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Reference panel guided topological structure annotation of Hi-C data.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-35231-3
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- Article
A call for benchmarking transposable element annotation methods.
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- Mobile DNA, 2015, v. 6, n. 1, p. 1, doi. 10.1186/s13100-015-0044-6
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- Article
Functional 5′ UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks.
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- Nucleic Acids Research, 2017, v. 45, n. 18, p. 10415, doi. 10.1093/nar/gkx751
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- Article
A critical assessment of topologically associating domain prediction tools.
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- Nucleic Acids Research, 2017, v. 45, n. 6, p. 2994, doi. 10.1093/nar/gkx145
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- Article
Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences.
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- Nucleic Acids Research, 2017, v. 45, n. 2, p. 556, doi. 10.1093/nar/gkw1085
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- Article
A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data.
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- Nucleic Acids Research, 2015, v. 43, n. 16, p. 1, doi. 10.1093/nar/gkv476
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- Article
Hox in motion: tracking HoxA cluster conformation during differentiation.
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- Nucleic Acids Research, 2014, v. 42, n. 3, p. 1524, doi. 10.1093/nar/gkt998
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- Article
Computational prediction of the localization of microRNAs within their pre-miRNA.
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- Nucleic Acids Research, 2013, v. 41, n. 15, p. 7200, doi. 10.1093/nar/gkt466
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- Article
Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2.
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- Nucleic Acids Research, 2013, v. 41, n. 14, p. 6881, doi. 10.1093/nar/gkt455
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- Article
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences.
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- Nucleic Acids Research, 2013, v. 41, p. W480, doi. 10.1093/nar/gkt461
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- Article
The three-dimensional architecture of Hox cluster silencing.
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- Nucleic Acids Research, 2010, v. 38, n. 21, p. 7472, doi. 10.1093/nar/gkq644
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- Article
PReMod: a database of genome-wide mammalian cis-regulatory module predictions.
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- Nucleic Acids Research, 2007, v. 35, p. d122, doi. 10.1093/nar/gkl879
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- Article
PERFUMES: pipeline to extract RNA functional motifs and exposed structures.
- Published in:
- Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae056
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- Article
Reference panel-guided super-resolution inference of Hi-C data.
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- Bioinformatics, 2023, v. 39, p. i386, doi. 10.1093/bioinformatics/btad266
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- Article
PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information.
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- Bioinformatics, 2022, v. 38, p. i299, doi. 10.1093/bioinformatics/btac259
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- Article
Positional Mapping and Candidate Gene Analysis of the Mouse <i>Ccs3</i> Locus That Regulates Differential Susceptibility to Carcinogen-Induced Colorectal Cancer.
- Published in:
- PLoS ONE, 2013, v. 8, n. 3, p. 1, doi. 10.1371/journal.pone.0058733
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- Article
Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment.
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- PLoS ONE, 2012, v. 7, n. 3, p. 1, doi. 10.1371/journal.pone.0031362
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- Article
An N-Ethyl-N-Nitrosourea (ENU)-Induced Dominant Negative Mutation in the JAK3 Kinase Protects against Cerebral Malaria.
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- PLoS ONE, 2012, v. 7, n. 2, p. 1, doi. 10.1371/journal.pone.0031012
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- Article
Combining Computational Prediction of Cis-Regulatory Elements with a New Enhancer Assay to Efficiently Label Neuronal Structures in the Medaka Fish.
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- PLoS ONE, 2011, v. 6, n. 5, p. 1, doi. 10.1371/journal.pone.0019747
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- Article
A flexible ancestral genome reconstruction method based on gapped adjacencies.
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- BMC Bioinformatics, 2012, v. 13, n. Suppl 19, p. 1, doi. 10.1186/1471-2105-13-S19-S4
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- Article
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites.
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- BMC Bioinformatics, 2012, v. 13, n. Suppl 19, p. 1, doi. 10.1186/1471-2105-13-S19-S2
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- Article
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania.
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- BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-158
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- Article
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences.
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- BMC Bioinformatics, 2004, v. 5, p. 170, doi. 10.1186/1471-2105-5-170
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- Article
Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes.
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- Molecular Biology & Evolution, 2019, v. 36, n. 4, p. 766, doi. 10.1093/molbev/msz016
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- Article
Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements.
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- Molecular Biology & Evolution, 2016, v. 33, n. 8, p. 1937, doi. 10.1093/molbev/msw067
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- Article
FootPrinter3: phylogenetic footprinting in partially alignable sequences.
