114(top 2%)
PR articles
24.1K(top 1%)
PR citations
53(top 1%)
PR h-index
58(top 1%)
h-index
131
documents
29.4K
doc citations
2.2K
citing journals
100
times ranked

Publications

115 peer-reviewed articles • 25,672 peer-reviewed citations • Sorted by year • Download PDF (PDF by citations)
Sort: Year | Citations
#ArticleIFCitationsLinks
13‐D substructure search by transitive closure in AlphaFold database
Protein Science, 2025, 34,
3.54Citations (PDF)
2DALI shines a light on remote homologs: One hundred discoveries
Protein Science, 2023, 32,
3.5757Citations (PDF)
3Fragmented habitat compensates for the adverse effects of genetic bottleneck
Current Biology, 2023, 33, 1009-1018.e7
2.524Citations (PDF)
4The giant diploid faba genome unlocks variation in a global protein crop
Nature, 2023, 615, 652-659
31.3161Citations (PDF)
5PANNZER—A practical tool for protein function prediction
Protein Science, 2022, 31, 118-128
3.5203Citations (PDF)
6Novel split quality measures for stratified multilabel cross validation with application to large and sparse gene ontology datasets
Applied Computing and Intelligence, 2022, 2, 49-62
1.02Citations (PDF)
7Dali server: structural unification of protein families
Nucleic Acids Research, 2022, 50, W210-W215
11.21,026Citations (PDF)
8Metatranscriptomic assessment of burn wound infection clearance
Clinical Microbiology and Infection, 2021, 27, 144-146
3.410Citations (PDF)
9DALI and the persistence of protein shape
Protein Science, 2020, 29, 128-140
3.5730Citations (PDF)
10Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types
Virus Evolution, 2020, 6,
2.252Citations (PDF)
11Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study
Bioscience Reports, 2020, 40,
2.513Citations (PDF)
12Benchmarking fold detection by DaliLite v.5
Bioinformatics, 2019, 35, 5326-5327
3.2332Citations (PDF)
13Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences
PLoS Computational Biology, 2019, 15, e1007419
1.914Citations (PDF)
14The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Genome Biology, 2019, 20,
4.8447Citations (PDF)
15Mlh1 deficiency in normal mouse colon mucosa associates with chromosomally unstable colon cancer
Carcinogenesis, 2018, 39, 788-797
2.223Citations (PDF)
16Bracketing phenogenotypic limits of mammalian hybridization
Royal Society Open Science, 2018, 5, 180903
1.634Citations (PDF)
17AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination
Nucleic Acids Research, 2018, 46, W479-W485
11.2161Citations (PDF)
18PANNZER2: a rapid functional annotation web server
Nucleic Acids Research, 2018, 46, W84-W88
11.2528Citations (PDF)
19An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Genome Biology, 2016, 17,
4.8386Citations (PDF)
20Robust multi-group gene set analysis with few replicates
BMC Bioinformatics, 2016, 17,
2.54Citations (PDF)
21Dali server update
Nucleic Acids Research, 2016, 44, W351-W355
11.2969Citations (PDF)
22BluB/CobT2 fusion enzyme activity reveals mechanisms responsible for production of active form of vitamin B12 by Propionibacterium freudenreichii
Microbial Cell Factories, 2015, 14,
3.664Citations (PDF)
23PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment
Bioinformatics, 2015, 31, 1544-1552
3.2144Citations (PDF)
24SANSparallel: interactive homology search against Uniprot
Nucleic Acids Research, 2015, 43, W24-W29
11.256Citations (PDF)
25Flight‐induced changes in gene expression in the Glanville fritillary butterfly
Molecular Ecology, 2015, 24, 4886-4900
2.233Citations (PDF)
26Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation
PLoS ONE, 2014, 9, e101467
1.527Citations (PDF)
27Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species
PLoS Computational Biology, 2014, 10, e1003465
1.992Citations (PDF)
28The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
Nature Communications, 2014, 5,
11.0224Citations (PDF)
29Reply to Sasso et al.: Distribution and phylogeny of nonribosomal peptide and polyketide biosynthetic pathways in eukaryotes
Proceedings of the National Academy of Sciences of the United States of America, 2014, 111,
5.32Citations (PDF)
30Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis
BMC Genomics, 2014, 15, 1070
2.1128Citations (PDF)
31Pfam: the protein families database
Nucleic Acids Research, 2014, 42, D222-D230
11.26,222Citations (PDF)
32Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains
Journal of Proteome Research, 2014, 13, 3748-3762
2.318Citations (PDF)
33Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes
Proceedings of the National Academy of Sciences of the United States of America, 2014, 111, 9259-9264
