Halfon Lab

Halfon Lab Publications

• Asma, H., Liu, L., and Halfon, M.S. (2024). SCRMshaw: Supervised cis-regulatory module prediction for insect genomes. PLoS One, 19(12):e0311752. doi: 10.1371/journal.pone.0311752. PMID: 39637210.
• Sterling-Lentsch, G., Halfon, M.S. (2024). Identification of a novel downstream single-minded midline regulatory element in Drosophila melanogaster. microPublication Biology. 10.17912/micropub.biology.001317.
• Dyer, N.A., Lucas, E.R., Nagi, S.C., McDermott, D.P., Brenas, H., Miles, A., Clarkson, C.S., Mawejje, H.D., Wilding, C.S., Halfon, M.S., Asma, A., Heinz, E., and Donnelly, M.J. (2024). Mechanisms of transcriptional regulation in Anopheles gambiae revealed by allele specific expression. Proc. R. Soc. B. 291:20241142. doi: 10.1098/rspb.2024.1142. PMID: 39288798.
• Asma, H., Tieke, E. Deem, K.D., Rahmat, J., Dong, T., Huang, X., Tomoyasu, Y. and Halfon, M.S. (2024). Regulatory genome annotation of 33 insect species. eLife, 13:RP96738. doi: 10.7554/eLife.96738.1.
• Reid, W., Sterling-Lentsch, G., and Halfon, M.S. (2024). Improved methodology for fixation and preparation of Aedes aegypti embryos. PLoS One, 19(5): e0304802. doi: 10.1371/journal.pone.0304802. PMID: 38820371.
• Schember, I., Reid, W., Sterling-Lentsch, G. and Halfon, M.S. (2024). Conserved and novel enhancers in the Aedes aegypti single-minded locus recapitulate embryonic ventral midline gene expression. PLoS Genetics, 20(4): e1010891. doi: 10.1371/journal.pgen.1010891. PMID: 38683842.
• Deem, K.D., Halfon, M.S. and Tomoyasu, Y. (2024). A new suite of reporter vectors and a novel landing site survey system to study cis-regulatory elements in diverse insect species. Scientific Reports, 14(1):10078. doi: 10.1038/s41598-024-60432-9. PMID: 38698030.
• Garza, A.B., Garcia, R, Halfon, M.S., Girgis, H.Z. (2023). Evaluation of metric and representation learning approaches: Effects of representations driven by relative distance on the performance. Intell Method Syst Appl. doi: 10.1109/imsa58542.2023.10217475. PMID: 37822849.
• Weinstein, M.L., Jaenke, C.M., Asma, H. G, Spangler, M., Kohnen, K.A., Konys, C., Williams, M.E., Williams, A.V., Rebeiz, M., Halfon, M.S., and Williams, T.M. (2023). A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait. PLoS Genetics, 19(2):e1010653. doi: 10.1371/journal.pgen.1010653. PMID: 36795790.
• Lindhorst, D. and Halfon, M.S. (2023). Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences. BMC Genomics, 24(17). doi: 10.1186/s12864-023-09123-9. PMID: 36639739.
• Keränen, S.V.E., Villahoz-Baleta, A., Bruno, A.E., and Halfon, M.S. (2022). REDfly: An integrated knowledgebase for insect regulatory genomics. Insects, 13:618. doi: 10.3390/ insects13070618. PMID: 35886794.
• Schember, I. and Halfon, M.S. (2022). Common Themes and Future Challenges in Understanding Gene Regulatory Network Evolution. Cells 11(3): 510. doi: 10.3390/cells11030510. PMID: 35159319.
• Asma, H. and Halfon, M.S. (2021). Annotating the insect regulatory genome. Insects, 12(7):591. doi: 10.3390/insects12070591. PMID: 34209769.
• Schember, I. and Halfon, M.S. (2021). Identification of new Anopheles gambiae transcriptional enhancers using a cross-species prediction approach. Insect Mol. Biol., doi: 10.1111/imb.12705. PMID: 33866636.
• Nowling, R.J., Behura, S.K., Halfon, M.S., Emrich, S.J., and Duman-Scheel, M. (2021). PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map. Hereditas, 158(1):7. doi: 10.1186/s41065-021-00172-2. PMID: 33509290.
• Halfon, M.S. (2020). Silencers, enhancers, and the multifunctional regulatory genome. Trends Genet. 35(3):149-151. doi: 10.1016/j.tig.2019.12.005. PMID: 31918861.
• Sinha, S., Jones, B., Traniello, I., Bukhari, S.A., Halfon, M.S., Hofmann, H.A., Huang, S., Katz, P., Keagy, J., Lynch, V.J., Sokolowski, M., Stubbs, L.J., Tabe-Bordbar, S., Wolfner, M., and Robinson, G.E. (2020). Behavior-related gene regulatory networks: a new level of organization in the brain. Proc. Natl. Acad. Sci. USA, doi:10.1073/pnas.1921625117. PMID: 32661177.
