Research Topics
Genomes and Genes | Rob DeSalleSummaryAffiliation: American Museum of Natural History Country: USA Publications
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Publications
Determination of enriched histone modifications in non-genic portions of the human genomeJeffrey A Rosenfeld
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
BMC Genomics 10:143. 2009..Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has recently been used to identify the modification patterns for the methylation and acetylation of many different histone tails in genes and enhancers...- Finishing genomes with limited resources: lessons from an ensemble of microbial genomesNiranjan Nagarajan
Computational and Mathematical Biology, Genome Institute of Singapore 127726, Singapore
BMC Genomics 11:242. 2010.... - Polytene chromosomes as indicators of phylogeny in several species groups of DrosophilaP M O'Grady
Division of Invertebrate Zoology, American Museum of Natural History, New York, USA
BMC Evol Biol 1:6. 2001..We place the classical Drosophila evolutionary biology tools of polytene chromosome inversion analysis in a phylogenetic context and assess their utility in comparison to nucleotide sequences... - Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomicsIndra Neil Sarkar
MBLWHOI Library, Marine Biological Laboratory, Woods Hole, MA, USA
BMC Bioinformatics 9:103. 2008..A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices... 
Species discovery versus species identification in DNA barcoding efforts: response to RubinoffRob DeSalle
Division of Invertebrates, American Museum of Natural History, New York, NY 10024, USA
Conserv Biol 20:1545-7. 2006- The expansion of conservation geneticsRob DeSalle
American Museum of Natural History, New York, New York 10024, USA
Nat Rev Genet 5:702-12. 2004..Such expansion will allow for more precise conservation decisions to be made and, more importantly, will allow conservation genetics to contribute to area- and landscape-based decision-making processes... - The unholy trinity: taxonomy, species delimitation and DNA barcodingRob DeSalle
Division of Invertebrate Zoology, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
Philos Trans R Soc Lond B Biol Sci 360:1905-16. 2005.... - Crossroads, milestones and landmarks in insect development and evolution: implications for systematicsR DeSalle
Department of Entomology, American Museum of Natural History, New York 10024, USA
Aliso 14:305-21. 1996..Both approaches will aid greatly in expanding our understanding of homology in particular, and insect development in general... 
Evolution of cysteine patterns in the large extracellular loop of tetraspanins from animals, fungi, plants and single-celled eukaryotesRob DeSalle
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
Mol Phylogenet Evol 56:486-91. 2010..Our study provides a framework to better understand tetraspanin formation, diversification and the evolutionary history of these important proteins...- What's in a character?Rob DeSalle
Division of Invertebrates and the Molecular Systematics Laboratories, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
J Biomed Inform 39:6-17. 2006.... - The evolution of HOM-C homeoboxes in the Dipteran family DrosophilidaeR DeSalle
Division of Invertebrates, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
Insect Mol Biol 12:345-51. 2003..In addition, different patterns of codon bias were detected in homeoboxes interrupted with introns when compared to homeoboxes that are uninterrupted... - An even "newer" animal phylogenyRob DeSalle
American Museum of Natural History, New York, Sackler Institute for Comparative Genomics, New York, NY 10024, USA
Bioessays 30:1043-7. 2008..First, the methods used by the authors to generate their phylogenetic hypotheses call for close examination. Second, the relationships of animal taxa in their resultant trees also prompt further discussion... - The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST dataJose Eduardo de la Torre-Bárcena
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
PLoS ONE 4:e5764. 2009..Although most recent studies support the notion that gymnosperms and angiosperms are monophyletic and sister groups, they differ on the topological arrangements within each major group... - Catching the phylogenic history through the ontogenic hourglass: a phylogenomic analysis of Drosophila body segmentation genesAmir Yassin
Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th St at Central Park West, NY 10024, USA
Evol Dev 12:288-95. 2010..We suggest that simultaneous character-based analyses give better macroevolutionary support to the hourglass model of the developmental constraints on genome evolution than pairwise phenetic comparisons... - A functional phylogenomic view of the seed plantsErnest K Lee
