Sean R. Eddy

The share of this author’s assessed papers carrying a ⚑ flag. A concentration is a prompt for expert review — never, on its own, a determination about the person.

Collaborators, sized by shared output and coloured by their own reproducibility (green = high, red = low). Click a node to open their card. A pattern is a prompt for review, never a determination.

How this author’s assessed papers reproduced — the outcome of reproduction attempts, not a judgement of the person. Coverage is partial and grows over time.

Assessed papers (1)

• Free circular introns with an unusual branchpoint in neuronal projections.
  2019 L1 99/100

1 assessed by us (1 reproduced) · 198 not yet assessed — every PubMed paper on record, linked below.

• HMMER web server: 2026 update ↗

  Nucleic Acids Research · 2026 · PMID 42037125
  not yet assessed
• Presence of group II introns in phage genomes ↗

  Nucleic Acids Research · 2025 · PMID 40808305
  not yet assessed
• Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice ↗

  eLife · 2025
  not yet assessed
• Induction of menstruation in mice reveals the regulation of menstrual shedding ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 41332577
  not yet assessed
• Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice ↗

  eLife · 2025
  not yet assessed
• Author response: Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice ↗

  2025
  not yet assessed
• Author response: Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice ↗

  2025
  not yet assessed
• Prevalence of Group II Introns in Phage Genomes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 40475605
  not yet assessed
• Mammalian cells repress random DNA that yeast transcribes ↗

  Nature · 2024 · PMID 38448526
  not yet assessed
• Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice ↗

  eLife · 2024 · PMID 40191998
  not yet assessed
• Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024 · PMID 39253506
  not yet assessed
• Protein sequence domain annotation using a language model ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice ↗

  eLife · 2024
  not yet assessed
• Author response: Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice ↗

  2024
  not yet assessed
• ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events ↗

  BMC Bioinformatics · 2023 · PMID 38093195
  not yet assessed
• Correction: Constructing Benchmark Test Sets for Biological Sequence Analysis Using Independent Set Algorithms ↗

  PLoS Computational Biology · 2023 · PMID 36888579
  not yet assessed
• ORFeus: A Computational Method to Detect Programmed Ribosomal Frameshifts and Other Non-Canonical Translation Events ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• Metabolic Acidosis in Pediatric Participants with Glomerular Disease in the NEPTUNE and CureGN Cohorts ↗

  Journal of the American Society of Nephrology · 2023
  not yet assessed
• Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes ↗

  Current Biology · 2022 · PMID 35588743
  not yet assessed
• Codetta: predicting the genetic code from nucleotide sequence ↗

  Bioinformatics · 2022 · PMID 36511586
  not yet assessed
• Constructing benchmark test sets for biological sequence analysis using independent set algorithms ↗

  PLoS Computational Biology · 2022 · PMID 35255082
  not yet assessed
• Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Mixing Genome Annotation Methods in a Comparative Analysis Inflates the Apparent Number of Lineage-Specific Genes ↗

  SSRN Electronic Journal · 2022
  not yet assessed
• A glomerular transcriptomic landscape of apolipoprotein L1 in Black patients with focal segmental glomerulosclerosis ↗

  Kidney International · 2021 · PMID 34929253
  not yet assessed
• Constructing benchmark test sets for biological sequence analysis using independent set algorithms ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• A computational screen for alternative genetic codes in over 250,000 genomes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Author response: A computational screen for alternative genetic codes in over 250,000 genomes ↗

  2021
  not yet assessed
• Referee report. For: Overlap of vitamin A and vitamin D target genes with CAKUT-related processes [version 1; peer review: 4 approved with reservations] ↗

  Faculty of 1000 Research Ltd · 2021
  not yet assessed
• A computational screen for alternative genetic codes in over 250,000 genomes ↗

  eLife · 2021 · PMID 34751130
  not yet assessed
• Rfam 14: expanded coverage of metagenomic, viral and microRNA families ↗

  Nucleic Acids Research · 2020 · PMID 33211869
  not yet assessed
• A genetic, genomic, and computational resource for exploring neural circuit function ↗

  eLife · 2020 · PMID 31939737
  not yet assessed
• Many, but not all, lineage-specific genes can be explained by homology detection failure ↗

