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1

Discovering viral genomes in human metagenomic data by predicting unknown protein families

Barrientos-Somarribas, Mauricio, Messina, David N., Pou, Christian, Lysholm, Fredrik, Bjerkner, Annelie, Allander, Tobias, Andersson, Björn, Sonnhammer, Erik L. L.

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 3.84 MB

english, 2018

2

Pfam: A comprehensive database of protein domain families based on seed alignments

Erik L.L. Sonnhammer, Sean R. Eddy, Richard Durbin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 761 KB

english, 1997

3

Predicting transmembrane protein topology with a hidden markov model: application to complete genomes

Anders Krogh, Björn Larsson, Gunnar von Heijne, Erik L.L Sonnhammer

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 980 KB

english, 2001

4

TreeDom - a graphical web tool for analysing domain architecture evolution

Haider, Christian, Kavic, Marina, Sonnhammer, Erik L.L.

Journal:

Year:

2016

Language:

english

File:

PDF, 342 KB

english, 2016

5

The Pfam protein families database in 2019

El-Gebali, Sara, Mistry, Jaina, Bateman, Alex, Eddy, Sean R, Luciani, Aurélien, Potter, Simon C, Qureshi, Matloob, Richardson, Lorna J, Salazar, Gustavo A, Smart, Alfredo, Sonnhammer, Erik L L, Hirsh,

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 818 KB

english, 2018

6

Putative regulatory domains in the human and mouse CVADR genes

Björn Andersson, Richard P. Tomko, Kimberly Edwards, Momina Mirza, Hamid Darban, Delal Öncü, Erik Sonnhammer, Kerstin Sollerbrant, Lennart Philipson

Journal:

Gene Function & Disease

Year:

2000

Language:

english

File:

PDF, 143 KB

english, 2000

7

Exploring the foundation of genomics: a Northern blot reference set for the comparative analysis of transcript profiling technologies

Danielle Kemmer, Margareta Faxén, Emily Hodges, Jonathan Lim, Elena Herzog, Elsebrit Ljungström, Anders Lundmark, Mary K. Olsen, Raf Podowski, Erik L. L. Sonnhammer, Peter Nilsson, Mark Reimers, Boris

Journal:

Comparative and Functional Genomics

Year:

2004

Language:

english

File:

PDF, 445 KB

english, 2004

8

OrthoDisease: A database of human disease orthologs

Kevin P. O'Brien, Isabelle Westerlund, Erik L.L. Sonnhammer

Journal:

Year:

2004

Language:

english

File:

PDF, 195 KB

english, 2004

9

Dynamic contact maps of protein structures

Erik L.L. Sonnhammer, John C. Wootton

Journal:

Journal of Molecular Graphics and Modelling

Year:

1998

Language:

english

File:

PDF, 458 KB

english, 1998

10

Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III

Peer Bork, Christos Ouzounis, Chris Sander, Michael Scharf, Reinhard Schneider, Erik Sonnhammer

Journal:

Protein Science

Year:

1992

Language:

english

File:

PDF, 1.25 MB

english, 1992

11

Modular arrangement of proteins as inferred from analysis of homology

Erik L.L. Sonnhammer, Daniel Kahn

Journal:

Protein Science

Year:

1994

Language:

english

File:

PDF, 1.70 MB

english, 1994

12

Integrated graphical analysis of protein sequence features predicted from sequence composition

Erik L.L. Sonnhammer, John C. Wootton

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 763 KB

english, 2001

13

Large-scale prediction of function shift in protein families with a focus on enzymatic function

Saraswathi Abhiman, Erik L.L. Sonnhammer

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 394 KB

english, 2005

14

Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony

Ann-Charlotte Berglund-Sonnhammer, Pär Steffansson, Matthew J. Betts, David A. Liberles

Journal:

Journal of Molecular Evolution

Year:

2006

Language:

english

File:

PDF, 545 KB

english, 2006

15

Conspicuous accumulation of transcription elongation repressor hrp130/CA150 on the intron-rich Balbiani ring 3 gene

Xin Sun, Jian Zhao, Karin Kylberg, Teresa Soop, Kevin Palka, Erik Sonnhammer, Neus Visa, Alla T. Alzhanova-Ericsson, Bertil Daneholt

Journal:

Year:

2004

Language:

english

File:

PDF, 670 KB

english, 2004

16

A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence

Anna Henricson, Lukas Käll, Erik L. L. Sonnhammer

Journal:

Year:

2005

Language:

english

File:

PDF, 265 KB

english, 2005

17

What's in a genome?

