Works by Holm, Liisa

Results: 77

3‐D substructure search by transitive closure in AlphaFold database.

Published in:

Protein Science: A Publication of the Protein Society, 2025, v. 34, n. 6, p. 1, doi. 10.1002/pro.70169

By:

Liu, Hao;
Laiho, Aleksi;
Törönen, Petri;
Holm, Liisa

Publication type:

Article

Mismatch repair analysis of inherited MSH2 and/or MSH6 variation pairs found in cancer patients.

Published in:

Human Mutation, 2012, v. 33, n. 8, p. 1294, doi. 10.1002/humu.22119

By:

Kantelinen, Jukka;
Kansikas, Minttu;
Candelin, Satu;
Hampel, Heather;
Smith, Betsy;
Holm, Liisa;
Kariola, Reetta;
Nyström, Minna

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

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

BluB/CobT2 fusion enzyme activity reveals mechanisms responsible for production of active form of vitamin B<sub>12</sub> by Propionibacterium freudenreichii.

Published in:

Microbial Cell Factories, 2015, v. 14, p. 1, doi. 10.1186/s12934-015-0363-9

By:

Deptula, Paulina;
Kylli, Petri;
Chamlagain, Bhawani;
Holm, Liisa;
Kostiainen, Risto;
Piironen, Vieno;
Savijoki, Kirsi;
Varmanen, Pekka

Publication type:

Article

Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193.

Published in:

PLoS Pathogens, 2012, v. 8, n. 11, p. 1, doi. 10.1371/journal.ppat.1003013

By:

Nykyri, Johanna;
Niemi, Outi;
Koskinen, Patrik;
Nokso-Koivisto, Jussi;
Pasanen, Miia;
Broberg, Martin;
Plyusnin, Ilja;
Törönen, Petri;
Holm, Liisa;
Pirhonen, Minna;
Palva, E. Tapio

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

Mlh1 deficiency in normal mouse colon mucosa associates with chromosomally unstable colon cancer.

Published in:

Carcinogenesis, 2018, v. 39, n. 6, p. 788, doi. 10.1093/carcin/bgy056

By:

Pussila, Marjaana;
Törönen, Petri;
Einarsdottir, Elisabet;
Katayama, Shintaro;
Krjutškov, Kaarel;
Holm, Liisa;
Kere, Juha;
Peltomäki, Päivi;
Mäkinen, Markus J.;
Linden, Jere;
Nyström, Minna

Publication type:

Article

In vivo and in vitro distribution of type 5 and fiber-modified oncolytic adenoviruses in human blood compartments.

Published in:

Annals of Medicine, 2011, v. 43, n. 2, p. 151, doi. 10.3109/07853890.2010.538079

By:

Escutenaire, Sophie;
Cerullo, Vincenzo;
Diaconu, Iulia;
Ahtiainen, Laura;
Hannuksela, Päivi;
Oksanen, Minna;
Haavisto, Elina;
Karioja-Kallio, Aila;
Holm, Sirkka-Liisa;
Kangasniemi, Lotta;
Ribacka, Camilla;
Kauppinen, Satu;
Joensuu, Timo;
Petteri Arstila, T.;
Pesonen, Sari;
Kanerva, Anna;
Hemminki, Akseli

Publication type:

Article

Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation.

Published in:

PLoS ONE, 2014, v. 9, n. 7, p. 1, doi. 10.1371/journal.pone.0101467

By:

Somervuo, Panu;
Kvist, Jouni;
Ikonen, Suvi;
Auvinen, Petri;
Paulin, Lars;
Koskinen, Patrik;
Holm, Liisa;
Taipale, Minna;
Duplouy, Anne;
Ruokolainen, Annukka;
Saarnio, Suvi;
Sirén, Jukka;
Kohonen, Jukka;
Corander, Jukka;
Frilander, Mikko J.;
Ahola, Virpi;
Hanski, Ilkka

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

Flight-induced changes in gene expression in the Glanville fritillary butterfly.

Published in:

Molecular Ecology, 2015, v. 24, n. 19, p. 4886, doi. 10.1111/mec.13359

By:

Kvist, Jouni;
Mattila, Anniina L. K.;
Somervuo, Panu;
Ahola, Virpi;
Koskinen, Patrik;
Paulin, Lars;
Salmela, Leena;
Fountain, Toby;
Rastas, Pasi;
Ruokolainen, Annukka;
Taipale, Minna;
Holm, Liisa;
Auvinen, Petri;
Lehtonen, Rainer;
Frilander, Mikko J.;
Hanski, Ilkka

Publication type:

Article

Oligomerization of Uukuniemi virus nucleocapsid protein.