  PLoS Biology · 2020 · PMID 33137085
  not yet assessed
• Estimating the power of sequence covariation for detecting conserved RNA structure ↗

  Bioinformatics · 2020 · PMID 32031582
  not yet assessed
• Remote homology search with hidden Potts models ↗

  PLoS Computational Biology · 2020 · PMID 33253143
  not yet assessed
• Remote homology search with hidden Potts models ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Many but not all lineage-specific genes can be explained by homology detection failure ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Response to Tavares et al., “Covariation analysis with improved parameters reveals conservation in lncRNA structures” ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Representation learning of genomic sequence motifs with convolutional neural networks ↗

  PLoS Computational Biology · 2019 · PMID 31856220
  not yet assessed
• Free circular introns with an unusual branchpoint in neuronal projections

  eLife · 2019 · PMID 31697236
  L1 99/100
• Estimating the power of sequence covariation for detecting conserved RNA structure ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Author response: Free circular introns with an unusual branchpoint in neuronal projections ↗

  2019
  not yet assessed
• Author response: A genetic, genomic, and computational resource for exploring neural circuit function ↗

  2019
  not yet assessed
• Free circular introns with an unusual branchpoint in neuronal projections ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• The Pfam protein families database in 2019 ↗

  Nucleic Acids Research · 2018 · PMID 30357350
  not yet assessed
• HMMER web server: 2018 update ↗

  Nucleic Acids Research · 2018 · PMID 29905871
  not yet assessed
• Group I introns are widespread in archaea ↗

  Nucleic Acids Research · 2018 · PMID 29788499
  not yet assessed
• A genetic, genomic, and computational resource for exploring neural circuit function ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Inferring Sequence-Structure Preferences of RNA-Binding Proteins with Convolutional Residual Networks ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Representation Learning of Genomic Sequence Motifs with Convolutional Neural Networks ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• A Genetic, Genomic, and Computational Resource for Exploring Neural Circuit Function ↗

  SSRN Electronic Journal · 2018
  not yet assessed
• Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families ↗

  Nucleic Acids Research · 2017 · PMID 29112718
  not yet assessed
• Identification and Characterization of a Class of MALAT1-like Genomic Loci ↗

  Cell Reports · 2017 · PMID 28538188
  not yet assessed
• Gene Evolution: Getting Something from Nothing ↗

  Current Biology · 2017 · PMID 28697368
  not yet assessed
• A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs ↗

  Nature Methods · 2016 · PMID 27819659
  not yet assessed
• Epigenomic landscapes of retinal rods and cones ↗

  eLife · 2016 · PMID 26949250
  not yet assessed
• The Pfam protein families database: towards a more sustainable future ↗

  Nucleic Acids Research · 2015 · PMID 26673716
  not yet assessed
• HMMER web server: 2015 update ↗

  Nucleic Acids Research · 2015 · PMID 25943547
  not yet assessed
• The Dfam database of repetitive DNA families ↗

  Nucleic Acids Research · 2015 · PMID 26612867
  not yet assessed
• Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain ↗

  Neuron · 2015 · PMID 26087164
  not yet assessed
• Parameterizing sequence alignment with an explicit evolutionary model ↗

  BMC Bioinformatics · 2015 · PMID 26652060
  not yet assessed
• Combinatorial DNA rearrangement facilitates the origin of new genes in ciliates ↗

  Genome Biology and Evolution · 2015 · PMID 26338187
  not yet assessed
• Homology searches for structural RNAs: from proof of principle to practical use ↗

  RNA · 2015 · PMID 25780158
  not yet assessed
• Comparison of key ciliate macronuclear genomes. ↗

  Figshare · 2015
  not yet assessed
• Author response: Epigenomic landscapes of retinal rods and cones ↗

  2015
  not yet assessed
• Additional file 2 of Parameterizing sequence alignment with an explicit evolutionary model ↗

