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Innate immunity in the simplest animals - placozoans.

Kamm K, Schierwater B, DeSalle R.

BMC Genomics. 2019 Jan 5;20(1):5. doi: 10.1186/s12864-018-5377-3.


Correction for Birger et al., "Asymptomatic Shedding of Respiratory Virus among an Ambulatory Population across Seasons".

Birger R, Morita H, Comito D, Filip I, Galanti M, Lane B, Ligon C, Rosenbloom D, Shittu A, Ud-Dean M, Desalle R, Planet P, Shaman J.

mSphere. 2018 Dec 12;3(6). pii: e00667-18. doi: 10.1128/mSphere.00667-18. No abstract available.


Good Citizenship Made Easy: A Step-by-Step Guide to Submitting RNA-Seq Data to NCBI.

Feindt W, Oppenheim SJ, DeSalle R, Mehr S.

Curr Protoc Bioinformatics. 2018 Dec;64(1):e67. doi: 10.1002/cpbi.67. Epub 2018 Nov 13.


Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans.

Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, Clifford GM, Chan PKS, Burk RD.

PLoS Pathog. 2018 Nov 1;14(11):e1007352. doi: 10.1371/journal.ppat.1007352. eCollection 2018 Nov.


Uroplakins play conserved roles in egg fertilization and acquired additional urothelial functions during mammalian divergence.

Liao Y, Chang HC, Liang FX, Chung PJ, Wei Y, Nguyen TP, Zhou G, Talebian S, Krey LC, Deng FM, Wong TW, Chicote JU, Grifo JA, Keefe DL, Shapiro E, Lepor H, Wu XR, DeSalle R, Garcia-España A, Kim SY, Sun TT.

Mol Biol Cell. 2018 Oct 10:mbcE18080496. doi: 10.1091/mbc.E18-08-0496. [Epub ahead of print]


Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction.

Kamm K, Osigus HJ, Stadler PF, DeSalle R, Schierwater B.

Sci Rep. 2018 Jul 24;8(1):11168. doi: 10.1038/s41598-018-29400-y.


Asymptomatic Shedding of Respiratory Virus among an Ambulatory Population across Seasons.

Birger R, Morita H, Comito D, Filip I, Galanti M, Lane B, Ligon C, Rosenbloom D, Shittu A, Ud-Dean M, Desalle R, Planet P, Shaman J.

mSphere. 2018 Jul 11;3(4). pii: e00249-18. doi: 10.1128/mSphere.00249-18. Erratum in: mSphere. 2018 Dec 12;3(6):.


ICTV Virus Taxonomy Profile: Papillomaviridae.

Van Doorslaer K, Chen Z, Bernard HU, Chan PKS, DeSalle R, Dillner J, Forslund O, Haga T, McBride AA, Villa LL, Burk RD, Ictv Report Consortium.

J Gen Virol. 2018 Aug;99(8):989-990. doi: 10.1099/jgv.0.001105. Epub 2018 Jun 21.


Phylogeny of the Genus Drosophila.

O'Grady PM, DeSalle R.

Genetics. 2018 May;209(1):1-25. doi: 10.1534/genetics.117.300583. Review.


Hawaiian Drosophila as an Evolutionary Model Clade: Days of Future Past.

O'Grady P, DeSalle R.

Bioessays. 2018 May;40(5):e1700246. doi: 10.1002/bies.201700246. Epub 2018 Mar 30. Review.



Schierwater B, DeSalle R.

Curr Biol. 2018 Feb 5;28(3):R97-R98. doi: 10.1016/j.cub.2017.11.042. Review.


New Insights Into Beclin-1: Evolution and Pan-Malignancy Inhibitor Activity.

Wechman SL, Pradhan AK, DeSalle R, Das SK, Emdad L, Sarkar D, Fisher PB.

Adv Cancer Res. 2018;137:77-114. doi: 10.1016/bs.acr.2017.11.002. Epub 2017 Dec 27.


De Novo characterization of transcriptomes from two North American Papaipema stem-borers (Lepidoptera: Noctuidae).

Oppenheim SJ, Feindt W, DeSalle R, Goldstein PZ.

PLoS One. 2018 Jan 24;13(1):e0191061. doi: 10.1371/journal.pone.0191061. eCollection 2018.


Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61).

Chen Z, Schiffman M, Herrero R, DeSalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Chan PKS, Burk RD.

Virology. 2018 Mar;516:86-101. doi: 10.1016/j.virol.2018.01.002. Epub 2018 Jan 11.


