Anders Krogh

Anders Krogh

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Anders Krogh

Publications by authors named "Anders Krogh"

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Accurate genotyping across variant classes and lengths using variant graphs.

Nat Genet 2018 07 18;50(7):1054-1059. Epub 2018 Jun 18.

The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41588-018-0145-5DOI Listing
July 2018

Erratum.

Eur Heart J Qual Care Clin Outcomes 2017 10;3(4):328

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http://dx.doi.org/10.1093/ehjqcco/qcx024DOI Listing
October 2017

RNA Sequencing of Trigeminal Ganglia in Rattus Norvegicus after Glyceryl Trinitrate Infusion with Relevance to Migraine.

PLoS One 2016 23;11(5):e0155039. Epub 2016 May 23.

Danish Headache Center, Department of Neurology, Glostrup Research Institute, Rigshospitalet, and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155039PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877077PMC
July 2017

Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors.

PLoS Comput Biol 2017 04 14;13(4):e1005460. Epub 2017 Apr 14.

Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.1005460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409497PMC
April 2017

Evolving quality standards for large-scale registries: the GARFIELD-AF experience.

Eur Heart J Qual Care Clin Outcomes 2017 04;3(2):114-122

Thrombosis Research Institute, Emmanuel Kaye Building, Manresa Road, Chelsea, London SW3 6LR, UK.

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http://dx.doi.org/10.1093/ehjqcco/qcw058DOI Listing
April 2017

Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale.

Gigascience 2015 24;4:64. Epub 2015 Dec 24.

BGI-Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen N, Denmark ; Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.

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https://academic.oup.com/gigascience/article-lookup/doi/10.1
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http://dx.doi.org/10.1186/s13742-015-0103-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690232PMC
July 2016

Transcriptome dynamics of the microRNA inhibition response.

Nucleic Acids Res 2016 05 9;44(9):4486. Epub 2016 Feb 9.

The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671

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http://dx.doi.org/10.1093/nar/gkw091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872088PMC
May 2016

Fast and sensitive taxonomic classification for metagenomics with Kaiju.

Nat Commun 2016 Apr 13;7:11257. Epub 2016 Apr 13.

Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark.

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http://dx.doi.org/10.1038/ncomms11257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833860PMC
April 2016

Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs.

Environ Microbiol 2016 Mar 21;18(3):863-74. Epub 2015 Dec 21.

Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, DK-2200, Denmark.

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http://doi.wiley.com/10.1111/1462-2920.13079
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http://dx.doi.org/10.1111/1462-2920.13079DOI Listing
March 2016

Bayesian transcriptome assembly.

Genome Biol 2014 ;15(10):501

The Bioinformatics Centre, Department of Biology and Biotech Research andInnovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.

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http://dx.doi.org/10.1186/s13059-014-0501-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4397945PMC
October 2015

Transcriptome dynamics of the microRNA inhibition response.

Nucleic Acids Res 2015 07 18;43(13):6207-21. Epub 2015 Jun 18.

The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671

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http://dx.doi.org/10.1093/nar/gkv603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513874PMC
July 2015

De novo assembly of a haplotype-resolved human genome.

Nat Biotechnol 2015 Jun 25;33(6):617-22. Epub 2015 May 25.

1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia. [4] Macau University of Science and Technology, Taipa, Macau, China. [5] Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China.

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http://dx.doi.org/10.1038/nbt.3200DOI Listing
June 2015

Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation.

Genome Biol 2015 Jun 9;16:123. Epub 2015 Jun 9.

Department of Biology, Center for Computational and Applied Transcriptomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark.

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http://dx.doi.org/10.1186/s13059-015-0687-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477473PMC
June 2015

SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data.

RNA 2015 May 24;21(5):1042-52. Epub 2015 Mar 24.

Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1261/rna.047068.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408784PMC
May 2015

SNPest: a probabilistic graphical model for estimating genotypes.

BMC Res Notes 2014 Oct 7;7:698. Epub 2014 Oct 7.

Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaloes Vej, 2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1756-0500-7-698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203901PMC
October 2014

Adaptable probabilistic mapping of short reads using position specific scoring matrices.