  Figshare · 2015
  not yet assessed
• Additional file 1 of Parameterizing sequence alignment with an explicit evolutionary model ↗

  Figshare · 2015
  not yet assessed
• Additional file 1 of Parameterizing sequence alignment with an explicit evolutionary model ↗

  Figshare · 2015
  not yet assessed
• Rfam 12.0: updates to the RNA families database ↗

  Nucleic Acids Research · 2014 · PMID 25392425
  not yet assessed
• Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes ↗

  Annual Review of Biophysics · 2014 · PMID 24895857
  not yet assessed
• Pfam: the protein families database ↗

  Nucleic Acids Research · 2013 · PMID 24288371
  not yet assessed
• Infernal 1.1: 100-fold faster RNA homology searches ↗

  Bioinformatics · 2013 · PMID 24008419
  not yet assessed
• Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions ↗

  Nucleic Acids Research · 2013 · PMID 23598997
  not yet assessed
• nhmmer: DNA homology search with profile HMMs ↗

  Bioinformatics · 2013 · PMID 23842809
  not yet assessed
• The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes ↗

  PLoS Biology · 2013 · PMID 23382650
  not yet assessed
• The ENCODE project: Missteps overshadowing a success ↗

  Current Biology · 2013 · PMID 23578867
  not yet assessed
• Computational identification of functional RNA homologs in metagenomic data ↗

  RNA Biology · 2013 · PMID 23722291
  not yet assessed
• Transcription Factors That Convert Adult Cell Identity Are Differentially Polycomb Repressed ↗

  PLoS ONE · 2013 · PMID 23650565
  not yet assessed
• Rfam 11.0: 10 years of RNA families ↗

  Nucleic Acids Research · 2012 · PMID 23125362
  not yet assessed
• Dfam: a database of repetitive DNA based on profile hidden Markov models ↗

  Nucleic Acids Research · 2012 · PMID 23203985
  not yet assessed
• The C-value paradox, junk DNA and ENCODE ↗

  Current Biology · 2012 · PMID 23137679
  not yet assessed
• Cell type–specific genomics of Drosophila neurons ↗

  Nucleic Acids Research · 2012 · PMID 22855560
  not yet assessed
• 492 Frequency and Co-occurrence of MAPK and PI3K Pathway Driver Mutations to Guide Single-agent and Combination Therapies: an Analysis of Next Generation Sequence Data From 2700 Patients ↗

  European Journal of Cancer · 2012
  not yet assessed
• Accelerated Profile HMM Searches ↗

  PLoS Computational Biology · 2011 · PMID 22039361
  not yet assessed
• HMMER web server: interactive sequence similarity searching ↗

  Nucleic Acids Research · 2011 · PMID 21593126
  not yet assessed
• The Pfam protein families database ↗

  Nucleic Acids Research · 2011
  not yet assessed
• A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more ↗

  RNA · 2011 · PMID 22194308
  not yet assessed
• Fast filtering for RNA homology search ↗

  Bioinformatics · 2011 · PMID 21965818
  not yet assessed
• Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes ↗

  Nucleic Acids Research · 2011 · PMID 21715380
  not yet assessed
• Hidden Markov model speed heuristic and iterative HMM search procedure ↗

  BMC Bioinformatics · 2010 · PMID 20718988
  not yet assessed
• Rfam: Wikipedia, clans and the "decimal" release ↗

  Nucleic Acids Research · 2010 · PMID 21062808
  not yet assessed
• The Pfam protein families database ↗

  Nucleic Acids Research · 2009 · PMID 19920124
  not yet assessed
• Infernal 1.0: inference of RNA alignments ↗

  Bioinformatics · 2009 · PMID 19307242
  not yet assessed
• A new generation of homology search tools based on probabilistic inference. ↗

  PubMed · 2009 · PMID 20180275
  not yet assessed
• A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE ↗

  2009
  not yet assessed
• Infernal 1.0: inference of RNA alignments ↗

  Bioinformatics · 2009
  not yet assessed
• Local RNA structure alignment with incomplete sequence ↗

  Bioinformatics · 2009 · PMID 19304875
  not yet assessed
• A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas ↗