Transcriptome profiling with focus on potential key genes for wing development and evolution in Megaloprepus caerulatus, the damselfly species with the world's largest wings.

Feindt W, Oppenheim SJ, DeSalle R, Goldstein PZ, Hadrys H.

PLoS One. 2018 Jan 12;13(1):e0189898. doi: 10.1371/journal.pone.0189898. eCollection 2018.


Asymptomatic Summertime Shedding of Respiratory Viruses.

Shaman J, Morita H, Birger R, Boyle M, Comito D, Lane B, Ligon C, Smith H, Desalle R, Planet P.

J Infect Dis. 2018 Mar 13;217(7):1074-1077. doi: 10.1093/infdis/jix685.


Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans.

Simon S, Sagasser S, Saccenti E, Brugler MR, Schranz ME, Hadrys H, Amato G, DeSalle R.

Sci Rep. 2017 Oct 19;7(1):13547. doi: 10.1038/s41598-017-13176-8.


Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants.

Chen Z, Ho WCS, Boon SS, Law PTY, Chan MCW, DeSalle R, Burk RD, Chan PKS.

J Virol. 2017 Oct 13;91(21). pii: e01285-17. doi: 10.1128/JVI.01285-17. Print 2017 Nov 1.


Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing.

Tessler M, Neumann JS, Afshinnekoo E, Pineda M, Hersch R, Velho LFM, Segovia BT, Lansac-Toha FA, Lemke M, DeSalle R, Mason CE, Brugler MR.

Sci Rep. 2017 Jul 31;7(1):6589. doi: 10.1038/s41598-017-06665-3.


Conservation Genetics, Precision Conservation, and De-extinction.

Desalle R, Amato G.

Hastings Cent Rep. 2017 Jul;47 Suppl 2:S18-S23. doi: 10.1002/hast.747.


The marker choice: Unexpected resolving power of an unexplored CO1 region for layered DNA barcoding approaches.

Rach J, Bergmann T, Paknia O, DeSalle R, Schierwater B, Hadrys H.

PLoS One. 2017 Apr 13;12(4):e0174842. doi: 10.1371/journal.pone.0174842. eCollection 2017.


Applying evolutionary genetics to developmental toxicology and risk assessment.

Leung MCK, Procter AC, Goldstone JV, Foox J, DeSalle R, Mattingly CJ, Siddall ME, Timme-Laragy AR.

Reprod Toxicol. 2017 Apr;69:174-186. doi: 10.1016/j.reprotox.2017.03.003. Epub 2017 Mar 4. Review.


Phosphotyrosine phosphatase R3 receptors: Origin, evolution and structural diversification.

Chicote JU, DeSalle R, García-España A.

PLoS One. 2017 Mar 3;12(3):e0172887. doi: 10.1371/journal.pone.0172887. eCollection 2017.


Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors.

Oppenheim SJ, Rosenfeld JA, DeSalle R.

BMC Genomics. 2017 Feb 27;18(1):205. doi: 10.1186/s12864-017-3590-0.


Correction: The Tetraspanin-Associated Uroplakins Family (UPK2/3) Is Evolutionarily Related to PTPRQ, a Phosphotyrosine Phosphatase Receptor.

Chicote JU, DeSalle R, Segarra J, Sun TT, García-España A.

PLoS One. 2017 Feb 13;12(2):e0172416. doi: 10.1371/journal.pone.0172416. eCollection 2017.


The Tetraspanin-Associated Uroplakins Family (UPK2/3) Is Evolutionarily Related to PTPRQ, a Phosphotyrosine Phosphatase Receptor.

Chicote JU, DeSalle R, Segarra J, Sun TT, García-España A.

PLoS One. 2017 Jan 18;12(1):e0170196. doi: 10.1371/journal.pone.0170196. eCollection 2017. Erratum in: PLoS One. 2017 Feb 13;12 (2):e0172416.


Genetic differentiation and adaptive evolution at reproductive loci in incipient Drosophila species.

Almeida FC, DeSalle R.

J Evol Biol. 2017 Mar;30(3):524-537. doi: 10.1111/jeb.13021. Epub 2016 Dec 19.


A whole genome gene content phylogenetic analysis of anopheline mosquitoes.

Rosenfeld JA, Oppenheim S, DeSalle R.

Mol Phylogenet Evol. 2017 Feb;107:266-269. doi: 10.1016/j.ympev.2016.11.006. Epub 2016 Nov 16.


MtDNA: The small workhorse of evolutionary studies.

Desalle R, Schierwater B, Hadrys H.

Front Biosci (Landmark Ed). 2017 Jan 1;22:873-887. Review.


