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77 peer-reviewed articles • 94,020 peer-reviewed citations • Sorted by year • Download PDF (PDF by citations)
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1Transcriptomic characterization of postnatal muscle maturation
DMM Disease Models and Mechanisms, 2025, 18,
2.02Citations (PDF)
2StopKB: a comprehensive knowledgebase for nonsense suppression therapies
Database: the Journal of Biological Databases and Curation, 2024, 2024,
2.72Citations (PDF)
3Graph-based machine learning model for weight prediction in protein–protein networks
BMC Bioinformatics, 2024, 25,
3.03Citations (PDF)
4De-MISTED: Image-based classification of erroneous multiple sequence alignments using convolutional neural networks
Applied Intelligence, 2023, 53, 18806-18820
2.84Citations (PDF)
5CeGAL: Redefining a Widespread Fungal-Specific Transcription Factor Family Using an In Silico Error-Tracking Approach
Journal of Fungi (Basel, Switzerland), 2023, 9, 424
3.47Citations (PDF)
6Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events
Frontiers in Bioinformatics, 2023, 3,
3.316Citations (PDF)
7Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR
Genome Biology and Evolution, 2021, 13,
2.43Citations (PDF)
8Potential role of the X circular code in the regulation of gene expression
BioSystems, 2021, 203, 104368
1.66Citations (PDF)
9Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes
BMC Bioinformatics, 2020, 21,
3.037Citations (PDF)
10MISTIC: A prediction tool to reveal disease-relevant deleterious missense variants
PLoS ONE, 2020, 15, e0236962
2.346Citations (PDF)
11Characterization of accessory genes in coronavirus genomes
Virology Journal, 2020, 17,
3.6163Citations (PDF)
12Identification of a circular code periodicity in the bacterial ribosome: origin of codon periodicity in genes?
RNA Biology, 2020, 17, 571-583
3.315Citations (PDF)
13A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms
BMC Genomics, 2020, 21,
3.391Citations (PDF)
14Optimality of circular codes versus the genetic code after frameshift errors
BioSystems, 2020, 195, 104134
1.69Citations (PDF)
15Circular code motifs in the ribosome: a missing link in the evolution of translation?
Rna, 2019, 25, 1714-1730
3.833Citations (PDF)
16BNO—An ontology for understanding the transittability of complex biomolecular networks
Web Semantics, 2019, 57, 100495
2.43Citations (PDF)
17Evolutionary conservation and functional implications of circular code motifs in eukaryotic genomes
BioSystems, 2019, 175, 57-74
1.619Citations (PDF)
18OrthoInspector 3.0: open portal for comparative genomics
Nucleic Acids Research, 2019, 47, D411-D418
15.571Citations (PDF)
19PROBE: analysis and visualization of protein block-level evolution
Bioinformatics, 2018, 34, 3390-3392
4.74Citations (PDF)
20Recessive MYPN mutations cause cap myopathy with occasional nemaline rods
Annals of Neurology, 2017, 81, 467-473
6.633Citations (PDF)
21Common and variable clinical, histological, and imaging findings of recessive RYR1-related centronuclear myopathy patients
Neuromuscular Disorders, 2017, 27, 975-985
0.744Citations (PDF)
22Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae
Life, 2017, 7, 52
2.69Citations (PDF)
23LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system
BMC Bioinformatics, 2016, 17,
3.012Citations (PDF)
24Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and Evolutionary Analyses
Nutrients, 2015, 7, 1-16
4.413Citations (PDF)
25OrthoInspector 2.0: Software and database updates
Bioinformatics, 2015, 31, 447-448
4.724Citations (PDF)
26Heterogeneous biological data integration with declarative query language
IBM Journal of Research and Development, 2014, 58, 15:1-15:12
0.55Citations (PDF)
27A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i)
BMC Bioinformatics, 2014, 15,
3.025Citations (PDF)
28SIBIS: a Bayesian model for inconsistent protein sequence estimation
Bioinformatics, 2014, 30, 2432-2439
4.78Citations (PDF)
29Functional insights into the core-TFIIH from a comparative survey
Genomics, 2013, 101, 178-186
2.819Citations (PDF)
30Knowledge Discovery in Variant Databases Using Inductive Logic Programming
Bioinformatics and Biology Insights, 2013, 7, BBI.S11184
2.26Citations (PDF)
31The Chordate Proteome History Database
Evolutionary Bioinformatics, 2012, 8,
1.35Citations (PDF)
32KD4v: comprehensible knowledge discovery system for missense variant
Nucleic Acids Research, 2012, 40, W71-W75
15.526Citations (PDF)
33EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data
Evolutionary Bioinformatics, 2012, 8,
1.34Citations (PDF)
34MSV3d: database of human MisSense variants mapped to 3D protein structure
Database: the Journal of Biological Databases and Curation, 2012, 2012, bas018-bas018
2.725Citations (PDF)
35Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism
BMC Genomics, 2012, 13,
3.338Citations (PDF)
36Controversies in modern evolutionary biology: the imperative for error detection and quality control
BMC Genomics, 2012, 13,
3.342Citations (PDF)
37A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives
PLoS ONE, 2011, 6, e18093
2.3228Citations (PDF)
38Identifying Single Copy Orthologs in Metazoa
PLoS Computational Biology, 2011, 7, e1002269
3.125Citations (PDF)
