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CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction.
- Published in:
- Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad687
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- Publication type:
- Article
Association Plots: visualizing cluster-specific associations in high-dimensional correspondence analysis biplots.
- Published in:
- Journal of the Royal Statistical Society: Series C (Applied Statistics), 2023, v. 72, n. 4, p. 1023, doi. 10.1093/jrsssc/qlad039
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- Article
Prediction of protein–protein interactions using sequences of intrinsically disordered regions.
- Published in:
- Proteins, 2023, v. 91, n. 7, p. 980, doi. 10.1002/prot.26486
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- Publication type:
- Article
2023 Outstanding Contributions to ISCB Award: Shoba Ranganathan.
- Published in:
- Bioinformatics, 2023, v. 39, p. i3, doi. 10.1093/bioinformatics/btad306
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- Publication type:
- Article
2023 ISCB Overton Prize: Jingyi Jessica Li.
- Published in:
- Bioinformatics, 2023, v. 39, p. i5, doi. 10.1093/bioinformatics/btad307
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- Publication type:
- Article
2023 ISCB innovator award: Dana Pe'er.
- Published in:
- Bioinformatics, 2023, v. 39, p. i7, doi. 10.1093/bioinformatics/btad318
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- Publication type:
- Article
2023 ISCB accomplishments by a senior scientist award: Mark Gerstein.
- Published in:
- Bioinformatics, 2023, v. 39, p. i9, doi. 10.1093/bioinformatics/btad316
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- Publication type:
- Article
IsoTools: a flexible workflow for long-read transcriptome sequencing analysis.
- Published in:
- Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad364
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- Publication type:
- Article
Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries.
- Published in:
- Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-02971-4
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- Article
2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir.
- Published in:
- Bioinformatics, 2022, v. 38, p. i1, doi. 10.1093/bioinformatics/btac339
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- Article
2022 ISCB Overton Prize: Po-Ru Loh.
- Published in:
- Bioinformatics, 2022, v. 38, p. i3, doi. 10.1093/bioinformatics/btac338
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- Publication type:
- Article
2022 ISCB Innovator Award: Núria López-Bigas.
- Published in:
- Bioinformatics, 2022, v. 38, p. i5, doi. 10.1093/bioinformatics/btac336
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- Article
2022 Outstanding Contributions to ISCB Award: Reinhard Schneider.
- Published in:
- Bioinformatics, 2022, v. 38, p. i7, doi. 10.1093/bioinformatics/btac337
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- Publication type:
- Article
TADA—a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs.
- Published in:
- Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02631-z
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- Publication type:
- Article
RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes.
- Published in:
- EMBO Journal, 2021, v. 40, n. 24, p. 1, doi. 10.15252/embj.2020105862
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- Publication type:
- Article
Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.
- Published in:
- Nucleic Acids Research, 2021, v. 49, n. 21, p. 12178, doi. 10.1093/nar/gkab1100
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- Publication type:
- Article
Quantifying the tissue-specific regulatory information within enhancer DNA sequences.
- Published in:
- NAR Genomics & Bioinformatics, 2021, v. 3, n. 4, p. 1, doi. 10.1093/nargab/lqab095
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- Publication type:
- Article
ISCB Honors 2021 Award Recipients Peer Bork, Barbara Engelhardt, Ben Raphael, Teresa Attwood.
- Published in:
- Bioinformatics, 2021, v. 37, p. i1, doi. 10.1093/bioinformatics/btab383
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- Publication type:
- Article
A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion.
- Published in:
- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02397-w
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- Publication type:
- Article
Conserved DNA sequence features underlie pervasive RNA polymerase pausing.
- Published in:
- Nucleic Acids Research, 2021, v. 49, n. 8, p. 4402, doi. 10.1093/nar/gkab208
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- Publication type:
- Article
SVIM-asm: structural variant detection from haploid and diploid genome assemblies.
- Published in:
- Bioinformatics, 2020, v. 36, n. 22/23, p. 5519, doi. 10.1093/bioinformatics/btaa1034
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- Publication type:
- Article
Ranbow: A fast and accurate method for polyploid haplotype reconstruction.
- Published in:
- PLoS Computational Biology, 2020, v. 16, n. 5, p. 1, doi. 10.1371/journal.pcbi.1007843
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- Publication type:
- Article
Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication.
- Published in:
- Viruses (1999-4915), 2020, v. 12, n. 1, p. 71, doi. 10.3390/v12010071
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- Publication type:
- Article
SVIM: structural variant identification using mapped long reads.
- Published in:
- Bioinformatics, 2019, v. 35, n. 17, p. 2907, doi. 10.1093/bioinformatics/btz041
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- Publication type:
- Article
Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks.
