Rob DeSalle

@ AMNH




2012 & In Press

Amato G, DeSalle R. 2012. Assessing biodiversity funding during the sixth extinction. BioEssays

Oliveira DC, Almeida FC, O'Grady PM, Armella MA, Desalle R, Etges WJ. 2012. Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group. Mol Phylogenet Evol 64(3):533–544.

Sancho A, Duran J, García-España A, Mauvezin C, Alemu EA, Lamark T, Macias MJ, DeSalle R, Royo M, Sala D, Chicote JU, Palacín M, Johansen T, Zorzano A. 2012. DOR/Tp53inp2 and Tp53inp1 constitute a metazoan gene family encoding dual regulators of autophagy and transcription. PLoS ONE 7(3):e34034.

Rosenfeld JA, Payne A, DeSalle R. 2012. Random roots and lineage sorting. Mol Phylogenet Evol 64(1):12-20.

Pentony MM, Winters P, Penfold-Brown D, Drew K, Narechania A, DeSalle R, Bonneau R, Purugganan MD. 2012. The Plant Proteome Folding Project: structure and positive selection in plant protein families. Genome Biol Evol 4(3):360-371.

Rosenfeld J, DeSalle R. 2012. E value cutoff and eukaryotic genome content phylogenetics. Mol Phylogenet Evol 63(2):342-350.

Karched M, Furgang D, Planet PJ, Desalle R, Fine DH. 2012. Genome sequence of Aggregatibacter actinomycetemcomitans RHAA1, isolated from a rhesus macaque, an Old World primate. J Bacteriol 194(5):1275-1276.

Lazzarini LC, Rosenfeld J, Huard RC, Hill V, Lapa E Silva JR, DeSalle R, Rastogi N, Ho JL. 2012. Mycobacterium tuberculosis spoligotypes that may derive from mixed strain infections are revealed by a novel computational approach. Infect Genet Evol

Narechania A, Baker RH, Sit R, Kolokotronis SO, DeSalle R, Planet PJ. 2012. Random Addition Concatenation Analysis: a novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the Cyanobacteria. Genome Biol Evol

2011

Lee EK*, Cibrian-Jaramillo A*, Kolokotronis SO*, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, DeSalle R. 2011. A functional phylogenomics view of the seed plants. PLoS Genet 7(12):e1002411. *equal contribution

Hanner R, DeSalle R, Ward RD, Kolokotronis SO. 2011. The Fish Barcode of Life (FISH-BOL) special issue. [edited issue] Mitochondrial DNA 22(S1):1-2.

Almeida FC, Giannini NP, Desalle R, Simmons NB. 2011. Evolutionary relationships of the old world fruit bats (Chiroptera, Pteropodidae): Another star phylogeny? BMC Evol Biol 11:281.

Hekkala E, Shirley MH, Amato G, Austin JD, Charter S, Thorbjarnarson J, Vliet KA, Houck ML, Desalle R, Blum MJ. 2011. An ancient icon reveals new mysteries: mummy DNA resurrects a cryptic species within the Nile crocodile. Mol Ecol 20(20):4199-4215.

Reid BN, LE M, McCord WP, Iverson JB, Georges A, Bergmann T, Amato G, DeSalle R, Naro-Maciel E. 2011. Comparing and combining distance-based and character-based approaches for barcoding turtles. Mol Ecol Resources 11(6):956-967.

Bennett CE, Wilson BS, DeSalle R. 2011. DNA barcoding of an invasive mammal species, the small Indian mongoose (Herpestes javanicus; E. Geoffroy Saint-Hillaire 1818) in the Caribbean and Hawaiian Islands. Mitochondrial DNA 22(1-2):12-18.

Lienau EK, DeSalle R, Allard M, Brown EW, Swofford D, Rosenfeld JA, Sarkar IN, Planet PJ. 2011. The mega-matrix tree of life: using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life. Cladistics 27(4):417-427.

Smith B, Chen Z, Reimers L, van Doorslaer K, Schiffman M, DeSalle R, Herrero R, Yu K, Wacholder S, Wang T, Burk RT. 2011. Sequence imputation of HPV16 genomes for genetic association studies. PLoS ONE 6(6):e21375.

Chen Z, Schiffman M, Herrero R, DeSalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Burk RD. 2011. Evolution and taxonomic classification of human papillomavirus 16 (HPV16)-related variant genomes: HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67. PLoS ONE 6(5):e20183.

