Group publications

 

Publikationer rss feed

2019
 

A Brief History of Protein Sorting Prediction

Nielsen, Henrik ; Tsirigos, Konstantinos D. ; Brunak, Søren ; von Heijne, Gunnar
in: Protein Journal, vol: 38, issue: 3, pages: 200-216

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/s10930-019-09838-3

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A generic deep convolutional neural network framework for prediction of receptor–ligand interactions—NetPhosPan: application to kinase phosphorylation prediction

Fenoy, Emilio ; Gonzalez-Izarzugaza, Jose Maria ; Jurtz, Vanessa ; Brunak, Søren ; Nielsen, Morten
in: Bioinformatics, vol: 35, issue: 7, pages: 1098-1107

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/bioinformatics/bty715

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Conflicting associations between dietary patterns and changes of anthropometric traits across subgroups of middle-aged women and men

Jiang, Li ; Audouze, Karine ; Romero Herrera, Jose Alejandro ; Ängquist, Lars Henrik ; Kjærulff, Sonny Kim ; Izarzugaza, Jose M.G. ; Tjønneland, Anne ; Halkjær, Jytte ; Overvad, Kim ; Sørensen, Thorkild I.A. ; Brunak, Søren
in: Clinical Nutrition

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.clnu.2019.02.003

 

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

Asplund, Maria ; Kjartansdóttir, Kristín Rós ; Mollerup, Sarah ; Vinner, Lasse ; Fridholm, Helena ; Herrera, José A. R. ; Friis-Nielsen, Jens ; Hansen, Thomas Arn ; Jensen, Randi Holm ; Nielsen, Ida Broman ; Richter, Stine Raith ; Rey-Iglesia, Alba ; Matey-Hernandez, Maria Luisa ; Alquezar-Planas, David E. ; Olsen, Pernille V. S. ; Sicheritz-Pontén, Thomas ; Willerslev, Eske ; Lund, Ole ; Brunak, Søren ; Mourier, Tobias ; Nielsen, Lars Peter ; Izarzugaza, Jose M. G. ; Hansen, Anders Johannes
in: Clinical Microbiology and Infection

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.cmi.2019.04.028

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Detection of co-expressed pathway modules associated with mineral concentration and meat quality in Nelore cattle

Diniz, Wellison J. S. ; Mazzoni, Gianluca ; Coutinho, Luiz L. ; Banerjee, Priyanka ; Geistlinger, Ludwig ; Cesar, Aline S. M. ; Bertolini, Francesca ; Afonso, Juliana ; de Oliveira, Priscila S. N. ; Tizioto, Polyana C. ; Kadarmideen, Haja ; Regitano, Luciana C. A.
in: Frontiers in Genetics, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.3389/fgene.2019.00210

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Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: descriptive characteristics of the epidemiological studies within the IMI DIRECT Consortium

Koivula, Robert W. ; Forgie, Ian M. ; Kurbasic, Azra ; Viñuela, Ana ; Heggie, Alison ; Giordano, Giuseppe N. ; Hansen, Tue H. ; Hudson, Michelle ; Koopman, Anitra D. M. ; Rutters, Femke ; Siloaho, Maritta ; Allin, Kristine H. ; Brage, Søren ; Brorsson, Caroline A. ; Dawed, Adem Y. ; De Masi, Federico ; Groves, Christopher J. ; Kokkola, Tarja ; Mahajan, Anubha ; Perry, Mandy H. ; Rauh, Simone P. ; Ridderstråle, Martin ; Teare, Harriet J. A. ; Thomas, E. Louise ; Tura, Andrea ; Vestergaard, Henrik ; White, Tom ; Adamski, Jerzy ; Bell, Jimmy D. ; Beulens, Joline W. ; Brunak, Søren ; Dermitzakis, Emmanouil T. ; Froguel, Philippe ; Frost, Gary ; Gupta, Ramneek ; Hansen, Torben ; Hattersley, Andrew ; Jablonka, Bernd ; Kaye, Jane ; Laakso, Markku ; McDonald, Timothy J. ; Pedersen, Oluf ; Schwenk, Jochen M. ; Pavo, Imre ; Mari, Andrea ; McCarthy, Mark I. ; Ruetten, Hartmut ; Walker, Mark ; Pearson, Ewan ; Franks, Paul W. ; ,
in: Diabetologia, vol: 62, issue: 9, pages: 1601-1615