  Bioinformatics · 2009 · PMID 19414530
  not yet assessed
• A survey of nematode SmY RNAs ↗

  RNA Biology · 2009 · PMID 19106623
  not yet assessed
• Broadening Pfam Protein Sequence Annotations ↗

  Nature Precedings · 2009
  not yet assessed
• Broadening Pfam Protein Sequence Annotations ↗

  Nature Precedings · 2009
  not yet assessed
• Open Revolution ↗

  PLoS Biology · 2009
  not yet assessed
• Rfam: updates to the RNA families database ↗

  Nucleic Acids Research · 2008 · PMID 18953034
  not yet assessed
• A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation ↗

  PLoS Computational Biology · 2008 · PMID 18516236
  not yet assessed
• Probabilistic Phylogenetic Inference with Insertions and Deletions ↗

  PLoS Computational Biology · 2008 · PMID 18787703
  not yet assessed
• Ethanol intake patterns in female mice: Influence of allopregnanolone and the inhibition of its synthesis ↗

  Drug and Alcohol Dependence · 2008 · PMID 18486362
  not yet assessed
• The Pfam protein families database ↗

  Nucleic Acids Research · 2007 · PMID 18039703
  not yet assessed
• Query-Dependent Banding (QDB) for Faster RNA Similarity Searches ↗

  PLoS Computational Biology · 2007 · PMID 17397253
  not yet assessed
• Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints ↗

  BMC Bioinformatics · 2006 · PMID 16952317
  not yet assessed
• Total Information Awareness for Worm Genetics ↗

  Science · 2006 · PMID 16527956
  not yet assessed
• Computational Analysis of RNAs ↗

  Cold Spring Harbor Symposia on Quantitative Biology · 2006 · PMID 17381287
  not yet assessed
• Generation and annotation of the DNA sequences of human chromosomes 2 and 4 ↗

  Nature · 2005 · PMID 15815621
  not yet assessed
• “Antedisciplinary” Science ↗

  PLoS Computational Biology · 2005 · PMID 16103907
  not yet assessed
• Query-Dependent Banding (QDB) for Faster RNA Similarity Searches ↗

  PLoS Computational Biology · 2005
  not yet assessed
• Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes ↗

  Genes & Development · 2005 · PMID 15805463
  not yet assessed
• Pack-MULE transposable elements mediate gene evolution in plants ↗

  Nature · 2004 · PMID 15457261
  not yet assessed
• What is a hidden Markov model? ↗

  Nature Biotechnology · 2004 · PMID 15470472
  not yet assessed
• Where did the BLOSUM62 alignment score matrix come from? ↗

  Nature Biotechnology · 2004 · PMID 15286655
  not yet assessed
• Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction ↗

  BMC Bioinformatics · 2004 · PMID 15180907
  not yet assessed
• What is dynamic programming? ↗

  Nature Biotechnology · 2004 · PMID 15229554
  not yet assessed
• What is Bayesian statistics? ↗

  Nature Biotechnology · 2004 · PMID 15340486
  not yet assessed
• How do RNA folding algorithms work? ↗

  Nature Biotechnology · 2004 · PMID 15529172
  not yet assessed
• A Model of the Statistical Power of Comparative Genome Sequence Analysis ↗

  PLoS Biology · 2004 · PMID 15660152
  not yet assessed
• Circular box C/D RNAs in <i>Pyrococcus furiosus</i> ↗

  Proceedings of the National Academy of Sciences · 2004 · PMID 15375211
  not yet assessed
• Rna structural alignment using stochastic context-free grammars

  2004
  not yet assessed
• A uniform system for microRNA annotation ↗

  RNA · 2003 · PMID 12592000
  not yet assessed
• An active DNA transposon family in rice ↗

  Nature · 2003 · PMID 12520302
  not yet assessed
• The DNA sequence of human chromosome 7 ↗

  Nature · 2003 · PMID 12853948
  not yet assessed
• RSEARCH: Finding homologs of single structured RNA sequences ↗

  BMC Bioinformatics · 2003 · PMID 14499004
  not yet assessed
• Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences ↗

