Works matching AU Holm, Liisa

Results: 77

Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1.

Published in:

Standards in Genomic Sciences, 2017, v. 12, p. 1, doi. 10.1186/s40793-017-0301-z

By:

Niemi, Outi;
Laine, Pia;
Koskinen, Patrik;
Pasanen, Miia;
Pennanen, Ville;
Harjunpää, Heidi;
Nykyri, Johanna;
Holm, Liisa;
Paulin, Lars;
Auvinen, Petri;
Palva, E. Tapio;
Pirhonen, Minna

Publication type:

Article

Unraveling protein interaction networks with near-optimal efficiency.

Published in:

Nature Biotechnology, 2004, v. 22, n. 1, p. 98, doi. 10.1038/nbt921

By:

Holm, Liisa;
Lappe, Michael

Publication type:

Article

The Pfam protein families database.

Published in:

Nucleic Acids Research, 2012, p. D290, doi. 10.1093/nar/gkr1065

By:

Punta, Marco;
Coggill, Penny C.;
Eberhardt, Ruth Y.;
Mistry, Jaina;
Tate, John;
Boursnell, Chris;
Pang, Ningze;
Forslund, Kristoffer;
Ceric, Goran;
Clements, Jody;
Heger, Andreas;
Holm, Liisa;
Sonnhammer, Erik L. L.;
Eddy, Sean R.;
Bateman, Alex;
Finn, Robert D.

Publication type:

Article

Dali server: conservation mapping in 3D.

Published in:

Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W545, doi. 10.1093/nar/gkq366

By:

Holm, Liisa;
Rosenström, Päivi

Publication type:

Article

PairsDB atlas of protein sequence space.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D276, doi. 10.1093/nar/gkm879

By:

Heger, Andreas;
Korpelainen, Eija;
Hupponen, Taavi;
Mattila, Kimmo;
Ollikainen, Vesa;
Holm, Liisa

Publication type:

Article

Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 18, p. e124, doi. 10.1093/nar/gkl694

By:

Kankainen, Matti;
Brader, Günter;
Törönen, Petri;
Palva, E. Tapio;
Holm, Liisa

Publication type:

Article

POXO: a web-enabled tool series to discover transcription factor binding sites.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 11, p. w534, doi. 10.1093/nar/gkl296

By:

Kankainen, Matti;
Pehkonen, Petri;
Rosenstöm, Päivi;
Törönen, Petri;
Wong, Garry;
Holm, Liisa

Publication type:

Article

POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 2, p. w427, doi. 10.1093/nar/gki467

By:

Kankainen, Matti;
Holm, Liisa

Publication type:

Article

ADDA: a domain database with global coverage of the protein universe.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d188

By:

Heger, Andreas;
Wilton, Christopher Andrew;
Sivakumar, Ashwin;
Holm, Liisa

Publication type:

Article

POBO, transcription factor binding site verification with bootstrapping.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w222, doi. 10.1093/nar/gkh463

By:

Kankainen, Matti;
Holm, Liisa

Publication type:

Article

Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study.

Published in:

Bioscience Reports, 2020, v. 40, n. 7, p. 1, doi. 10.1042/BSR20200596

By:

Mishra, Pashupati P.;
Hänninen, Ismo;
Raitoharju, Emma;
Marttila, Saara;
Mishra, Binisha H.;
Mononen, Nina;
KahÖnen, Mika;
Hurme, Mikko;
Raitakari, Ollix;
ToÖroÖnen, Petri;
Holm, Liisa;
Lehtimaki, Terho

Publication type:

Article

Rapid automatic detection and alignment of repeats in protein sequences.

Published in:

Proteins, 2000, v. 41, n. 2, p. 224, doi. 10.1002/1097-0134(20001101)41:2<224::AID-PROT70>3.0.CO;2-Z

By:

Heger, Andreas;
Holm, Liisa

Publication type:

Article

Dictionary of Recurrent Domains in Protein Structures

Published in:

Proteins, 1998, v. 33, n. 1, p. 88

By:

Holm, Liisa;
Sander, Chris

Publication type:

Article

An evolutionary treasure: unification of a broad set of amidohydrolases related to urease.

Published in:

Proteins, 1997, v. 28, n. 1, p. 72, doi. 10.1002/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L

By:

Holm, Liisa;
Sander, Chris

Publication type:

Article

Predicting protein structure using hidden Markov models.

Published in:

Proteins, 1997, v. 29, n. S1, p. 134, doi. 10.1002/(SICI)1097-0134(1997)1+<134::AID-PROT18>3.0.CO;2-P

By:

Karplus, Kevin;
Sjölander, Kimmen;
Barrett, Christian;
Cline, Melissa;
Haussler, David;
Hughey, Richard;
Holm, Liisa;
Sander, Chris

Publication type:

Article

The cytidylyltransferase superfamily: Identification of the nucleotide-binding site and fold prediction.