• Tomoyasu, Y. and Halfon, M.S. (2020). How to study enhancers in non-traditional insect models. J. Exp. Biol., 223(Pt Suppl 1). doi: 10.1242/jeb.212241. PMID: 32034049
• Asma, H. and Halfon, M.S. (2019). Computational enhancer prediction: evaluation and improvements. BMC Bioinformatics, 20:174. doi: 10.1186/s12859-019-2781-x. PMID: 30953451
• Zhou, Y., Popadowski, S.E., Deutschman, E. and Halfon, M.S. (2019). Distinct roles and requirements for Ras pathway signaling in visceral versus somatic muscle founder specification in the Drosophila mesoderm. Development, 146:dev169003. doi: 10.1242/dev.169003. PMID: 30630823
• Halfon, M.S. (2018). Studying transcriptional enhancers: the founder fallacy, validation creep, and other biases. Trends Genet. doi: 10.1016/j.tig.2018.11.004 PMID: 30553552
• Kazemian, M. and Halfon, M.S. (2019). CRM Discovery beyond model insects. Methods Mol. Biol., 1858:117-139. doi: 10.1007/978-1-4939-8775-7_10. PMID: 30414115
• Rivera, J., Keränen, S.V.E., Gallo, S.M. and Halfon, M.S. (2018). REDfly: the transcriptional regulatory element database for Drosophila. Nucl. Acids Res., epub 17 October 2018, doi:10.1093/nar/gky957. PMID: 30329093
• Lai, Y-T., Deem, K.D., Borras-Castells, F., Sambrani, N., Rudolf, H., Suryamohan, K., El-Sherif, E., Halfon, M.S., McKay, D.J. and Tomoyasu, Y. (2018). Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum. Development, 145(7):dev160663. PMID: 29540499
• Halfon, M.S. (2017). Perspectives on gene regulatory network evolution. Trends Genet., 33(7):436-447. doi: 10.1016/j.tig.2017.04.005. PMID: 28528721
• Suryamohan, K. , Hanson, C., Andrews, E., Sinha, S., Duman Scheel, M. and Halfon, M.S. (2016). Redeployment of a conserved gene regulatory network during Aedes aegypti development. Developmental Biology, 416(2):402-413. doi:10.1016/j.ydbio.2016.06.031. PMID: 27341759
• Suryamohan, K. and Halfon, M.S. (2015). Insect Regulatory Genomics. In Short Views on Insect Genomics and Proteomics, C. Raman, M.R. Goldsmith, and T.A. Agunbiade, eds. (Springer International Publishing), pp. 119-155. [invited book chapter.] doi: 10.1007/978-3-319-24235-4_6.
• Suryamohan, K. and Halfon, M.S. (2015). Identifying transcriptional cis-regulatory modules in animal genomes. WIREs Dev Biol. 4:59-89. doi: 10.1002/wdev.168. PMID: 25704908 PMCID: PMC4339228
• Kazemian, M.*, Suryamohan, K.*, Chen, J. *, Zhang, Y., Samee, M.A.H., Halfon, M.S.† and Sinha, S.† (2014). Evidence for Deep Regulatory Similarities in Early Developmental Programs across Highly Diverged Insects. Genome Biology and Evolution, 6(9):2301-2320. doi: 10.1093/gbe/evu184. PMID: 25173756 PMCID: PMC4217690 *equal contribution, †co-corresponding authors
• Dobi, K.C., Halfon, M.S. and Baylies, M.K. (2014). Whole genome analysis of muscle founder cells implicates the chromatin regulator Sin3A in muscle identity. Cell Reports, 8(3):858-870. doi: 10.1016/j.celrep.2014.07.005. PMID: 25088419
• Atkinson, T.J. and Halfon, M.S. (2014). Gene regulation in the genomic context. Comput Struct Biotechnol J, 9(13):e201401001. doi: 10.5936/csbj.201401001. PMID: 24688749 PMCID: PMC3962188
• Halfon, M.S., Zhu, Q. , Brennan, E.R. , and Zhou, Y. (2011). Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules. BMC Genomics,12:578- epub Nov 25. PMID: 22115527 PMCID: PMC3235160
• Kazemian, M., Zhu, Q. , Halfon, M.S.*, Sinha, S*. (2011). Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. Nucl. Acids Res., 39:9463-9472. doi: 10.1093/nar/gkr621. PMID: 21821659 PMCID: PMC3239187 *co-corresponding authors
• Tu, C., Li, J., Young, R., Page, B.J., Engler, F., Halfon, M.S., Canty, J.M. and Qu, J. (2011). 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. Anal Chem. 83(12):4802-13. PMID: 21491903 PMCID: PMC3125109
• Zhu, Q., Miecznikowski, J.C., and Halfon, M.S. (2011). A wholly-defined Agilent microarray spike-in dataset. Bioinformatics, 27:1290-1298. doi:10.1093/bioinformatics/btr135. PMID: 21414985 PMCID: PMC3109518
• Gallo, S.M., Gerrard, D.T., Miner, D., Simich, M., Des Soye, B., Bergman, C.M. and Halfon, M.S. (2011). REDfly v3.0: Toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucl. Acids Res. First published online October 21, 2010 doi:10.1093/nar/gkq999. PMID: 20965965 PMCID: PMC3013816
