Full Text Journal Articles by
Author Marc S Halfon

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

Saurabh Sinha, Beryl M Jones, Ian M Traniello, Syed A Bukhari, Marc S Halfon, Hans A Hofmann, Sui Huang, Paul S Katz, Jason Keagy, Vincent J Lynch, Marla B Sokolowski, Lisa J Stubbs, Shayan Tabe-Bordbar, Mariana F Wolfner, Gene E Robinson,

Neuronal networks are the standard heuristic model today for describing brain activity associated with animal behavior. Recent studies have revealed an extensive role for a completely distinct layer of networked activities in the brain-the gene regulatory network (GRN)-that orchestrates expression levels of hundreds to thousands of genes in a behavior-related ... Read more >>

Proc Natl Acad Sci U S A (Proceedings of the National Academy of Sciences of the United States of America)
[2020, 117(38):23270-23279]

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How to study enhancers in non-traditional insect models.

Yoshinori Tomoyasu, Marc S Halfon,

Transcriptional enhancers are central to the function and evolution of genes and gene regulation. At the organismal level, enhancers play a crucial role in coordinating tissue- and context-dependent gene expression. At the population level, changes in enhancers are thought to be a major driving force that facilitates evolution of diverse ... Read more >>

J Exp Biol (The Journal of experimental biology)
[2020, 223(Pt Suppl 1):]

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Silencers, Enhancers, and the Multifunctional Regulatory Genome.

Marc S Halfon,

Negative regulation of gene expression by transcriptional silencers has been difficult to study due to limited defined examples. A new study by Gisselbrecht et al. has dramatically increased the number of identified silencers and reveals that they are bifunctional regulatory sequences that also act as gene expression-promoting enhancers. ... Read more >>

Trends Genet (Trends in genetics : TIG)
[2020, 36(3):149-151]

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Computational enhancer prediction: evaluation and improvements.

Hasiba Asma, Marc S Halfon,

BACKGROUND:Identifying transcriptional enhancers and other cis-regulatory modules (CRMs) is an important goal of post-sequencing genome annotation. Computational approaches provide a useful complement to empirical methods for CRM discovery, but it is critical that we develop effective means to evaluate their performance in terms of estimating their sensitivity and specificity. RESULTS:We ... Read more >>

BMC Bioinformatics (BMC bioinformatics)
[2019, 20(1):174]

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Correction: Distinct roles and requirements for Ras pathway signaling in visceral versus somatic muscle founder specification (doi: 10.1242/dev.169003).

Yiyun Zhou, Sarah E Popadowski, Emily Deutschman, Marc S Halfon,

Development (Development (Cambridge, England))
[2019, 146(4):]

Cited: 0 times

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Distinct roles and requirements for Ras pathway signaling in visceral versus somatic muscle founder specification.

Yiyun Zhou, Sarah E Popadowski, Emily Deutschman, Marc S Halfon,

Pleiotropic signaling pathways must somehow engender specific cellular responses. In the Drosophila mesoderm, Ras pathway signaling specifies muscle founder cells from among the broader population of myoblasts. For somatic muscles, this is an inductive process mediated by the ETS-domain downstream Ras effectors Pointed and Aop (Yan). We demonstrate here that ... Read more >>

Development (Development (Cambridge, England))
[2019, 146(2):]

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CRM Discovery Beyond Model Insects.

Majid Kazemian, Marc S Halfon,

Although the number of sequenced insect genomes numbers in the hundreds, little is known about gene regulatory sequences in any species other than the well-studied Drosophila melanogaster. We provide here a detailed protocol for using SCRMshaw, a computational method for predicting cis-regulatory modules (CRMs, also "enhancers") in sequenced insect genomes. ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2019, 1858:117-139]

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REDfly: the transcriptional regulatory element database for Drosophila.

John Rivera, Soile V E Keränen, Steven M Gallo, Marc S Halfon,

The REDfly database provides a comprehensive curation of experimentally-validated Drosophila transcriptional cis-regulatory elements and includes information on DNA sequence, experimental evidence, patterns of regulated gene expression, and more. Now in its thirteenth year, REDfly has grown to over 23 000 records of tested reporter gene constructs and 2200 tested transcription ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2019, 47(D1):D828-D834]

Cited: 6 times

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

Marc S Halfon,

Transcriptional enhancers play a major role in regulating metazoan gene expression. Recent developments in genomics and next-generation sequencing have accelerated and revitalized the study of this important class of sequence elements. Increased interest and attention, however, has also led to troubling trends in the enhancer literature. In this Opinion, I ... Read more >>