Published in:

Proteins, 1995, v. 22, n. 3, p. 259, doi. 10.1002/prot.340220306

By:

Bork, Peer;
Holm, Liisa;
Koonin, Eugene V.;
Sander, Chris

Publication type:

Article

Parser for protein folding units.

Published in:

Proteins, 1994, v. 19, n. 3, p. 256, doi. 10.1002/prot.340190309

By:

Holm, Liisa;
Sander, Chris

Publication type:

Article

Searching protein structure databases has come of age.

Published in:

Proteins, 1994, v. 19, n. 3, p. 165, doi. 10.1002/prot.340190302

By:

Holm, Liisa;
Sander, Chris

Publication type:

Article

Adhesive polypeptides of Staphylococcus aureus identified using a novel secretion library technique in Escherichia coli.

Published in:

BMC Microbiology, 2011, v. 11, n. 1, p. 117, doi. 10.1186/1471-2180-11-117

By:

Kylväjä, Riikka;
Kankainen, Matti;
Holm, Liisa;
Westerlund-Wikström, Benita

Publication type:

Article

The global trace graph, a novel paradigm for searching protein sequence databases.

Published in:

Bioinformatics, 2007, v. 23, n. 18, p. 2361, doi. 10.1093/bioinformatics/btm358

By:

Andreas Heger;
Swapan Mallick;
Christopher Wilton;
Liisa Holm

Publication type:

Article

Bayesian search of functionally divergent protein subgroups and their function specific residues.

Published in:

Bioinformatics, 2006, v. 22, n. 20, p. 2466, doi. 10.1093/bioinformatics/btl411

By:

Pekka Marttinen;
Jukka Corander;
Petri Törönen;
Liisa Holm

Publication type:

Article

PSIbase: a database of Protein Structural Interactome map (PSIMAP).

Published in:

Bioinformatics, 2005, v. 21, n. 10, p. 2541, doi. 10.1093/bioinformatics/bti366

By:

Sungsam Gong;
Giseok Yoon;
Insoo Jang;
Dan Bolser;
Panos Dafas;
Michael Schroeder;
Hansol Choi;
Yoobok Cho;
Kyungsook Han;
Sunghoon Lee;
Hwanho Choi;
Michael Lappe;
Liisa Holm;
Sangsoo Kim;
Donghoon Oh;
Jonghwa Bhak

Publication type:

Article

Generating protein interaction maps from incomplete data: application to fold assignment.

Published in:

Bioinformatics, 2001, v. 17, p. 149, doi. 10.1093/bioinformatics/17.suppl_1.s149

By:

Lappe, Michael;
Park, Jong;
Niggemann, Oliver;
Holm, Liisa

Publication type:

Article

Picasso: generating a covering set of protein family profiles.

Published in:

Bioinformatics, 2001, v. 17, n. 3, p. 272, doi. 10.1093/bioinformatics/17.3.272

By:

Heger, Andreas;
Holm, Liisa

Publication type:

Article

Estimating the significance of sequence order in protein secondary structure and prediction.

Published in:

Bioinformatics, 2000, v. 16, n. 11, p. 978, doi. 10.1093/bioinformatics/16.11.978

By:

Park, Jong;
Dietmann, Sabine;
Heger, Andreas;
Holm, Liisa

Publication type:

Article

DaliLite workbench for protein structure comparison.

Published in:

Bioinformatics, 2000, v. 16, n. 6, p. 566, doi. 10.1093/bioinformatics/16.6.566

By:

Holm, Liisa;
Park, Jong

Publication type:

Article

RSDB: representative protein sequence databases have high information content.

Published in:

Bioinformatics, 2000, v. 16, n. 5, p. 458, doi. 10.1093/bioinformatics/16.5.458

By:

Park, Jong;
Holm, Liisa;
Heger, Andreas;
Chothia, Cyrus

Publication type:

Article

Sequence search algorithm assessment and testing toolkit (SAT).

Published in:

Bioinformatics, 2000, v. 12, n. 2, p. 104, doi. 10.1093/bioinformatics/16.2.104

By:

Park, Jong;
Holm, Liisa;
Chothia, Cyrus

Publication type:

Article

Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.

Published in:

2022

By:

Plyusnin, Ilya;
Holm, Liisa;
Törönen, Petri

Publication type:

Correction Notice

DALI shines a light on remote homologs: One hundred discoveries.

Published in:

Protein Science: A Publication of the Protein Society, 2023, v. 32, n. 1, p. 1, doi. 10.1002/pro.4519

By:

Holm, Liisa;
Laiho, Aleksi;
Törönen, Petri;
Salgado, Marco

Publication type:

Article

PANNZER—A practical tool for protein function prediction.

Published in:

Protein Science: A Publication of the Protein Society, 2022, v. 31, n. 1, p. 118, doi. 10.1002/pro.4193

By:

Törönen, Petri;
Holm, Liisa

Publication type:

Article

DALI and the persistence of protein shape.

