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Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases

Trends in genetics, 2019-02, Vol.35 (2), p.93-103

Halfon, Marc S.

2019

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Silencers, Enhancers, and the Multifunctional Regulatory Genome

Trends in genetics, 2020-03, Vol.36 (3), p.149-151

Halfon, Marc S.

2020

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Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences

BMC genomics, 2023-01, Vol.24 (1), p.17-17, Article 17

2023

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Improved methodology for fixation and preparation of Aedes aegypti embryos

PloS one, 2024-05, Vol.19 (5), p.e0304802

2024

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Conserved and novel enhancers in the Aedes aegypti single-minded locus recapitulate embryonic ventral midline gene expression

PLoS genetics, 2024-04, Vol.20 (4), p.e1010891-e1010891

2024

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Computational enhancer prediction: evaluation and improvements

BMC bioinformatics, 2019-04, Vol.20 (1), p.174-15, Article 174

2019

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A new suite of reporter vectors and a novel landing site survey system to study cis-regulatory elements in diverse insect species

Scientific reports, 2024-05, Vol.14 (1), p.10078-10078, Article 10078

2024

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Behavior-related gene regulatory networks: A new level of organization in the brain

Proceedings of the National Academy of Sciences - PNAS, 2020-09, Vol.117 (38), p.23270-23279

2020

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A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait

PLoS genetics, 2023-02, Vol.19 (2), p.e1010653-e1010653

2023

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Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum

Development (Cambridge), 2018-04, Vol.145 (7), p.dev160663-dev160663

2018

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Annotating the Insect Regulatory Genome

Insects (Basel, Switzerland), 2021-06, Vol.12 (7), p.591

2021

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Identifying transcriptional cis-regulatory modules in animal genomes

Wiley interdisciplinary reviews. Developmental biology, 2015-03, Vol.4 (2), p.59-84

2015

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Common Themes and Future Challenges in Understanding Gene Regulatory Network Evolution

Cells (Basel, Switzerland), 2022-02, Vol.11 (3), p.510

2022

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Regulatory genome annotation of 33 insect species

eLife, 2024-10, Vol.13

2024

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Perspectives on Gene Regulatory Network Evolution

Trends in genetics, 2017-07, Vol.33 (7), p.436-447

Halfon, Marc S

2017

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Whole-Genome Analysis of Muscle Founder Cells Implicates the Chromatin Regulator Sin3A in Muscle Identity

Cell reports (Cambridge), 2014-08, Vol.8 (3), p.858-870

2014

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REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics

Insects (Basel, Switzerland), 2022-07, Vol.13 (7), p.618

2022

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PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map

Hereditas, 2021-01, Vol.158 (1), p.7-7, Article 7

2021

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Regulation of gene expression in the genomic context

Computational and structural biotechnology journal, 2014-01, Vol.9 (13), p.e201401001-e201401001, Article e201401001

2014

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Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset

BMC bioinformatics, 2010-05, Vol.11 (1), p.285-285, Article 285

2010

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How to study enhancers in non-traditional insect models

Journal of experimental biology, 2020-02, Vol.223 (Pt Suppl 1)

2020

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REDfly: a Regulatory Element Database for Drosophila

Bioinformatics, 2006-02, Vol.22 (3), p.381-383

2006

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Ras Pathway Specificity Is Determined by the Integration of Multiple Signal-Activated and Tissue-Restricted Transcription Factors

Cell, 2000-09, Vol.103 (1), p.63-74

2000

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Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

BMC genomics, 2009-01, Vol.10 (1), p.9-9

2009

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Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules

BMC genomics, 2011-11, Vol.12 (1), p.578-578, Article 578

2011

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Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases

Silencers, Enhancers, and the Multifunctional Regulatory Genome

Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences

Improved methodology for fixation and preparation of Aedes aegypti embryos

Conserved and novel enhancers in the Aedes aegypti single-minded locus recapitulate embryonic ventral midline gene expression

Computational enhancer prediction: evaluation and improvements

A new suite of reporter vectors and a novel landing site survey system to study cis-regulatory elements in diverse insect species

Behavior-related gene regulatory networks: A new level of organization in the brain

A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait

Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum

Annotating the Insect Regulatory Genome

Identifying transcriptional cis-regulatory modules in animal genomes

Common Themes and Future Challenges in Understanding Gene Regulatory Network Evolution

Regulatory genome annotation of 33 insect species

Perspectives on Gene Regulatory Network Evolution

Whole-Genome Analysis of Muscle Founder Cells Implicates the Chromatin Regulator Sin3A in Muscle Identity

REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics

PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map

Regulation of gene expression in the genomic context

Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset

How to study enhancers in non-traditional insect models

REDfly: a Regulatory Element Database for Drosophila

Ras Pathway Specificity Is Determined by the Integration of Multiple Signal-Activated and Tissue-Restricted Transcription Factors

Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules

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