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
PLoS Genet 7:e1002411. 2011..Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification... - Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolutionAngélica Cibrián-Jaramillo
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
Genome Biol Evol 2:225-39. 2010.... - A whole-genome phylogeny of the family PasteurellaceaeMaria Pia Di Bonaventura
Sackler Institute of Comparative Genomics, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
Mol Phylogenet Evol 54:950-6. 2010..We show that a very large number of concatenated gene sequences (>160) are needed to reliably obtain the same topology as the overall analysis... - Orthology, function and evolution of accessory gland proteins in the Drosophila repleta groupFrancisca C Almeida
Department of Biology, New York University, New York, NY 10003, USA
Genetics 181:235-45. 2009..We found that positive selection is a strong force in the early divergence of these gene pairs... - The phylogenetic relationships of cynopterine fruit bats (Chiroptera: Pteropodidae: Cynopterinae)Francisca C Almeida
American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA
Mol Phylogenet Evol 53:772-83. 2009..Biogeographic analyses indicate a Sundaland origin of the Cynopterinae and divergence date estimates suggest different timing of diversification of the two major cynopterine clades... - OrthologID: automation of genome-scale ortholog identification within a parsimony frameworkJoanna C Chiu
Department of Biology, New York University, New York, NY 10003, USA
Bioinformatics 22:699-707. 2006..AVAILABILITY: http://nypg.bio.nyu.edu/orthologid/.. - Evolutionary relationships of the old world fruit bats (Chiroptera, Pteropodidae): another star phylogeny?Francisca C Almeida
American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA
BMC Evol Biol 11:281. 2011.... - ESTimating plant phylogeny: lessons from partitioningJose E B de la Torre
Department of Biology, New York University, 100 Washington Sq East, New York, NY 10003, USA
BMC Evol Biol 6:48. 2006.... - ORFcurator: molecular curation of genes and gene clusters in prokaryotic organismsJeffrey A Rosenfeld
Division of Invertebrate Zoology, Central Park West, 79th Street, American Museum of Natural History, New York, NY 10024, USA
Bioinformatics 20:3462-5. 2004..AVAILABILITY: ORFcurator and all associated scripts are freely available as supplementary information. SUPPLEMENTARY INFORMATION: http://www.genomecurator.org/ORFcurator/.. - Animal phylogenomics: multiple interspecific genome comparisonsRob DeSalle
Department of Interbrate Zoology, American Museum of Natural History, New York, New York 10024, USA
Methods Enzymol 395:104-33. 2005..Finally, genome-enabled technologies that are affecting comparative biology are also discussed... - Reciprocal illumination in the gene content tree of lifeE Kurt Lienau
American Museum of Natural History, Molecular Laboratories, Central Park West at 79th Street, P.J.P, New York, New York 10024, USA
Syst Biol 55:441-53. 2006..It also can serve as a technique for identifying well-corroborated sets of homologous genes for functional genomic applications... - Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae)R H Baker
Department of Entomology, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
Syst Biol 50:87-105. 2001..In general, inclusion of the more rapidly evolving data consistently improves the congruence among partitions... - Evidence of adaptive evolution of accessory gland proteins in closely related species of the Drosophila repleta groupFrancisca C Almeida
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
Mol Biol Evol 25:2043-53. 2008..Among these, the ones with a conserved protein domain had positively selected sites within the functional region of the sequence. We also detected one instance of lineage-specific adaptive evolution in a clade formed by 2 sister species... - Testing taxonomic boundaries and the limit of DNA barcoding in the Siberian sturgeon, Acipenser baeriiVadim J Birstein
Sturgeon Conservation International, New York, USA
Mitochondrial DNA 20:110-8. 2009..baerii at the species level. Although control region variation among subspecies was significant, diagnostic differences were not found for any of the subspecies... - Random Addition Concatenation Analysis: a novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the cyanobacteriaApurva Narechania
Sackler Institute for Comparative Genomics, American Museum of Natural History, USA
Genome Biol Evol 4:30-43. 2012..Our method also demonstrates that most emergent phylogenetic signal appears early in the concatenation process. The software is freely available at http://desalle.amnh.org... - Mitochondrial DNA extraction and sequencing of formalin-fixed archival snake tissueMike Friedman