- Published in:
- Nucleic Acids Research, 2006, v. 34, n. 11, p. w617, doi. 10.1093/nar/gkl123
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- Article
FootPrinter: a program designed for phylogenetic footprinting.
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- Nucleic Acids Research, 2003, v. 31, n. 13, p. 3840, doi. 10.1093/nar/gkg606
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- Article
Models and algorithms for genome rearrangement with positional constraints.
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- Algorithms for Molecular Biology, 2016, v. 11, p. 1, doi. 10.1186/s13015-016-0065-9
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- Article
Predicting direct protein interactions from affinitypurification mass spectrometry data.
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- Algorithms for Molecular Biology, 2010, v. 5, p. 34, doi. 10.1186/1748-7188-5-34
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- Article
Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human.
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- PLoS Computational Biology, 2010, v. 6, n. 7, p. 1, doi. 10.1371/journal.pcbi.1000849
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- Article
PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing.
- Published in:
- Nature Communications, 2015, v. 6, n. 12, p. 10124, doi. 10.1038/ncomms10124
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- Article
Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation.
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- Genome Biology, 2015, v. 16, p. 1, doi. 10.1186/s13059-015-0856-1
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- Article
Classifying leukemia types with chromatin conformation data.
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- Genome Biology, 2014, v. 15, n. 4, p. R60, doi. 10.1186/gb-2014-15-4-r60
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- Article
The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts.
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- Genome Biology, 2014, v. 15, n. 2, p. 1, doi. 10.1186/gb-2014-15-2-r37
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- Article
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment.
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- Genome Biology, 2013, v. 14, n. 10, p. 2, doi. 10.1186/gb-2013-14-10-r116
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- Article
LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads.
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- BMC Research Notes, 2020, v. 13, n. 1, p. 1, doi. 10.1186/s13104-020-05106-1
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- Article
ARGV: 3D genome structure exploration using augmented reality.
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- BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05882-8
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- Article
Specific Dysregulation of IFNγ Production by Natural Killer Cells Confers Susceptibility to Viral Infection.
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- PLoS Pathogens, 2014, v. 10, n. 12, p. 1, doi. 10.1371/journal.ppat.1004511
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- Article
Genome-Wide Mouse Mutagenesis Reveals CD45-Mediated T Cell Function as Critical in Protective Immunity to HSV-1.
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- PLoS Pathogens, 2013, v. 9, n. 9, p. 1, doi. 10.1371/journal.ppat.1003637
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- Article
Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning.
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- PLoS Biology, 2005, v. 3, n. 12, p. e384, doi. 10.1371/journal.pbio.0030384
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- Article
Posterior inference of Hi-C contact frequency through sampling.
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- Frontiers in Bioinformatics, 2024, p. 1, doi. 10.3389/fbinf.2023.1285828
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- Article
Into the heart of darkness: large-scale clustering of human non-coding DNA.
- Published in:
- Bioinformatics, 2004, v. 20, n. suppl_1, p. i40, doi. 10.1093/bioinformatics/bth946
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- Article
Into the heart of darkness: large-scale clustering of human non-coding DNA.
- Published in:
- Bioinformatics, 2004, v. 20, p. i40, doi. 10.1093/bioinformatics/bth946
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- Publication type:
- Article
Separating real motifs from their artifacts.
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- Bioinformatics, 2001, v. 17, p. 30, doi. 10.1093/bioinformatics/17.suppl_1.s30
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- Publication type:
- Article
Reconstruction of full-length LINE-1 progenitors from ancestral genomes.
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- Genetics, 2022, v. 221, n. 3, p. 1, doi. 10.1093/genetics/iyac074
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- Article
oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species.
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- Nucleic Acids Research, 2020, v. 48, n. D1, p. D166, doi. 10.1093/nar/gkz986
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- Article
2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing.
- Published in:
- BMC Genomics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12864-019-5532-5
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- Article
Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data.
- Published in:
- BMC Cancer, 2022, v. 22, n. 1, p. 1, doi. 10.1186/s12885-022-10359-z
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- Article
Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora.
- Published in:
- PLoS Genetics, 2014, v. 10, n. 9, p. 1, doi. 10.1371/journal.pgen.1004622
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- Article
A Newly Uncovered Group of Distantly Related Lysine Methyltransferases Preferentially Interact with Molecular Chaperones to Regulate Their Activity.
- Published in:
- PLoS Genetics, 2013, v. 9, n. 1, p. 1, doi. 10.1371/journal.pgen.1003210
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- Article