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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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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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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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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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The role of the Bhattacharyya distance in stochastic model updating

Mechanical systems and signal processing, 2019-02, Vol.117, p.437-452

2019

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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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gkmSVM: an R package for gapped-kmer SVM

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

2016

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Advanced Line Sampling for efficient robust reliability analysis

Structural safety, 2015-01, Vol.52, p.170-182

2015

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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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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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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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Understanding Human Errors in Construction Industry: Where, When, How and Why We Make Mistakes

1, 2023

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Long-term performance assessment and design of offshore structures

Computers & structures, 2015-07, Vol.154, p.101-115

2015

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Predicting Gene Expression from Sequence

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

2004

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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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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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Arts Therapies for Anxiety, Depression, and Quality of Life in Breast Cancer Patients: A Systematic Review and Meta-Analysis

Evidence-based complementary and alternative medicine, 2014-01, Vol.2014 (2014), p.1-9

2014

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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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Enhancer Predictions and Genome-Wide Regulatory Circuits

Annual review of genomics and human genetics, 2020-08, Vol.21 (1), p.37-54

2020

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Engineering computation under uncertainty – Capabilities of non-traditional models

Computers & structures, 2008-05, Vol.86 (10), p.1024-1041

2008

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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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Enhanced regulatory sequence prediction using gapped k-mer features

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

Predicting enhancer activity and variant impact using gkm‐SVM

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

The role of the Bhattacharyya distance in stochastic model updating

Comparison of the transcriptional landscapes between human and mouse tissues

gkmSVM: an R package for gapped-kmer SVM

Advanced Line Sampling for efficient robust reliability analysis

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

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

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

Understanding Human Errors in Construction Industry: Where, When, How and Why We Make Mistakes

Long-term performance assessment and design of offshore structures

Predicting Gene Expression from Sequence

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

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

Arts Therapies for Anxiety, Depression, and Quality of Life in Breast Cancer Patients: A Systematic Review and Meta-Analysis

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

Enhancer Predictions and Genome-Wide Regulatory Circuits

Engineering computation under uncertainty – Capabilities of non-traditional models

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

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