Sackler Insitute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
Mitochondrial DNA 19:433-7. 2008..We reiterate previous caution about minimizing amplicon size and maximizing controls for contamination when working with formalin-preserved reptile tissues... - Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700Maria Pia Di Bonaventura
Sackler Institute for Comparative Genetics, American Museum of Natural History, New York, NY 10024, USA
J Bacteriol 191:4693-4. 2009..This strain has a rough appearance, and its genome contains genes encoding a type VI secretion system and several factors that may participate in host colonization... - Using whole genome presence/absence data to untangle function in 12 Drosophila genomesJeffrey A Rosenfeld
Department of Biology, New York University, New York, New York 10024, USA
Fly (Austin) 2:291-9. 2008..We propose that measures of phylogenetic congruence can be used as criteria to identify loci with related GO terms that have a significant impact on cladogenesis... - The genus Drosophila as a model for testing tree- and character-based methods of species identification using DNA barcodingAmir Yassin
Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, USA
Mol Phylogenet Evol 57:509-17. 2010..In conclusion, DNA barcoding of Drosophila shows no reason to alter the 250 years old tradition of character-based taxonomy, and many reasons to shy away from the alternatives... - Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiationAngélica Cibrián-Jaramillo
Department of Ecology, Evolution and Environmental Biology, Columbia University, 1200 Amsterdam Avenue, Mail Code 5557, New York, NY 10027, USA
BMC Genet 10:65. 2009..We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size... - Integrating DNA barcode data and taxonomic practice: determination, discovery, and descriptionPaul Z Goldstein
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
Bioessays 33:135-47. 2011..This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice... - Preparation of samples for comparative studies of arthropod chromosomes: visualization, in situ hybridization, and genome size estimationRob DeSalle
Department of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
Methods Enzymol 395:460-88. 2005..As well, advances in Genome size measurement and theory are described herein... - A novel analytical framework for dissecting the genetic architecture of behavioral symptoms in neuropsychiatric disordersAnthony J Deo
Department of Biology, New York University, New York, New York, United States of America
PLoS ONE 5:e9714. 2010..CONCLUSIONS: The findings presented are novel and demonstrate the efficacy of this approach in detection of genes underlying such complex human disorders as schizophrenia and depression... - Genetic assessment of a white-collared x red-fronted lemur hybrid zone at Andringitra, MadagascarYael M Wyner
Department of Entomology, American Museum of Natural History, New York, New York 10024, USA
Am J Primatol 57:51-66. 2002..f. rufus populations. The remaining three individuals were found to contain only markers for E. albocollaris. These results indicate that the population at Andringitra is a hybrid population between E. albocollaris and E.f. rufus... - The origin of polynucleotide phosphorylase domainsMagdalena Leszczyniecka
Division of Invertebrates, American Museum of Natural History, New York, NY 10024, USA
Mol Phylogenet Evol 31:123-30. 2004..This result suggests that RPH experienced different evolutionary divergence patterns than the PNPase domains, consistent with the linked nature of the two PNPase domains... - The Widespread Colonization Island of Actinobacillus actinomycetemcomitansPaul J Planet
Department of Microbiology, College of Physicians and Surgeons, Columbia University, 701 West 168th Street, New York, New York 10032, USA
Nat Genet 34:193-8. 2003..We present evidence for a specific horizontal transfer event leading to the establishment of this region as a determinant of disease... - An automated phylogenetic key for classifying homeoboxesI Neil Sarkar
Department of Medical Informatics, Columbia University College of Physicians and Surgeons, New York, NY, USA
Mol Phylogenet Evol 24:388-99. 2002..Using a subset of homeobox protein sequences as a test case, we show that our method approximates classification based on full-scale phylogenetic analysis with very high accuracy in a tiny fraction of the time... - A molecular phylogeny of Costaceae (Zingiberales)C D Specht
Department of Biology, New York University, New York, New York 10003, USA