39Lessons from genome-wide studies: an integrated definition of the coactivator function of histone acetyl transferases
Epigenetics and Chromatin, 2010, 3,
3.248Citations (PDF)
40Visualization of multiple alignments, phylogenies and gene family evolution
Nature Methods, 2010, 7, S16-S25
24.677Citations (PDF)
41AQUA: automated quality improvement for multiple sequence alignments
Bioinformatics, 2010, 26, 263-265
4.756Citations (PDF)
42AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis
Nucleic Acids Research, 2010, 38, 6338-6349
15.511Citations (PDF)
43Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
Nucleic Acids Research, 2010, 38, 7353-7363
15.578Citations (PDF)
44Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods
BMC Bioinformatics, 2009, 10,
3.019Citations (PDF)
45Initial Implementation of a Comparative Data Analysis Ontology
Evolutionary Bioinformatics, 2009, 5,
1.331Citations (PDF)
46A new protein linear motif benchmark for multiple sequence alignment software
BMC Bioinformatics, 2008, 9,
3.024Citations (PDF)
47Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis
Briefings in Bioinformatics, 2008, 10, 11-23
6.616Citations (PDF)
48Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
Evolutionary Bioinformatics, 2008, 4,
1.317Citations (PDF)
49MAGOS: multiple alignment and modelling server
Bioinformatics, 2006, 22, 2164-2165
4.72Citations (PDF)
50BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
Proteins: Structure, Function and Bioinformatics, 2005, 61, 127-136
2.6370Citations (PDF)
51GOAnno: GO annotation based on multiple alignment
Bioinformatics, 2005, 21, 2095-2096
4.737Citations (PDF)
52MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences
Nucleic Acids Research, 2005, 33, 4164-4171
15.523Citations (PDF)
53Identifying sigma factors in Mycobacterium smegmatis by comparative genomic analysis
Trends in Microbiology, 2005, 13, 505-509
8.162Citations (PDF)
54LEON: multiple aLignment Evaluation Of Neighbours
Nucleic Acids Research, 2004, 32, 1298-1307
15.525Citations (PDF)
55Multiple sequence alignment with the Clustal series of programs
Nucleic Acids Research, 2003, 31, 3497-3500
15.54,379Citations (PDF)
56Multiple Sequence Alignment Using ClustalW and ClustalX
Current Protocols in Bioinformatics, 2003, 00,
3.32,243Citations (PDF)
57PipeAlign: a new toolkit for protein family analysis
Nucleic Acids Research, 2003, 31, 3829-3832
15.5113Citations (PDF)
58RASCAL: rapid scanning and correction of multiple sequence alignments
Bioinformatics, 2003, 19, 1155-1161
4.7132Citations (PDF)
59BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations
Nucleic Acids Research, 2001, 29, 323-326
15.5159Citations (PDF)
60Towards a reliable objective function for multiple sequence alignments 1 1Edited by J. Karn
Journal of Molecular Biology, 2001, 314, 937-951
4.1132Citations (PDF)
61Multiple alignment of complete sequences (MACS) in the post-genomic era
Gene, 2001, 270, 17-30
2.363Citations (PDF)
62Ballast: Blast post-processing based on locally conserved segments
Bioinformatics, 2000, 16, 750-759
4.722Citations (PDF)
63DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches
Nucleic Acids Research, 2000, 28, 2919-2926
15.5165Citations (PDF)
64BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
Bioinformatics, 1999, 15, 87-88
4.7422Citations (PDF)
65A comprehensive comparison of multiple sequence alignment programs
Nucleic Acids Research, 1999, 27, 2682-2690
15.5669Citations (PDF)
66Multiple sequence alignment with Clustal X
Trends in Biochemical Sciences, 1998, 23, 403-405
6.72,530Citations (PDF)
67The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
Nucleic Acids Research, 1997, 25, 4876-4882
15.535,968Citations (PDF)
68PairWise and SearchWise: Finding the Optimal Alignment in a Simultaneous Comparison of a Protein Profile against All DNA Translation Frames
Nucleic Acids Research, 1996, 24, 2730-2739
15.5159Citations (PDF)
69Introducing variable gap penalties to sequence alignment in linear space
Bioinformatics, 1995, 11, 181-186
4.76Citations (PDF)
70Evidence for a protein domain superfamily shared by the cyclins, TFIIB and RB/p107
Nucleic Acids Research, 1994, 22, 946-952
15.574Citations (PDF)
71Improved sensitivity of profile searches through the use of sequence weights and gap excision
Bioinformatics, 1994, 10, 19-29
4.7192Citations (PDF)
72Detection of dsRNA-binding domains in RNA helicase A andDrosophilamaleless: implications for monomeric RNA helicases
Nucleic Acids Research, 1994, 22, 2552-2556
15.5104Citations (PDF)
73CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
Nucleic Acids Research, 1994, 22, 4673-4680
15.562,187Citations (PDF)
74The KH domain occurs in a diverse set of RNA‐binding proteins that include the antiterminator NusA and is probably involved in binding to nucleic acid
FEBS Letters, 1993, 324, 361-366
2.7193Citations (PDF)
75KH domains within the FMR1 sequence suggest that fragile X syndrome stems from a defect in RNA metabolism
Trends in Biochemical Sciences, 1993, 18, 331-333
6.774Citations (PDF)
76X-ray scattering study of ribosomes from Escherichia coli
Journal of Molecular Biology, 1969, 44, 89-102
4.182Citations (PDF)
77Integrative Multi-Omics and Network Analyses Reveal Pathogenic and Protective Pathways in Centronuclear Myopathies
International Journal of Molecular Sciences, 0, 26, 11572
4.40Citations (PDF)