  PLANT PHYSIOLOGY · 2003 · PMID 12746507
  not yet assessed
• Unrestricted free access works and must continue ↗

  Nature · 2003 · PMID 12712164
  not yet assessed
• Genomic Analysis of Noncoding RNAs

  Annual Review of Biochemistry · 2003
  not yet assessed
• Role of differential gene and protein regulation in hibernating mammals ↗

  2003
  not yet assessed
• Initial sequencing and comparative analysis of the mouse genome ↗

  Nature · 2002 · PMID 12466850
  not yet assessed
• Noncoding RNA genes identified in AT-rich hyperthermophiles ↗

  Proceedings of the National Academy of Sciences · 2002 · PMID 12032319
  not yet assessed
• A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure ↗

  BMC Bioinformatics · 2002 · PMID 12095421
  not yet assessed
• Computational Genomics of Noncoding RNA Genes ↗

  Cell · 2002 · PMID 12007398
  not yet assessed
• RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs ↗

  BMC Bioinformatics · 2002 · PMID 12028595
  not yet assessed
• Archaeal Guide RNAs Function in rRNA Modification in the Eukaryotic Nucleus ↗

  Current Biology · 2002 · PMID 11839271
  not yet assessed
• Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes ↗

  Genome Research · 2002 · PMID 12176934
  not yet assessed
• Initial sequencing and analysis of the human genome ↗

  Nature · 2001 · PMID 11237011
  not yet assessed
• Non–coding RNA genes and the modern RNA world ↗

  Nature Reviews Genetics · 2001 · PMID 11733745
  not yet assessed
• Noncoding RNA gene detection using comparative sequence analysis ↗

  BMC Bioinformatics · 2001 · PMID 11801179
  not yet assessed
• The Distributed Annotation System ↗

  BMC Bioinformatics · 2001 · PMID 11667947
  not yet assessed
• Computational identification of noncoding RNAs in E. coli by comparative genomics ↗

  Current Biology · 2001 · PMID 11553332
  not yet assessed
• ATV: display and manipulation of annotated phylogenetic trees ↗

  Bioinformatics · 2001 · PMID 11301314
  not yet assessed
• A simple algorithm to infer gene duplication and speciation events on a gene tree ↗

  Bioinformatics · 2001 · PMID 11590098
  not yet assessed
• Changes in Gene Expression Associated with Developmental Arrest and Longevity in <i>Caenorhabditis elegans</i> ↗

  Genome Research · 2001 · PMID 11483575
  not yet assessed
• Analisis Faktor Shift, Dan Mesin Produksi Wafer Terhadap Cacat Produk Dengan Menggunakan Metode Perencanaan Eksperimen Faktorial Dwifaktor Di PT.Interbis Sejahtera

  ePrints Repository Musi Charitas Catholic University · 2001
  not yet assessed
• Homologs of Small Nucleolar RNAs in Archaea ↗

  Science · 2000 · PMID 10775111
  not yet assessed
• Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs ↗

  Bioinformatics · 2000 · PMID 11038329
  not yet assessed
• The language of RNA: a formal grammar that includes pseudoknots ↗

  Bioinformatics · 2000 · PMID 10869031
  not yet assessed
• A Computational Screen for Methylation Guide snoRNAs in Yeast ↗

  Science · 1999 · PMID 10024243
  not yet assessed
• Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins ↗

  Nucleic Acids Research · 1999 · PMID 9847196
  not yet assessed
• Noncoding RNA genes ↗

  Current Opinion in Genetics & Development · 1999 · PMID 10607607
  not yet assessed
• A dynamic programming algorithm for RNA structure prediction including pseudoknots 1 1Edited by I. Tinoco ↗

  Journal of Molecular Biology · 1999 · PMID 9925784
  not yet assessed
• Shotgun coverage of human genome computing ↗

  Trends in Biochemical Sciences · 1999
  not yet assessed
• Profile hidden Markov models. ↗

  Bioinformatics · 1998 · PMID 9918945
  not yet assessed
• Biological sequence analysis: probabilistic models of proteins and nucleic acids

