Publications
Google Scholar
* authors contributed equally; Rebeiz lab members appear in bold
35. Smith SJ, Davidson L, Rebeiz M, Evolutionary expansion of apical extracellular matrix is required for the elongation of cells in a novel structure. (2019) Elife doi: 10.7554/eLife.55965 (2020)
Accompanied by an insight article written by Jocelyn McDonald and Yoshi Tomoyasu
34. Vincent BJ*, Rice GR*, Wong GM, Glassford WJ, Downs K, Shastay J, Charles-Obi K, Natarajan M, Gogol MM, Zeitlinger J, Rebeiz M. An atlas of transcription factors expressed in the Drosophila melanogaster pupal terminalia. G3 9(12):3961-3972 (2019) (COVER IMAGE)
33. Camino EM, List MP, Vellky J, Rebeiz M, and Williams. TM Red light/green light, a dual fluorescent protein reporter system to study enhancer-promoter specificity in Drosophila. G3 10(3):985-997 (2020)
32. Rice GR, David J, Kamimura Y, Masly JP, Mcgregor A, Nagy O, Noselli, S, Nunes MDS, O'Grady, P, Sánchez-Herrero E, Siegal, Toda MJ*, Rebeiz M*, Courtier-Orgogozo V*, Yassin A*. A standardized nomenclature and atlas of the male terminalia of Drosophila melanogaster. Fly 19: 1-14(2019)
31. Liu Y, Ramos-Womack M, Han C, Reilly P, LaRue K, Rogers W, Williams T, Andolfatto P, Stern D, Rebeiz M. Changes throughout a genetic network mask the contribution of Hox gene evolution. Current Biology 29(13): 2157-66 (2019)
Accompanied by a Dispatch article written by Nicolas Gompel and Benjamin Prud’homme
30. Grover S, Williams M, Kaiser R, Hughes JT, Gresham L, Spradling V, Rebeiz M, Williams TM. Co-option of a wound response element accompanies the origin of a Hox-regulated Drosophila abdominal pigmentation trait. Developmental Biology, 441(1), 159-175 (2018)
29. Roeske MJ, Camino EM, Grover S, Rebeiz M, Williams TM. Cis-regulatory evolution integrated the Bric-à-brac transcription factors into a novel fruit fly gene regulatory network. Elife e32273 (2018)
28. Smith AF, Posakony JW, Rebeiz M. Automated tools for comparative sequence analysis of genic regions using the GenePalette application. Developmental Biology, 429 (1), 158-164 (2017)
27. Pham T, Glassford WJ, Johnson WC, Williams TM, Rebeiz M. The evolutionary origination of a novel expression pattern through an extreme heterochronic shift. (in revision at Evolution & Development) (2016)
26. Signor SA, Liu Y, Rebeiz M, and Kopp A. Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila. Current Biology, pii: S0960-9822(16)30785-0 (2016).
25. Glassford WJ, Johnson WC, Dall NR, Liu Y, Boll W, Noll M, Rebeiz M. Co-option of an ancestral Hox-regulated network underlies a recently evolved morphological novelty. Developmental Cell, 34(5): 520-531 (2015) (COVER IMAGE)
Accompanied by a Preview article written by Ella Preger-Ben Noon and Nicolas Frankel
24. Johnson WC*, Ordway AJ*, Watada M, Pruitt JN, Williams TM, Rebeiz M. Genetic Changes to a Transcriptional Silencer Element Confers Phenotypic Diversity Within and Between Drosophila Species. PLoS Genetics, 11(6): e1005279 (2015)
23. Camino EM, Butts JC, Ordway AJ, Velky JE, Rebeiz M, Williams TM. The evolutionary origination and diversification of a dimorphic gene regulatory network through parallel innovations in cis and trans. PLoS Genetics, 11(4): e1005136 (2015)
22. Miller SW, Rebeiz M, Atanasov JE, and Posakony JW. Neural precursor-specific expression of multiple Drosophila genes is driven by dual enhancer modules with overlapping function. PNAS, 111(48) 17194-17199. (2014)
21. Ordway JA*, Hancuch KN*, Johnson WC, Williams TW, Rebeiz M. The expansion of body coloration involves coordinated evolution in cis and trans within the pigmentation regulatory network of Drosophila prostipennis. Dev Biol, 392(2):431-440 (2014)
20. Rogers WA, Grover S, Stringer SJ, Parks J, Rebeiz M, Williams TW. A survey of the trans-regulatory landscape for Drosophila melanogaster abdominal pigmentation. Dev Biol, 385(2):417-432 (2014) [Faculty of 1000]