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/s00125-019-4906-1

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Genome-wide association studies for 30 haematological and blood clinical-biochemical traits in Large White pigs reveal genomic regions affecting intermediate phenotypes

Bovo, Samuele ; Mazzoni, Gianluca ; Bertolini, Francesca ; Schiavo, Giuseppina ; Galimberti, Giuliano ; Gallo, Maurizio ; Dall'Olio, Stefania ; Fontanesi, Luca
in: Scientific Reports, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41598-019-43297-1

 

High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach

Mollerup, Sarah ; Asplund, Maria ; Friis-Nielsen, Jens ; Kjartansdóttir, Kristín Rós ; Fridholm, Helena ; Hansen, Thomas Arn ; Herrera, José Alejandro Romero ; Barnes, Christopher James ; Jensen, Randi Holm ; Richter, Stine Raith ; Nielsen, Ida Broman ; Pietroni, Carlotta ; Alquezar-Planas, David E. ; Rey-Iglesia, Alba ; Olsen, Pernille V. S. ; Rajpert-De Meyts, Ewa ; Groth-Pedersen, Line ; von Buchwald, Christian ; Jensen, David H. ; Gniadecki, Robert ; Høgdall, Estrid ; Langhoff, Jill Levin ; Pete, Imre ; Vereczkey, Ildikó ; Baranyai, Zsolt ; Dybkaer, Karen ; Johnsen, Hans Erik ; Steiniche, Torben ; Hokland, Peter ; Rosenberg, Jacob ; Baandrup, Ulrik ; Sicheritz-Pontén, Thomas ; Willerslev, Eske ; Brunak, Søren ; Lund, Ole ; Mourier, Tobias ; Vinner, Lasse ; Izarzugaza, Jose M. G. ; Nielsen, Lars Peter ; Hansen, Anders Johannes
in: Journal of Infectious Diseases

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1093/infdis/jiz318

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Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types

Hjaltelin, Jessica Xin ; Izarzugaza, Jose M. G. ; Jensen, Lars Juhl ; Russo, Francesco ; Westergaard, David ; Brunak, Søren
in: n p j Systems Biology and Applications, vol: 5

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41540-019-0104-5

 

SignalP 5.0 improves signal peptide predictions using deep neural networks

Almagro Armenteros, Jose Juan ; Tsirigos, Konstantinos D. ; Sønderby, Casper Kaae ; Petersen, Thomas Nordahl ; Winther, Ole ; Brunak, Søren ; von Heijne, Gunnar ; Nielsen, Henrik
in: Nature Biotechnology, vol: 37, pages: 420-423

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41587-019-0036-z

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The bio.tools registry of software tools and data resources for the life sciences

Ison, Jon ; Ienasescu, Hans ; Chmura, Piotr Jaroslaw ; Rydza, Emil Karol ; Menager, Herve ; Kalaš, Matuš ; Schwammle, Veit ; Gruning, Björn ; Beard, Niall ; Lopez, Rodrigo ; Duvaud, Severine ; Stockinger, Heinz ; Persson, Bengt ; Vařekova, Radka Svobodova ; Raček, Tomaš ; Vondrašek, Jiři ; Peterson, Hedi ; Salumets, Ahto ; Jonassen, Inge ; Hooft, Rob ; Nyronen, Tommi ; Valencia, Alfonso ; Capella, Salvador ; Gelpi, Josep ; Zambelli, Federico ; Savakis, Babis ; Leskošek, Brane ; Rapacki, Kristoffer ; Blanchet, Christophe ; Jimenez, Rafael ; Oliveira, Arlindo ; Vriend, Gert ; Collin, Olivier ; Van Helden, Jacques ; Løngreen, Peter ; Brunak, Søren
in: Genome Biology, vol: 20, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s13059-019-1772-6

