Williams TM and Rebeiz M. (2023) “JEZB special issue on animal gene regulatory network evolution.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 1-3.

Williams TM. (2021) “In the Spotlight-Early career researcher.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 1-2.

       **Included in “Gene Regulatory Network Evolution in Animals” special issue **

Finet C, Kassner VA, Carvalho AB, Chung H, Day JP, Delaney EK, De Re FC, Dufour HD, Dupim E, Izumitani HF, Gauterio TB, Justen J, Katoh T,  Kopp A, Koshikawa S, Ben Longdon, Elgion L Loreto, Maria DS Nunes, Komal KB Raja, Mark Rebeiz, Michael G Ritchie, Gayane Saakyan, Sneddon T, Teramoto M, Tyukmaeva V, Vanderlinde T, Wey EE, Werner T, Williams TM, Robe LJ, Toda MJ, Marletaz F. (2021) “DrosoPhyla: genomic resources for drosophilid phylogeny and systematics.” Accepted for publication in Molecular Biology and Evolution (July 29 2021).

Hughes JT, Williams ME, Rebeiz M, and Williams TM. (2021) “Widespread cis- and trans-regulatory evolution underlies the origin, diversification, and loss of a sexually dimorphic fruit fly pigmentation trait.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 1–19.

       **Included in “Gene Regulatory Network Evolution in Animals” special issue **

Hughes JT, Williams ME, Johnson R, Grover S, Rebeiz M, and Williams TM. (2020) “Gene Regulatory Network Homoplasy Underlies Recurrent Sexually Dimorphic Fruit Fly Pigmentation.” Frontiers in Ecology and Evolution. March 26; 8. DOI=10.3389/fevo.2020.00080.

This article is part of the Research Topic Evo-Devo of Color Pattern Formation

Camino EM, Weinstein ML, List MP, Vellky JE, Rebeiz M, and Williams TM. (2020) “Red light/green light, a dual fluorescent protein reporter system to study enhancer-promoter specificity in Drosophila.” G3: Genes, Genomes, Genetics. March 1; 10(3): 985-997.

Liu Y, Ramos-Womack M, Han C, Reilly P, Brackett KL, Rogers W, Williams TM, Andolfatto P, Stern DL, and Rebeiz M. (2019) “Changes throughout a genetic network mask the contribution of Hox gene evolution.” Current Biology. Jun 21. DOI: 10.1016/j.cub.2019.05.074, PMID: 31257142

Grover S, Williams ME, Hughes JT, Kaiser R, Gresham L, Rebeiz M, and Williams TM. (2018) “Augmentation of a wound response element accompanies the origin of a Hox-regulated Drosophila abdominal pigmentation trait.” Developmental Biology Sep 1; 441(1):159-175. doi: 10.1016/j.ydbio.2018.07.001. PMID: 29981311

Roeske MJ, Camino EM, Grover S, Rebeiz M, and Williams TM. (2018) “Cis-regulatory evolution integrated the Bric-à-brac transcription factors into a novel fruit fly gene regulatory network.” eLife. 2018;7:e32273 doi: 10.7554/eLife.32273

Pham T, Glassford WJ, Johnson WC, Williams TM, and Rebeiz M. (2017) “The evolutionary origination of a novel expression pattern through an extreme heterochronic shift”. Evolution and Development.  Mar;19(2):43-55. DOI: 10.1111/ede.12215

Rebeiz, M and Williams TM. (2017) “Using Drosophila pigmentation traits to study the mechanisms of cis-regulatory evolution”. Current Opinion in Insect Science. Feb; 19: 1-7. doi: 10.1016/j.cois.2016.10.002

Johnson WC, Ordway AJ, Watada M, Pruitt JN, Williams TM, and Rebeiz M. “Genetic Variation in a Transcriptional Silencer Element Confers Phenotypic Diversity in a Drosophila Population.” (PLoS Genet 11(6): e1005279. doi: 10.1371/journal.pgen.1005279. ).

Camino EM, Butts JC, Ordway AJ, Vellky JE, Rebeiz, MR, and Williams TM. (2015) “The evolutionary origination and diversification of a dimorphic gene regulatory network through parallel innovations in cis and trans.” (PLoS Genet 11(4): e1005136. doi:10.1371/journal.pgen.1005136).

Ordway A, Hancuch K, Johnson W, Parks J, Williams TM, and Rebeiz M. (2014) The expansion of body coloration involves coordinated evolution in cis and trans within the pigmentation regulatory network of Drosophila prostipennisDevelopmental Biology. DOI: 10.1016/j.ydbio.2014.05.023

Rogers WA, Grover S, Stringer SJ, Parks J, Rebeiz M, and Williams TM. (2014) A survey of the trans-regulatory landscape for Drosophila melanogaster abdominal pigmentation. Developmental Biology. 385: 417-432.

