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Enhanced regulatory sequence prediction using gapped k-mer features

PLoS computational biology, 2014-07, Vol.10 (7), p.e1003711-e1003711

2014

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Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals

Nature communications, 2024-07, Vol.15 (1), p.6464-16, Article 6464

2024

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Loop competition and extrusion model predicts CTCF interaction specificity

Nature communications, 2021-02, Vol.12 (1), p.1046-1046, Article 1046

2021

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Discriminative prediction of mammalian enhancers from DNA sequence

Genome research, 2011-12, Vol.21 (12), p.2167-2180

2011

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A method to predict the impact of regulatory variants from DNA sequence

Nature genetics, 2015-08, Vol.47 (8), p.955-961

2015

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Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy

PLoS computational biology, 2018-12, Vol.14 (12), p.e1006625-e1006625

2018

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Comparison of the transcriptional landscapes between human and mouse tissues

Proceedings of the National Academy of Sciences - PNAS, 2014-12, Vol.111 (48), p.17224-17229

2014

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Indicators of Successful Career Transitions from Physical Sciences and Engineering to Biomedical Research

Current genomics, 2021-12, Vol.22 (4), p.301-305

Beer, Michael A

2021

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Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis

Molecular cell, 2007-06, Vol.26 (5), p.745-752

2007

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Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

Nature genetics, 2023-08, Vol.55 (8), p.1336-1346

2023

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Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation

Proceedings of the National Academy of Sciences - PNAS, 2009-03, Vol.106 (9), p.3384-3389

2009

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Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space

PloS one, 2015-10, Vol.10 (10), p.e0140557-e0140557

2015

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Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X

PloS one, 2017-04, Vol.12 (4), p.e0170403

2017

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Epigenomic landscapes of retinal rods and cones

eLife, 2016-03, Vol.5, p.e11613-e11613

2016

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Predicting enhancer activity and variant impact using gkm‐SVM

Human mutation, 2017-09, Vol.38 (9), p.1251-1258

Beer, Michael A.

2017

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Early Transcriptional Responses of Human Nasal Epithelial Cells to Infection with Influenza A and SARS-CoV-2 Virus Differ and Are Influenced by Physiological Temperature

Pathogens (Basel), 2023-03, Vol.12 (3), p.480

2023

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Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach

Proteomics (Weinheim), 2009-03, Vol.9 (5), p.1374-1384

2009

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Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression

Nature communications, 2015-01, Vol.6 (1), p.5903, Article 5903

2015

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Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer

Genome medicine, 2021-10, Vol.13 (1), p.158-158, Article 158

2021

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Group normalization for genomic data

PloS one, 2012-08, Vol.7 (8), p.e38695-e38695

2012

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gkmSVM: an R package for gapped-kmer SVM

Bioinformatics (Oxford, England), 2016-07, Vol.32 (14), p.2205-2207

2016

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Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b

Genome Research, 2008-02, Vol.18 (2), p.252-260

2008

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Sequence-based correction of barcode bias in massively parallel reporter assays

Genome research, 2021-09, Vol.31 (9), p.1638-1645

2021

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Predicting Gene Expression from Sequence

Cell, 2004-04, Vol.117 (2), p.185-198

2004

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kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

Nucleic acids research, 2013-07, Vol.41 (Web Server issue), p.W544

2013

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Enhanced regulatory sequence prediction using gapped k-mer features

Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals

Loop competition and extrusion model predicts CTCF interaction specificity

Discriminative prediction of mammalian enhancers from DNA sequence

A method to predict the impact of regulatory variants from DNA sequence

Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy

Comparison of the transcriptional landscapes between human and mouse tissues

Indicators of Successful Career Transitions from Physical Sciences and Engineering to Biomedical Research

Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis

Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation

Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space

Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X

Epigenomic landscapes of retinal rods and cones

Predicting enhancer activity and variant impact using gkm‐SVM

Early Transcriptional Responses of Human Nasal Epithelial Cells to Infection with Influenza A and SARS-CoV-2 Virus Differ and Are Influenced by Physiological Temperature

Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression

Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer

Group normalization for genomic data

gkmSVM: an R package for gapped-kmer SVM

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b

Sequence-based correction of barcode bias in massively parallel reporter assays

Predicting Gene Expression from Sequence

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

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