2008
Chen, C. Opazo, J.C., Erez, O., Uddin, M., Santolaya-Forgas, J.,Goodman, M., Grossman, L.I., Romero, R., Wildman, D.E., The human progesterone receptor shows evidence of adaptive evolution associated with its ability to act as a transcription factor. Molecular Phylogenet Evolution, 2008, 47(2): 637-49. PDF
Uddin, M., Goodman, M., Erez, O., Romero, R., Liu, G., Islam, M., Opazo, J.C., Sherwood, C.C., Grossman, L.I., Wildman, D.E. Distinct Genomic Signatures of adaptation in pre- and postnatal environments during human evolution. Proceedings of the National Academy of Sciences, 2008, 105(9): 3215-20. PDF
Uddin, M., Opazo, J.C.,Wildman, D.E., Goodman, M., Grossman, L.I. Molecular evolution of the cytochrome c oxidase submit 5A gene in primates, BMC Evolution, 2008, 8: 8. PDF
2007
Wildman, D.E.,Source for Comparative Studies of Placentation. II. Genomic Resources, Placenta, 2007, 144-7, PDF
Liu, G., Uddin, M., Islam, M., Goodman, M., Grossman, L.I., Romero, R.Wildman, D.E., OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences, Source Code for Biology and Medicine. 2007, 2:5. PDF
Wildman, D.E., Uddin, M., Opazo, J.C., Liu, G., Lefort, V., Guindon, S., Gascuel, O., Grossman, L.I., Romero, R., Goodman, M. Genomics, biogeography, and the diversification of placental mammals. Proceedings of the National Academy of Sciences USA. 2007, 104: 14395-14400. PDF
Koike, C., Uddin, M., Wildman, D.E., Gray, E.A., Trucco, M., Starzl, T.E., Goodman, M. Functionally important glycosyltransferase gain and loss during catarrhine primate emergence. Proceedings of the National Academy of Sciences USA. 2007, 104: 559-564. PDF
2006
Johnson, R.M., Prychitko, T., Gumucio, D., Wildman, D.E., Uddin, M., Goodman, M. Phylogenetic comparison suggest that distance from the locus control region guides developmental expression of primate b-type globin genes. Proceedings of the National Academy of Sciences USA. 2006, 103: 3186-3191. PDF
Khatri, P., Desai, V., Tarca, A.L., Sallamuthu, S., Wildman, D.E., Romero, R., Draghici, S. New Onto-Tools: Promoter-express, nsSNPCounter and Onto-translate. Nucleic Acids Research. 2006, 34: W626-631. PDF
Opazo, J.C., Wildman, D.E., Prychitko, T., Johnson, R.M., Goodman, M. Phylogenetic relationships and divergence times amog New World monkeys (Platyrrhini, Primates). Molecular Phylogenetics and Evolution. 2006, 40: 274-280. PDF
Sherwood, C.C., Stimpson, C.D., Raghanti, M.A., Wildman, D.E., Uddin, M., Grossman, L.I., Goodman, M., Redmon, J.C., Bonar, C.J., Erwin, J.M., Hof, P.R. Evolution of increased glia-neuron ratios in the human frontal cortex. Proceedings of the National Academy of Sciences USA. 2006, 103: 13606-13611. PDF
Wildman, D.E., Chen, C., Erez, O., Grossman, L.I., Goodman, M., Romero, R. Evolution of the mammalian placenta revealed by phylogenetic analysis. Proceedings of the National Academy of Sciences USA. 2006, 103: 3203-3208. PDF
2005
Doan, J.W., Schmidt, T.R., Wildman, D.E., Goodman, M., Weiss, M.L., Grossman, L.I. Rapid nonsynonymous evolution of the iron-sulfur protein in anthropoids primates. Journal of Bioenergetics and Biomembranes. 2005, 37:35-41. PDF
Goodman, M., Grossman, L.I., Wildman, D.E. Moving primate genomics beyond the chimpanzee genome. Trends in Genetics. 2005, 21:511-517. PDF
Prychitko, T., Johnson, R.M., Wildman, D.E., Gumucio, D., Goodman, M. The phylogenetic history of the New World monkey beta globin reveals a platyrrhine beta to delta gene conversion in the atelid ancestry. Molecular Phylogenetics and Evolution. 2005, 35:225-234. PDF
Schmidt, T.R., Wildman, D.E., Uddin, M., Opazo, J.C., Goodman, M., Grossman, L.I. Rapid electrostatic evolution at the binding site for cytochrome c on cytochrome c oxidase in anthropoid primates. Proceedings of the National Academy of Sciences USA. 2005, 102: 6379-6384. PDF
2004
Doan, J.W., Schmidt, T.R., Wildman, D.E., Uddin, M., Goldberg, S., Huttemann, M., Goodman, M., Weiss, M.L., Grossman, L.I. Coadaptive evolution in cytochrome c oxidase: 9 of 13 subunits show accelerated rates of nonsynonymous substitutions in anthropoid primates. Molecular Phylogenetics and Evolution. 2004, 33:944-950. PDF