Goldstein PZ, DeSalle R. 2011. Integrating DNA barcode data and taxonomic practice: determination, discovery, and description. BioEssays 33(2):135-147.

O'Grady PM, Lapoint RT, Bonacum J, Lasola J, Owen E, Wu Y, DeSalle R. 2011. Phylogenetic and ecological relationships of the Hawaiian Drosophila inferred by mitochondrial DNA analysis. Mol Phylogenet Evol 58(2):244-256.

2010

Escalante P, DeSalle R, Kolokotronis SO. 2010. The MexBOL initiative. [edited issue] Mitochondrial DNA 21(S1): 1-2.

Yassin A, Markow TA, Narechania A, O'Grady PM, DeSalle R. 2010. The genus Drosophila as a model for testing tree- and character-based methods of species identification using DNA barcoding. Mol Phylogenet Evol 57(2):509-517.

Perez-Sweeney B, DeSalle R, Ho JL. 2010. An introduction of a novel population genetic approach for HIV characterization. Infect Genet Evol 10(8):1155-1164.

Schiffman M, Rodriguez AC, Chen Z, Wacholder S, Herrero R, Hildesheim A, DeSalle R, Befano B, Yu K, Safaeian M, Sherman ME, Morales J, Guillen D, Alfaro M, Hutchinson M, Solomon D, Castle PE, Burk RD. 2010. A population-based prospective study of carcinogenic human papillomavirus variant lineages, viral persistence, and cervical neoplasia. Cancer Res 70(8):3159-3169.

Wyner Y, DeSalle R. 2010. Taking the conservation biology perspective to secondary school classrooms. Conserv Biol 24(3):649-654.

DeSalle R, Mares R, Garcia-España A. 2010. Evolution of cysteine patterns in the large extracellular loop of tetraspanins from animals, fungi, plants and single-celled eukaryotes. Mol Phylogenet Evol 56(1):486-491.

Gruber DF, DeSalle R, Lienau EK, Tchernov D, Pieribone VA, Kao HT. 2010. Novel internal regions of fluorescent proteins undergo divergent evolutionary patterns. Mol Biol Evol 26(12):2841-2848.

Dias IMG, Almeida FC, Amato G, DeSalle R, Fonseca CG. 2010. Delineating geographic boundaries of the woolly mouse opossums, Micoureus demerarae and Micoureus paraguayanus (Didelphimorphia: Didelphidae). Conserv Genet 11(4):1579-1585.

Hekkala ER, Amato G, DeSalle R, Blum MJ. 2010. Molecular assessment of population differentiation and individual assignment potential of Nile crocodile (Crocodylus niloticus) populations. Conserv Genet 11(4):1435-1443.

Cibrián-Jaramillo A, Daly AC, Brenner E, DeSalle R, Marler TE. 2010. When North and South don't mix: genetic connectivity of a recently endangered oceanic cycad, Cycas micronesica, in Guam using EST-microsatellites. Mol Ecol 19(12):2364-2379.

Cibrián-Jaramillo A, De la Torre-Bárcena E, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R. 2010. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol Evol 2:225.

Yassin A, Lienau EK, Narechania A, DeSalle R. 2010. Catching the phylogenic history through the ontogenic hourglass: a phylogenomic analysis of Drosophila body segmentation genes. Evol Dev 12(3):288-295.

Nagarajan N, Cook C, Di Bonaventura M, Ge H, Richards A, Bishop-Lilly KA, DeSalle R, Read TD, Pop M. 2010. Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC Genomics 11(1):242.

Deo AJ, Costa R, DeLisi LE, DeSalle R, Haghighi F. 2010. A novel analytical framework for dissecting the genetic architecture of behavioral symptoms in neuropsychiatric disorders. PLoS ONE 5(3):e9714.

Bonaventura MD, Lee E, DeSalle R, Planet P. 2010. A whole-genome phylogeny of the family Pasteurellaceae. Mol Phylogenet Evol 54(3):950-956.

2009

Camp EM, Sánchez-Sánchez AV, Garcia-España A, DeSalle R, Odqvist L, O'Connor JE, Mullor JL. 2009. Nanog regulates proliferation during early fish development. Stem Cells 27(9):2081-2091.

Lienau EK, DeSalle. 2009. Is the microbial tree of life verificationist? Cladistics 26(2):195-201.