19. Glassford WJ, Rebeiz M. Assessing constraints on regulatory sequence evolution. Phil Trans B, 368(1632):20130026 (2013) [Faculty of 1000]
18. Salomone JR, Rogers WA, Rebeiz M, and Williams TM. The evolution of Bab paralog expression and abdominal pigmentation among Sophophora fruit fly species. Evolution and Development, 15(6):442-457 (2013)
17. Rogers WA, Salomone J, Tacy DJ, Camino EM, Davis K, Rebeiz M, and Williams TM. Recurrent modification of a conserved cis-regulatory element underlies the diversity for a sexually dimorphic fruit fly pigmentation trait. PLoS Genetics, 9(8):e1003740 (2013)
16. Rebeiz M, Castro B, Liu F, Yue F, Posakony JW. Ancestral and conserved cis-regulatory architectures in developmental control genes. Dev Biol, 362:282-294 (2012) [Faculty of 1000]
15. Rebeiz M*, Jikomes N*, Kassner VA, Carroll SB. The evolutionary origin of a novel gene expression pattern through co-option of latent activities of existing regulatory sequences. PNAS, 108:10036-10043 (2011) [Faculty of 1000]
14. Rebeiz M*, Miller SJ*, Posakony JW. Notch regulates numb: Integration of conditional and autonomous cell fate specification. Development, 138:215-225 (2011)
13. Rebeiz M, Pool JE, Kassner VA, Aquadro CF, Carroll SB. Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population. Science, 326(5960):1663-1667 (2009) [Faculty of 1000]
12. Rebeiz M*, Ramos-Womack M*, Jeong S, Andolfatto P, Werner T, True J, Stern DL, Carroll SB. Evolution of the tan locus underlies pigment loss in Drosophila santomea: A response to Matute et al. Cell, 139(6):1189-1196 (2009)
11. Jeong S, Rebeiz M, Andolfatto P, Werner T, True J, Carroll SB. The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell, 132(5):783-793 (2008) [Faculty of 1000]
10. Rebeiz M, Stone T, Posakony JW. An ancient transcriptional regulatory linkage. Dev Biol, 281(2):299-308 (2005) [Faculty of 1000]
9. Rebeiz M, Posakony JW. GenePalette: a universal software tool for genome sequence visualization and analysis, Dev Biol. 271(2):431-438 (2004)
8. Everts-van der Wind A, Kata SR, Band MR, Rebeiz M, Larkin DM, Everts RE, Green CA, Liu L, Natarajan S, Goldammer T, Lee JH, McKay S, Womack JE, Lewin HA. A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Res, 14(7):1424-37 (2004)
7. Liu L, Gong G, Liu Y, Natarajan S, Larkin DM, Everts-van der Wind A, Rebeiz M, Beever JE. Multi-species comparative mapping in silico using the COMPASS strategy. Bioinformatics, 20(2):148-154 (2004)
6. Larkin DM, Everts-van der Wind A, Rebeiz M, Schweitzer PA, Bachman S, Green C, Wright CL, Campos EJ, Benson LD, Edwards J, Liu L, Osoegawa K, Womack JE, de Jong PJ, Lewin HA. A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res, 13(8):1966-1972 (2003)
5. Larson JH, Rebeiz MJ, Stiening CM, Windish RL, Beever JE, Lewin HA. MHC class I-like genes in cattle, MHCLA, with similarity to genes encoding NK cell stimulatory ligands. Immunogenetics, 55(1):16-22 (2003)
4. Rebeiz M, Reeves NL, Posakony JW. SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. PNAS, 99(15):9888-9893 (2002)
3. Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW, Donovan J, Windish R, Steining C, Mahyuddin P, Womack JE, Lewin HA. An ordered comparative map of the cattle and human genomes. Genome Res, 10(9):1359-1368 (2000)
2. Rebeiz M, Lewin HA. Compass of 47,787 cattle ESTs. Anim Biotechnol, 11(2):75-241 (2000)
1. Rebeiz M, Miller DJ. Porcine sperm surface ß1,4galactosyltransferase binds to the zona pellucida but is not necessary or sufficient to mediate sperm-zona pellucida binding. Mol Reprod Dev, 54(4):379-387 (1999)
BOOK CHAPTERS AND REVIEWS
8. Govindjee G, Briskin DP, Benning C, Daniell H, Kolossov V, Scheer H, Rebeiz M. From δ-aminolevulinic acid to chlorophyll and every step in between: In memory of Constantin (Tino) A. Rebeiz, 1936 – 2019. Photosynthesis Res (In Press)
7. McQueen E, Rebeiz M. On the specificity of gene regulatory networks: How does network co-option affect subsequent evolution? Current Topics Developmental Biology 139:375-405 (2020)
