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Author Details

Liisa Holm
Institute of Biotechnology, University of Helsinki
1986
144
65
PMIDPaper TitleJournal TitlePublished Year
36822202Fragmented habitat compensates for the adverse effects of genetic bottleneck.Curr Biol2023
37699397Global analysis of aging-related protein structural changes uncovers enzyme-polymerization-based control of longevity.Mol Cell2023
36890232The giant diploid faba genome unlocks variation in a global protein crop.Nature2023
36419248DALI shines a light on remote homologs: One hundred discoveries.Protein Sci2023
34562305PANNZER-A practical tool for protein function prediction.Protein Sci2022
35679225Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.PLoS Comput Biol2022
35610055Dali server: structural unification of protein families.Nucleic Acids Res2022
32712245Metatranscriptomic assessment of burn wound infection clearance.Clin Microbiol Infect2021
31606894DALI and the persistence of protein shape.Protein Sci2020
32006276Using Dali for Protein Structure Comparison.Methods Mol Biol2020
33408878Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types.Virus Evol2020
32583859Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study.Biosci Rep2020
31263867Benchmarking fold detection by DaliLite v.5.Bioinformatics2019
31744546The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.Genome Biol2019
31682632Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.PLoS Comput Biol2019
29762724AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination.Nucleic Acids Res2018
29976145BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing.BMC Bioinformatics2018
30064374TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases.BMC Bioinformatics2018
30564397Bracketing phenogenotypic limits of mammalian hybridization.R Soc Open Sci2018
29701748Mlh1 deficiency in normal mouse colon mucosa associates with chromosomally unstable colon cancer.Carcinogenesis2018
29741643PANNZER2: a rapid functional annotation web server.Nucleic Acids Res2018
29276572Genome sequence of the model plant pathogen <i>Pectobacterium carotovorum</i> SCC1.Stand Genomic Sci2017
27131377Dali server update.Nucleic Acids Res2016
27938331Robust multi-group gene set analysis with few replicates.BMC Bioinformatics2016
27604469An expanded evaluation of protein function prediction methods shows an improvement in accuracy.Genome Biol2016
25653249PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.Bioinformatics2015
26331775Flight-induced changes in gene expression in the Glanville fritillary butterfly.Mol Ecol2015
26597297BluB/CobT2 fusion enzyme activity reveals mechanisms responsible for production of active form of vitamin B⿁⿿ by Propionibacterium freudenreichii.Microb Cell Fact2015
25855811SANSparallel: interactive homology search against Uniprot.Nucleic Acids Res2015
24288371Pfam: the protein families database.Nucleic Acids Res2014
25480015Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis.BMC Genomics2014
25199204Reply to Sasso et al.: Distribution and phylogeny of nonribosomal peptide and polyketide biosynthetic pathways in eukaryotes.Proc Natl Acad Sci U S A2014
25189940The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.Nat Commun2014
24988207Transcriptome analysis reveals signature of adaptation to landscape fragmentation.PLoS One2014
25014494Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains.J Proteome Res2014
24903419Gene set analysis: limitations in popular existing methods and proposed improvements.Bioinformatics2014
24927540Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes.Proc Natl Acad Sci U S A2014
24516375Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.PLoS Comput Biol2014
23353650A large-scale evaluation of computational protein function prediction.Nat Methods2013
23815736Defense-related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis.New Phytol2013
23927037GOParGenPy: a high throughput method to generate gene ontology data matrices.BMC Bioinformatics2013
21630267Integrin targeted oncolytic adenoviruses Ad5-D24-RGD and Ad5-RGD-D24-GMCSF for treatment of patients with advanced chemotherapy refractory solid tumors.Int J Cancer2012
22962464SANS: high-throughput retrieval of protein sequences allowing 50% mismatches.Bioinformatics2012
23045508Genome sequence of Pectobacterium sp. strain SCC3193.J Bacteriol2012
23133391Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193.PLoS Pathog2012
22808531Mutational analysis of positively charged amino acid residues of Uukuniemi phlebovirus nucleocapsid protein.Virus Res2012
22828500An oncolytic adenovirus enhanced for toll-like receptor 9 stimulation increases antitumor immune responses and tumor clearance.Mol Ther2012
22540977Comprehensive comparison of graph based multiple protein sequence alignment strategies.BMC Bioinformatics2012
22581703Mismatch repair analysis of inherited MSH2 and/or MSH6 variation pairs found in cancer patients.Hum Mutat2012
22335941BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins.BMC Bioinformatics2012
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Collaborators

Chris Sander
Broad Institute of MIT and Harvard
Co-authored papers 32
Petri T??r??nen
Institute of Biotechnology, University of Helsinki
Co-authored papers 24
Pekka Koskinen
University of Helsinki and Helsinki University Hospital
Co-authored papers 14
Alan Medlar
Institute of Biotechnology, University of Helsinki
Co-authored papers 6
Prajwal Bhat
Royal Holloway University of London
Co-authored papers 3
Marco Falda
University of Padova
Co-authored papers 3
Erik L L Sonnhammer
Stockholm University
Co-authored papers 3
Alex Bateman
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 3
Alfonso E Romero
University of Miami
Co-authored papers 3
Enrico Lavezzo
University of Padova
Co-authored papers 3
Robert D Finn
European Bioinformatics Institute
Co-authored papers 3
Paolo Fontana
San Pio Hospital
Co-authored papers 3
Predrag Radivojac
Indiana University
Co-authored papers 3
Jaina Mistry
Co-authored papers 3
Fran Supek
Catalan Institution for Research and Advanced Studies (ICREA)
Co-authored papers 3
Haixuan Yang
University of Galway
Co-authored papers 3
Sean D Mooney
University of Washington
Co-authored papers 3
Hai Fang
University of Bristol
Co-authored papers 3
Stefano Toppo
University of Padova
Co-authored papers 3
John Tate
Co-authored papers 3
Patricia C Babbitt
University of California san francisco
Co-authored papers 3
Asa Ben-Hur
Colorado State University
Co-authored papers 3
Michal Linial
Institute of Life Sciences, The Hebrew University of Jerusalem
Co-authored papers 3
Daisuke Kihara
Purdue University
Co-authored papers 3
Iddo Friedberg
Iowa State University
Co-authored papers 3
David T Jones
University College London
Co-authored papers 3
Steven E Brenner
University of California berkeley
Co-authored papers 3
Rita Casadio
Department of Pharmacy and Biotechnology, University of Bologna
Co-authored papers 3
Burkhard Rost
Technical University of Munich (TUM)
Co-authored papers 3
Domenico Cozzetto
Imperial College London
Co-authored papers 3
Release 1.2