Calcagnotto D, DeSalle R. 2009. Population genetic structuring in pacu (Piaractus mesopotamicus) across the Parana-Paraguay basin: evidence from microsatellites. Neotrop Ichthyol 7(4):607-616.

Naro-Maciel E, Reid B, FitzSimmons NN, Le M, DeSalle R, Amato G. 2009. DNA barcodes for globally threatened marine turtles: a registry approach to documenting biodiversity. Mol Ecol Resources 10(2):252-263.

Almeida FC, Giannini NP, DeSalle R, Simmons NB. 2009. The phylogenetic relationships of cynopterine fruit bats (Chiroptera: Pteropodidae: Cynopterinae). Mol Phylogenet Evol 53(3):772-783.

Chen Z, van Doorslaer K, DeSalle R, Wood CE, Kaplan JR, Wagner JD, Burk RD. 2009. Genomic diversity and interspecies host infection of α12 Macaca fascicularis papillomaviruses (MfPVs). Virology 393(2):304-310.

Birstein VJ, DeSalle R, Doukakis P, Hanner R, Ruban GI, Wong E. 2009. Testing taxonomic boundaries and the limit of DNA barcoding in the Siberian sturgeon, Acipenser baerii. Mitochondrial DNA 5(9):e1000655.

Cibrián-Jaramillo A, Bacon CD, Garwood NC, Bateman RM, Thomas MM, Russell S, Bailey DC, Hahn WJ, Bridgewater SGM, DeSalle R. 2009. Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation. BMC Genetics 10:65.

DeSalle R. 2009. Molecular tooth decay. PLoS Genet 5(9):e1000655.

Garcia-España A, DeSalle R. 2009. Intron sliding in tetraspanins. Commun Integr Biol 2(5):1-3.

Rosenfeld JA, Xuan Z, DeSalle R. 2009. Investigating repetitively matching short sequencing reads: the enigmatic nature of H3K9me3. Epigenetics 4(7):476-486.

Barral PM, Sarkar D, Su ZZ, Barber GN, DeSalle R, Racaniello VR, Fisher PB. 2009. Functions of the cytoplasmic RNA sensors RIG-I and MDA-5: key regulators of innate immunity. Pharmacol Ther 124(2):219-234.

Schierwater B, Kolokotronis SO, Eitel M, DeSalle R. 2009. The Diploblast-Bilateria Sister hypothesis: parallel evolution of a nervous system may have been a simple step. Commun Integr Biol 2(5):1-3.

Di Bonaventura MP, DeSalle R, Pop M, Nagarajan N, Figurski DH, Fine DH, Kaplan JB, Planet PJ. 2009. Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700. J Bacteriol 191(14):4693-4694.

de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R. 2009. The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS ONE 4(6):e5764.

de Jong D, Eitel M, Jakob W, Osigus HJ, Hadrys H, DeSalle R, Schierwater B. 2009. Multiple Dicer genes in the early diverging Metazoa. Mol Biol Evol 26(6):1333-1340.

Lienau EK, DeSalle R. 2009. Evidence, content and corroboration and the Tree of Life. Acta Biotheor 57(1-2):187-199.

Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. 2009. Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics 10(1):143.

Garcia-España A, Mares R, Sun TT, DeSalle R. 2009. Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins. PLoS ONE 4(3):e4680.

Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, DeSalle R. 2009. Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis. PLoS Biol 7(1):e1000020.

Schierwater B, de Jong D, DeSalle R. 2009. Placozoa and the evolution of Metazoa and intrasomatic cell differentiation. Int J Biochem Cell Biol 41(2):370-379.

Lemke MJ, Lienau EK, Rothe J, Pagioro TA, Rosenfeld J, DeSalle R. 2009. Description of freshwater bacterial assemblages from the Upper Paraná river floodpulse system, Brazil. Microb Ecol 57(1):94-103.

Chen Z, DeSalle R, Schiffman M, Herrero R, Burk RD. 2009. Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97. J Virol 83(3):1443-1455.

Ameida FC, DeSalle R. 2009. Orthology, function, and evolution of accessory gland proteins in the Drosophila repleta group. Genetics 181(1):235-245.

2008

Rosenfeld JR, DeSalle R, Lee EK, O'Grady P. 2008. Using whole genome presence/absence data to untangle function in 12 Drosophila genomes. Fly 2(6):291-299.