6. Rice G, Rebeiz M. Evolution: How Many Phenotypes Do Regulatory Mutations Affect?
Current Biology, 29(1):R21-R23 (2019)
5. Smith SJ, Rebeiz M, Davidson L. From pattern to process: studies at the interface of gene regulatory networks, morphogenesis, and evolution. Current Opinion in Genetics and Development, 51:103-110 (2018) (COVER IMAGE)
4. Rebeiz M, Tsiantis M. Enhancer evolution and the origins of morphological novelty. Current Opinion in Genetics & Development, 45:115-123 (2017)
3. Rebeiz M, Williams TM. “Using Drosophila pigmentation traits to study the mechanisms of cis-regulatory evolution”. (In Press, Current Opinion in Insect Science)
2. Rebeiz M, Patel NH, Hinman VH. “Unraveling the tangled skein: the evolution of transcriptional regulatory networks in development”. Annual Reviews of Genomics and Human Genetics, 16:103-131 (2015)
1. Rebeiz M, Williams TM. “Experimental approaches to evaluate the contribution of candidate cis-regulatory mutations to phenotypic evolution” Methods in Molecular Biology: Molecular Methods for Evolutionary Genetics. Humana Press. Edited by V. Orgogozo and M. Rockman. 772:351-75 (2011)
* authors contributed equally; Rebeiz lab members appear in bold
35. Smith SJ, Davidson L, Rebeiz M, Evolutionary expansion of apical extracellular matrix is required for the elongation of cells in a novel structure. (2019) Elife doi: 10.7554/eLife.55965 (2020)
Accompanied by an insight article written by Jocelyn McDonald and Yoshi Tomoyasu
34. Vincent BJ*, Rice GR*, Wong GM, Glassford WJ, Downs K, Shastay J, Charles-Obi K, Natarajan M, Gogol MM, Zeitlinger J, Rebeiz M. An atlas of transcription factors expressed in the Drosophila melanogaster pupal terminalia. G3 9(12):3961-3972 (2019) (COVER IMAGE)
33. Camino EM, List MP, Vellky J, Rebeiz M, and Williams. TM Red light/green light, a dual fluorescent protein reporter system to study enhancer-promoter specificity in Drosophila. G3 10(3):985-997 (2020)
32. Rice GR, David J, Kamimura Y, Masly JP, Mcgregor A, Nagy O, Noselli, S, Nunes MDS, O'Grady, P, Sánchez-Herrero E, Siegal, Toda MJ*, Rebeiz M*, Courtier-Orgogozo V*, Yassin A*. A standardized nomenclature and atlas of the male terminalia of Drosophila melanogaster. Fly 19: 1-14(2019)
31. Liu Y, Ramos-Womack M, Han C, Reilly P, LaRue K, Rogers W, Williams T, Andolfatto P, Stern D, Rebeiz M. Changes throughout a genetic network mask the contribution of Hox gene evolution. Current Biology 29(13): 2157-66 (2019)
Accompanied by a Dispatch article written by Nicolas Gompel and Benjamin Prud’homme
30. Grover S, Williams M, Kaiser R, Hughes JT, Gresham L, Spradling V, Rebeiz M, Williams TM. Co-option of a wound response element accompanies the origin of a Hox-regulated Drosophila abdominal pigmentation trait. Developmental Biology, 441(1), 159-175 (2018)
29. Roeske MJ, Camino EM, Grover S, Rebeiz M, Williams TM. Cis-regulatory evolution integrated the Bric-à-brac transcription factors into a novel fruit fly gene regulatory network. Elife e32273 (2018)
28. Smith AF, Posakony JW, Rebeiz M. Automated tools for comparative sequence analysis of genic regions using the GenePalette application. Developmental Biology, 429 (1), 158-164 (2017)
27. Pham T, Glassford WJ, Johnson WC, Williams TM, Rebeiz M. The evolutionary origination of a novel expression pattern through an extreme heterochronic shift. (in revision at Evolution & Development) (2016)
26. Signor SA, Liu Y, Rebeiz M, and Kopp A. Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila. Current Biology, pii: S0960-9822(16)30785-0 (2016).
