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Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-33194-z
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- Publication type:
- Article
Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-30624-w
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- Publication type:
- Article
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.
- Published in:
- BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1274-4
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- Article
Quantifying Differences Between Machine Learning Classification Models Applied to Cancer Microscopy Data.
- Published in:
- 2022
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- Publication type:
- Abstract
RECOGNICER: A coarse-graining approach for identifying broad domains from ChIP-seq data.
- Published in:
- Quantitative Biology, 2020, v. 8, n. 4, p. 359, doi. 10.1007/s40484-020-0225-2
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- Publication type:
- Article
Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. 2, p. 1, doi. 10.1093/nar/gkx1053
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- Publication type:
- Article
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. D1, p. D658, doi. 10.1093/nar/gkw983
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- Publication type:
- Article
Genome-wide identification and characterization of Notch transcription complex–binding sequence-paired sites in leukemia cells.
- Published in:
- Science Signaling, 2017, v. 10, n. 477, p. 1, doi. 10.1126/scisignal.aag1598
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- Publication type:
- Article
Partitioning heritability by functional annotation using genome-wide association summary statistics.
- Published in:
- Nature Genetics, 2015, v. 47, n. 11, p. 1228, doi. 10.1038/ng.3404
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- Publication type:
- Article
H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions.
- Published in:
- Nature Genetics, 2009, v. 41, n. 8, p. 941, doi. 10.1038/ng.409
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- Publication type:
- Article
Combinatorial patterns of histone acetylations and methylations in the human genome.
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- Nature Genetics, 2008, v. 40, n. 7, p. 897, doi. 10.1038/ng.154
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- Publication type:
- Article
Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.
- Published in:
- Nature Methods, 2014, v. 11, n. 1, p. 73, doi. 10.1038/nmeth.2762
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- Publication type:
- Article
Assessing acute myeloid leukemia susceptibility in rearrangement‐driven patients by DNA breakage at topoisomerase II and CCCTC‐binding factor/cohesin binding sites.
- Published in:
- Genes, Chromosomes & Cancer, 2021, v. 60, n. 12, p. 808, doi. 10.1002/gcc.22993
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- Publication type:
- Article
Interpretable meta-learning of multi-omics data for survival analysis and pathway enrichment.
- Published in:
- Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad113
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- Publication type:
- Article
BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data.
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- Bioinformatics, 2021, v. 37, n. 18, p. 3075, doi. 10.1093/bioinformatics/btab173
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- Publication type:
- Article
NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes.
- Published in:
- Scientific Reports, 2016, p. 30255, doi. 10.1038/srep30255
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- Publication type:
- Article
Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation.
- Published in:
- Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02152-7
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- Publication type:
- Article
Integrative analysis of DNA replication origins and ORC-/MCM- binding sites in human cells reveals a lack of overlap.
- Published in:
- eLife, 2024, p. 1, doi. 10.7554/eLife.89548
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- Publication type:
- Article
An epilepsy-associated mutation in the nuclear import receptor KPNA7 reduces nuclear localization signal binding.
- Published in:
- Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-61369-5
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- Publication type:
- Article
High-dimensional genomic data bias correction and data integration using MANCIE.
- Published in:
- Nature Communications, 2016, v. 7, n. 4, p. 11305, doi. 10.1038/ncomms11305
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- Publication type:
- Article
Network analysis of gene essentiality in functional genomics experiments.
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- Genome Biology, 2015, v. 16, p. 1, doi. 10.1186/s13059-015-0808-9
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- Publication type:
- Article
MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes.
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- Genome Biology, 2014, v. 15, n. 7, p. 1, doi. 10.1186/s13059-014-0419-x
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- Publication type:
- Article
Nickel exposure induces persistent mesenchymal phenotype in human lung epithelial cells through epigenetic activation of ZEB1.
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- Molecular Carcinogenesis, 2018, v. 57, n. 6, p. 794, doi. 10.1002/mc.22802
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- Publication type:
- Article
The Role of Notch Receptors in Transcriptional Regulation.
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- Journal of Cellular Physiology, 2015, v. 230, n. 5, p. 982, doi. 10.1002/jcp.24872
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- Publication type:
- Article
DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity.
- Published in:
- Nucleic Acids Research, 2024, v. 52, n. 7, p. 3837, doi. 10.1093/nar/gkae164
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- Publication type:
- Article
Transcriptional Regulation of Rod Photoreceptor Homeostasis Revealed by In Vivo NRL Targetome Analysis.
- Published in:
- PLoS Genetics, 2012, v. 8, n. 4, p. 1, doi. 10.1371/journal.pgen.1002649
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- Publication type:
- Article
DARDN: A Deep-Learning Approach for CTCF Binding Sequence Classification and Oncogenic Regulatory Feature Discovery.
- Published in:
- Genes, 2024, v. 15, n. 2, p. 144, doi. 10.3390/genes15020144
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- Publication type:
- Article
Nickel-induced transcriptional changes persist post exposure through epigenetic reprogramming.
- Published in:
- Epigenetics & Chromatin, 2019, v. 12, n. 1, p. 1, doi. 10.1186/s13072-019-0324-3
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- Publication type:
- Article
Target analysis by integration of transcriptome and ChIP-seq data with BETA.
- Published in:
- Nature Protocols, 2013, v. 8, n. 12, p. 2502, doi. 10.1038/nprot.2013.150
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- Publication type:
- Article
Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III.
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- PLoS Genetics, 2023, v. 18, n. 4, p. 1, doi. 10.1371/journal.pgen.1010705
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- Publication type:
- Article
YY1 is a cis-regulator in the organoid models of high mammographic density.
- Published in:
- Bioinformatics, 2020, v. 36, n. 6, p. 1663, doi. 10.1093/bioinformatics/btz812
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- Publication type:
- Article
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.
- Published in:
- Bioinformatics, 2009, v. 25, n. 15, p. 1952, doi. 10.1093/bioinformatics/btp340
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- Publication type:
- Article