  1998
  not yet assessed
• Biological Sequence Analysis ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• Multiple sequence alignment methods ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• Studies in Probabilistic Sequence Alignment and Evolution

  1998
  not yet assessed
• Markov chains and hidden Markov models ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• Multiple-alignment and -sequence searches ↗

  Trends in biotechnology · 1998
  not yet assessed
• Pairwise alignment ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• Building phylogenetic trees ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• Pairwise alignment using HMMs ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• Probabilistic approaches to phylogeny ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• Transformational grammars ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• Introduction ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• A dynamic programming algorithm for RNA structure prediction including\n pseudoknots ↗

  arXiv (Cornell University) · 1998
  not yet assessed
• A dynamic programming algorithm for RNA structure prediction including pseudoknots ↗

  arXiv (Cornell University) · 1998
  not yet assessed
• Bibliography ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• Profile HMMs for sequence families ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• RNA structure analysis ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• [Invited Lecture] Genome sequence analysis and profile hidden Markov models.

  German Conference on Bioinformatics · 1998
  not yet assessed
• Preface ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• Background on probability ↗

  Cambridge University Press eBooks · 1998
  not yet assessed
• tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence ↗

  Nucleic Acids Research · 1997 · PMID 9023104
  not yet assessed
• tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence ↗

  Nucleic Acids Research · 1997
  not yet assessed
• Pfam: A comprehensive database of protein domain families based on seed alignments ↗

  Proteins Structure Function and Bioinformatics · 1997 · PMID 9223186
  not yet assessed
• A Member of the Immunoglobulin Superfamily in Bacteriophage T4 ↗

  Virus Genes · 1997 · PMID 9237357
  not yet assessed
• Inside the black boxes Computer methods for macromolecular sequence analysis (Methods in enzymology vol. 266) ↗

  Trends in Biochemical Sciences · 1997
  not yet assessed
• Hidden Markov models ↗

  Current Opinion in Structural Biology · 1996 · PMID 8804822
  not yet assessed
• Members of the immunoglobulin superfamily in bacteria ↗

  Protein Science · 1996 · PMID 8880921
  not yet assessed
• Is the Pope the Pope? ↗

  Nature · 1996
  not yet assessed
• Molecular genetics in silico ↗

  Trends in Genetics · 1996
  not yet assessed
• Molecular genetics in silico ↗

  Trends in Genetics · 1996
  not yet assessed
• Multiple alignment using hidden Markov models. ↗

  PubMed · 1995 · PMID 7584426
  not yet assessed
• Maximum Discrimination Hidden Markov Models of Sequence Consensus ↗

  Journal of Computational Biology · 1995 · PMID 7497123
  not yet assessed
• Genome maps. VI. Caenorhabditis elegans. Wall chart. ↗

  PubMed · 1995 · PMID 7569996
  not yet assessed
• RNA structure alignment on a massively parallel computer ↗

  Lecture notes in computer science · 1995
  not yet assessed
• RNA sequence analysis using covariance models ↗

  Nucleic Acids Research · 1994 · PMID 8029015
  not yet assessed
• Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns ↗

  Trends in Biochemical Sciences · 1994 · PMID 7817395
  not yet assessed
• The Caenorhabditis Elegans Genome Project ↗

  1994
  not yet assessed
• 19 RNA: The Shape of Things to Come ↗

  1993
  not yet assessed
• Artificial mobile DNA element constructed from the EcoRI endonuclease gene. ↗

  Proceedings of the National Academy of Sciences · 1992 · PMID 1311841
  not yet assessed
• The phage T4 nrdB intron: a deletion mutant of a version found in the wild. ↗

  Genes & Development · 1991 · PMID 2044951
  not yet assessed
• Autogenous translational operator recognized by bacteriophage T4 DNA polymerase ↗

  Journal of Molecular Biology · 1990 · PMID 2359122
  not yet assessed
• Nucleotide Sequence of Yellow Fever Virus: Implications for Flavivirus Gene Expression and Evolution ↗

  Science · 1985 · PMID 4023707
  not yet assessed