Sarkar D, DeSalle R, Fisher PB. 2008. Evolution of MDA-5/RIG-I-dependent innate immunity: independent evolution by domain grafting. Proc Natl Acad Sci USA 105(44):17040-17045.

Friedman M, DeSalle R. 2008. Mitochondrial DNA extraction and sequencing of formalin-fixed archival snake tissue. Mitochondrial DNA 19(5):433-437.

Wyatt KB, Campos PF, Gilbert MT, Kolokotronis SO, Hynes WH, DeSalle R, Daszak P, MacPhee RD, Greenwood AD. 2008. Historical mammal extinction on Christmas Island (Indian Ocean) correlates with introduced infectious disease. PLoS ONE 3(11):e3602.

DeSalle R, Schierwater B. 2008. An even "newer" animal phylogeny. Bioessays 30(11-12):1043-1047.

Almeida FC, Leszczyniecka M, Fisher PB, DeSalle R. 2008. Examining ancient inter-domain horizontal gene transfer. Evol Bioinform 4:109-119.

Cibrián-Jaramillo A, Marler TE, DeSalle R, Brenner ED. 2008. Development of EST-microsatellites from the cycad Cycas rumphii, and their use in the recently endangered Cycas micronesica. Conserv Genet 9(4):1051-1054.

Almeida FC, DeSalle R. 2008. Evidence of adaptive evolution of accessory gland proteins in closely related species of the Drosophila repleta group. Mol Biol Evol 25(9):2043-2053.

Garcia-España A, Chung PJ, Sarkar IN, Stiner E, Sun TT, DeSalle R. 2008. Appearance of new tetraspanin genes during vertebrate evolution. Genomics 91(4):326-334.

O'Grady P, DeSalle R. 2008. Out of Hawaii: the origin and biogeography of the genus Scaptomyza (Diptera: Drosophilidae). Biol Lett 4(2):195-199.

Sarkar IN, Egan MG, Coruzzi G, Lee EK, DeSalle R. 2008. Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phylogenomics. BMC Bioinform 9:103.

Sarkar IN, Planet PJ, DeSalle R. 2008. CAOS software for use in character-based DNA barcoding. Mol Ecol Resources 8(6):1256-1259.

Cibrián-Jaramillo A, Hahn WJ, DeSalle R. 2008. Development of microsatellite markers of the Mexican understory palm Chamaedorea elegans, cross-species genotyping, and amplification in congeners. Mol Ecol Resources 8(2):322–324.

Rach J, DeSalle R, Sarkar IN, Schierwater B, Hadrys H. 2008. Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proc Biol Sci 275(1632):237-247.

2007

Kao HT, Sturgis S, DeSalle R, Tsai J, Davis D, Gruber DF, Pieribone VA. 2007. Dynamic regulation of fluorescent proteins from a single species of coral. Mar Biotechnol 9(6):733-746.

DeSalle R. 2007. Phenetic and DNA taxonomy; a comment on Waugh. Bioessays 29(12):1289-1290.

DeSalle R, Schierwater B. 2007. Key transitions in animal evolution. Integr Comp Biol 47(5):667-669.

Schierwater B, DeSalle R. 2007. Can we ever identify the Urmetazoan? Integr Comp Biol 47(5):670-676.

Gatesy J, DeSalle R, Wahlberg N. 2007. How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence. Syst Biol 56(2):355-363.

Naro-Maciel E, Becker JH, Lima EH, Marcovaldi MA, DeSalle R. 2007. Testing dispersal hypotheses in foraging green sea turtles (Chelonia mydas) of Brazil. J Hered 98(1):29-39.

Chen Z, Schiffman M, Herrero R, DeSalle R, Burk RD. 2007. Human papillomavirus (HPV) types 101 and 103 isolated from cervicovaginal cells lack an E6 open reading frame (ORF) and are related to gamma-papillomaviruses. Virology 360(2):447-453.

2006

DeSalle R. 2006. Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conserv Biol 20(5):1545-1547.

Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, Depamphilis C, DeSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. 2006. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS 10(2):231-237.

Burk RD, DeSalle R. 2006. The tango and tangle of human papillomavirus and the human genome. J Natl Cancer Inst 98(15):1026-1027.

Lienau EK, DeSalle R, Rosenfeld JA, Planet PJ. 2006. Reciprocal illumination in the gene content tree of life. Syst Biol 55(3):441-453.