Trends Genet (Trends in genetics : TIG)
[2019, 35(2):93-103]

Cited: 6 times

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

Yi-Ting Lai, Kevin D Deem, Ferran Borràs-Castells, Nagraj Sambrani, Heike Rudolf, Kushal Suryamohan, Ezzat El-Sherif, Marc S Halfon, Daniel J McKay, Yoshinori Tomoyasu,

Evolution of cis-regulatory elements (such as enhancers) plays an important role in the production of diverse morphology. However, a mechanistic understanding is often limited by the absence of methods for studying enhancers in species other than established model systems. Here, we sought to establish methods to identify and test enhancer ... Read more >>

Development (Development (Cambridge, England))
[2018, 145(7):]

Cited: 4 times

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Perspectives on Gene Regulatory Network Evolution.

Marc S Halfon,

Animal development proceeds through the activity of genes and their cis-regulatory modules (CRMs) working together in sets of gene regulatory networks (GRNs). The emergence of species-specific traits and novel structures results from evolutionary changes in GRNs. Recent work in a wide variety of animal models, and particularly in insects, has ... Read more >>

Trends Genet (Trends in genetics : TIG)
[2017, 33(7):436-447]

Cited: 16 times

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Redeployment of a conserved gene regulatory network during Aedes aegypti development.

Kushal Suryamohan, Casey Hanson, Emily Andrews, Saurabh Sinha, Molly Duman Scheel, Marc S Halfon,

Changes in gene regulatory networks (GRNs) underlie the evolution of morphological novelty and developmental system drift. The fruitfly Drosophila melanogaster and the dengue and Zika vector mosquito Aedes aegypti have substantially similar nervous system morphology. Nevertheless, they show significant divergence in a set of genes co-expressed in the midline of ... Read more >>

Dev Biol (Developmental biology)
[2016, 416(2):402-413]

Cited: 5 times

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Identifying transcriptional cis-regulatory modules in animal genomes.

Kushal Suryamohan, Marc S Halfon,

Gene expression is regulated through the activity of transcription factors (TFs) and chromatin-modifying proteins acting on specific DNA sequences, referred to as cis-regulatory elements. These include promoters, located at the transcription initiation sites of genes, and a variety of distal cis-regulatory modules (CRMs), the most common of which are transcriptional ... Read more >>

Wiley Interdiscip Rev Dev Biol (Wiley interdisciplinary reviews. Developmental biology)
[2015, 4(2):59-84]

Cited: 23 times

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Evidence for deep regulatory similarities in early developmental programs across highly diverged insects.

Majid Kazemian, Kushal Suryamohan, Jia-Yu Chen, Yinan Zhang, Md Abul Hassan Samee, Marc S Halfon, Saurabh Sinha,

Many genes familiar from Drosophila development, such as the so-called gap, pair-rule, and segment polarity genes, play important roles in the development of other insects and in many cases appear to be deployed in a similar fashion, despite the fact that Drosophila-like "long germband" development is highly derived and confined ... Read more >>

Genome Biol Evol (Genome biology and evolution)
[2014, 6(9):2301-2320]

Cited: 14 times

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Whole-genome analysis of muscle founder cells implicates the chromatin regulator Sin3A in muscle identity.

Krista C Dobi, Marc S Halfon, Mary K Baylies,

Skeletal muscles are formed in numerous shapes and sizes, and this diversity impacts function and disease susceptibility. To understand how muscle diversity is generated, we performed gene expression profiling of two muscle subsets from Drosophila embryos. By comparing the transcriptional profiles of these subsets, we identified a core group of ... Read more >>

Cell Rep (Cell reports)
[2014, 8(3):858-870]

Cited: 11 times

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Regulation of gene expression in the genomic context.

Taylor J Atkinson, Marc S Halfon,

Metazoan life is dependent on the proper temporal and spatial control of gene expression within the many cells-essentially all with the identical genome-that make up the organism. While much is understood about how individual gene regulatory elements function, many questions remain about how they interact to maintain correct regulation globally ... Read more >>

Comput Struct Biotechnol J (Computational and structural biotechnology journal)
[2014, 9:e201401001]

Cited: 12 times

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

Marc S Halfon, Qianqian Zhu, Elizabeth R Brennan, Yiyun Zhou,

Cis-regulatory modules are bound by transcription factors to regulate gene expression. Characterizing these DNA sequences is central to understanding gene regulatory networks and gaining insight into mechanisms of transcriptional regulation, but genome-scale regulatory module discovery remains a challenge. One popular approach is to scan the genome for clusters of transcription ... Read more >>

BMC Genomics (BMC genomics)
[2011, 12:578]

Cited: 9 times

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Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.