BMC Bioinformatics 2014 Apr 9;15:100. Epub 2014 Apr 9.

Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1471-2105-15-100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021105PMC
April 2014

Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors.

Front Endocrinol (Lausanne) 2014 15;5:46. Epub 2014 Apr 15.

Center for Genomic Medicine, Rigshospitalet, University of Copenhagen , Copenhagen , Denmark.

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http://dx.doi.org/10.3389/fendo.2014.00046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995063PMC
April 2014

On the accuracy of short read mapping.

Methods Mol Biol 2013 ;1038:39-59

Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1007/978-1-62703-514-9_3DOI Listing
February 2014

Alterations in polyadenylation and its implications for endocrine disease.

Front Endocrinol (Lausanne) 2013 8;4:53. Epub 2013 May 8.

Genomic Medicine, Rigshospitalet, Copenhagen University Hospital Copenhagen, Denmark.

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http://dx.doi.org/10.3389/fendo.2013.00053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3647115PMC
May 2013

cWords - systematic microRNA regulatory motif discovery from mRNA expression data.

Silence 2013 May 20;4(1). Epub 2013 May 20.

Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark.

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http://dx.doi.org/10.1186/1758-907X-4-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682869PMC
May 2013

MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells.

BMC Cancer 2012 Jun 12;12:232. Epub 2012 Jun 12.

Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, DK-2200, Copenhagen N, Denmark.

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http://dx.doi.org/10.1186/1471-2407-12-232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3480834PMC
June 2012

Improving ancient DNA read mapping against modern reference genomes.

BMC Genomics 2012 May 10;13:178. Epub 2012 May 10.

Centre for GeoGenetics; Natural History Museum of Denmark, University of Copenhagen, 5-7 Øster Voldgade, 1350, Kobenhavns K, Denmark.

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http://dx.doi.org/10.1186/1471-2164-13-178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468387PMC
May 2012

Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns.

Genome Biol 2012 May 24;13(5):R35. Epub 2012 May 24.

The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1186/gb-2012-13-5-r35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446288PMC
May 2012

microRNA-101 is a potent inhibitor of autophagy.

EMBO J 2011 Sep 13;30(22):4628-41. Epub 2011 Sep 13.

Biotech Research and Innovation Centre, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1038/emboj.2011.331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243595PMC
September 2011

MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action.

RNA 2011 May 9;17(5):820-34. Epub 2011 Mar 9.

The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.

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http://dx.doi.org/10.1261/rna.2387911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078732PMC
May 2011

miR-449 inhibits cell proliferation and is down-regulated in gastric cancer.

Mol Cancer 2011 Mar 18;10:29. Epub 2011 Mar 18.

BRIC-Biotech Research & Innovation Centre and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1476-4598-10-29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070685PMC
March 2011

Signatures of RNA binding proteins globally coupled to effective microRNA target sites.

Genome Res 2010 Aug 27;20(8):1010-9. Epub 2010 May 27.

The Bioinformatics Centre, Department of Biology, and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen 2200, Denmark.

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http://dx.doi.org/10.1101/gr.103259.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909566PMC
August 2010

miRMaid: a unified programming interface for microRNA data resources.

BMC Bioinformatics 2010 Jan 14;11:29. Epub 2010 Jan 14.

The Bioinformatics Centre, Department of biology, University of Copenhagen, 2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1186/1471-2105-11-29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831003PMC
January 2010

MicroRNA-145 targets YES and STAT1 in colon cancer cells.

PLoS One 2010 Jan 21;5(1):e8836. Epub 2010 Jan 21.

Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark.

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http://www.bric.ku.dk/staff/?pure=files%2F44137612%2FMicroRN
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http://dx.plos.org/10.1371/journal.pone.0008836
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008836PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2809101PMC
January 2010

CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information.

Bioinformatics 2009 Nov 10;25(21):2757-63. Epub 2009 Sep 10.

Biocomputing Group, Department of Biology, University of Bologna, 40126 Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btp539DOI Listing
November 2009

Discovery of regulatory elements is improved by a discriminatory approach.