Grossman, L.I., Wildman, D.E., Schmidt, T.R., Goodman, M. Accelerated evolution of the electron transport chain in antropoid primates. Trends in Genetics. 2004, 20:579-585. PDF
Ling, J., Zhang, L., Jin, H., Pi, W., Kosteas, T., Anagnou, N.P., Goodman, M., Tuan, D. Dynamic retrotransposition of ERV-9 LRT and L1 in the beta-globin gene locus during primate evolution. Molecular Phylogenetics and Evolution. 2004, 30:867-871. PDF
Uddin, M., Wildman, D.E., Lui, G., Xu, W., Johnson, R.M., Hof, P.R., Kapatos, G., Grossman, L.I., Goodman, M. Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. Proceedings of the National Academy of Sciences USA. 2004, 101:2957-2962. PDF
Wildman, D.E., Bergman, T.J., al-Aghbari, A., Sterner, K.N., Newman, T.K., Phillips-Conroy, J.E., Jolly, C.J., Disotell, T.R. Mitochondrial evidence for the origin of hamadryas baboons. Molecular Phylogenetics and Evolution. 2004, 32:287-296. PDF
2003
Goldberg, A., Wildman, D.E., Schmidt, T.R., Huttemann, M., Goodman, M., Weiss, M.L., Grossman, L.I. Adaptive evolution of cytochrome c oxidase subunit VIII in anthropid primates. Proceedings of the National Academy of Sciences USA. 2003, 100:5873-5878. PDF
Schmidt, T.R., Doan, J.W., Goodman, M., Grossman, L.I. Retention of a duplicate gene through changes in subcellular targeting: an electron transport protein homologue localizes to the golgi. Journal of Molecular Evolution. 2003, 57:222-228. PDF
Wildman, D.E., Uddin, M., Liu, G., Grossman, Goodman, M. Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo. Proceedings of the National Academy of Sciences USA. 2003, 100:7181-7188. PDF
2002
Johnson, R.M., Gumucio, D., Goodman, M. Globin gene swtching in primates. Comparative Biochemistry and Physiology A. 2002. 133:877-883. PDF
Schmidt, T.R., Goodman, M., Grossman, L.I. Amino acid replacement is rapid in primates for the mature polypeptides of COX subunits, but not for their targeting presequences. Gene. 2002, 286:13-19. PDF
Wildman, D.E. A map of the common chimpanzee genome. Bioessays. 2002, 24:490-493. PDF
Wildman, D.E., Wu, W., Goodman, M., Grossman, L.I. Episodic positive selection in ape cytochrome c oxidase subunnit IV. Molecular Biology and Evolution. 2002, 19:1812-1815. PDF
Yu, T., Thomas, D.M., Goodman, M., Gumucio, D.L. Regulation of fetal versus embrionic gamma globin genes: appropiate developmental stage expression patterns in the presence of HS2 of the locus control region. Blood. 2002, 99:1082-1084. PDF
2001
Grossman, L.I., Schmidt, T.R., Wildman, D.E., Goodman, M. Molecular evolution of aerobic energy metabolism in primates. Molecular Phylogenetics and Evolution. 2001. 18:26-36. PDF
Page, S.L., Goodman, M. Catarrhine phylogeny:noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade. Molecular Phylogenetics and Evolution. 2001, 18:14-25. PDF
Schmidt, T.R., Wu, W., Goodman, M., Grossman, L.I. Evolution of nuclear- and mitochondrial-encoded subunits interaction in cytochrome c oxidase. Molecular Biology and Evolution. 2001, 18:563-569. PDF
Wheeler, D., Hope, R., Cooper, S.B., Dolman, G., Webb, G.C., Bottema, C.D., Gooley, A.A., Goodman, M., Holland, R.A. An orphaned mammalian beta-globin gene of ancient evolutionary origin. Proceedings of the National Academy of Sciences USA. 2001, 98:1327-1329. PDF
2000
Johnson, R.M., Buck, S., Chiu, C-H., Gage, D.A., Shen, T-L., Hendrickx, A.G., Gumucio, D.L., Goodman, M. Humans and Old World monkeys have similar patterns of fetal globin expression. Journal of Experimental Zoology (Mol. Dev. Evol.). 2000, 288:318-326. PDF
McConkey, E.H., Fouts, R., Goodman, M., Nelson, D., Penny, D., Ruvolo, M., Sikela, J., Stewart, C-B., Varki, A., Wise, S. A proposal for a human evolution project. Molecular Phylogenetics and Evolution. 2000, 15:1-4. PDF
Miyamoto, M.M., Porter, C.A., Goodman, M. c-Myc gene sequences and the phylogeny of bats and other eutherian mammals. Systematic Biology. 2000, 49:501-514. PDF
Wu, W., Schmidt, T.R., Goodman, M., Grossman, L.I. Molecular evolution of cytochrome c oxidase subunit I in primates: is there coevolution between mitochondrial and nuclear genomes? Molecular Phylogenetics and Evolution. 2000, 17:294-304. PDF