Bork, Peer, Ouzounis, Christos, Sander, Chris, Scharf, Michael, Schneider, Reinhard, Sonnhammer, Erik

Journal:

Year:

1992

File:

PDF, 148 KB

1992

18

A general model of G protein-coupled receptor sequences and its application to detect remote homologs

Markus Wistrand, Lukas Käll, Erik L.L. Sonnhammer

Journal:

Protein Science

Year:

2006

Language:

english

File:

PDF, 435 KB

english, 2006

19

Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis

Andrey Alexeyenko, A. Harvey Millar, James Whelan, Erik L.L. Sonnhammer

Journal:

Trends in Genetics

Year:

2006

Language:

english

File:

PDF, 404 KB

english, 2006

20

Orthology, paralogy and proposed classification for paralog subtypes

Erik L.L Sonnhammer, Eugene V Koonin

Journal:

Trends in Genetics

Year:

2002

Language:

english

File:

PDF, 29 KB

english, 2002

21

The C. elegans expression pattern database: a beginning

Ian A. Hope, Donna G. Albertson, Sylvia D. Martinelli, Andrew S. Lynch, Erik Sonnhammer, Richard Durbin

Journal:

Trends in Genetics

Year:

1996

Language:

english

File:

PDF, 338 KB

english, 1996

22

Widespread eukaryotic sequences, highly similar to bacterial DNA polymerase I, looking for functions

Erik L.L. Sonnhammer, John C. Wootton

Journal:

Current Biology

Year:

1997

Language:

english

File:

PDF, 880 KB

english, 1997

23

FAT: a novel domain in PIK-related kinases

Roberta Bosotti, Antonella Isacchi, Erik L.L. Sonnhammer

Journal:

Trends in Biochemical Sciences

Year:

2000

Language:

english

File:

PDF, 1.16 MB

english, 2000

24

MetaTM - a consensus method for transmembrane protein topology prediction

Martin Klammer, David N Messina, Thomas Schmitt, Erik LL Sonnhammer

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 264 KB

english, 2009

25

Domain architecture conservation in orthologs

Kristoffer Forslund, Isabella Pekkari, Erik LL Sonnhammer

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 324 KB

english, 2011

26

Profiled support vector machines for antisense oligonucleotide efficacy prediction

Gustavo Camps-Valls, Alistair M Chalk, Antonio J Serrano-López, José D Martín-Guerrero, Erik LL Sonnhammer

Journal:

BMC Bioinformatics

Year:

2004

Language:

english

File:

PDF, 307 KB

english, 2004

27

Scoredist: A simple and robust protein sequence distance estimator

Erik LL Sonnhammer, Volker Hollich

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.17 MB

english, 2005

28

Kalign – an accurate and fast multiple sequence alignment algorithm

Timo Lassmann, Erik LL Sonnhammer

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 292 KB

english, 2005

29

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER

Markus Wistrand, Erik LL Sonnhammer

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 424 KB

english, 2005

30

primetv: a viewer for reconciled trees

Bengt Sennblad, Eva Schreil, Ann-Charlotte Berglund Sonnhammer, Jens Lagergren, Lars Arvestad

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 340 KB

english, 2007

31

Automatic extraction of reliable regions from multiple sequence alignments

Timo Lassmann, Erik LL Sonnhammer

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 1023 KB

english, 2007

32

Orthology confers intron position conservation

Anna Henricson, Kristoffer Forslund, Erik LL Sonnhammer

Journal:

Year:

2010

Language:

english

File:

PDF, 1.71 MB

english, 2010

33

Functional characterization inCaenorhabditis elegansof transmembrane worm-human orthologs

Anna Henricson, Erik LL Sonnhammer, David L Baillie, Ana Vaz Gomes

Journal:

Year:

2004

Language:

english

File:

PDF, 987 KB

english, 2004

34

NovelFam3000 - Uncharacterized human protein domains conserved across model organisms

