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A genetic, genomic, and computational resource for exploring neural circuit function.
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- eLife, 2020, p. 1, doi. 10.7554/eLife.50901
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Free circular introns with an unusual branchpoint in neuronal projections.
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- eLife, 2019, p. 1, doi. 10.7554/eLife.47809
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Epigenomic landscapes of retinal rods and cones.
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- eLife, 2016, p. 1, doi. 10.7554/eLife.11613
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- Article
B Cell Signatures Distinguish Cutaneous Lupus Erythematosus Subtypes and the Presence of Systemic Disease Activity.
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- Frontiers in Immunology, 2021, v. 12, p. 1, doi. 10.3389/fimmu.2021.775353
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The Pfam protein families database in 2019.
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- Nucleic Acids Research, 2019, v. 47, n. D1, p. D427, doi. 10.1093/nar/gky995
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Group I introns are widespread in archaea.
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- Nucleic Acids Research, 2018, v. 46, n. 15, p. 7970, doi. 10.1093/nar/gky414
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HMMER web server: 2018 update.
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- Nucleic Acids Research, 2018, v. 46, n. W1, p. W200, doi. 10.1093/nar/gky448
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Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.
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- Nucleic Acids Research, 2018, v. 46, n. D1, p. D335, doi. 10.1093/nar/gkx1038
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The Pfam protein families database: towards a more sustainable future.
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- Nucleic Acids Research, 2016, v. 44, p. D279, doi. 10.1093/nar/gkv1344
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The Dfam database of repetitive DNA families.
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- Nucleic Acids Research, 2016, v. 44, p. D81, doi. 10.1093/nar/gkv1272
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HMMER web server: 2015 update.
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- Nucleic Acids Research, 2015, v. 43, n. W1, p. W30, doi. 10.1093/nar/gkv397
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Rfam 12.0: updates to the RNA families database.
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- Nucleic Acids Research, 2015, v. 43, n. D1, p. D130, doi. 10.1093/nar/gku1063
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Pfam: the protein families database.
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- Nucleic Acids Research, 2014, v. 42, n. D1, p. D222, doi. 10.1093/nar/gkt1223
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Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.
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- Nucleic Acids Research, 2013, v. 41, n. 12, p. e121, doi. 10.1093/nar/gkt263
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Dfam: a database of repetitive DNA based on profile hidden Markov models.
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- Nucleic Acids Research, 2013, v. 41, p. D70, doi. 10.1093/nar/gks1265
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Rfam 11.0: 10 years of RNA families.
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- Nucleic Acids Research, 2013, v. 41, p. D226, doi. 10.1093/nar/gks1005
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Cell type–specific genomics of Drosophila neurons.
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- Nucleic Acids Research, 2012, v. 40, n. 19, p. 9691, doi. 10.1093/nar/gks671
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The Pfam protein families database.
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- Nucleic Acids Research, 2012, p. D290, doi. 10.1093/nar/gkr1065
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Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes.
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- Nucleic Acids Research, 2011, v. 39, n. 17, p. 7529, doi. 10.1093/nar/gkr501
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HMMER web server: interactive sequence similarity searching.
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- Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W29, doi. 10.1093/nar/gkr367
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Rfam: Wikipedia, clans and the “decimal” release.
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- Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D141, doi. 10.1093/nar/gkq1129
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Rfam: updates to the RNA families database.
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- Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D136, doi. 10.1093/nar/gkn766
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The Pfam protein families database.
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- Nucleic Acids Research, 2008, v. 36, p. D281
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How do RNA folding algorithms work?
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- Nature Biotechnology, 2004, v. 22, n. 11, p. 1457, doi. 10.1038/nbt1104-1457
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What is a hidden Markov model?
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- Nature Biotechnology, 2004, v. 22, n. 10, p. 1315, doi. 10.1038/nbt1004-1315
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What is Bayesian statistics?
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- Nature Biotechnology, 2004, v. 22, n. 9, p. 1177, doi. 10.1038/nbt0904-1177
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Where did the BLOSUM62 alignment score matrix come from?
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- Nature Biotechnology, 2004, v. 22, n. 8, p. 1035, doi. 10.1038/nbt0804-1035
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What is dynamic programming?
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- Nature Biotechnology, 2004, v. 22, n. 7, p. 909, doi. 10.1038/nbt0704-909
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An integrated organoid omics map extends modeling potential of kidney disease.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-39740-7
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Transcription Factors That Convert Adult Cell Identity Are Differentially Polycomb Repressed
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- PLoS ONE, 2013, v. 8, n. 5, p. 1, doi. 10.1371/journal.pone.0063407
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Pfam: A comprehensive database of protein domain families based on seed alignments.
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- Proteins, 1997, v. 28, n. 3, p. 405, doi. 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L
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ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05602-8
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NF-κB and epithelial to mesenchymal transition of cancer.
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- Journal of Cellular Biochemistry, 2008, v. 104, n. 3, p. 733, doi. 10.1002/jcb.21695
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NON-CODING RNA GENES AND THE MODERN RNA WORLD.
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- Nature Reviews Genetics, 2001, v. 2, n. 12, p. 919, doi. 10.1038/35103511
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A computational screen for alternative genetic codes in over 250,000 genomes.
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- eLife, 2021, p. 1, doi. 10.7554/eLife.71402
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The association of low birthweight and prematurity on outcomes in children and adults with nephrotic syndrome—a NEPTUNE cohort study.
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- Pediatric Nephrology, 2023, v. 38, n. 10, p. 3297, doi. 10.1007/s00467-023-05876-3
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Parameterizing sequence alignment with an explicit evolutionary model.
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- BMC Bioinformatics, 2015, v. 16, p. 1, doi. 10.1186/s12859-015-0832-5
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Hidden Markov model speed heuristic anditerative HMM search procedure.
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- BMC Bioinformatics, 2010, v. 11, p. 431, doi. 10.1186/1471-2105-11-431
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Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction.
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- BMC Bioinformatics, 2004, v. 5, p. 71, doi. 10.1186/1471-2105-5-71
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RSEARCH: Finding homologs of single structured RNA sequences.
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- BMC Bioinformatics, 2003, v. 4, p. 44, doi. 10.1186/1471-2105-4-44
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A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.
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- BMC Bioinformatics, 2002, v. 3, p. 18, doi. 10.1186/1471-2105-3-18
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RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs.
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- BMC Bioinformatics, 2002, v. 3, p. 14, doi. 10.1186/1471-2105-3-14
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Noncoding RNA gene detection using comparative sequence analysis.
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- BMC Bioinformatics, 2001, v. 2, p. 8, doi. 10.1186/1471-2105-2-8
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The Distributed Annotation System.
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- BMC Bioinformatics, 2001, v. 2, p. 7, doi. 10.1186/1471-2105-2-7
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Constructing benchmark test sets for biological sequence analysis using independent set algorithms.
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- PLoS Computational Biology, 2022, v. 18, n. 3, p. 1, doi. 10.1371/journal.pcbi.1009492
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Pfam: clans, web tools and services.
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- Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d247, doi. 10.1093/nar/gkj149
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Rfam: annotating non-coding RNAs in complete genomes.
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- Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d121
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Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics.
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- Nucleic Acids Research, 2004, v. 32, n. 15, p. 4713, doi. 10.1093/nar/gkh801
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The Pfam protein families database.
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- Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d138
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Computational identification of non‐coding RNAs in Saccharomyces cerevisiae by comparative genomics.
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- Nucleic Acids Research, 2003, v. 31, n. 14, p. 4119, doi. 10.1093/nar/gkg438
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- Article