Publications by authors named "Olof Emanuelsson"

27Publications

Detecting sequence signals in targeting peptides using deep learning.

Life Sci Alliance 2019 10 30;2(5). Epub 2019 Sep 30.

Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongen Lyngby, Denmark

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http://dx.doi.org/10.26508/lsa.201900429DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769257PMC
October 2019

Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana.

Nucleic Acids Res 2017 04;45(6):3253-3265

Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Solna SE-171 65, Sweden.

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http://dx.doi.org/10.1093/nar/gkx087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389543PMC
April 2017

GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information.

Sci Rep 2016 Feb 18;6:21134. Epub 2016 Feb 18.

KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, SE-171 65, Solna, Sweden.

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http://dx.doi.org/10.1038/srep21134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758070PMC
February 2016

Nuclease-assisted suppression of human DNA background in sepsis.

PLoS One 2014 30;9(7):e103610. Epub 2014 Jul 30.

Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden; Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden; Karolinska University Hospital, Department of Clinical Microbiology, Stockholm, Sweden.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103610PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116218PMC
November 2015

Analysis of stranded information using an automated procedure for strand specific RNA sequencing.

BMC Genomics 2014 Jul 28;15:631. Epub 2014 Jul 28.

Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Tomtebodavägen 23A, 17165 Solna, Stockholm, Sweden.

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http://dx.doi.org/10.1186/1471-2164-15-631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247151PMC
July 2014

Sequencing degraded RNA addressed by 3' tag counting.

PLoS One 2014 14;9(3):e91851. Epub 2014 Mar 14.

Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Solna, Sweden.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091851PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954844PMC
November 2014

The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.

Nucleic Acids Res 2014 Mar 24;42(5):3330-45. Epub 2013 Dec 24.

Ribogenetics@Biochemistry Lab, School of Engineering and Science, Molecular Life Sciences Research Center, Jacobs University Bremen, Campus Ring 1, DE-28759 Bremen, Germany, Abteilung Genetik, Universität Kassel, Heinrich-Plett-Strasse 40, DE-34132 Kassel, Germany, Friedrich-Schiller-Universität Jena, Institut für Pharmazie, Lehrstuhl für Pharmazeutische Biologie, Semmelweisstraße 10, DE-07743 Jena, Germany, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, SE-171 65 Solna, Sweden, Garvan Institute of Medical Research, 384 Victoria St Darlinghurst, NSW 2010, Australia, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, PO Box 596, S-75124 Uppsala, Sweden and Science for Life Laboratory, SE-75124 Uppsala, Sweden.

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http://dx.doi.org/10.1093/nar/gkt1337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950715PMC
March 2014

Hereditary uveal melanoma: a report of a germline mutation in BAP1.

Genes Chromosomes Cancer 2013 Apr 23;52(4):378-84. Epub 2013 Jan 23.

Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Solna, Stockholm, Sweden.

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http://dx.doi.org/10.1002/gcc.22035DOI Listing
April 2013

Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor.

Plant Physiol 2013 Feb 7;161(2):813-23. Epub 2012 Dec 7.

Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden.

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http://dx.doi.org/10.1104/pp.112.207746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561021PMC
February 2013

Analysis of transcript and protein overlap in a human osteosarcoma cell line.

BMC Genomics 2010 Dec 2;11:684. Epub 2010 Dec 2.

Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, SE-171 65 Solna, Sweden.

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http://dx.doi.org/10.1186/1471-2164-11-684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014981PMC
December 2010

In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.

PLoS One 2010 Mar 25;5(3):e9762. Epub 2010 Mar 25.

Division of Gene Technology, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009762PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845605PMC
March 2010

Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.

PLoS One 2008 Apr 23;3(4):e1994. Epub 2008 Apr 23.

Department of Plant Biology, Cornell University, Ithaca, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001994PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2291561PMC
April 2008

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

What is a gene, post-ENCODE? History and updated definition.

Genome Res 2007 Jun;17(6):669-81

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA.

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http://dx.doi.org/10.1101/gr.6339607DOI Listing
June 2007

Locating proteins in the cell using TargetP, SignalP and related tools.

Nat Protoc 2007 ;2(4):953-71

Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1038/nprot.2007.131DOI Listing
June 2007

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.

Methods Enzymol 2006 ;411:282-311

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1016/S0076-6879(06)11015-0DOI Listing
December 2006

Design optimization methods for genomic DNA tiling arrays.

Genome Res 2006 Feb 19;16(2):271-81. Epub 2005 Dec 19.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CN 06520, USA. P50 HG02357

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http://dx.doi.org/10.1101/gr.4452906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1361723PMC
February 2006

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.

Proc Natl Acad Sci U S A 2004 Dec 10;101(51):17771-6. Epub 2004 Dec 10.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.

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http://dx.doi.org/10.1073/pnas.0408170101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539744PMC
December 2004

Analysis of curated and predicted plastid subproteomes of Arabidopsis. Subcellular compartmentalization leads to distinctive proteome properties.

Plant Physiol 2004 Jun;135(2):723-34

Computational Biology Service Unit, Cornell Theory Center, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1104/pp.104.040717DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC514110PMC
June 2004

LumenP--a neural network predictor for protein localization in the thylakoid lumen.

Protein Sci 2003 Oct;12(10):2360-6

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2366911PMC
http://dx.doi.org/10.1110/ps.0306003DOI Listing
October 2003

In silico prediction of the peroxisomal proteome in fungi, plants and animals.

J Mol Biol 2003 Jul;330(2):443-56

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

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http://dx.doi.org/10.1016/s0022-2836(03)00553-9DOI Listing
July 2003

Predicting protein subcellular localisation from amino acid sequence information.

Authors:
Olof Emanuelsson

Brief Bioinform 2002 Dec;3(4):361-76

Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1093/bib/3.4.361DOI Listing
December 2002