25. Glassford WJ, Johnson WC, Dall NR, Liu Y, Boll W, Noll M, Rebeiz M. Co-option of an ancestral Hox-regulated network underlies a recently evolved morphological novelty. Developmental Cell, 34(5): 520-531 (2015) (COVER IMAGE)
Accompanied by a Preview article written by Ella Preger-Ben Noon and Nicolas Frankel
24. Johnson WC*, Ordway AJ*, Watada M, Pruitt JN, Williams TM, Rebeiz M. Genetic Changes to a Transcriptional Silencer Element Confers Phenotypic Diversity Within and Between Drosophila Species. PLoS Genetics, 11(6): e1005279 (2015)
23. Camino EM, Butts JC, Ordway AJ, Velky JE, Rebeiz M, Williams TM. The evolutionary origination and diversification of a dimorphic gene regulatory network through parallel innovations in cis and trans. PLoS Genetics, 11(4): e1005136 (2015)
22. Miller SW, Rebeiz M, Atanasov JE, and Posakony JW. Neural precursor-specific expression of multiple Drosophila genes is driven by dual enhancer modules with overlapping function. PNAS, 111(48) 17194-17199. (2014)
21. Ordway JA*, Hancuch KN*, Johnson WC, Williams TW, Rebeiz M. The expansion of body coloration involves coordinated evolution in cis and trans within the pigmentation regulatory network of Drosophila prostipennis. Dev Biol, 392(2):431-440 (2014)
20. Rogers WA, Grover S, Stringer SJ, Parks J, Rebeiz M, Williams TW. A survey of the trans-regulatory landscape for Drosophila melanogaster abdominal pigmentation. Dev Biol, 385(2):417-432 (2014) [Faculty of 1000]
19. Glassford WJ, Rebeiz M. Assessing constraints on regulatory sequence evolution. Phil Trans B, 368(1632):20130026 (2013) [Faculty of 1000]
18. Salomone JR, Rogers WA, Rebeiz M, and Williams TM. The evolution of Bab paralog expression and abdominal pigmentation among Sophophora fruit fly species. Evolution and Development, 15(6):442-457 (2013)
17. Rogers WA, Salomone J, Tacy DJ, Camino EM, Davis K, Rebeiz M, and Williams TM. Recurrent modification of a conserved cis-regulatory element underlies the diversity for a sexually dimorphic fruit fly pigmentation trait. PLoS Genetics, 9(8):e1003740 (2013)
16. Rebeiz M, Castro B, Liu F, Yue F, Posakony JW. Ancestral and conserved cis-regulatory architectures in developmental control genes. Dev Biol, 362:282-294 (2012) [Faculty of 1000]
15. Rebeiz M*, Jikomes N*, Kassner VA, Carroll SB. The evolutionary origin of a novel gene expression pattern through co-option of latent activities of existing regulatory sequences. PNAS, 108:10036-10043 (2011) [Faculty of 1000]
14. Rebeiz M*, Miller SJ*, Posakony JW. Notch regulates numb: Integration of conditional and autonomous cell fate specification. Development, 138:215-225 (2011)
13. Rebeiz M, Pool JE, Kassner VA, Aquadro CF, Carroll SB. Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population. Science, 326(5960):1663-1667 (2009) [Faculty of 1000]
12. Rebeiz M*, Ramos-Womack M*, Jeong S, Andolfatto P, Werner T, True J, Stern DL, Carroll SB. Evolution of the tan locus underlies pigment loss in Drosophila santomea: A response to Matute et al. Cell, 139(6):1189-1196 (2009)
11. Jeong S, Rebeiz M, Andolfatto P, Werner T, True J, Carroll SB. The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell, 132(5):783-793 (2008) [Faculty of 1000]
10. Rebeiz M, Stone T, Posakony JW. An ancient transcriptional regulatory linkage. Dev Biol, 281(2):299-308 (2005) [Faculty of 1000]
