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Marc S. Halfon - Publications

Affiliations: 
State University of New York, Buffalo, Buffalo, NY, United States 
Area:
mesoderm development, transcriptional regulatory elements
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52/58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Dyer NA, Lucas ER, Nagi SC, McDermott D, Brenas JH, Miles A, Clarkson CS, Mawejje HD, Wilding CS, Halfon MS, Asma H, Heinz E, Donnelly MJ. Mechanisms of transcriptional regulation in revealed by allele specific expression. Biorxiv : the Preprint Server For Biology. PMID 38045426 DOI: 10.1101/2023.11.22.568226  0.323
2023 Weinstein ML, Jaenke CM, Asma H, Spangler M, Kohnen KA, Konys CC, Williams ME, Williams AV, Rebeiz M, Halfon MS, Williams TM. A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait. Plos Genetics. 19: e1010653. PMID 36795790 DOI: 10.1371/journal.pgen.1010653  0.422
2023 Lindhorst D, Halfon MS. Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences. Bmc Genomics. 24: 17. PMID 36639739 DOI: 10.1186/s12864-023-09123-9  0.301
2022 Keränen SVE, Villahoz-Baleta A, Bruno AE, Halfon MS. REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. Insects. 13. PMID 35886794 DOI: 10.3390/insects13070618  0.385
2021 Asma H, Halfon MS. Annotating the Insect Regulatory Genome. Insects. 12. PMID 34209769 DOI: 10.3390/insects12070591  0.311
2021 Schember I, Halfon MS. Identification of new Anopheles gambiae transcriptional enhancers using a cross-species prediction approach. Insect Molecular Biology. PMID 33866636 DOI: 10.1111/imb.12705  0.325
2020 Tomoyasu Y, Halfon MS. How to study enhancers in non-traditional insect models. The Journal of Experimental Biology. 223. PMID 32034049 DOI: 10.1242/jeb.212241  0.411
2020 Halfon MS. Silencers, Enhancers, and the Multifunctional Regulatory Genome. Trends in Genetics : Tig. PMID 31918861 DOI: 10.1016/j.tig.2019.12.005  0.468
2019 Asma H, Halfon MS. Computational enhancer prediction: evaluation and improvements. Bmc Bioinformatics. 20: 174. PMID 30953451 DOI: 10.1186/s12859-019-2781-x  0.389
2019 Zhou Y, Popadowski SE, Deutschman E, Halfon MS. Correction: Distinct roles and requirements for Ras pathway signaling in visceral versus somatic muscle founder specification (doi: 10.1242/dev.169003). Development (Cambridge, England). 146. PMID 30770381 DOI: 10.1242/Dev.176743  0.609
2019 Zhou Y, Popadowski SE, Deustchman E, Halfon MS. Distinct roles and requirements for Ras pathway signaling in visceral versus somatic muscle founder specification. Development (Cambridge, England). 146. PMID 30630823 DOI: 10.1242/Dev.169003  0.638
2019 Halfon MS. Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases. Trends in Genetics : Tig. 35: 93-103. PMID 30553552 DOI: 10.1016/j.tig.2018.11.004  0.442
2019 Kazemian M, Halfon MS. CRM Discovery Beyond Model Insects. Methods in Molecular Biology (Clifton, N.J.). 1858: 117-139. PMID 30414115 DOI: 10.1007/978-1-4939-8775-7_10  0.431
2018 Rivera J, Keränen SVE, Gallo SM, Halfon MS. REDfly: the transcriptional regulatory element database for Drosophila. Nucleic Acids Research. PMID 30329093 DOI: 10.1093/nar/gky957  0.488
2018 Lai YT, Deem KD, Borràs-Castells F, Sambrani N, Rudolf H, Suryamohan K, El-Sherif E, Halfon MS, McKay DJ, Tomoyasu Y. Enhancer identification and activity evaluation in the red flour beetle,. Development (Cambridge, England). PMID 29540499 DOI: 10.1242/Dev.160663  0.745
2017 Halfon MS. Perspectives on Gene Regulatory Network Evolution. Trends in Genetics : Tig. PMID 28528721 DOI: 10.1016/j.tig.2017.04.005  0.41
2016 Suryamohan K, Hanson C, Andrews E, Sinha S, Scheel MD, Halfon MS. Redeployment of a conserved gene regulatory network during Aedes aegypti development. Developmental Biology. PMID 27341759 DOI: 10.1016/J.Ydbio.2016.06.031  0.773
2015 Suryamohan K, Halfon MS. Identifying transcriptional cis-regulatory modules in animal genomes. Wiley Interdisciplinary Reviews. Developmental Biology. 4: 59-84. PMID 25704908 DOI: 10.1002/Wdev.168  0.775
2014 Kazemian M, Suryamohan K, Chen JY, Zhang Y, Samee MA, Halfon MS, Sinha S. Evidence for deep regulatory similarities in early developmental programs across highly diverged insects. Genome Biology and Evolution. 6: 2301-20. PMID 25173756 DOI: 10.1093/Gbe/Evu184  0.764