Mol Phylogenet Evol 21:333-45. 2001..This represents the first detailed investigation into intrageneric and interspecific evolutionary relationships within the family Costaceae and presents some novel evolutionary trends with respect to floral morphology and biogeography... - Character congruence of multiple data partitions and the origin of the Hawaiian DrosophilidaeJ Remsen
Department of Entomology, American Museum of Natural History, New York, New York 10024, USA
Mol Phylogenet Evol 9:225-35. 1998.... - The evolution and development of dipteran wing veins: a systematic approachJ Stark
Department of Biology, New York University, New York 10003, USA
Annu Rev Entomol 44:97-129. 1999..We argue that further developmental evolutionary studies, and the interpretation of data therefrom, must be conducted within the context of a well-supported phylogeny of the organisms under study... - Captive breeding, reintroduction, and the conservation genetics of black and white ruffed lemurs, Varecia variegata variegataY M Wyner
Department of Biology, New York University, NY 10003 6688, USA
Mol Ecol 8:S107-15. 1999..This study demonstrates the utility of combining genetic information with a consideration of conservation priorities in evaluating the implementation of management strategies... - Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relativesA D Greenwood
Division of Vertebrate Zoology, American Museum of Natural History, New York, New York 10024 5192, USA
Mol Biol Evol 18:840-7. 2001.... - Molecular genetic analysis among subspecies of two Eurasian sturgeon species, Acipenser baerii and A. stellatusP Doukakis
American Museum of Natural History, New York, NY 10024, USA
Mol Ecol 8:S117-27. 1999.... - Multiple sources of character information and the phylogeny of Hawaiian drosophilidsR H Baker
Department of Entomology, American Museum of Natural History, 79th Street at Central Park West, New York, New York 10024, USA
Syst Biol 46:654-73. 1997..We present a new method, partitioned Bremer support, for examining the contribution of a particular data partition to the topological support of the simultaneous analysis tree... - Assessing biodiversity funding during the sixth extinctionGeorge Amato
Sackler Institute for Comparative Genomics, American Museum of Natural History New York, NY, USA
Bioessays 34:658-60. 2012..A true solution to the biodiversity crisis will require greater attention from governmental and international funding agencies... - Evidence, content and corroboration and the Tree of LifeE Kurt Lienau
Department of Biology, New York University, New York, NY 10003, USA
Acta Biotheor 57:187-99. 2009..Discussion of this "total evidence" approach leads to several interesting conclusions about generating ToL hypotheses... - An application of tissue and DNA banking for genomics and conservation: the Ambrose Monell Cryo-Collection (AMCC)Angelique Corthals
American Museum of Natural History, New York, NY, 10024, USA
Syst Biol 54:819-23. 2005 - Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97Zigui Chen
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
J Virol 83:1443-55. 2009.... - Relationships among characiform fishes inferred from analysis of nuclear and mitochondrial gene sequencesDaniela Calcagnotto
Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024 5192, USA
Mol Phylogenet Evol 36:135-53. 2005.... - Patterns of mitochondrial versus nuclear DNA sequence divergence among nymphalid butterflies: the utility of wingless as a source of characters for phylogenetic inferenceA V Brower
Department of Entomology, American Museum of Natural History, New York, NY, USA
Insect Mol Biol 7:73-82. 1998..We suggest that wg will be a useful source of characters for phylogenetic studies of butterflies, and perhaps other insect taxa, with divergence times up to 60 million years ago... - PERMANENT GENETIC RESOURCES: Development of microsatellite markers of the Mexican understorey palm Chamaedorea elegans, cross-species genotyping, and amplification in congenersAngélica Cibrián-Jaramillo
Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Avenue, MC5557, New York, NY 10027, USA, Department of Biology, Georgetown University, 37th and O Streets, NW, Washington, D C 20057, USA, Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
Mol Ecol Resour 8:322-4. 2008..All nine multiplexing loci amplified in other five congeneric species, which will facilitate comparisons within the genus and contribute to the conservation of its genetic resources... - Taking the conservation biology perspective to secondary school classroomsYael Wyner
Secondary Education, City College of New York, New York, NY 10031, USA
Conserv Biol 24:649-54. 2010..Nevertheless, if the research is placed in the context of larger ecological processes that are being taught, students can gain a better understanding of ecology and a better understanding of their effect on the world... - DNA barcoding of an invasive mammal species, the small Indian mongoose (Herpestes javanicus; E. Geoffroy Saint-Hillaire 1818) in the Caribbean and Hawaiian IslandsChanda E Bennett
