Erik L. Sonnhammer: search on Z-Library

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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

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

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

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

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

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

7

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

8

Optimal Sparsity Criteria for Network Inference

Tjärnberg, Andreas, Nordling, Torbjörn E.M., Studham, Matthew, Sonnhammer, Erik L.L.

Journal:

Journal of Computational Biology

Year:

2013

Language:

english

File:

PDF, 925 KB

english, 2013

9

MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

Friedrich, Stefanie, Barbulescu, Remus, Helleday, Thomas, Sonnhammer, Erik L. L.

Journal:

BMC Medical Genomics

Year:

2020

File:

PDF, 1.20 MB

2020

10

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

11

Overview and comparison of ortholog databases

Andrey Alexeyenko, Julia Lindberg, Åsa Pérez-Bercoff, Erik L.L. Sonnhammer

Journal:

Drug Discovery Today: Technologies

Year:

2006

Language:

english

File:

PDF, 213 KB

english, 2006

12

A genome-wide IR-induced RAD51 foci RNAi screen identifies CDC73 involved in chromatin remodeling for DNA repair

Herr, Patrick, Lundin, Cecilia, Evers, Bastiaan, Ebner, Daniel, Bauerschmidt, Christina, Kingham, Guy, Palmai-Pallag, Timea, Mortusewicz, Oliver, Frings, Oliver, Sonnhammer, Erik, Helleday, Thomas

Journal:

Year:

2015

Language:

english

File:

PDF, 4.18 MB

english, 2015

13

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

14

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

15

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

16

GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties

Tjärnberg, Andreas, Morgan, Daniel C., Studham, Matthew, Nordling, Torbjörn E. M., Sonnhammer, Erik L. L.

Journal:

Molecular BioSystems

Year:

2017

Language:

english

File:

PDF, 4.30 MB

english, 2017

17

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

18

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

19

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

20

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

21

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

22

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

23

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

24

MGclus: network clustering employing shared neighbors

Frings, Oliver, Alexeyenko, Andrey, Sonnhammer, Erik L. L.

Journal:

Molecular BioSystems

Year:

2013

Language:

english

File:

PDF, 1.59 MB

english, 2013

25

HieranoiDB: a database of orthologs inferred by Hieranoid

Kaduk, Mateusz, Riegler, Christian, Lemp, Oliver, Sonnhammer, Erik L. L.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 600 KB

english, 2016

26

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

27

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

28

Comparison of the Human Germline and Rearranged VH Repertoire Reveals Complementarity between Germline Variability and Somatic Mutation

GERALD WALTER, IAN M. TOMLINSON, PAUL H. DEAR, ERIK L. L. SONNHAMMER, GRAHAM P. COOK, GREG WINTER

Journal:

Annals of the New York Academy of Sciences

Year:

1995

Language:

english

File:

PDF, 141 KB

english, 1995

29

Avoiding pitfalls in gene (co)expression meta-analysis

Östlund, Gabriel, Sonnhammer, Erik L.L.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.28 MB

english, 2014

30

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

Kutsenko, Alexey, Svensson, Thomas, Nystedt, Björn, Lundeberg, Joakim, Björk, Petra, Sonnhammer, Erik, Giacomello, Stefania, Visa, Neus, Wieslander, Lars

Journal:

Year:

2014

Language:

english

File:

PDF, 1.93 MB

english, 2014

31

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

32

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

33

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

34

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

35

Hieranoid: Hierarchical Orthology Inference

Schreiber, Fabian, Sonnhammer, Erik L.L.

Journal:

Journal of Molecular Biology

Year:

2013

Language:

english

File:

PDF, 620 KB

english, 2013

36

PathwAX: a web server for network crosstalk based pathway annotation

Ogris, Christoph, Helleday, Thomas, Sonnhammer, Erik L.L.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 549 KB

english, 2016

37

Pathway-specific model estimation for improved pathway annotation by network crosstalk

Castresana-Aguirre, Miguel, Sonnhammer, Erik L. L.

Journal:

Scientific Reports

Year:

2020

File:

PDF, 3.18 MB

2020

38

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

39

Orthology confers intron position conservation

Anna Henricson, Kristoffer Forslund, Erik LL Sonnhammer

Journal:

Year:

2010

Language:

english

File:

PDF, 1.71 MB

english, 2010

40

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

41

Genome informatics: taming the avalanche of genomic data

Erik LL Sonnhammer

Journal:

Year:

2005

Language:

english

File:

PDF, 50 KB

english, 2005

42

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

43

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

44

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

45

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

46

A novel ACKR2-dependent role of fibroblast-derived CXCL14 in epithelial-to-mesenchymal transition and metastasis of breast cancer

Sjöberg, Elin, Meyrath, Max, Milde, Laura, Herrera, Mercedes, Lövrot, John, Hägerstrand, Daniel, Frings, Oliver, Bartish, Margarita, Rolny, Charlotte, Sonnhammer, Erik, Chevigné, Andy, Augsten, Martin

Journal:

Clinical Cancer Research

Year:

2019

Language:

english

File:

PDF, 2.80 MB

english, 2019

47

Experimental validation of predicted cancer genes using FRET

Guala, Dimitri, Bernhem, Kristoffer, Ait Blal, Hammou, Jans, Daniel, Lundberg, Emma, Brismar, Hjalmar, Sonnhammer, Erik L L

Journal:

Methods and Applications in Fluorescence

Year:

2018

Language:

english

File:

PDF, 1.24 MB

english, 2018

48

Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks

McCormack, Theodore, Frings, Oliver, Alexeyenko, Andrey, Sonnhammer, Erik L. L., Ouzounis, Christos A.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.09 MB

english, 2013

49

A large-scale benchmark of gene prioritization methods

Guala, Dimitri, Sonnhammer, Erik L. L.

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 820 KB

english, 2017

50

Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms

Morgan, Daniel, Studham, Matthew, TjÃ¤rnberg, Andreas, Weishaupt, Holger, Swartling, Fredrik J., Nordling, TorbjÃ¶rn E. M., Sonnhammer, Erik L. L.

Journal:

Scientific Reports

Year:

2020

File:

PDF, 1.83 MB

2020

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