Published in:

Virology Journal, 2010, v. 7, p. 187, doi. 10.1186/1743-422X-7-187

By:

Katz, Anna;
Freiberg, Alexander N.;
Backström, Vera;
Schulz, Axel R.;
Mateos, Angelo;
Holm, Liisa;
Pettersson, Ralf F.;
Vaheri, Antti;
Flick, Ramon;
Plyusnin, Alexander

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

A Theoretical Model for the Regulation of Sex-lethal, a Gene That Controls Sex Determination and Dosage Compensation in Drosophila melanogaster.

Published in:

Genetics, 2003, v. 165, n. 3, p. 1355, doi. 10.1093/genetics/165.3.1355

By:

Louis, Matthieu;
Holm, Liisa;
Sánchez, Lucas;
Kaufman, Marcelle

Publication type:

Article

Integrin targeted oncolytic adenoviruses Ad5-D24-RGD and Ad5-RGD-D24-GMCSF for treatment of patients with advanced chemotherapy refractory solid tumors.

Published in:

International Journal of Cancer, 2012, v. 130, n. 8, p. 1937, doi. 10.1002/ijc.26216

By:

Pesonen, Sari;
Diaconu, Iulia;
Cerullo, Vincenzo;
Escutenaire, Sophie;
Raki, Mari;
Kangasniemi, Lotta;
Nokisalmi, Petri;
Dotti, Gianpietro;
Guse, Kilian;
Laasonen, Leena;
Partanen, Kaarina;
Karli, Eerika;
Haavisto, Elina;
Oksanen, Minna;
Karioja-Kallio, Aila;
Hannuksela, Päivi;
Holm, Sirkka-Liisa;
Kauppinen, Satu;
Joensuu, Timo;
Kanerva, Anna

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

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

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

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

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

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

Identification of homology in protein structure classification.

Published in:

Nature Structural Biology, 2001, v. 8, n. 11, p. 953, doi. 10.1038/nsb1101-953

By:

Dietmann, Sabine;
Holm, Liisa

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

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

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 2, p. 1, doi. 10.1371/journal.pcbi.1003465

By:

Pitkänen, Esa;
Jouhten, Paula;
Hou, Jian;
Syed, Muhammad Fahad;
Blomberg, Peter;
Kludas, Jana;
Oja, Merja;
Holm, Liisa;
Penttilä, Merja;
Rousu, Juho;
Arvas, Mikko

Publication type:

Article

An Oncolytic Adenovirus Enhanced for Toll-like Receptor 9 Stimulation Increases Antitumor Immune Responses and Tumor Clearance.

Published in:

Molecular Therapy, 2012, v. 20, n. 11, p. 2076, doi. 10.1038/mt.2012.137

By:

Cerullo, Vincenzo;
Diaconu, Iulia;
Romano, Valentina;
Hirvinen, Mari;
Ugolini, Matteo;
Escutenaire, Sophie;
Holm, Sirkka-Liisa;
Kipar, Anja;
Kanerva, Anna;
Hemminki, Akseli

Publication type:

Article

Immunological Effects of Low-dose Cyclophosphamide in Cancer Patients Treated With Oncolytic Adenovirus.

Published in:

Molecular Therapy, 2011, v. 19, n. 9, p. 1737, doi. 10.1038/mt.2011.113

By:

Cerullo, Vincenzo;
Diaconu, Iulia;
Kangasniemi, Lotta;
Rajecki, Maria;
Escutenaire, Sophie;
Koski, Anniina;
Romano, Valentina;
Rouvinen, Noora;
Tuuminen, Tamara;
Laasonen, Leena;
Partanen, Kaarina;
Kauppinen, Satu;
Joensuu, Timo;
Oksanen, Minna;
Holm, Sirkka-Liisa;
Haavisto, Elina;
Karioja-Kallio, Aila;
Kanerva, Anna;
Pesonen, Sari;
Arstila, Petteri T

Publication type:

Article

Treatment of Cancer Patients With a Serotype 5/3 Chimeric Oncolytic Adenovirus Expressing GMCSF.

Published in:

Molecular Therapy, 2010, v. 18, n. 10, p. 1874, doi. 10.1038/mt.2010.161

By:

Koski, Anniina;
Kangasn2iemi, Lotta;
Escutenaire, Sophie;
Pesonen, Sari;
Cerullo, Vincenzo;
Diaconu, Iulia;
Nokisalmi, Petri;
Raki, Mari;
Rajecki, Maria;
Guse, Kilian;
Ranki, Tuuli;
Oksanen, Minna;
Holm, Sirkka-Liisa;
Haavisto, Elina;
Karioja-Kallio, Aila;
Laasonen, Leena;
Partanen, Kaarina;
Ugolini, Matteo;
Helminen, Andreas;
Karli, Eerika

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

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

Dali server: structural unification of protein families.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W210, doi. 10.1093/nar/gkac387

By:

Holm, Liisa

Publication type:

Article

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination.

Published in:

Nucleic Acids Research, 2018, v. 46, n. W1, p. W478, doi. 10.1093/nar/gky359

By:

Medlar, Alan J;
Törönen, Petri;
Holm, Liisa

Publication type:

Article