Danielle Kemmer, Raf M Podowski, David Arenillas, Jonathan Lim, Emily Hodges, Peggy Roth, Erik LL Sonnhammer, Christer Höög, Wyeth W Wasserman

Journal:

Year:

2006

Language:

english

File:

PDF, 1.06 MB

english, 2006

35

Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family

Nicolas Joannin, Saraswathi Abhiman, Erik L Sonnhammer, Mats Wahlgren

Journal:

Year:

2008

Language:

english

File:

PDF, 1.55 MB

english, 2008

36

Employing conservation of co-expression to improve functional inference

Carsten O Daub, Erik LL Sonnhammer

Journal:

BMC Systems Biology

Year:

2008

Language:

english

File:

PDF, 2.33 MB

english, 2008

37

Analysis of Protein Domain Families inCaenorhabditis elegans

Erik L.L. Sonnhammer, Richard Durbin

Journal:

Year:

1997

Language:

english

File:

PDF, 1.03 MB

english, 1997

38

The Imprint of Somatic Hypermutation on the Repertoire of Human Germline V Genes

Ian M. Tomlinson, Gerald Walter, Peter T. Jones, Paul H. Dear, Erik L.L. Sonnhammer, Greg Winter

Journal:

Journal of Molecular Biology

Year:

1996

Language:

english

File:

PDF, 536 KB

english, 1996

39

Sequence of the human immunoglobulin diversity (D) segment locus: a systematic analysis provides no evidence for the use of DIR segments, inverted D segments, “minor” D segments or D-D recombination

Simon J Corbett, Ian M Tomlinson, Erik L.L Sonnhammer, David Buck, Greg Winter

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 328 KB

english, 1997

40

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

Maido Remm, Christian E.V. Storm, Erik L.L. Sonnhammer

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 225 KB

english, 2001

41

Volume changes in protein evolution

Mark Gerstein, Erik L.L. Sonnhammer, Cyrus Chothia

Journal:

Journal of Molecular Biology

Year:

1994

Language:

english

File:

PDF, 1.09 MB

english, 1994

42

A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis

Erik L.L. Sonnhammer, Richard Durbin

Journal:

Year:

1995

Language:

english

File:

PDF, 804 KB

english, 1995

43

Improved and automated prediction of effective siRNA

Alistair M Chalk, Claes Wahlestedt, Erik L.L Sonnhammer

Journal:

Biochemical and Biophysical Research Communications

Year:

2004

Language:

english

File:

PDF, 672 KB

english, 2004

44

Focusing on RISC assembly in mammalian cells

Junmei Hong, Na Wei, Alistair Chalk, Jue Wang, Yutong Song, Fan Yi, Ren-Ping Qiao, Erik L.L. Sonnhammer, Claes Wahlestedt, Zicai Liang, Quan Du

Journal:

Biochemical and Biophysical Research Communications

Year:

2008

Language:

english

File:

PDF, 199 KB

english, 2008

45

Quality criteria for finding genes with high mRNA–protein expression correlation and coexpression correlation

Gabriel Östlund, Erik L.L. Sonnhammer

Journal:

Year:

2012

Language:

english

File:

PDF, 564 KB

english, 2012

46

Improving Profile HMM Discrimination by Adapting Transition Probabilities

Markus Wistrand, Erik L.L. Sonnhammer

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 244 KB

english, 2004

47

A Combined Transmembrane Topology and Signal Peptide Prediction Method

Lukas Käll, Anders Krogh, Erik L.L Sonnhammer

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 601 KB

english, 2004

48

Quality assessment of multiple alignment programs

Timo Lassmann, Erik L.L Sonnhammer

Journal:

Year:

2002

Language:

english

File:

PDF, 376 KB

english, 2002

49

Reliability of transmembrane predictions in whole-genome data

Lukas Käll, Erik L.L Sonnhammer

Journal:

Year:

2002

Language:

english

File:

PDF, 540 KB

english, 2002

50

Membrane topology of the Drosophila OR83b odorant receptor

Carolina Lundin, Lukas Käll, Scott A. Kreher, Katja Kapp, Erik L. Sonnhammer, John R. Carlson, Gunnar von Heijne, IngMarie Nilsson

Journal:

Year:

2007

Language:

english

File:

PDF, 519 KB

english, 2007