Patrice Duroux, Marzio Pennisi, Arianna Palladini, Olivo Miotto, Daniel Churchill, Elda Rossi, Adrian J. Shepherd, David S. Moss, Filippo Castiglione, Massimo Bernaschi, Marie-Paule Lefranc, Søren Brunak, Santo Motta, Pierluigi Lollini, Kaye E. Basford, Vladimir Brusic
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. Briefings Bioinform. 10 (3) (2009)
Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak, Thomas Skøt Jensen
Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res. 36 (Database-Issue) (2008)
Frank Panitz, Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B. Madsen, Anette Høj, Rikke K. Vingborg, Bujie Zahn, Xuegang Wang, Xuefei Wang, Rasmus Wernersson, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob Hull Havgaard, Søren Brunak, Merete Fredholm, Christian Bendixen
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen
Modeling the adaptive immune system: predictions and simulations. Bioinform. 23 (24) (2007)
Niclas Tue Hansen, Irene Kouskoumvekaki, Flemming Steen Jørgensen, Søren Brunak, Svava Ósk Jónsdóttir
Prediction of pH-Dependent Aqueous Solubility of Druglike Molecules. J. Chem. Inf. Model. 46 (6) (2006)
Philip E. Bourne, Søren Brunak
ISMB 2006. ISMB (Supplement of Bioinformatics) (2006)
Goran Neshich, Philip E. Bourne, Søren Brunak
ISMB 2006. PLoS Comput. Biol. 2 (2) (2006)
Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer, Søren Brunak
Prediction of twin-arginine signal peptides. BMC Bioinform. 6 (2005)
Ulrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork, Søren Brunak
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinform. 21 (7) (2005)
Svava Ósk Jónsdóttir, Flemming Steen Jørgensen, Søren Brunak
Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. Bioinform. 21 (10) (2005)
Claus A. F. Andersen, Søren Brunak
Representation of Protein-Sequence Information by Amino Acid Subalphabets. AI Mag. 25 (1) (2004)
Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom
proteinase cleavage sites: Possible relevance to SARS virus pathology. BMC Bioinform. 5 (2004)
Claus Lundegaard, Morten Nielsen, Kasper Lamberth, Peder Worning, Christina Sylvester-Hvid, Søren Buus, Søren Brunak, Ole Lund
MHC Class I Epitope Binding Prediction Trained on Small Data Sets. ICARIS (2004)
Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinform. 20 (9) (2004)
Tanja la Cour, Ramneek Gupta, Kristoffer Rapacki, Karen Skriver, Flemming M. Poulsen, Søren Brunak
NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Res. 31 (1) (2003)
Claus Lundegaard, Thomas Nordahl Petersen, Morten Nielsen, Henrik Bohr, Jakob Bohr, Søren Brunak, Garry Gippert, Ole Lund
Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks. Mathematical Methods for Protein Structure Analysis and Design (2003)
Jens Kaae Christensen, Kasper Lamberth, Morten Nielsen, Claus Lundegaard, Peder Worning, Sanne Lise Lauemøller, Søren Buus, Søren Brunak, Ole Lund
Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach. Neural Comput. 15 (12) (2003)
Lars Juhl Jensen, Ramneek Gupta, Hans Henrik Stærfeldt, Søren Brunak
Prediction of human protein function according to Gene Ontology categories. Bioinform. 19 (5) (2003)
Ramneek Gupta, Søren Brunak
Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function. Pacific Symposium on Biocomputing (2002)
David Ussery, Dikeos Mario Soumpasis, Søren Brunak, Hans Henrik Stærfeldt, Peder Worning, Anders Krogh
Bias of Purine Stretches in Sequenced Chromosomes. Comput. Chem. 26 (5) (2002)
Jeppe S. Spicker, Friedrik Wikman, Ming-Lan Lu, Carlos Cordon-Cardo, Christopher T. Workman, Torben F. Ørntoft, Søren Brunak, Steen Knudsen
Neural network predicts sequence of TP53 gene based on DNA chip. Bioinform. 18 (8) (2002)
Søren Brunak, Anders Krogh
ISMB 2001. ISMB (Supplement of Bioinformatics) (2001)
Pierre Baldi, Søren Brunak
Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. Pacific Symposium on Biocomputing (2001)
Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen
Flexibility of the genetic code with respect to DNA structure. Bioinform. 17 (3) (2001)
Pierre Baldi, Søren Brunak, Paolo Frasconi, Gianluca Pollastri, Giovanni Soda
Bidirectional Dynamics for Protein Secondary Structure Prediction. Sequence Learning (2001)
Jan Gorodkin, Bodil Søgaard, Hanne Bay, Hans Doll, Per Kølster, Søren Brunak
Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks. Comput. Chem. 25 (3) (2001)
Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen
Assessing the accuracy of prediction algorithms for classification: an overview. Bioinform. 16 (5) (2000)
Thomas M. Frimurer, Robert Bywater, Lars Nærum, Leif Nørskov Lauritsen, Søren Brunak
Improving the Odds in Discriminating "Drug-like" from "Non Drug-like" Compounds. J. Chem. Inf. Comput. Sci. 40 (6) (2000)
Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Søren Brunak
Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. ISMB (2000)
Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Søren Brunak
Protein β-Sheet Partner Prediction by Neural Networks. ANNIMAB (2000)
Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen
Structural basis for triplet repeat disorders: a computational analysis. Bioinform. 15 (11) (1999)
Anders Gorm Pedersen, Pierre Baldi, Yves Chauvin, Søren Brunak
The Biology of Eukaryotic Promoter Prediction - A Review. Comput. Chem. 23 (3-4) (1999)
Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak
MatrixPlot: visualizing sequence constraints. Bioinform. 15 (9) (1999)
Andres Kreegipuu, Nikolaj Blom, Søren Brunak
PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res. 27 (1) (1999)
Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri
Exploiting the past and the future in protein secondary structure prediction. Bioinform. 15 (11) (1999)
Ramneek Gupta, Hanne Birch, Kristoffer Rapacki, Søren Brunak, Jan E. Hansen
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. Nucleic Acids Res. 27 (1) (1999)
Jan Gorodkin, Ole Lund, Claus A. F. Andersen, Søren Brunak
Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints. ISMB (1999)
Nikolaj Blom, Andres Kreegipuu, Søren Brunak
PhosphoBase: a database of phosphorylation sites. Nucleic Acids Res. 26 (1) (1998)
Jan E. Hansen, Ole Lund, Jette Nilsson, Kristoffer Rapacki, Søren Brunak
O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins. Nucleic Acids Res. 26 (1) (1998)
Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen
Computational Applications of DNA Structural Scales. ISMB (1998)
Jan E. Hansen, Ole Lund, Kristoffer Rapacki, Søren Brunak
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins. Nucleic Acids Res. 25 (1) (1997)
Henrik Nielsen, Jacob Engelbrecht, Søren Brunak, Gunnar von Heijne
A Neural Network Method for Identification of Prokaryotic and Eukaryotic Signal Peptides and Prediction of their Cleavage Sites. Int. J. Neural Syst. 8 (5-6) (1997)
Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo
Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci. 13 (6) (1997)
Jan E. Hansen, Ole Lund, Jens O. Nielsen, John-E. S. Hansen, Søren Brunak
O-GLYCBASE: a revised database of O-glycosylated proteins. Nucleic Acids Res. 24 (1) (1996)
Anders Gorm Pedersen, Pierre Baldi, Søren Brunak, Yves Chauvin
Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. ISMB (1996)
Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh
Periodic Sequence Patterns in Human Exons. ISMB (1995)
Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh
Hidden Markov Models for Human Genes. NIPS (1993)
Henrik Fredholm, Henrik Bohr, Jakob Bohr, Søren Brunak, Rodney M. J. Cotterill, Benny Lautrup, Steffen B. Petersen
A Novel Approach to Prediction of the 3-Dimensional Structures. NIPS (1990)
Henrik Bohr, Søren Brunak
A Travelling Salesman Approach to Protein Conformation. Complex Syst. 3 (1) (1989)