• Escamilla-Hernandez, R., Chakrabarti, R., Romano, R., Smalley, K., Zhu, Q., Lai, W., Halfon, M.S., Buck, M.J. and Sinha, S. (2010). Genome-wide search identifies Ccnd2 as a direct transcriptional target of Elf5 in mouse mammary gland. BMC Molecular Biology, 10:68. PMID: 20831799 PMCID: PMC2949602
• Zhu, Q., Miecznikowski, J.C., and Halfon, M.S. (2010). Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. BMC Bioinformatics, 11:285. PMID: 20507584. PMCID: PMC2897828
• Kantorovitz, M.R., Kazemian, M., Kinston, S., Miranda-Saavedra, D., Zhu, Q., Robinson, G.E., Göttgens, B., Halfon, M.S.* and Sinha, S.* (2009). Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Developmental Cell, 17:568-579. PMID: 19853570. PMCID: PMC2768654. *co-corresponding authors
• Leatherbarrow, J.R. and Halfon, M.S. (2009). Identification of receptor tyrosine kinase signaling target genes reveals receptor-specific activities and pathway branchpoints during Drosophila development. Genetics, 181:1335-1345. doi:10.1534/genetics.108.098475. PMID: 19189950. PMCID: PMC2666503.
• Zhu, Q. and Halfon, M.S. (2009). Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster. BMC Genomics, 10:9, doi:10.1186/1471-2164-10-9. PMID: 19128496. PMCID: PMC2631479.
• Yakoby, N., Bristow, C.A., Gong, D., Schafer, X.L., Lembong, J., Zartman, J.J., Halfon, M.S., Schüpbach, T., Shavartsman, S.Y. (2008). A combinatorial code for pattern formation in Drosophila oogenesis. Developmental Cell, 15:725-737. PMID: 19000837. PMCID: PMC2822874.
• Ivan, A., Halfon, M. S. and Sinha, S. (2008). Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biology, 9:R22. PMID: 18226245. PMCID: PMC2395258. *A Genome Biology “highly accessed” publication
• Griffith OL, Montgomery SB, Bernier B, Chu B, Aerts S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Mahony S, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJM, and The Open Regulatory Annotation Consortium. (2008). ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 36(suppl_1):D107-113. doi:10.1093/nar/gkm967. PMID: 18006570. PMCID: PMC2239002.
• Halfon, M. S., Gallo, S. M. and Bergman, C. M. (2008). REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Res., 36(suppl_1):D594-598. doi: 10.1093/nar/gkm876. PMID: 18039705. PMCID: PMC2238825.
• Halfon, M. S. and Arnosti, David N. (2007). New tools, resources for gene regulatory analysis in Drosophila. Fly, 1:123-124. PMID: 18690057
• Li, L., Zhu, Q., He, X., Sinha, S. and Halfon, M. S. (2007). Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biology, 8:R101. PMID: 17550599. PMCID: PMC2394749. *A Genome Biology “highly accessed” publication and Faculty of 1000 “recommended” selection
• Zhu, Q. and Halfon, M. S. (2007). Vector-dependent gene expression driven by insulated P-element reporter vectors. Fly, 1(1) 55-56.
• Estrada, B., Choe, S. E., Gisselbrecht, S., Michaud, S.,Raj, L., Busser, B. W., Halfon, M. S., Church, G. M. and Michelson, A. M. (2006). An integrated strategy for analyzing the developmental programs of different myoblast subtypes. PLoS Genetics, 2:e16. PMID: 16482229. PMCID: PMC1366495.
• Halfon, M.S. (2006). (Re)Modeling the transcriptional enhancer. Nature Genetics, 38:1102-1103. PMID: 17006462
• Gallo, S. M., Li, L., Hu, Z. and Halfon, M. S. (2006). REDfly: a regulatory element database for Drosophila. Bioinformatics, 22:381-383. Published online 22 Nov 2005, doi:10.1093/bioinformatics/bti794. PMID: 16303794
• Choe, S. E., Boutros, M., Michelson, A. M., Church, G. M. and Halfon, M. S. (2005). Preferred analysis methods for Affymetrix GeneChips revealed by a wholly-defined control dataset. Genome Biology, 6:R16. PMID: 15693945. PMCID: PMC551536. *A Genome Biology “highly accessed” publication and Faculty of 1000 “must read” selection
• Grad, Y., Roth, F. P., Halfon, M. S. and Church, G. M. (2004). Prediction of similarly-acting cis -regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D. pseudoobscura. Bioinformatics. 20:2738-2750. PMID: 15145800
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