1999
Chaves, R., Sampaio, I., Schneider, M.P., Schneider, H., Page, S.L., Goodman, M. The place of Callimico goeldii in the callitrichine phylogenetic tree: evidence from the von Willebrand factor gene (vWF) intron II sequences. Molecular Phylogenetics and Evolution. 1999, 13:392-404. PDF
Chiu, C-H., Gregoire, L., Gumucio, D.L., Muniz, J.A.P.C., Lancaster, W.D., Goodman, M. A model for the fetal recruitment of simian g-globin genes based on findings from two New World monkeys Cebus apella and Callithrix jacchus (Platyrrhini, Primates). Journal of Experimental Zoology (Mol. Dev. Evol.). 1999, 285:27-40. PDF
Goodman, M. The genomic record of humankind's evolutionary roots. American Journal of Humans Genetics. 1999, 64:31-39. PDF
Meireles, C.M., Czelusniak, J., Schneider, M.P., Muniz, J.A.P.C., Brigido, M.C., Ferreira, H.S., Goodman, M. Molecular phylogeny of ateline New Worls monkeys (Platyrrhini, Primates) based on g-globin gene sequences: evidence that Brachyteles is the sister group of Lagothrix. Molecular Phylogenetics and Evolution. 1999, 12:10-30. PDF
Meireles, C.M., Czelusniak, J., Ferrari, S.F., Schneider, M.P., Goodman, M. Phylogenetic relationships among brazilian howler monkeys, genus Alouatta (Platyrrhini, Atelinae) base on g-globin1 pseudogene sequences. Genetics and Molecular Biology. 1999, 22:337-344. PDF
Meireles, C.M., Czelusniak, J., Goodman, M. The Tarsius g-globin gene: pseudogene or active gene? Molecular Phylogenetics and Evolution. 1999, 13:434-439. PDF
Page, S.L., Chiu, C-H., Goodman, M. Molecular phylogeny of Old World monkeys (Cercopithecidae) as inferred from g-globin DNA sequences. Molecular Phylogenetics and Evolution. 1999, 13:348-359. PDF
Porter, C.A., Czelusniak, J., Schneider, H., Schneider, M.P.C., Sampaio, I., Goodman, M. Sequence from the 5' flanking region of the e-globin gene support the relationship of Callicebus with the pitheciins. American Journal of Primatology. 1999, 48:69-75. PDF
Schmidt, T.R., Goodman, M., Grossman, L.I. Molecular evolution of the COX7A gene family in primates. Molecular Biology and Evolution. 1999, 16:619-626. PDF
Stojanovic, N., Florea, L., Riemer, C., Gumucio, D., Slightom, J., Goodman, M., Miller, W., Hardison, R. Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Research. 1999, 27:3899-3910. PDF
Zhu, W., TomHon, C., Shelden, E., Mason, M., Campbell, T., Richards, N., Goodman, M., Gumucio, D.L. Analysis of linked human e and g transgenes:effect of locus control region hypersensitive sites 2 and 3 or a distal YY1 mutation on stage-specific expression patterns. Blood. 1999, 93:3540-3549. PDF
1998
Goodman, M., Porter, C.A., Czelusniak, J., Page, S.L., Schneider, H., Shoshani, J., Gunnell, G., Groves, C.P. Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil record. Molecular Phylogenetics and Evolution. 1998, 9:585-598. PDF
Meireles, C.M., Czelusniak, J., Page, S.L., Gumucio, D.L., Schneider, M.P.C., Goodman, M. Testing a model of the fetal recruitment of g-globin genes in callitrichine New World monkeys. Blood Cells, Molecules and Diseases. 1998, 24:491.
1997
Barroso, C.M.L., Schneider, H., Schneider, M.P.C., Sampaio, I., Harada, M.L., Czelusniak, J., Goodman, M. Update on the phylogenetic systematics of New World monkeys: further DNA evidence for placing the pygmy marmoset (Cebuella) within the marmoset genus Callithrix. International Journal of Primatology. 1997, 18:651-674. PDF
Chiu, C-H., Schneider, H., Slightom, J.L., Gumucio, D.L., Goodman, M. Dynamics of the regulatory evolution in primate beta-globin gene clusters: cis-mediated aquisition of simian gamma expression patterns. Gene. 1997, 205:47-57. PDF
Hardison, R., Slightom, J.L., Gumucio, D.L., Goodman, M., Stojanovic, N., Miller, W. Locus control regions of mammalian beta-globin gne clusters: combinig phylogenetic analyses and experimental results to gain functional insights. Gene. 1997, 205:73-94. PDF
Johnson, R.M., Buck, S., Schneider, H., Sampaio, I., Gage, D.A., Shen, T-L., Schneider, M.P.C., Goodman, M. Identification of pre-gamma-globin. Hemoglobin. 1997, 21:143-153.