9. Rebeiz M, Posakony JW. GenePalette: a universal software tool for genome sequence visualization and analysis, Dev Biol. 271(2):431-438 (2004)
8. Everts-van der Wind A, Kata SR, Band MR, Rebeiz M, Larkin DM, Everts RE, Green CA, Liu L, Natarajan S, Goldammer T, Lee JH, McKay S, Womack JE, Lewin HA. A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Res, 14(7):1424-37 (2004)
7. Liu L, Gong G, Liu Y, Natarajan S, Larkin DM, Everts-van der Wind A, Rebeiz M, Beever JE. Multi-species comparative mapping in silico using the COMPASS strategy. Bioinformatics, 20(2):148-154 (2004)
6. Larkin DM, Everts-van der Wind A, Rebeiz M, Schweitzer PA, Bachman S, Green C, Wright CL, Campos EJ, Benson LD, Edwards J, Liu L, Osoegawa K, Womack JE, de Jong PJ, Lewin HA. A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res, 13(8):1966-1972 (2003)
5. Larson JH, Rebeiz MJ, Stiening CM, Windish RL, Beever JE, Lewin HA. MHC class I-like genes in cattle, MHCLA, with similarity to genes encoding NK cell stimulatory ligands. Immunogenetics, 55(1):16-22 (2003)
4. Rebeiz M, Reeves NL, Posakony JW. SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. PNAS, 99(15):9888-9893 (2002)
3. Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW, Donovan J, Windish R, Steining C, Mahyuddin P, Womack JE, Lewin HA. An ordered comparative map of the cattle and human genomes. Genome Res, 10(9):1359-1368 (2000)
2. Rebeiz M, Lewin HA. Compass of 47,787 cattle ESTs. Anim Biotechnol, 11(2):75-241 (2000)
1. Rebeiz M, Miller DJ. Porcine sperm surface ß1,4galactosyltransferase binds to the zona pellucida but is not necessary or sufficient to mediate sperm-zona pellucida binding. Mol Reprod Dev, 54(4):379-387 (1999)
BOOK CHAPTERS AND REVIEWS
8. Govindjee G, Briskin DP, Benning C, Daniell H, Kolossov V, Scheer H, Rebeiz M. From δ-aminolevulinic acid to chlorophyll and every step in between: In memory of Constantin (Tino) A. Rebeiz, 1936 – 2019. Photosynthesis Res (In Press)
7. McQueen E, Rebeiz M. On the specificity of gene regulatory networks: How does network co-option affect subsequent evolution? Current Topics Developmental Biology 139:375-405 (2020)
6. Rice G, Rebeiz M. Evolution: How Many Phenotypes Do Regulatory Mutations Affect?
Current Biology, 29(1):R21-R23 (2019)
5. Smith SJ, Rebeiz M, Davidson L. From pattern to process: studies at the interface of gene regulatory networks, morphogenesis, and evolution. Current Opinion in Genetics and Development, 51:103-110 (2018) (COVER IMAGE)
4. Rebeiz M, Tsiantis M. Enhancer evolution and the origins of morphological novelty. Current Opinion in Genetics & Development, 45:115-123 (2017)
3. Rebeiz M, Williams TM. “Using Drosophila pigmentation traits to study the mechanisms of cis-regulatory evolution”. (In Press, Current Opinion in Insect Science)
2. Rebeiz M, Patel NH, Hinman VH. “Unraveling the tangled skein: the evolution of transcriptional regulatory networks in development”. Annual Reviews of Genomics and Human Genetics, 16:103-131 (2015)
1. Rebeiz M, Williams TM. “Experimental approaches to evaluate the contribution of candidate cis-regulatory mutations to phenotypic evolution” Methods in Molecular Biology: Molecular Methods for Evolutionary Genetics. Humana Press. Edited by V. Orgogozo and M. Rockman. 772:351-75 (2011)