5.3383Citations (PDF)
34Gene set analysis: limitations in popular existing methods and proposed improvements
Bioinformatics, 2014, 30, 2747-2756
3.217Citations (PDF)
35A large-scale evaluation of computational protein function prediction
Nature Methods, 2013, 10, 221-227
13.61,011Citations (PDF)
36Genome Sequence of Dickeya solani, a New soft Rot Pathogen of Potato, Suggests its Emergence May Be Related to a Novel Combination of Non-Ribosomal Peptide/Polyketide Synthetase Clusters
Diversity, 2013, 5, 824-842
1.257Citations (PDF)
37Defense‐related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis
New Phytologist, 2013, 200, 457-472
5.3280Citations (PDF)
38Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193
PLoS Pathogens, 2012, 8, e1003013
2.9106Citations (PDF)
39SANS: high-throughput retrieval of protein sequences allowing 50% mismatches
Bioinformatics, 2012, 28, i438-i443
3.222Citations (PDF)
40Mutational analysis of positively charged amino acid residues of Uukuniemi phlebovirus nucleocapsid protein
Virus Research, 2012, 167, 118-123
2.01Citations (PDF)
41Comprehensive comparison of graph based multiple protein sequence alignment strategies
BMC Bioinformatics, 2012, 13,
2.56Citations (PDF)
42Mismatch repair analysis of inherited MSH2 and/or MSH6 variation pairs found in cancer patients
Human Mutation, 2012, 33, 1294-1301
1.014Citations (PDF)
43Adhesive polypeptides of Staphylococcus aureus identified using a novel secretion library technique in Escherichia coli
BMC Microbiology, 2011, 11,
2.97Citations (PDF)
44A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees
Bioinformatics, 2011, 27, 700-706
3.219Citations (PDF)
45MPEA—metabolite pathway enrichment analysis
Bioinformatics, 2011, 27, 1878-1879
3.297Citations (PDF)
46Inferring the physical connectivity of complex networks from their functional dynamics
BMC Systems Biology, 2010, 4,
2.87Citations (PDF)
47Oligomerization of Uukuniemi virus nucleocapsid protein
Virology Journal, 2010, 7,
2.218Citations (PDF)
48Dali server: conservation mapping in 3D
Nucleic Acids Research, 2010, 38, W545-W549
11.23,635Citations (PDF)
49LOCP—locating pilus operons in Gram-positive bacteria
Bioinformatics, 2009, 25, 1187-1188
3.29Citations (PDF)
50Advances and pitfalls of protein structural alignment
Current Opinion in Structural Biology, 2009, 19, 341-348
4.8350Citations (PDF)
51Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function
BMC Bioinformatics, 2009, 10,
2.540Citations (PDF)
52Evaluation of different domain-based methods in protein interaction prediction
Biochemical and Biophysical Research Communications, 2009, 390, 357-362
1.526Citations (PDF)
53Searching protein structure databases with DaliLite v.3
Bioinformatics, 2008, 24, 2780-2781
3.2971Citations (PDF)
54PairsDB atlas of protein sequence space
Nucleic Acids Research, 2008, 36, D276-D280
11.213Citations (PDF)
55The global trace graph, a novel paradigm for searching protein sequence databases
Bioinformatics, 2007, 23, 2361-2367
3.220Citations (PDF)
56Loss of neurturin in frog—Comparative genomics study of GDNF family ligand-receptor pairs
Molecular and Cellular Neurosciences, 2007, 34, 155-167
2.229Citations (PDF)
57The RPSP: Web server for prediction of signal peptides
Polymer, 2007, 48, 5493-5496
3.419Citations (PDF)
58From sequences to a functional unit
Physiological Genomics, 2006, 25, 1-8
1.41Citations (PDF)
59Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana
Nucleic Acids Research, 2006, 34, e124-e124
11.213Citations (PDF)
60POXO: a web-enabled tool series to discover transcription factor binding sites
Nucleic Acids Research, 2006, 34, W534-W540
11.210Citations (PDF)
61Oligomerization of Hantavirus Nucleocapsid Protein: Analysis of the N-Terminal Coiled-Coil Domain
Journal of Virology, 2006, 80, 9073-9081
2.430Citations (PDF)
62Bayesian search of functionally divergent protein subgroups and their function specific residues
Bioinformatics, 2006, 22, 2466-2474
3.240Citations (PDF)
63POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets
Nucleic Acids Research, 2005, 33, W427-W431
11.217Citations (PDF)
64POBO, transcription factor binding site verification with bootstrapping
Nucleic Acids Research, 2004, 32, W222-W229
11.249Citations (PDF)
65ADDA: a domain database with global coverage of the protein universe
Nucleic Acids Research, 2004, 33, D188-D191
11.239Citations (PDF)
66Accurate Detection of Very Sparse Sequence Motifs
Journal of Computational Biology, 2004, 11, 843-857
0.818Citations (PDF)
67Title is missing!