Garcia-España A, Chung PJ, Zhao X, Lee A, Pellicer A, Yu J, Sun TT, DeSalle R. 2006. Origin of the tetraspanin uroplakins and their co-evolution with associated proteins: Implications for uroplakin structure and function. Mol Phylogenet Evol 41(2):355-367.

de la Torre JE, Egan MG, Katari M, Brenner ED, Stevenson DW, Coruzzi GM, DeSalle R. 2006. ESTimating plant phylogeny: lessons from partitioning. BMC Evol Biol 6(1):48

Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R. 2006. OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 22(6):699-707.

DeSalle R. 2006. What's in a character? J Biomed Inform 39(1):6-17.

2005

Narechania A, Chen Z, DeSalle R, Burk RD. 2005. Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses. J Virol 79(24):15503-15510.

Corthals A, DeSalle R. 2005. An application of tissue and DNA banking for genomics and conservation: the Ambrose Monell Cryo-Collection (AMCC). Syst Biol 54(5):819-823.

DeSalle R, Egan MG, Siddall M. 2005. The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc Lond B Biol Sci 360(1462):1905-1916.

Bonacum J, O'Grady PM, Kambysellis M, DeSalle R. 2005. Phylogeny and age of diversification of the planitibia species group of the Hawaiian Drosophila. Mol Phylogenet Evol 37(1):73-82.

Schiffman M, Herrero R, DeSalle R, et al. 2005. The carcinogenicity of human papillomavirus types reflects viral evolution. Virology 337(1):76-84.

Calcagnotto D, Schaefer SA, DeSalle R. 2005. Relationships among characiform fishes inferred from analysis of nuclear and mitochondrial gene sequences. Mol Phylogenet Evol 36(1):135-153.

Chen Z, Terai M, Fu L, Herrero R, DeSalle R, Burk RD. 2005. Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses. J Virol 79(11):7014-7023.

Hadrys T, DeSalle R, Sagasser S, Fischer N, Schierwater B. 2005. The Trichoplax PaxB gene: a putative proto-PaxA/B/C gene predating the origin of nerve and sensory cells. Mol Biol Evol 22(7):1569-1578.

Helfenbein KG, DeSalle R. 2005. Falsifications and corroborations: Karl Popper's influence on systematics. Mol Phylogenet Evol 35(1):271-280. [Corrigendum ]

DeSalle R. 2005. Genetics at the brink of extinction. Heredity 94(4):386-387.

Birstein VJ, Ruban G, Ludwig A, Doukakis P, DeSalle R. 2005. The enigmatic Caspian Sea Russian sturgeon: how many cryptic forms does it contain? Syst Biodiv 3:203-218.

Goldstein P, Wyner Y, Doukakis P, Egan MG, Amato G, Rosenbaum H, DeSalle R. 2005. Theory and methods for diagnosing species and populations in conservation. Ann MO Bot Gard 92:12-27.

2004

DeSalle R, Amato G. 2004. The expansion of conservation genetics. Nat Rev Genet 5(9):702-712.

Herbst L, Ene A, Su M, Desalle R, Lenz J. 2004. Tumor outbreaks in marine turtles are not due to recent herpesvirus mutations. Curr Biol 14(17):R697-R699.

Rosenfeld JA, Sarkar IN, Planet PJ, Figurski DH, DeSalle R. 2004. ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms. Bioinformatics 20(18):3462-3465. [ORFcurator website]

Narechania A, Terai M, Chen Z, DeSalle R, Burk RD. 2004. Lack of the canonical pRB-binding domain in the E7 ORF of artiodactyl papillomaviruses is associated with the development of fibropapillomas. J Gen Virol 85(Pt 5):1243-1250.

2003

Oliveira DC, Wintermute EH, Etges WJ, Heed WB, O'Grady PM, Desalle R. 2003. Hierarchical structure in the Drosophila mojavensis cluster (Diptera: Drosophilidae). Hereditas 139(3):223-227.

Leszczyniecka M, DeSalle R, Kang DC, Fisher PB. 2003. The origin of polynucleotide phosphorylase domains. Mol Phylogenet Evol 31(1):123-130.

DeSalle R, Branham MA, O'Grady P, Gatesy J. 2003. The evolution of HOM-C homeoboxes in the Dipteran family Drosophilidae. Insect Mol Biol 12(4):345-351.

Goldstein PZ, Desalle R. 2003. Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimens. Mol Ecol 12(7):1993-1998.

