default search action
Søren Brunak
Person information
Refine list
refinements active!
zoomed in on ?? of ?? records
view refined list in
export refined list as
showing all ?? records
2020 – today
- 2024
- [j69]Victorine P. Muse, Davide Placido, Amalie Dahl Haue, Søren Brunak:
Seasonally adjusted laboratory reference intervals to improve the performance of machine learning models for classification of cardiovascular diseases. BMC Medical Informatics Decis. Mak. 24(1): 62 (2024) - 2023
- [j68]Jessica Xin Hjaltelin, Hannah Currant, Isabella Friis Jørgensen, Søren Brunak:
Visualising disease trajectories from population-wide data. Frontiers Bioinform. 3 (2023) - [j67]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): 100778 (2023) - [j66]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) - 2022
- [j65]Laust Hvas Mortensen, Søren Brunak:
Reply to: Immortal time bias in the analysis of drug prescription trajectories. npj Digit. Medicine 5 (2022) - [j64]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) - 2021
- [j63]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) - [j62]Isabella Friis Jørgensen, Søren Brunak:
Time-ordered comorbidity correlations identify patients at risk of mis- and overdiagnosis. npj Digit. Medicine 4 (2021) - 2020
- [j61]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) - [j60]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): 94 (2020) - [j59]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 Glynne Gut, David Haan, Arif Ozgun 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): 102-111 (2020) - [j58]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) - [c23]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: 389-390
2010 – 2019
- 2019
- [j57]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): 1098-1107 (2019) - [j56]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): 5391-5392 (2019) - [j55]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: 107-113 (2019) - 2018
- [j54]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): 239:1-239:12 (2018) - [j53]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): D354-D359 (2018) - [j52]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) - 2017
- [j51]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): D995-D1002 (2017) - [j50]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:
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nat. 548(7665): 87-91 (2017) - [c22]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: 380-389 - 2016
- [j49]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) - [j48]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. Jiménez, 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): 38-47 (2016) - [j47]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): 207-214 (2016) - 2015
- [j46]Kristoffer Forslund, Falk Hildebrand, Trine 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): 262-266 (2015) - [c21]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 - [c20]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: 8-9 - 2014
- [j45]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): 942-952 (2014) - [j44]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: 160-170 (2014) - [j43]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 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): 516 (2014) - [c19]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: 64-68 - [c18]Søren Brunak, Francisco M. de la Vega, Gunnar Rätsch, Joshua M. Stuart:
Session Introduction. Pacific Symposium on Biocomputing 2014: 1-2 - 2013
- [j42]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): 947-953 (2013) - [j41]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): 464-469 (2013) - [j40]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): 104-108 (2013) - [c17]Bente Maegaard, Udo Hahn, Søren Brunak, Stefan Schulz, Ulrich Andersen, Sebastian Welter:
Question Answering for Health Professionals and Laypersons. MedInfo 2013: 1244 - 2011
- [j39]Kai Wang, Rasmus Wernersson, Søren Brunak:
The strength of intron donor splice sites in human genes displays a bell-shaped pattern. Bioinform. 27(22): 3079-3084 (2011) - [j38]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: 310 (2011) - [j37]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): 367-372 (2011) - [j36]Francisco S. Roque, Peter Bjødstrup Jensen, Henriette Schmock, Marlene Dalgaard, Massimo Andreatta, Thomas Folkmann 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) - 2010
- [j35]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): 699-702 (2010) - [j34]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)
2000 – 2009
- 2009
- [j33]Francesco Pappalardo, Mark D. Halling-Brown, Nicolas Rapin, Ping Zhang, Davide Alemani, Andrew P. J. 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): 330-340 (2009) - 2008
- [j32]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): 854-859 (2008) - 2007
- [j31]Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen:
Modeling the adaptive immune system: predictions and simulations. Bioinform. 23(24): 3265-3275 (2007) - [c16]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: 387-391 - 2006