Majid Kazemian, Qiyun Zhu, Marc S Halfon, Saurabh Sinha,

Despite recent advances in experimental approaches for identifying transcriptional cis-regulatory modules (CRMs, 'enhancers'), direct empirical discovery of CRMs for all genes in all cell types and environmental conditions is likely to remain an elusive goal. Effective methods for computational CRM discovery are thus a critically needed complement to empirical approaches. ... Read more >>

Nucleic Acids Res (Nucleic acids research)
[2011, 39(22):9463-9472]

Cited: 17 times

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A wholly defined Agilent microarray spike-in dataset.

Qianqian Zhu, Jeffrey C Miecznikowski, Marc S Halfon,

Spike-in datasets provide a valuable resource for assessing and comparing among competing microarray analysis strategies. Our previous wholly defined spike-in datasets, the Golden and Platinum Spikes, have provided insights for the analysis of Affymetrix GeneChips. However, a similar dataset, in which all cRNA identities and relative levels are known prospectively, ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2011, 27(9):1284-1289]

Cited: 6 times

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REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila.

Steven M Gallo, Dave T Gerrard, David Miner, Michael Simich, Benjamin Des Soye, Casey M Bergman, Marc S Halfon,

The REDfly database of Drosophila transcriptional cis-regulatory elements provides the broadest and most comprehensive available resource for experimentally validated cis-regulatory modules and transcription factor binding sites among the metazoa. The third major release of the database extends the utility of REDfly as a powerful tool for both computational and experimental ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2011, 39(Database issue):D118-23]

Cited: 111 times

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Genome-wide search identifies Ccnd2 as a direct transcriptional target of Elf5 in mouse mammary gland.

Rosalba Escamilla-Hernandez, Rumela Chakrabarti, Rose-Anne Romano, Kirsten Smalley, Qianqian Zhu, William Lai, Marc S Halfon, Michael J Buck, Satrajit Sinha,

The ETS transcription factor Elf5 (also known as ESE-2) is highly expressed in the mammary gland and plays an important role in its development and differentiation. Indeed studies in mice have illustrated an essential role for Elf5 in directing alveologenesis during pregnancy. Although the molecular mechanisms that underlie the developmental ... Read more >>

BMC Mol. Biol. (BMC molecular biology)
[2010, 11:68]

Cited: 10 times

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

Qianqian Zhu, Jeffrey C Miecznikowski, Marc S Halfon,

Concomitant with the rise in the popularity of DNA microarrays has been a surge of proposed methods for the analysis of microarray data. Fully controlled "spike-in" datasets are an invaluable but rare tool for assessing the performance of various methods.We generated a new wholly defined Affymetrix spike-in dataset consisting of ... Read more >>

BMC Bioinformatics (BMC bioinformatics)
[2010, 11:285]

Cited: 23 times

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Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse.

Miriam R Kantorovitz, Majid Kazemian, Sarah Kinston, Diego Miranda-Saavedra, Qiyun Zhu, Gene E Robinson, Berthold Göttgens, Marc S Halfon, Saurabh Sinha,

We present new approaches to cis-regulatory module (CRM) discovery in the common scenario where relevant transcription factors and/or motifs are unknown. Beginning with a small list of CRMs mediating a common gene expression pattern, we search genome-wide for CRMs with similar functionality, using new statistical scores and without requiring known ... Read more >>

Dev Cell (Developmental cell)
[2009, 17(4):568-579]

Cited: 41 times

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A combinatorial code for pattern formation in Drosophila oogenesis.

Nir Yakoby, Christopher A Bristow, Danielle Gong, Xenia Schafer, Jessica Lembong, Jeremiah J Zartman, Marc S Halfon, Trudi Schüpbach, Stanislav Y Shvartsman,

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations ... Read more >>

Dev Cell (Developmental cell)
[2008, 15(5):725-737]

Cited: 48 times

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Identification of receptor-tyrosine-kinase-signaling target genes reveals receptor-specific activities and pathway branchpoints during Drosophila development.

John R Leatherbarrow, Marc S Halfon,

Receptor tyrosine kinases (RTKs) are an important family of signaling molecules with the unusual property that they are able to transduce their signals using the same downstream pathways. This has led to an unresolved debate as to whether individual receptors are interchangeable, or if each receptor can mediate specific downstream ... Read more >>

Genetics (Genetics)
[2009, 181(4):1335-1345]

Cited: 5 times

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