Center for Biodiversity and Conservation, American Museum of Natural History, New York, USA
Mitochondrial DNA 22:12-8. 2011..Although the small Indian mongoose is recognized as Herpestes javanicus, this nomenclature has been used interchangeably with Herpestes auropunctatus... - Testing dispersal hypotheses in foraging green sea turtles (Chelonia mydas) of BrazilEugenia Naro-Maciel
the Center for Biodiversity and Conservation and the Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, USA
J Hered 98:29-39. 2007..The results are consistent with a model of juvenile natal homing impacted by other factors. Effective protection of turtles foraging along the extensive Brazilian coast may enhance breeding populations thousands of kilometers away... - caos software for use in character-based DNA barcodingIndra Neil Sarkar
MBLWHOI Library, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA, Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street at CPW, New York, NY 10024, USA
Mol Ecol Resour 8:1256-9. 2008..The software is publicly available from http://sarkarlab.mbl.edu/CAOS... - The effect of differential reproductive success on population genetic structure: correlations of life history with matrilines in humpback whales of the gulf of maineH C Rosenbaum
Molecular Systematics Laboratory, American Museum of Natural History, 79th Street and CPW, New York, NY 10024, USA
J Hered 93:389-99. 2002..These results indicate that population structure can be influenced by interactions or associations between reproductive success, genetic structure, and environmental factors in a natural population of long-lived mammals... - Hierarchical structure in the Drosophila mojavensis cluster (Diptera: Drosophilidae)D C S G Oliveira
Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
Hereditas 139:223-7. 2003..arizonae. Our results suggest that either these taxa are still undergoing differentiation at the molecular level or have experienced gene flow in the recent past... - How the fruit fly changed (some of) its spotsP M O'Grady
Division of Invertebrates, American Museum of Natural History, New York 10024, USA
Curr Biol 10:R75-7. 2000..While several genes have been shown to play a role in melanization, changes in a single gene - the one encoding tyrosine hydroxylase - are sufficient to generate novel pigmentation patterns... - Genetic divergence within the Drosophila mayaguana subcluster, a closely related triad of Caribbean species in the repleta species groupC M Durando
American Museum of Natural History, Division of Invertebrate Zoology, Central Park West @ 79th St, New York, NY 10024, USA
Hereditas 136:240-5. 2002..straubae from D. parisiena, highlighting the importance of examining a diverse array of data (morphological, molecular, ecological, and behavioral) when defining species limits... - Gene family evolution and homology: genomics meets phylogeneticsJ W Thornton
Department of Biological Sciences and Center for Environmental Research and Conservation, Columbia University, New York, New York 10027, USA
Annu Rev Genomics Hum Genet 1:41-73. 2000..A marriage of the principles of phylogenetic systematics with the copious data generated by genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it... - Molecular evolution of the synapsin gene familyH T Kao
Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York 10021, USA
J Exp Zool 285:360-77. 1999..This was accompanied by the emergence of an additional conserved domain, termed A. J. Exp. Zool. ( Mol. Dev. Evol. ) 285:360-377, 1999... - Random roots and lineage sortingJeffrey A Rosenfeld
IST High Performance and Research Computing, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
Mol Phylogenet Evol 64:12-20. 2012..Likelihood tends to stabilize incongruence as outgroups get further and further away from the ingroup. In one extreme case, likelihood overcompensates for sequence divergence but increases random rooting causing long branch repulsion... - Mycobacterium tuberculosis spoligotypes that may derive from mixed strain infections are revealed by a novel computational approachLuiz Claudio O Lazzarini
Institute of Thoracic Disease, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
Infect Genet Evol 12:798-806. 2012.... - An introduction to a novel population genetic approach for HIV characterizationBeatriz Perez-Sweeney
American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, NY, USA
Infect Genet Evol 10:1155-64. 2010..This strategy may prove to be a helpful way to characterize HIV genetic variation among hosts with suspected selection pressure differences, like progressors versus non-progressors... - Can we ever identify the Urmetazoan?Bernd Schierwater