2014 Dobi KC, Halfon MS, Baylies MK. Whole-genome analysis of muscle founder cells implicates the chromatin regulator Sin3A in muscle identity. Cell Reports. 8: 858-70. PMID 25088419 DOI: 10.1016/j.celrep.2014.07.005  0.394
2014 Atkinson TJ, Halfon MS. Regulation of gene expression in the genomic context. Computational and Structural Biotechnology Journal. 9: e201401001. PMID 24688749 DOI: 10.5936/csbj.201401001  0.366
2011 Halfon MS, Zhu Q, Brennan ER, Zhou Y. Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules. Bmc Genomics. 12: 578. PMID 22115527 DOI: 10.1186/1471-2164-12-578  0.706
2011 Kazemian M, Zhu Q, Halfon MS, Sinha S. Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. Nucleic Acids Research. 39: 9463-72. PMID 21821659 DOI: 10.1093/Nar/Gkr621  0.583
2011 Zhu Q, Miecznikowski JC, Halfon MS. A wholly defined Agilent microarray spike-in dataset. Bioinformatics (Oxford, England). 27: 1284-9. PMID 21414985 DOI: 10.1093/Bioinformatics/Btr135  0.48
2011 Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, Bergman CM, Halfon MS. REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Research. 39: D118-23. PMID 20965965 DOI: 10.1093/Nar/Gkq999  0.428
2010 Escamilla-Hernandez R, Chakrabarti R, Romano RA, Smalley K, Zhu Q, Lai W, Halfon MS, Buck MJ, Sinha S. Genome-wide search identifies Ccnd2 as a direct transcriptional target of Elf5 in mouse mammary gland. Bmc Molecular Biology. 11: 68. PMID 20831799 DOI: 10.1186/1471-2199-11-68  0.602
2010 Zhu Q, Miecznikowski JC, Halfon MS. Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. Bmc Bioinformatics. 11: 285. PMID 20507584 DOI: 10.1186/1471-2105-11-285  0.49
2009 Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Göttgens B, Halfon MS, Sinha S. Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Developmental Cell. 17: 568-79. PMID 19853570 DOI: 10.1016/J.Devcel.2009.09.002  0.602
2009 Leatherbarrow JR, Halfon MS. Identification of receptor-tyrosine-kinase-signaling target genes reveals receptor-specific activities and pathway branchpoints during Drosophila development. Genetics. 181: 1335-45. PMID 19189950 DOI: 10.1534/genetics.108.098475  0.405
2009 Zhu Q, Halfon MS. Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster. Bmc Genomics. 10: 9. PMID 19128496 DOI: 10.1186/1471-2164-10-9  0.608
2008 Yakoby N, Bristow CA, Gong D, Schafer X, Lembong J, Zartman JJ, Halfon MS, Schüpbach T, Shvartsman SY. A combinatorial code for pattern formation in Drosophila oogenesis. Developmental Cell. 15: 725-37. PMID 19000837 DOI: 10.1016/J.Devcel.2008.09.008  0.392
2008 Ivan A, Halfon MS, Sinha S. Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biology. 9: R22. PMID 18226245 DOI: 10.1186/Gb-2008-9-1-R22  0.331
2008 Halfon MS, Gallo SM, Bergman CM. REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Research. 36: D594-8. PMID 18039705 DOI: 10.1093/nar/gkm876  0.437
2008 Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, ... ... Halfon MS, et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research. 36: D107-13. PMID 18006570 DOI: 10.1093/Nar/Gkm967  0.412
2007 Halfon MS, Arnosti DN. New tools, resources for gene regulatory analysis in Drosophila. Fly. 1: 123-4. PMID 19378457 DOI: 10.4161/Fly.4291  0.383
2007 Zhu Q, Halfon MS. Vector-dependent gene expression driven by insulated P-element reporter vectors. Fly. 1: 55-6. PMID 18690057 DOI: 10.4161/Fly.3892  0.521
2007 Li L, Zhu Q, He X, Sinha S, Halfon MS. Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biology. 8: R101. PMID 17550599 DOI: 10.1186/Gb-2007-8-6-R101  0.581
2006 Halfon MS. (Re)modeling the transcriptional enhancer. Nature Genetics. 38: 1102-3. PMID 17006462 DOI: 10.1038/ng1006-1102  0.439
2006 Estrada B, Choe SE, Gisselbrecht SS, Michaud S, Raj L, Busser BW, Halfon MS, Church GM, Michelson AM. An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes. Plos Genetics. 2: e16. PMID 16482229 DOI: 10.1371/Journal.Pgen.0020016  0.644
2006 Gallo SM, Li L, Hu Z, Halfon MS. REDfly: a Regulatory Element Database for Drosophila. Bioinformatics (Oxford, England). 22: 381-3. PMID 16303794 DOI: 10.1093/bioinformatics/bti794  0.48
2005 Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biology. 6: R16. PMID 15693945 DOI: 10.1186/Gb-2005-6-2-R16  0.557
2004 Grad YH, Roth FP, Halfon MS, Church GM. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics (Oxford, England). 20: 2738-50. PMID 15145800 DOI: 10.1093/Bioinformatics/Bth320  0.428