Salomone JR, Rogers WA, Rebeiz M, and Williams TM. (2013) The evolution of Bab paralog expression and abdominal pigmentation among Sophophora fruit fly species. Evolution and Development. Volume 15(6): 442-457.

Rogers WA, Salomone JR, Tacy DJ, Camino EM, Davis KA, Rebeiz M, and Williams TM. (2013) Recurrent Modification of a Conserved Cis-Regulatory Element Underlies Fruit Fly Pigmentation Diversity. PLoS Genet 9(8): e1003740. doi:10.1371/journal.pgen.1003740

Rogers WA and Williams TM. (2011) Quantitative comparison of cis-Regulatory Element (CRE) activities in transgenic Drosophila melanogaster. Journal of Visualized Experiments.  Dec; 58 ( e3395): 1-6.

Rebeiz M. and Williams TM. Experimental Approaches to Evaluate the Contributions of Candidate Cis-regulatory Mutations to Phenotypic Evolution. (2011) In: Orgogozo V, Rockman M, editors. Molecular Methods for Evolutionary Genetics. Humana Press (Vol. 772, ISBN 978-1-61779-227-4)

Werner T, Koshikawa S, Williams TM, and Carroll SB. (2010) Generation and evolution of a complex wing color pattern controlled by the Wingless morphogen. Nature. Apr; 22: 464 (7292): 1143-8. (Cover)

Williams TM and Carroll SB. (2009) Genetic and molecular insights into the development and evolution of sexual dimorphism. Nature Reviews Genetics. Nov; 10: 797-804.

Shirangi TR, Dufour HD, Williams TM, and Carroll SB. (2009) Rapid Evolution of Sex-Pheromone-producing Enzyme in Drosophila. PLoS Biology. Aug 7 (8): e1000168.doi:10.1371.pbio.1000168.

Williams TM, Selegue JE, Werner T, Gompel N, Kopp A, and Carroll SB. (2008) The Regulation and Evolution of a Genetic Switch Controlling Sexually Dimorphic Traits in Drosophila. Cell. Aug 22; 134: 610-623. (Cover).

Prud’homme B, Gompel N, Rokas A, Kassner VA, Williams TM, Yeh SD, True JR, Carroll SB. (2006) Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature. Apr 20; 440 (7087): 1050-3.

Williams TM, Williams ME, and Innis JW. (2005) Range of HOX/TALE superclass associations and protein domain requirements for HOXA13:MEIS interaction. Developmental Biology. 2005 Jan 15; 277 (2): 457-71.

Williams TM, Williams ME, Kuick R, Misek D, McDonagh K, Hanash S, & Innis JW. (2005) Candidate Downstream Regulated Genes of HOX Group 13 Transcription Factors with and without Monomeric DNA Binding Capability. Developmental Biology. Mar 15; 279(2): 462-80.

Williams TM, Williams ME, Heaton JH, Gelehrter TD, and Innis JW. (2005) Group 13 HOX Proteins Interact with the MH2 Domain of R-Smads and Modulate Smad Transcriptional Activation Functions Independent of HOX DNA Binding Capability. Nucleic Acids Research. Aug 8; 33 (14): 4475-84.

Innis JW, Mortlock D, Chen Z, Ludwig M, Williams ME, Williams TM, Doyle CD, Shao Z, Glynn M, Mikulic D, Lehmann K, Mundlos S, and Utsch B. (2004) Polyalanine expansion in HOXA13: Three new affected families and the molecular consequences in a mouse model. Human Molecular Genetics. 2004 Nov 15;13 (22): 2841-51.

Innis JW, Goodman FR, Bacchelli C, Williams TM, Mortlock DP, Sateesh P, Scambler PJ, McKinnon W, and Guttmacher AE. A HOXA13 allele with a missense mutation in the homeobox and a dinucleotide deletion in the promoter underlies Guttmacher syndrome. Hum Mutat. 2002 May; 19 (5): 573-4.

Hanash SM, Bobek MP, Rickman DS, Williams T, Rouillard JM, Kuick R, and Puravs E. Integrating cancer genomics and proteomics in the post-genome era. Proteomics. 2002 Jan; 2 (1): 69-75.

Dua K, Williams TM, and Beretta L. Translational control of the proteome: Relevance to cancer. Proteomics. 2001 Oct; 1 (10): 1191-9.

Kass DH, Raynor ME, and Williams TM. Evolutionary History of B1 Retroposons in the Genus Mus. Journal of Molecular Evolution. 2000 Sep; 51 (3): 256-64.


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