- Published in:
- Molecular Systems Biology, 2019, v. 15, n. 5, p. N.PAG, doi. 10.15252/msb.20188339
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- Publication type:
- Article
Predicting enhancers in mammalian genomes using supervised hidden Markov models.
- Published in:
- BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2708-6
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- Publication type:
- Article
The Distance Precision Matrix: computing networks from non-linear relationships.
- Published in:
- Bioinformatics, 2019, v. 35, n. 6, p. 1009, doi. 10.1093/bioinformatics/bty724
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- Publication type:
- Article
Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions.
- Published in:
- BMC Biology, 2018, v. 16, n. 1, p. 1, doi. 10.1186/s12915-018-0585-5
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- Publication type:
- Article
Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise.
- Published in:
- PLoS Genetics, 2018, v. 14, n. 11, p. 1, doi. 10.1371/journal.pgen.1007793
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- Publication type:
- Article
coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers.
- Published in:
- PLoS Computational Biology, 2018, v. 14, n. 8, p. 1, doi. 10.1371/journal.pcbi.1006372
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- Publication type:
- Article
Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance.
- Published in:
- Genome Medicine, 2018, v. 10, n. 1, p. N.PAG, doi. 10.1186/s13073-018-0562-1
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- Publication type:
- Article
Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. 6, p. 2868, doi. 10.1093/nar/gky051
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- Publication type:
- Article
Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. 6, p. 3258, doi. 10.1093/nar/gky122
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- Publication type:
- Article
An improved compound Poisson model for the number of motif hits in DNA sequences.
- Published in:
- Bioinformatics, 2017, v. 33, n. 24, p. 3929, doi. 10.1093/bioinformatics/btx539
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- Publication type:
- Article
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. 19, p. 11004, doi. 10.1093/nar/gkx756
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- Publication type:
- Article
Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. 4, p. 1805, doi. 10.1093/nar/gkw1163
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- Publication type:
- Article
Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns.
- Published in:
- PLoS Computational Biology, 2016, v. 12, n. 12, p. 1, doi. 10.1371/journal.pcbi.1005249
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- Publication type:
- Article
Corrigendum: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.
- Published in:
- Nature Communications, 2016, v. 7, n. 11, p. 13784, doi. 10.1038/ncomms13784
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- Publication type:
- Article
Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.
- Published in:
- Nature Communications, 2016, v. 7, n. 9, p. 12621, doi. 10.1038/ncomms12621
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- Publication type:
- Article
Genome-wide Chromatin Profiling of Legionella pneumophila-Infected Human Macrophages Reveals Activation of the Probacterial Host Factor TNFAIP2.
- Published in:
- 2016
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- Publication type:
- journal article
Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor.
- Published in:
- Molecular Biology & Evolution, 2016, v. 33, n. 1, p. 185, doi. 10.1093/molbev/msv210
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- Publication type:
- Article
Reconstruction of gene networks using prior knowledge.
- Published in:
- BMC Systems Biology, 2015, v. 9, p. 1, doi. 10.1186/s12918-015-0233-4
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- Publication type:
- Article
Somatic neurofibromatosis type 1 (NF1) inactivation events in cutaneous neurofibromas of a single NF1 patient.
- Published in:
- European Journal of Human Genetics, 2015, v. 23, n. 6, p. 870, doi. 10.1038/ejhg.2014.210
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- Publication type:
- Article
Translational regulation shapes the molecular landscape of complex disease phenotypes.
- Published in:
- Nature Communications, 2015, v. 6, n. 5, p. 7200, doi. 10.1038/ncomms8200
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- Publication type:
- Article
histoneHMM: Differential analysis of histone modifications with broad genomic footprints.
- Published in:
- BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0491-6
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- Publication type:
- Article
histoneHMM: Differential analysis of histone modifications with broad genomic footprints.
- Published in:
- BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0491-6
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- Publication type:
- Article
Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling.
- Published in:
- Nucleic Acids Research, 2014, v. 42, n. 22, p. 13689, doi. 10.1093/nar/gku1234
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- Publication type:
- Article
Inferring the paths of somatic evolution in cancer.
- Published in:
- Bioinformatics, 2014, v. 30, n. 17, p. 2456, doi. 10.1093/bioinformatics/btu319
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- Publication type:
- Article
Condition-specific target prediction from motifs and expression.
- Published in:
- Bioinformatics, 2014, v. 30, n. 12, p. 1643, doi. 10.1093/bioinformatics/btu066
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- Publication type:
- Article
Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana.
- Published in:
- Frontiers in Plant Science, 2014, v. 5, p. 1, doi. 10.3389/fpls.2014.00273
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- Publication type:
- Article