ITZ, Ecology and Evolution, TiHo Hannover, Bünteweg 17d, D 30559 Hannover, Germany American Museum of Natural History, Division of Invertebrate Zoology 79 St at Central Park West, New York, NY 10024, USA
Integr Comp Biol 47:670-6. 2007..Even considerable amounts of recent molecular data have not provided a generally accepted answer. Here, we review the major problems of this phylogenetic conundrum and provide some directions for solving it... - Key transitions in animal evolutionRob DeSalle
American Museum of Natural History, New York, Division of Invertebrate Zoology 79 St at Central Park West, New York, NY 10024 ITZ, Ecology and Evolution, TiHo Hannover, Bünteweg 17d, D 30559 Hannover, Germany
Integr Comp Biol 47:667-9. 2007..In order to address this subject further and to assess progress in the examination of animal origins and transitions, an international group of scientists was convened at the Society for Comparative Biology meeting in January 2007... - The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansionFrancois Roudier
Department of Biology, New York University, New York, NY 10003, USA
Plant Physiol 130:538-48. 2002..Together, these results indicate that COB family members are likely to be important new players at the plasma membrane-cell wall interface... - Falsifications and corroborations: Karl Popper's influence on systematicsKevin G Helfenbein
American Museum of Natural History, Department of Invertebrate Zoology, Central Park West at 79th Street, New York, NY 10024, USA
Mol Phylogenet Evol 35:271-80. 2005..We begin by presenting a synopsis of Popper's philosophical views to allow those views to be placed in the context of systematics... - flp-1, the first representative of a new pilin gene subfamily, is required for non-specific adherence of Actinobacillus actinomycetemcomitansS C Kachlany
Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
Mol Microbiol 40:542-54. 2001..actinomycetemcomitans. The duplication and divergence of flp genes in bacteria may be important to the diversification of the colonization properties of these organisms... - Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classificationP J Planet
Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
Proc Natl Acad Sci U S A 98:2503-8. 2001..This molecular key-based method can be applied to other gene superfamilies and represents a valuable tool for genome analysis... - Combined support for wholesale taxic atavism in gavialine crocodyliansJohn Gatesy
Department of Biology, University of California, Riverside, California 92521, USA
Syst Biol 52:403-22. 2003..Remaining inconsistencies in minimum length trees, including concentrated hierarchical patterns of homoplasy and extensive gaps in the fossil record, indicate where future work in crocodylian systematics should be directed... - Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thalianaJoanna C Chiu
Department of Biology, New York University, New York 10003, USA
Mol Biol Evol 19:1066-82. 2002..The three AtGLR clades do not show distinct clade-specific organ expression patterns. All 20 AtGLR genes are expressed in the root. Among them, five of the nine clade-II genes are root-specific in 8-week-old Arabidopsis plants... - Origin of the tetraspanin uroplakins and their co-evolution with associated proteins: implications for uroplakin structure and functionAntonio Garcia-Espana
Unitat de Recerca, University Hospital Joan XXIII, Universitat Rovira i Virgili, 46007 Tarragona, Spain
Mol Phylogenet Evol 41:355-67. 2006..The structure and function of uroplakins, which are also expressed in Xenopus kidney, oocytes and fat body, are much more versatile than hitherto appreciated... - Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimensPaul Z Goldstein
Division of Insects, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
Mol Ecol 12:1993-8. 2003..Implications for the phylogenetic species criterion and for the reintroduction of individuals to formerly occupied sites are discussed... - Phylogeny and age of diversification of the planitibia species group of the Hawaiian DrosophilaJames Bonacum
Department of Biology, University of Illinois at Springfield, 62703 5407, USA
Mol Phylogenet Evol 37:73-82. 2005.... - How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruenceJohn Gatesy
Department of Biology, University of California Riverside, Spieth Hall, Riverside, California 92521, USA
Syst Biol 56:355-63. 2007 - Phenetic and DNA taxonomy; a comment on WaughRob DeSalle
Bioessays 29:1289-90. 2007 - Tumor outbreaks in marine turtles are not due to recent herpesvirus mutationsLarry Herbst