Gatesy J, Amato G, Norell M, DeSalle R, Hayashi C. 2003. Combined support for wholesale taxic atavism in gavialine crocodylians. Syst Biol 52(3):403-422.

Planet PJ, Kachlany SC, Fine DH, DeSalle R, Figurski DH. 2003. The widespread colonization island of Actinobacillus actinomycetemcomitans. Nat Genet 34(2):193-198.

2002

Rosenbaum HC, Weinrich MT, Stoleson SA, Gibbs JP, Baker CS, DeSalle R. 2002. The effect of differential reproductive success on population genetic structure: correlations of life history with matrilines in humpback whales of the gulf of Maine. J Hered 93(6):389-399.

Sarkar IN, Planet PJ, Bael TE, Stanley SE, Siddall M, DeSalle R, Figurski DH. 2002. Characteristic attributes in cancer microarrays. J Biomed Inform 35(2):111-22.

O'Grady PM, Durando CM, Heed WB, Wasserman M, Etges W, Desalle R. 2002. Genetic divergence within the Drosophila mayaguana subcluster, a closely related triad of Caribbean species in the repleta species group. Hereditas 136(3):240-245.

Roudier F, Schindelman G, DeSalle R, Benfey PN. 2002. The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion. Plant Physiol 130(2):538-548.

Gatesy J, Matthee C, DeSalle R, Hayashi C. 2002. Resolution of a supertree/supermatrix paradox. Syst Biol 51(4):652-664.

Sarkar IN, Thornton JW, Planet PJ, Figurski DH, Schierwater B, DeSalle R. 2002. An automated phylogenetic key for classifying homeoboxes. Mol Phylogenet Evol 24(3):388-399.

Schierwater B, Dellaporta S, DeSalle R. 2002. Is the evolution of Cnox-2 Hox/ParaHox genes "multicolored" and "polygenealogical?". Mol Phylogenet Evol 24(3):374-378.

Terai M, DeSalle R, Burk RD. 2002. Lack of canonical E6 and E7 open reading frames in bird papillomaviruses: Fringilla coelebs papillomavirus and Psittacus erithacus timneh papillomavirus. J Virol 76(19):10020-10023.

Chiu JC, Brenner ED, DeSalle R, Nitabach MN, Holmes TC, Coruzzi GM. 2002. Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana. Mol Biol Evol 19(7):1066-1082.

Borchers MT, Ansay T, DeSalle R, Daugherty BL, Shen H, Metzger M, Lee NA, Lee JJ. 2002. In vitro assessment of chemokine receptor-ligand interactions mediating mouse eosinophil migration. J Leukoc Biol 71(6):1033-1041.

Wyner YM, Johnson SE, Stumpf RM, Desalle R. 2002. Genetic assessment of a white-collared x red-fronted lemur hybrid zone at Andringitra, Madagascar. Am J Primatol 57(2):51-66.

Birstein VJ, Doukakis P, DeSalle R. 2002. Molecular phylogeny of Acipenseridae: Nonmonophyly of Scaphirhynchinae. Copeia 2002(2):287-301.

DeSalle R. 2002. Bold yet austere. BioEssays 24(9):865-866.

Zilversmit M, O'Grady P, Desalle R. 2002. Shallow genomics, phylogenetics, and evolution in the family Drosophilidae. Pac Symp Biocomput 7:512-23.

2001

Baker RH, Wilkinson GS, DeSalle R. 2002. Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae). Syst Biol 50(1):87-105.

Specht CD, Kress WJ, Stevenson DW, DeSalle R. 2002. A molecular phylogeny of Costaceae (Zingiberales). Mol Phylogenet Evol 21(3):333-345. [Corrigendum ]

O'Grady PM, Baker RH, Durando CM, Etges WJ, DeSalle R. 2001. Polytene chromosomes as indicators of phylogeny in several species groups of Drosophila. BMC Evol Biol 1:6.

Kachlany SC, Planet PJ, DeSalle R, Fine DH, Figurski DH. 2001. Genes for tight adherence of Actinobacillus actinomycetemcomitans: from plaque to plague to pond scum. Trends Microbiol 9(9):429-437.

Schierwater B, Desalle R. 2001. Current problems with the zootype and the early evolution of Hox genes. J Exp Zool B Mol Dev Evol 291(2):169-174.

Planet PJ, DeSalle R, Siddall M, Bael T, Sarkar IN, Stanley SE. 2001. Systematic analysis of DNA microarray data: ordering and interpreting patterns of gene expression. Genome Res 11(7):1149-1155.