Journal of Structural and Functional Genomics, 2003, 4, 57-66
0.07Citations (PDF)
68Exhaustive Enumeration of Protein Domain Families
Journal of Molecular Biology, 2003, 328, 749-767
3.0119Citations (PDF)
69Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins
Bioinformatics, 2003, 19, i130-i137
3.241Citations (PDF)
70Unraveling protein interaction networks with near-optimal efficiency
Nature Biotechnology, 2003, 22, 98-103
20.277Citations (PDF)
71A Theoretical Model for the Regulation of Sex-lethal, a Gene That Controls Sex Determination and Dosage Compensation in Drosophila melanogaster
Genetics, 2003, 165, 1355-1384
3.322Citations (PDF)
72Automated detection of remote homology
Current Opinion in Structural Biology, 2002, 12, 362-367
4.827Citations (PDF)
73Title is missing!
2001, 8, 953-957
118Citations (PDF)
74A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3
Nucleic Acids Research, 2001, 29, 55-57
11.2172Citations (PDF)
75Generating protein interaction maps from incomplete data: application to fold assignment
Bioinformatics, 2001, 17, S149-S156
3.221Citations (PDF)
76Picasso: generating a covering set of protein family profiles
Bioinformatics, 2001, 17, 272-279
3.264Citations (PDF)
77Rapid automatic detection and alignment of repeats in protein sequences
Proteins: Structure, Function and Bioinformatics, 2000, 41, 224-237
1.9321Citations (PDF)
78Towards a covering set of protein family profiles
Progress in Biophysics and Molecular Biology, 2000, 73, 321-337
2.948Citations (PDF)
79Estimating the significance of sequence order in protein secondary structure and prediction
Bioinformatics, 2000, 16, 978-987
3.28Citations (PDF)
80Sequence search algorithm assessment and testing toolkit (SAT)
Bioinformatics, 2000, 16, 104-110
3.29Citations (PDF)
81DaliLite workbench for protein structure comparison
Bioinformatics, 2000, 16, 566-567
3.2833Citations (PDF)
82RSDB: representative protein sequence databases have high information content
Bioinformatics, 2000, 16, 458-464
3.237Citations (PDF)
83Protein folds and families: sequence and structure alignments
Nucleic Acids Research, 1999, 27, 244-247
11.2201Citations (PDF)
84Dictionary of recurrent domains in protein structures
1998, 33, 88-96
166Citations (PDF)
85Unification of protein families
Current Opinion in Structural Biology, 1998, 8, 372-379
4.850Citations (PDF)
86Touring protein fold space with Dali/FSSP
Nucleic Acids Research, 1998, 26, 316-319
11.2615Citations (PDF)
87COFFEE: an objective function for multiple sequence alignments
Bioinformatics, 1998, 14, 407-422
3.2211Citations (PDF)
88Removing near-neighbour redundancy from large protein sequence collections
Bioinformatics, 1998, 14, 423-429
3.2292Citations (PDF)
89Dali/FSSP classification of three-dimensional protein folds
Nucleic Acids Research, 1997, 25, 231-234
11.2421Citations (PDF)
90Enzyme HIT
Trends in Biochemical Sciences, 1997, 22, 116-117
7.421Citations (PDF)
91New structure —  novel fold?