PLoS Comput Biol 2009 Nov 13;5(11):e1000562. Epub 2009 Nov 13.

The Bioinformatics Centre, Department of Biology and the Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.1000562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770120PMC
November 2009

Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing.

BMC Med Genomics 2009 Jun 9;2:35. Epub 2009 Jun 9.

The Bioinformatics Centre, Department of biology, University of Copenhagen, 2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1186/1755-8794-2-35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702338PMC
June 2009

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

BayesMD: flexible biological modeling for motif discovery.

J Comput Biol 2008 Dec;15(10):1347-63

Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1089/cmb.2007.0176DOI Listing
December 2008

Modeling promoter grammars with evolving hidden Markov models.

Bioinformatics 2008 Aug 5;24(15):1669-75. Epub 2008 Jun 5.

The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btn254DOI Listing
August 2008

A generative, probabilistic model of local protein structure.

Proc Natl Acad Sci U S A 2008 Jul 25;105(26):8932-7. Epub 2008 Jun 25.

Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1073/pnas.0801715105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2440424PMC
July 2008

Hidden Markov Models for prediction of protein features.

Methods Mol Biol 2008 ;413:173-98

Department of Biology, Rensselaer Polytechnic Institute, Troy, NY, USA.

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http://dx.doi.org/10.1007/978-1-59745-574-9_7DOI Listing
June 2008

What are artificial neural networks?

Authors:
Anders Krogh

Nat Biotechnol 2008 Feb;26(2):195-7

Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark.

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http://www.nature.com/articles/nbt1386
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http://dx.doi.org/10.1038/nbt1386DOI Listing
February 2008

Asap: a framework for over-representation statistics for transcription factor binding sites.

PLoS One 2008 Feb 20;3(2):e1623. Epub 2008 Feb 20.

Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001623PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2229843PMC
February 2008

Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells.

J Biol Chem 2008 Jan 8;283(2):1026-33. Epub 2007 Nov 8.

Biotech Research and Innovation Centre, Bioinformatics Centre, University of Copenhagen, DK-2200 N Copenhagen, Denmark.

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http://dx.doi.org/10.1074/jbc.M707224200DOI Listing
January 2008

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.

Nucleic Acids Res 2008 Jan 15;36(Database issue):D102-6. Epub 2007 Nov 15.

Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.

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http://dx.doi.org/10.1093/nar/gkm955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238834PMC
January 2008

A code for transcription initiation in mammalian genomes.

Genome Res 2008 Jan 21;18(1):1-12. Epub 2007 Nov 21.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.6831208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134772PMC
January 2008

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.

Bioinformatics 2007 Dec 15;23(24):3304-11. Epub 2007 Nov 15.

Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btm525DOI Listing
December 2007

Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.

PLoS Comput Biol 2007 Nov;3(11):e238

Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.0030238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2098865PMC
November 2007

An evolutionary method for learning HMM structure: prediction of protein secondary structure.

BMC Bioinformatics 2007 Sep 21;8:357. Epub 2007 Sep 21.

Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1471-2105-8-357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2072961PMC
September 2007

Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server.

Nucleic Acids Res 2007 Jul 5;35(Web Server issue):W429-32. Epub 2007 May 5.

Center for Genomics and Bioinformatics, Karolinska Institutet, S-17177 Stockholm, Sweden.

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http://dx.doi.org/10.1093/nar/gkm256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933244PMC
July 2007

Molecular composition of IMP1 ribonucleoprotein granules.

Mol Cell Proteomics 2007 May 7;6(5):798-811. Epub 2007 Feb 7.

Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1074/mcp.M600346-MCP200DOI Listing
May 2007

Novel overlapping coding sequences in Chlamydia trachomatis.

FEMS Microbiol Lett 2006 Dec 13;265(1):106-17. Epub 2006 Oct 13.

Laboratory of Infectious Diseases Immunology, Chlamydia Vaccine Unit, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark.