Curr Biol 14:R697-9. 2004 - Is the evolution of Cnox-2 Hox/ParaHox genes "multicolored" and "polygenealogical?"Bernd Schierwater
ITZ, Ecology and Evolution, TiHo Hannover, Bünteweg 17d, D 30559 Hannover, Germany
Mol Phylogenet Evol 24:374-8. 2002..The existing data on possible gene functions also reveal a quite heterogeneous picture. It seems conceivable that part of the "multicolored" picture relates to a "polygenealogical" origin of the Cnox-2 gene... - Out of Hawaii: the origin and biogeography of the genus Scaptomyza (Diptera: Drosophilidae)Patrick O'Grady
Department of Environmental Science, Policy and Management, 117 Hilgard Hall, University of California, Berkeley, Berkeley, CA 94720, USA
Biol Lett 4:195-9. 2008..We propose that a combination of small body size, rapid generation time and unique ecological and physiological adaptations have allowed this genus to effectively disperse and diversify... - The Trichoplax PaxB gene: a putative Proto-PaxA/B/C gene predating the origin of nerve and sensory cellsThorsten Hadrys
ITZ, Ecology and Evolution, Hannover, Germany
Mol Biol Evol 22:1569-78. 2005..While PaxB, Pax2/5/8, and Pax6 genes have been linked to nerve cell and sensory system/organ development in virtually all animals investigated so far, our study suggests that Pax genes predate the origin of nerve and sensory cells... - Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)Jim Leebens-Mack
Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
OMICS 10:231-7. 2006..Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors... - Diversifying selection in human papillomavirus type 16 lineages based on complete genome analysesZigui Chen
Department of Microbiology and Immunology, Albert Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
J Virol 79:7014-23. 2005..Whether response to selective pressure upon the E5 and E6 ORFs contributes to the biological success of HPV16, its specific biological niche, and/or its oncogenic potential remains to be established... - The carcinogenicity of human papillomavirus types reflects viral evolutionMark Schiffman
Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MA, USA
Virology 337:76-84. 2005..These results present several clear clues and research directions in our ongoing efforts to understand HPV carcinogenesis... - In vitro assessment of chemokine receptor-ligand interactions mediating mouse eosinophil migrationMichael T Borchers
Mayo Clinic Scottsdale, Scottsdale, Arizona 85259, USA
J Leukoc Biol 71:1033-41. 2002..Collectively, these observations reveal physiologically relevant distinctions in mechanisms mediating human and mouse eosinophil migration that potentially reflect evolutionary disparities between these species... - Lack of the canonical pRB-binding domain in the E7 ORF of artiodactyl papillomaviruses is associated with the development of fibropapillomasApurva Narechania
Department of Microbiology and Immunology, Albert Einstein Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
J Gen Virol 85:1243-50. 2004.... - Phylogenetic incongruence among oncogenic genital alpha human papillomavirusesApurva Narechania
Department of Microbiology, Albert Einstein College of Medicine, Ullman Building, Room 515, 1300 Morris Park Ave, Bronx, NY 10461, USA
J Virol 79:15503-10. 2005..These data indicate that the phylogeny of the oncogenic HPVs is complex and that their evolution may not be monophyletic across all genes... - Resolution of a supertree/supermatrix paradoxJohn Gatesy
Department of Biology, University of California, Riverside, California 92521, USA
Syst Biol 51:652-64. 2002 - Appearance of new tetraspanin genes during vertebrate evolutionAntonio Garcia-Espana
Research Unit, Universitat Rovira i Virgili, Hospital Joan XXIII, Pere Virgily Institute, Tarragona 43007, Spain
Genomics 91:326-34. 2008.... - Human papillomavirus (HPV) types 101 and 103 isolated from cervicovaginal cells lack an E6 open reading frame (ORF) and are related to gamma-papillomavirusesZigui Chen
Department of Microbiology and Immunology, Albert Einstein Cancer Center, Albert Einstein College of Medicine of Yeshiva University, NY 10461, USA
Virology 360:447-53. 2007..Moreover, this is the first report of HPVs lacking an E6 ORF and phylogenetic evidence suggests this occurred subsequent to their emergence from the gamma-/pi-PVs... - Dynamic regulation of fluorescent proteins from a single species of coralHung Teh Kao
Department of Psychiatry and Human Behavior, Division of Biology and Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
Mar Biotechnol (NY) 9:733-46. 2007..These findings have implications for current hypotheses regarding the properties and natural function of fluorescent proteins...
Research Grants
- Genetic Transfer in the Evolution of Infectious DiseaseRob DeSalle; Fiscal Year: 2005....