2002 Halfon MS, Gisselbrecht S, Lu J, Estrada B, Keshishian H, Michelson AM. New fluorescent protein reporters for use with the Drosophila Gal4 expression system and for vital detection of balancer chromosomes. Genesis (New York, N.Y. : 2000). 34: 135-8. PMID 12324968 DOI: 10.1002/gene.10136  0.67
2002 Halfon MS, Michelson AM. Exploring genetic regulatory networks in metazoan development: methods and models. Physiological Genomics. 10: 131-43. PMID 12209016 DOI: 10.1152/physiolgenomics.00072.2002  0.578
2002 Halfon MS, Grad Y, Church GM, Michelson AM. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Research. 12: 1019-28. PMID 12097338 DOI: 10.1101/gr.228902  0.611
2002 Carmena A, Buff E, Halfon MS, Gisselbrecht S, Jiménez F, Baylies MK, Michelson AM. Reciprocal regulatory interactions between the Notch and Ras signaling pathways in the Drosophila embryonic mesoderm. Developmental Biology. 244: 226-42. PMID 11944933 DOI: 10.1006/dbio.2002.0606  0.714
2000 Halfon MS, Carmena A, Gisselbrecht S, Sackerson CM, Jiménez F, Baylies MK, Michelson AM. Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors. Cell. 103: 63-74. PMID 11051548 DOI: 10.1016/S0092-8674(00)00105-7  0.595
1998 Halfon MS, Keshishian H. The Toll pathway is required in the epidermis for muscle development in the Drosophila embryo. Developmental Biology. 199: 164-74. PMID 9676200 DOI: 10.1006/dbio.1998.8915  0.637
1997 Halfon MS, Kose H, Chiba A, Keshishian H. Targeted gene expression without a tissue-specific promoter: creating mosaic embryos using laser-induced single-cell heat shock. Proceedings of the National Academy of Sciences of the United States of America. 94: 6255-60. PMID 9177204 DOI: 10.1073/Pnas.94.12.6255  0.681
1995 Halfon MS, Hashimoto C, Keshishian H. The Drosophila toll gene functions zygotically and is necessary for proper motoneuron and muscle development. Developmental Biology. 169: 151-67. PMID 7750635 DOI: 10.1006/Dbio.1995.1134  0.651
1993 Tolias PP, Konsolaki M, Halfon MS, Stroumbakis ND, Kafatos FC. Elements controlling follicular expression of the s36 chorion gene during Drosophila oogenesis. Molecular and Cellular Biology. 13: 5898-906. PMID 8355717 DOI: 10.1128/Mcb.13.9.5898  0.647
1993 Keshishian H, Chiba A, Chang TN, Halfon MS, Harkins EW, Jarecki J, Wang L, Anderson M, Cash S, Halpern ME. Cellular mechanisms governing synaptic development in Drosophila melanogaster. Journal of Neurobiology. 24: 757-87. PMID 8251016 DOI: 10.1002/Neu.480240606  0.718
Low-probability matches (unlikely to be authored by this person)
2020 Sinha S, Jones BM, Traniello IM, Bukhari SA, Halfon MS, Hofmann HA, Huang S, Katz PS, Keagy J, Lynch VJ, Sokolowski MB, Stubbs LJ, Tabe-Bordbar S, Wolfner MF, Robinson GE. Behavior-related gene regulatory networks: A new level of organization in the brain. Proceedings of the National Academy of Sciences of the United States of America. PMID 32661177 DOI: 10.1073/Pnas.1921625117  0.3
2011 Tu C, Li J, Young R, Page BJ, Engler F, Halfon MS, Canty JM, Qu J. Combinatorial peptide ligand library treatment followed by a dual-enzyme, dual-activation approach on a nanoflow liquid chromatography/orbitrap/electron transfer dissociation system for comprehensive analysis of swine plasma proteome. Analytical Chemistry. 83: 4802-13. PMID 21491903 DOI: 10.1021/Ac200376M  0.263
2023 Garza AB, Garcia R, Solis LM, Halfon MS, Girgis HZ. EnhancerTracker: Comparing cell-type-specific enhancer activity of DNA sequence triplets via an ensemble of deep convolutional neural networks. Biorxiv : the Preprint Server For Biology. PMID 38187673 DOI: 10.1101/2023.12.23.573198  0.235
2022 Schember I, Halfon MS. Common Themes and Future Challenges in Understanding Gene Regulatory Network Evolution. Cells. 11. PMID 35159319 DOI: 10.3390/cells11030510  0.235
2021 Nowling RJ, Behura SK, Halfon MS, Emrich SJ, Duman-Scheel M. PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map. Hereditas. 158: 7. PMID 33509290 DOI: 10.1186/s41065-021-00172-2  0.202
2023 Garza AB, Garcia R, Halfon MS, Girgis HZ. Evaluation of metric and representation learning approaches: Effects of representations driven by relative distance on the performance. 2023 Intelligent Methods, Systems, and Applications. 2023: 545-550. PMID 37822849 DOI: 10.1109/imsa58542.2023.10217475  0.082
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