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https://academic.oup.com/femsle/article-lookup/doi/10.1111/j
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http://dx.doi.org/10.1111/j.1574-6968.2006.00480.xDOI Listing
December 2006

Sampling realistic protein conformations using local structural bias.

PLoS Comput Biol 2006 Sep 21;2(9):e131. Epub 2006 Aug 21.

Bioinformatics Center, Institute of Molecular Biology and Physiology, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.0020131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1570370PMC
September 2006

A hidden Markov model approach for determining expression from genomic tiling micro arrays.

BMC Bioinformatics 2006 May 3;7:239. Epub 2006 May 3.

Bioinformatics Centre, Institute of Molecular Biology and Physiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1471-2105-7-239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1481622PMC
May 2006

Automatic generation of gene finders for eukaryotic species.

BMC Bioinformatics 2006 May 21;7:263. Epub 2006 May 21.

Bioinformatics Centre, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark.

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http://dx.doi.org/10.1186/1471-2105-7-263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1522026PMC
May 2006

Large-scale prokaryotic gene prediction and comparison to genome annotation.

Bioinformatics 2005 Dec 25;21(24):4322-9. Epub 2005 Oct 25.

Bioinformatics Centre, Institute of Molecular Biology and Physiology, University of Copenhagen Universitetsparken 15, 2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bti701DOI Listing
December 2005

Computational evidence for hundreds of non-conserved plant microRNAs.

BMC Genomics 2005 Sep 13;6:119. Epub 2005 Sep 13.

Bioinformatics Centre, Institute of Molecular Biology, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1471-2164-6-119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1249568PMC
September 2005

An HMM posterior decoder for sequence feature prediction that includes homology information.

Bioinformatics 2005 Jun;21 Suppl 1:i251-7

Center for Genomics and Bioinformatics, Karolinska Institutet SE-17 177 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/bti1014DOI Listing
June 2005

Training HMM structure with genetic algorithm for biological sequence analysis.

Bioinformatics 2004 Dec 5;20(18):3613-9. Epub 2004 Aug 5.

ISIS Group, ECS, University of Southampton, SO17 1BJ, UK.

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http://dx.doi.org/10.1093/bioinformatics/bth454DOI Listing
December 2004

A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins.

Bioinformatics 2002 ;18 Suppl 1:S46-53

Laboratory of Biocomputing, CIRB/Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/18.suppl_1.s46DOI Listing
October 2004

Teaching computers to fold proteins.

Phys Rev E Stat Nonlin Soft Matter Phys 2004 Sep 27;70(3 Pt 1):030903. Epub 2004 Sep 27.

Center for Biological Sequence Analysis, The Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark.

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https://link.aps.org/doi/10.1103/PhysRevE.70.030903
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http://dx.doi.org/10.1103/PhysRevE.70.030903DOI Listing
September 2004

A combined transmembrane topology and signal peptide prediction method.

J Mol Biol 2004 May;338(5):1027-36

Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17 177 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jmb.2004.03.016DOI Listing
May 2004

Prediction of lipoprotein signal peptides in Gram-negative bacteria.

Protein Sci 2003 Aug;12(8):1652-62

Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby 2800, Denmark.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323952PMC
http://dx.doi.org/10.1110/ps.0303703DOI Listing
August 2003

EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance.

BMC Bioinformatics 2003 Jun 3;4:21. Epub 2003 Jun 3.

Center for Biological Sequence Analysis BioCentrum, Technical University of Denmark Building 208, 2800 Lyngby, Denmark.

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http://dx.doi.org/10.1186/1471-2105-4-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC521197PMC
June 2003

RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.

J Mol Biol 2003 Mar;326(5):1361-72

Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark.

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http://dx.doi.org/10.1016/s0022-2836(03)00034-2DOI Listing
March 2003

Reliability measures for membrane protein topology prediction algorithms.

J Mol Biol 2003 Mar;327(3):735-44

Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1016/s0022-2836(03)00182-7DOI Listing
March 2003

Bias of purine stretches in sequenced chromosomes.

Comput Chem 2002 Jul;26(5):531-41

Department of Biotechnology, Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby.

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July 2002