Marc S. Halfon - Publications

State University of New York, Buffalo, Buffalo, NY, United States 
mesoderm development, transcriptional regulatory elements

41 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
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  0.56
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2006 Halfon MS. (Re)modeling the transcriptional enhancer. Nature Genetics. 38: 1102-3. PMID 17006462 DOI: 10.1038/ng1006-1102  1
2006 Irizarry RA, Cope LM, Wu Z. Feature-level exploration of a published Affymetrix GeneChip control dataset. Genome Biology. 7: 404. PMID 16953902 DOI: 10.1186/Gb-2006-7-8-404  1
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  1
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  1
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  1
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  0.6
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  1
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  1
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  1
2002 GuhaThakurta D, Palomar L, Stormo GD, Tedesco P, Johnson TE, Walker DW, Lithgow G, Kim S, Link CD. Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. Genome Research. 12: 701-12. PMID 11997337 DOI: 10.1101/gr.228902  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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