 

Transcriptomics–genomics data integration and expression quantitative trait loci analyses in oocyte donors and embryo recipients for improving in vitro production of dairy cattle embryos

Kadarmideen, Haja ; Mazzoni, Gianluca
in: Reproduction, Fertility and Development, vol: 31, pages: 55–67

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1071/RD18338

2018
 

Accurate genotyping across variant classes and lengths using variant graphs

Sibbesen, Jonas Andreas ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Dam-Als, Thomas ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; van Beusekom, Johan ; Espeseth, Thomas ; Flindt, Esben ; Friborg, Rune M. ; Halager, Anders Egerup ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Matey-Hernandez, María Luisa ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick ; Ali , Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Rasmussen, Simon ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide
in: Nature Genetics

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41588-018-0145-5

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A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

Westergaard, David ; Stærfeldt, Hans Henrik ; Tønsberg, Christian ; Jensen, Lars Juhl ; Brunak, Søren
in: P L o S Computational Biology (Online), vol: 14, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1371/journal.pcbi.1005962

 

A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links

Pedersen, Helle Krogh ; Forslund, Sofia K ; Gudmundsdottir, Valborg ; Petersen, Anders Østergaard ; Hildebrand, Falk ; Hyötyläinen, Tuulia ; Nielsen, Trine ; Hansen, Torben ; Bork, Peer ; Ehrlich, S Dusko ; Brunak, Søren ; Oresic, Matej ; Pedersen, Oluf ; Nielsen, Henrik Bjørn
in: Nature Protocols, vol: 13, pages: 2781-2800

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41596-018-0064-z

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Analysis of a gene panel for targeted sequencing of colorectal cancer samples

Jensen, Klaus Højgaard ; Izarzugaza, Jose M.G ; Sierakowska Juncker, Agnieszka ; Borup Hansen, Rasmus ; Frøstrup Hansen, Torben ; Timshel, Pascal ; Blondal, Thorarinn ; Jensen, Thomas Skøt ; Rygaard-Hjalsted, Eske ; Mouritzen, Peter ; Thorsen, Michael ; Wernersson, Rasmus ; Nielsen, Henrik Bjørn ; Jakobsen, Anders ; Brunak, Søren ; Brandt Sørensen, Flemming
in: OncoTarget, vol: 9, issue: 10, pages: 9043-9060

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.18632/oncotarget.24138

 

A Novel Familial Cardiac Arrhythmia Syndrome with Widespread ST-Segment Depression

Bundgaard, Henning ; Jøns, Christian ; Lodder, Elisabeth ; Gonzalez-Izarzugaza, Jose Maria ; Herrera, Jose A. Romero ; Pehrson, Steen ; Tfelt-Hansen, Jacob ; Ahlberg, Gustav ; Olesen, Morten S ; Holst, Anders G ; Wellens, Hein ; de Villiers, Carin ; Hastings, Robert ; Graham, Stuart ; Wilde, Arthur A. M. ; Watkins, Hugh ; Christensen, Alex ; Brunak, Søren
in: The New England Journal of Medicine, vol: 379, pages: 1780-1782

Type: Comment/debate (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1056/NEJMc1807668

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Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

Matey-Hernandez, María Luisa ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Andreas Sibbesen, Jonas ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Als, Thomas D. ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; Beusekom, Johan v. ; Espeseth, Thomas ; Flindt, Esben N. ; Friborg, Rune M. ; Halager, Anders Egerup ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick F. ; Ali , Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide ; Izarzugaza, Jose M. G.
in: B M C Bioinformatics, vol: 19

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12859-018-2239-6

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Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency

Salleh, S. M. ; Mazzoni, Gianluca ; Løvendahl, P. ; Kadarmideen, Haja
in: B M C Bioinformatics, vol: 19

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12859-018-2553-z

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Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils

Sabino, Marcella ; Carmelo, Victor Adriano Okstoft ; Mazzoni, Gianluca ; Cappelli, Katia ; Capomaccio, Stefano ; Ajmone-Marsan, Paolo ; Verini-Supplizi, Andrea ; Trabalza-Marinucci, Massimo ; Kadarmideen, Haja N
in: B M C Genomics, vol: 19, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12864-018-4632-y

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Human MHC-II with Shared Epitope Motifs Are Optimal Epstein-Barr Virus Glycoprotein 42 Ligands—Relation to Rheumatoid Arthritis

Trier, Nicole ; Gonzalez-Izarzugaza, Jose Maria ; Chailyan, Anna ; Marcatili, Paolo ; Houen, Gunnar
in: International Journal of Molecular Sciences (Online), vol: 19, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.3390/ijms19010317

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Ibuprofen alters human testicular physiology to produce a state of compensated hypogonadism

Kristensen, David Møbjerg ; Desdoits-Lethimonier, Christèle ; Mackey, Abigail L ; Dalgaard, Marlene Danner ; De Masi, Federico ; Munkbøl, Cecilie Hurup ; Styrishave, Bjarne ; Antignac, Jean-Philippe ; Le Bizec, Bruno ; Platel, Christian ; Hay-Schmidt, Anders ; Jensen, Tina Kold ; Lesné, Laurianne ; Mazaud-Guittot, Séverine ; Kristiansen, Karsten ; Brunak, Søren ; Kjær, Michael ; Juul, Anders Christian ; Jégou, Bernard
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 115, issue: 17, pages: E715-E724

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1073/pnas.1715035115

 

Ibuprofen alters human testicular physiology to produce a state of compensated hypogonadism (vol 115, pg E715, 2018)

Kristensen, David Mobjerg ; Desdoits-Lethimonier, Christéle ; Mackey, Abigail L. ; Dalgaard, Marlene Danner ; De Masi, Federico ; Munkbol, Cecilie Hurup ; Styrishave, Bjarne ; Antignac, Jean-Philippe ; Le Bizec, Bruno ; Platel, Christian ; Hay-Schmidt, Anders ; Jensen, Tina Kold ; Lesne, Laurianne ; Mazaud-Guittot, SVerine ; Kristiansen, Karsten ; Brunak, Søren ; Kjær, Michael ; Juul, Anders Christian ; Jegou, Bernard
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 115, issue: 17, pages: E4143-E4143

Type: Comment/debate

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1073/pnas.1805313115

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Identification of Expression QTLs Targeting Candidate Genes for Residual Feed Intake in Dairy Cattle Using Systems Genomics

Salleh, MS ; Mazzoni, Gianluca ; Nielsen, M. O. ; Løvendahl, P ; Kadarmideen, Haja
in: Journal of Genetics and Genome Research, vol: 5, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.23937/2378-3648/1410035

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Integrative network analysis highlights biological processes underlying GLP-1 stimulated insulin secretion: A DIRECT study

Gudmundsdottir, Valborg ; Pedersen, Helle Krogh ; Allebrandt, Karla Viviani ; Brorsson, Caroline Anna ; van Leeuwen, Nienke ; Banasik, Karina ; Mahajan, Anubha ; Groves, Christopher J ; van de Bunt, Martijn ; Dawed, Adem Y ; Fritsche, Andreas ; Staiger, Harald ; Simonis-Bik, Annemarie M C ; Deelen, Joris ; Kramer, Mark H H ; Dietrich, Axel ; Hübschle, Thomas ; Willemsen, Gonneke ; Häring, Hans-Ulrich ; de Geus, Eco J C ; Boomsma, Dorret I ; Eekhoff, Elisabeth M W ; Ferrer, Jorge ; McCarthy, Mark I ; Pearson, Ewan R ; Gupta, Ramneek ; Brunak, Søren ; 't Hart, Leen M
in: P L o S One, vol: 13, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1371/journal.pone.0189886


https://www.bioinformatics.dtu.dk/research2018/research-groups/integrative-systems-biology/gruppens-publikationer
18 SEPTEMBER 2019