Published in:

Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 1, p. 128, doi. 10.1002/pro.3749

By:

Holm, Liisa

Publication type:

Article

TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2290-3

By:

Medlar, Alan;
Holm, Liisa

Publication type:

Article

BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2262-7

By:

Somervuo, Panu;
Koskinen, Patrik;
Mei, Peng;
Holm, Liisa;
Auvinen, Petri;
Paulin, Lars

Publication type:

Article

Benchmarking fold detection by DaliLite v.5.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5326, doi. 10.1093/bioinformatics/btz536

By:

Holm, Liisa

Publication type:

Article

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.

Published in:

2015

By:

Koskinen, Patrik;
Törönen, Petri;
Nokso-Koivisto, Jussi;
Holm, Liisa

Publication type:

Product Review

Gene set analysis: limitations in popular existing methods and proposed improvements.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2747, doi. 10.1093/bioinformatics/btu374

By:

Mishra, Pashupati;
Törönen, Petri;
Leino, Yrjö;
Holm, Liisa

Publication type:

Article

SANS: high-throughput retrieval of protein sequences allowing 50% mismatches.

Published in:

Bioinformatics, 2012, v. 28, n. 18, p. i438, doi. 10.1093/bioinformatics/bts417

By:

Koskinen, J. Patrik;
Holm, Liisa

Publication type:

Article

MPEA—metabolite pathway enrichment analysis.

Published in:

Bioinformatics, 2011, v. 27, n. 13, p. 1878, doi. 10.1093/bioinformatics/btr278

By:

Kankainen, Matti;
Gopalacharyulu, Peddinti;
Holm, Liisa;
Orešič, Matej

Publication type:

Article

A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees.

Published in:

Bioinformatics, 2011, v. 27, n. 5, p. 700, doi. 10.1093/bioinformatics/btq705

By:

Ta, Hung Xuan;
Koskinen, Patrik;
Holm, Liisa

Publication type:

Article

LOCP--locating pilus operons in Gram-positive bacteria.

Published in:

Bioinformatics, 2009, v. 25, n. 9, p. 1187, doi. 10.1093/bioinformatics/btp127

By:

Ilya Plyusnin;
Liisa Holm;
Matti Kankainen

Publication type:

Article

Defense-related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis.

Published in:

New Phytologist, 2013, v. 200, n. 2, p. 457, doi. 10.1111/nph.12378

By:

Li, Jing;
Besseau, Sebastien;
Törönen, Petri;
Sipari, Nina;
Kollist, Hannes;
Holm, Liisa;
Palva, E. Tapio

Publication type:

Article

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 1, p. 55, doi. 10.1093/nar/29.1.55

By:

Dietmann, Sabine;
Park, Jong;
Notredame, Cedric;
Heger, Andreas;
Lappe, Michael;
Holm, Liisa

Publication type:

Article

Protein folds and families: sequence and structure alignments.

Published in:

Nucleic Acids Research, 1999, v. 27, n. 1, p. 244, doi. 10.1093/nar/27.1.244

By:

Holm, Liisa;
Sander, Chris

Publication type:

Article

Touring protein fold space with Dali/FSSP.

Published in:

Nucleic Acids Research, 1998, v. 26, n. 1, p. 318, doi. 10.1093/nar/26.1.316

By:

Holm, Liisa;
Sander, Chris

Publication type:

Article

Dali/FSSP classification of three-dimensional protein folds.

Published in:

Nucleic Acids Research, 1997, v. 25, n. 1, p. 231, doi. 10.1093/nar/25.1.231

By:

Holm, Liisa;
Sander, Chris

Publication type:

Article

The FSSP Database: Fold Classification Based on Structure-Structure Alignment of Proteins.

Published in:

Nucleic Acids Research, 1996, v. 24, n. 1, p. 206, doi. 10.1093/nar/24.1.206

By:

Holm, Liisa;
Sander, Chris

Publication type:

Article

Inferring the physical connectivity of complex networks from their functional dynamics.

Published in:

BMC Systems Biology, 2010, v. 4, p. 70, doi. 10.1186/1752-0509-4-70

By:

Hung Xuan Ta;
Chang No Yoon;
Holm, Liisa;
Seung Kee Han

Publication type:

Article

Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis.

Published in:

BMC Genomics, 2014, v. 15, n. 1, p. 311, doi. 10.1186/1471-2164-15-1070

By:

Ojala, Teija;
Kankainen, Matti;
Castro, Joana;
Cerca, Nuno;
Edelman, Sanna;
Westerlund-Wikström, Benita;
Paulin, Lars;
Holm, Liisa;
Auvinen, Petri

Publication type:

Article

Robust multi-group gene set analysis with few replicates.

Published in:

BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1403-0

By:

Mishra, Pashupati P.;
Medlar, Alan;
Holm, Liisa;
Törönen, Petri

Publication type:

Article