McConkey, E.H., Goodman, M. A human genome evolution project is needed. Trends in Genetics. 1997, 13:350-351. PDF
Porter, C.A., Czelusniak, J., Schneider, H., Schneider, M.P.C., Sampaio, I., Goodman, M. Sequences of the primate epsilon-globin gene: implications for systematics of the marmosets and other New World primates. Gene. 1997, 205:59-71. PDF
Porter, C.A., Page, S.L., Czelusniak, J., Schneider, H., Schneider, M.P.C., Sampaio, I., Goodman, M. Phylogeny and evolution of selected primates as determined by sequences of the epsilon-globin locus and 5' flanking regions. International Journal of Primatology. 1997, 18:261-295. PDF
Shelton, D.A., Stegman, L., Hardison, R., Miller, W., Bock, J.H., Slightom, J.L., Goodman, M., Gumucio, D.L. Phylogenetic footprinting of hypersensitive site 3 of the beta-globin locus control region. Blood. 1997, 89:3457-3469. PDF
Schmidt, T.R., Jaradat, S.A., Goodman, M., Lomax, M.I., Grossman, L.I. Molecualr evolution of cytochrome c oxidase: rate variation between subunits VIa isoforms. Molecular Biology and Evolution. 1997, 14:595-601. PDF
Slightom, J.L., Bock, J.H., Tagle, D.A., Gumucio, D.L., Goodman, M., Stojanovic, N., Jackson, J., Miller, W., Hardison, R. The complete sequence of the galago and rabbit beta-globin locus control regions: extended sequence and functional conservation outside the cores of DNase hypersensitive sites. Genomics. 1997, 39:90-94. PDF
TomHon, C., Zhu, W., Millinoff, D., Hayasaka, K., Slightom, J.L., Goodman, M., Gumucio, D.L. Evolution of a fetal expression pattern via cis changes near the gamma globin gene. Journal of Biological Chemistry. 1997, 272:14062-14066. PDF
Wu, W., Goodman, M., Lomax, M.I., Grossman, L.I. Molecular evolution of cytochrome c oxidase subunit IV: evidence for positive selection in simian primates. Journal of Molecular Evolution. 1997, 44:477-491. PDF
1996
Chiu, C-H., Schneider, H., Schneider, M.P.C., Sampaio, Meireles, C.M., Slightom, J.L., Gumucio, D., Goodman, M. Reduction of two functional gamma-globin genes to one: an evolutionary trend in New World monkeys (Infraorder Platyrrhini). Proceedings of the National Academy of Sciences USA. 1996, 93:6510-6515. PDF
Goodman, M. Epilogue: a personal account of the origins of a new paradigm. Molecular Phylogenetics and Evolution. 1996, 5:269-285. PDF
Gumucio, D.L., Shelton, D.A., Zhu, W., Millinoff, D., Gray, T., Bock, J.H., Slightom, J.L., Goodman, M. Evolutionary strategies for the elucidation of cis and trans factors that regulate the developmental switching programs of the beta-like globin genes. Molecular Phylogenetics and Evolution. 1996, 5:18-32. PDF
Johnson, R.M., Buck, S., Chiu, C-H., Schneider, H, Sampaio, I., Gage, D.A., Shen, T-L., Schneider, M.P.C., Muniz, J.A., Gumucio, D.L., Goodman, M. Fetal globin expression in New World monkeys. Journal of Biological Chemistry. 1996, 271:14684-14691. PDF
Porter, C.A., Goodman, M., Stanhope, M.J. Evidence of mammalian phylogeny from sequences of exon 28 of the von Willebrand factor gene. Molecular Phylogenetics and Evolution. 1996, 5:89-101. PDF
Schneider, H., Sampaio, I., Harada, M.L., Barroso, C.M.L., Schneider, M.P.C., Czelusniak, J., Goodman, M. Molecular phylogeny of the New World monkeys (Platyrrhini, Primates) based on two unlinkek nuclear genes: IRBP intron 1 and epsilon-globin sequences. American Journal of Physical Anthropology. 1996, 100:153-179. PDF
Stanhope, M.J., Smith, M.R., Waddell, V.G., Porter, C.A., Shivji, M.S., Goodman, M. Mammalian evolution and the interphotoreceptor retinoid binding protein (IRBP) gene: convincing evidence for several superordinal clades. Journal of Molecular Evolution. 1996, 43:83-92.