Lacombe B, Becker D, Hedrich R, DeSalle R, Hollmann M, Kwak JM, Schroeder JI, Le Novère N, Nam HG, Spalding EP, Tester M, Turano FJ, Chiu J, Coruzzi G. 2001. The identity of plant glutamate receptors. Science 292(5521):1486-1487.

Kachlany SC, Planet PJ, DeSalle R, Fine DH, Figurski DH, Kaplan JB. 2001. flp-1, the first representative of a new pilin gene subfamily, is required for non-specific adherence of Actinobacillus actinomycetemcomitans. Mol Microbiol 40(3):542-54.

Greenwood AD, Lee F, Capelli C, DeSalle R, Tikhonov A, Marx PA, MacPhee RD. 2001. Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives. Mol Biol Evol 18(5):840-847.

Planet PJ, Kachlany SC, DeSalle R, Figurski DH. 2001. Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification. Proc Natl Acad Sci USA 98(5):2503-2508.


Books and Book Chapters

Stefani A, DeSalle R. 2013. A Pictorial Approach to Microbiology: Laboratory Guide.

Egan M, Lee EK, Chiu JC, Coruzzi G, DeSalle R. 2009. Gene orthology assessment with OrthologID. In: Methods in Molecular Biology. Bioinformatics for DNA Sequence Analysis. 537:23-38. (Posada D, Ed.)

DeSalle R, Tattersall I. 2008. Human Origins: What Bones and Genomes Tell Us about Ourselves. 216 p. Texas A&M University Press, College Station, TX. ISBN: 1585445673

Amato G, DeSalle R, Rosenbaum HC (Eds.) 2006. Conservation Genetics in the Age of Genomics. 400 p. Columbia University Press, New York, NY. ISBN: 0231128320

DeSalle R. 2005. Animal phylogenomics: multiple interspecific genome comparisons. In: Methods in Enzymology. Molecular Evolution: Producing the Biochemical Data 395:104-133. (Zimmer EA & Roalson EH, Eds.)

DeSalle R, Gregory TR, Johnston JS. 2005. Preparation of samples for comparative studies of arthropod chromosomes: visualization, in situ hybridization, and genome size estimation. In: Methods in Enzymology. Molecular Evolution: Producing the Biochemical Data. 395:460-488. (Zimmer EA & Roalson EH, Eds.)

Di Bonaventura MP, DeSalle R, Eveleigh DE, Baldwin AM, Koestler RJ. 2003. Studies of fungal infestations of the Tiffany’s drawings: limits and advantages of classical and molecular techniques. In: Art, Biology, and Conservation: Biodeterioration of Works of Art. pp. 94-109. (Koestler RJ, Koestler VH, Charola AE, Nieto-Fernandez FE, Eds.) Metropolitan Museum of Art, New York. ISBN: 0300104820

DeSalle R & Schierwater B (Eds.) 2003. Molecular Approaches to Ecology and Evolution. 300 p. Birkhauser, Basel. ISBN: 3764357258

DeSalle R & Yudell M (Eds.) 2002. Welcome to the Genome: A User's Guide to your Genetic Past, Present, and Future. 215 p. John Wiley & Sons, Hoboken, NJ. ISBN: 0471453315

DeSalle R, Giribet G, Wheeler W (Eds.) 2002. Molecular Systematics and Evolution: Theory and Practice. 316 p. Birkhauser, Basel. ISBN: 3764365447

DeSalle R, Giribet G, Wheeler W (Eds.) 2002. Techniques in Molecular Systematics and Evolution. Series: Methods and Tools in Biosciences and Medicine. 407 p. Birkhauser, Basel. ISBN: 3764362561

DeSalle R & Yudell M (Eds.) 2002. Genomic Revolution: Unveiling the Unity of Life. 250 p. National Academy Press, Washington, DC. ISBN: 0309074363

DeSalle R. 1999. Epidemic! The World of Infectious Disease. 246 p. The New Press, New York, NY. ISBN: 1565845463

DeSalle R & Lindley D. 1998. The Science of Jurassic Park and the Lost World. 224 p. HarperCollins, New York, NY. ISBN: 0060977353

Schierwater B, Streit B, Wagner GP, Desalle R. 1994. Molecular Ecology and Evolution: Approaches and Applications. 640 p. Birkhauser, Basel. ISBN: 0817629424

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