- [j30]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): 2601-2609 (2006) - [j29]Goran Neshich, Philip E. Bourne, Søren Brunak:
ISMB 2006. PLoS Comput. Biol. 2(2) (2006) - [c15]Philip E. Bourne, Søren Brunak:
ISMB 2006. ISMB (Supplement of Bioinformatics) 2006: 1-2 - 2005
- [b3]Ole Lund, Morten Nielsen, Claus Lundegaard, Can Kesmir, Søren Brunak:
Immunological bioinformatics. Computational molecular biology, AAAI Press 2005, ISBN 978-0-262-12280-1, pp. I-XII, 1-296 - [j28]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): 1164-1171 (2005) - [j27]Svava Ósk Jónsdóttir, Flemming Steen Jørgensen, Søren Brunak:
Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. Bioinform. 21(10): 2145-2160 (2005) - [j26]Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer, Søren Brunak:
Prediction of twin-arginine signal peptides. BMC Bioinform. 6: 167 (2005) - 2004
- [j25]Claus A. F. Andersen, Søren Brunak:
Representation of Protein-Sequence Information by Amino Acid Subalphabets. AI Mag. 25(1): 97-104 (2004) - [j24]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): 1388-1397 (2004) - [j23]Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom:
Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology. BMC Bioinform. 5: 72 (2004) - [c14]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: 217-225 - 2003
- [j22]Lars Juhl Jensen, Ramneek Gupta, Hans Henrik Stærfeldt, Søren Brunak:
Prediction of human protein function according to Gene Ontology categories. Bioinform. 19(5): 635-642 (2003) - [j21]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): 393-396 (2003) - [j20]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): 2931-2942 (2003) - [c13]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: 117-122 - 2002
- [j19]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): 1133-1134 (2002) - [j18]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): 531-541 (2002) - [c12]Ramneek Gupta, Søren Brunak:
Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function. Pacific Symposium on Biocomputing 2002: 310-322 - 2001
- [b2]Pierre Baldi, Søren Brunak:
Bioinformatics - the machine learning approach (2. ed.). MIT Press 2001, ISBN 978-0-262-02506-5, pp. I-XXI, 1-452 - [j17]Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen:
Flexibility of the genetic code with respect to DNA structure. Bioinform. 17(3): 237-248 (2001) - [j16]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): 301-307 (2001) - [c11]Søren Brunak, Anders Krogh:
ISMB 2001. ISMB (Supplement of Bioinformatics) 2001: 1-4 - [c10]Pierre Baldi, Søren Brunak:
Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. Pacific Symposium on Biocomputing 2001 - [c9]Pierre Baldi, Søren Brunak, Paolo Frasconi, Gianluca Pollastri, Giovanni Soda:
Bidirectional Dynamics for Protein Secondary Structure Prediction. Sequence Learning 2001: 80-104 - 2000
- [b1]Pierre Baldi, Søren Brunak:
Bioinformatics - the machine learning approach. MIT Press 2000, ISBN 978-0-262-02442-6, pp. 1-44 - [j15]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): 412-424 (2000) - [j14]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): 1315-1324 (2000) - [c8]Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Søren Brunak:
Protein β-Sheet Partner Prediction by Neural Networks. ANNIMAB 2000: 3-9 - [c7]Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Søren Brunak:
Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. ISMB 2000: 25-36
1990 – 1999
- 1999
- [j13]Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak:
MatrixPlot: visualizing sequence constraints. Bioinform. 15(9): 769-770 (1999) - [j12]Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen:
Structural basis for triplet repeat disorders: a computational analysis. Bioinform. 15(11): 918-929 (1999) - [j11]Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri:
Exploiting the past and the future in protein secondary structure prediction. Bioinform. 15(11): 937-946 (1999) - [j10]Anders Gorm Pedersen, Pierre Baldi, Yves Chauvin, Søren Brunak:
The Biology of Eukaryotic Promoter Prediction - A Review. Comput. Chem. 23(3-4): 191-207 (1999) - [j9]Andres Kreegipuu, Nikolaj Blom, Søren Brunak:
PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res. 27(1): 237-239 (1999) - [j8]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): 370-372 (1999) - [c6]Jan Gorodkin, Ole Lund, Claus A. F. Andersen, Søren Brunak:
Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints. ISMB 1999: 95-105 - 1998
- [j7]Nikolaj Blom, Andres Kreegipuu, Søren Brunak:
PhosphoBase: a database of phosphorylation sites. Nucleic Acids Res. 26(1): 382-386 (1998) - [j6]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): 387-389 (1998) - [c5]Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen:
Computational Applications of DNA Structural Scales. ISMB 1998: 35-42 - 1997
- [j5]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): 583-586 (1997) - [j4]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): 581-599 (1997) - [j3]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): 278-282 (1997) - 1996
- [j2]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): 248-252 (1996) - [c4]