Structure, 1997, 5, 165-171
2.566Citations (PDF)
92An evolutionary treasure: unification of a broad set of amidohydrolases related to urease
1997, 28, 72-82
462Citations (PDF)
93The FSSP database: fold classification based on structure-structure alignment of proteins
Nucleic Acids Research, 1996, 24, 206-209
11.2219Citations (PDF)
94DNA polymerase β belongs to an ancient nucleotidyltransferase superfamily
Trends in Biochemical Sciences, 1995, 20, 345-347
7.4277Citations (PDF)
95Dali: a network tool for protein structure comparison
Trends in Biochemical Sciences, 1995, 20, 478-480
7.41,475Citations (PDF)
96The cytidylyltransferase superfamily: Identification of the nucleotide-binding site and fold prediction
Proteins: Structure, Function and Bioinformatics, 1995, 22, 259-266
1.990Citations (PDF)
97Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme.
EMBO Journal, 1995, 14, 1287-1293
5.259Citations (PDF)
98LexA repressor and iron uptake regulator from Escherichia coli: new members of the CAP-like DNA binding domain superfamily
Protein Engineering, Design and Selection, 1994, 7, 1449-1453
2.236Citations (PDF)
99Searching protein structure databases has come of age
Proteins: Structure, Function and Bioinformatics, 1994, 19, 165-173
1.9243Citations (PDF)
100Parser for protein folding units
Proteins: Structure, Function and Bioinformatics, 1994, 19, 256-268
1.9230Citations (PDF)
101Three sisters, different names
Nature Structural Biology, 1994, 1, 146-147
11.032Citations (PDF)
102Structural similarity of plant chitinase and lysozymes from animals and phage
FEBS Letters, 1994, 340, 129-132
1.887Citations (PDF)
103Globin fold in a bacterial toxin
Nature, 1993, 361, 309-309
31.337Citations (PDF)
104Structural alignment of globins, phycocyanins and colicin A
FEBS Letters, 1993, 315, 301-306
1.879Citations (PDF)
105Protein Structure Comparison by Alignment of Distance Matrices
Journal of Molecular Biology, 1993, 233, 123-138
3.03,930Citations (PDF)
106Molecular dynamics simulations of hapten binding to structural models of 2-phenyloxazolone antibodies
ImmunoMethods, 1992, 1, 80-90
0.74Citations (PDF)
107Evaluation of protein models by atomic solvation preference
Journal of Molecular Biology, 1992, 225, 93-105
3.0201Citations (PDF)
108A database of protein structure families with common folding motifs
Protein Science, 1992, 1, 1691-1698
3.5195Citations (PDF)
109Fast and simple monte carlo algorithm for side chain optimization in proteins: Application to model building by homology
Proteins: Structure, Function and Bioinformatics, 1992, 14, 213-223
1.9152Citations (PDF)
110Database algorithm for generating protein backbone and side-chain co-ordinates from a Cα trace
Journal of Molecular Biology, 1991, 218, 183-194
3.0332Citations (PDF)
111Site-Directed Mutagenesis of a Thermostable α-Amylase from Bacillus stearothermophilus: Putative Role of Three Conserved Residues1
Journal of Biochemistry, 1990, 107, 267-272
1.475Citations (PDF)
112Molecular modelling study of antigen binding to oxazolone-specific antibodies: the Ox1 idiotypic IgG and its mature variant with increased affinity to 2-phenyloxazolone
Protein Engineering, Design and Selection, 1990, 3, 403-409
2.216Citations (PDF)
113Random mutagenesis used to probe the structure and function of Bacillus stearothermophilus alpha-amylase
Protein Engineering, Design and Selection, 1990, 3, 181-191
2.281Citations (PDF)
114Codon usage and gene expression
Nucleic Acids Research, 1986, 14, 3075-3087
11.2141Citations (PDF)
115Development and comparison of evaluation metrics for batch correction reveals performance differences
Bioinformatics Advances, 0, 6,
0.90Citations (PDF)