Co-existence of BRAF and NRAS driver mutations in the same melanoma cells results in heterogeneity of targeted therapy resistance.

Raaijmakers MI, Widmer DS, Narechania A, Eichhoff O, Freiberger SN, Wenzina J, Cheng PF, Mihic-Probst D, Desalle R, Dummer R, Levesque MP.

Oncotarget. 2016 Nov 22;7(47):77163-77174. doi: 10.18632/oncotarget.12848.


Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome.

Rutschmann S, Detering H, Simon S, Funk DH, Gattolliat JL, Hughes SJ, Raposeiro PM, DeSalle R, Sartori M, Monaghan MT.

Mol Phylogenet Evol. 2017 Feb;107:27-38. doi: 10.1016/j.ympev.2016.10.007. Epub 2016 Oct 11.


Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets.

Narechania A, Baker R, DeSalle R, Mathema B, Kolokotronis SO, Kreiswirth B, Planet PJ.

Gigascience. 2016 Oct 24;5(1):44.


The mitogenome of the bed bug Cimex lectularius (Hemiptera: Cimicidae).

Kolokotronis SO, Foox J, Rosenfeld JA, Brugler MR, Reeves D, Benoit JB, Booth W, Robison G, Steffen M, Sakas Z, Palli SR, Schal C, Richards S, Narechania A, Baker RH, Sorkin LN, Amato G, Mason CE, Siddall ME, DeSalle R.

Mitochondrial DNA B Resour. 2016;1(1):425-427. doi: 10.1080/23802359.2016.1180268. Epub 2016 Jun 20.


A Global eDNA Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil.

Tessler M, Brugler MR, DeSalle R, Hersch R, Velho LFM, Segovia BT, Lansac-Toha FA, Lemke MJ.

Microb Ecol. 2017 Jan;73(1):61-74. doi: 10.1007/s00248-016-0834-5. Epub 2016 Sep 9.


Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.

Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GR, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE; 1000 Genomes Project Consortium, Bustamante CD, Tyler-Smith C.

Nat Genet. 2016 Jun;48(6):593-9. doi: 10.1038/ng.3559. Epub 2016 Apr 25. Review.


What do our genes tell us about our past?

DeSalle R.

J Anthropol Sci. 2016 Jun 20;94:193-200. doi: 10.4436/JASS.94032. Epub 2015 Apr 11.


Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae).

Baker RH, Narechania A, DeSalle R, Johns PM, Reinhardt JA, Wilkinson GS.

Genome Biol Evol. 2016 Mar 26;8(3):896-914. doi: 10.1093/gbe/evw043.


SCIENCE AND SOCIETY. Taking race out of human genetics.

Yudell M, Roberts D, DeSalle R, Tishkoff S.

Science. 2016 Feb 5;351(6273):564-5. doi: 10.1126/science.aac4951. No abstract available.


Data for constructing insect genome content matrices for phylogenetic analysis and functional annotation.

Rosenfeld J, Foox J, DeSalle R.

Data Brief. 2015 Dec 17;6:279-81. doi: 10.1016/j.dib.2015.12.015. eCollection 2016 Mar.


Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius.

Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE.

Nat Commun. 2016 Feb 2;7:10164. doi: 10.1038/ncomms10164.


Comments on Smith (2015)-'The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs'.

DeSalle R.

Brief Funct Genomics. 2016 Sep;15(5):373. doi: 10.1093/bfgp/elv052. Epub 2015 Nov 17. No abstract available.


Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment.

Gruber DF, Gaffney JP, Mehr S, DeSalle R, Sparks JS, Platisa J, Pieribone VA.

PLoS One. 2015 Nov 11;10(11):e0140972. doi: 10.1371/journal.pone.0140972. eCollection 2015.


Insect genome content phylogeny and functional annotation of core insect genomes.

Rosenfeld JA, Foox J, DeSalle R.

Mol Phylogenet Evol. 2016 Apr;97:224-232. doi: 10.1016/j.ympev.2015.10.014. Epub 2015 Nov 5.


Degradation of Human PDZ-Proteins by Human Alphapapillomaviruses Represents an Evolutionary Adaptation to a Novel Cellular Niche.

Van Doorslaer K, DeSalle R, Einstein MH, Burk RD.

PLoS Pathog. 2015 Jun 18;11(6):e1004980. doi: 10.1371/journal.ppat.1004980. eCollection 2015 Jun.


Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae).

Mehr S, Verdes A, DeSalle R, Sparks J, Pieribone V, Gruber DF.

BMC Genomics. 2015 Jun 10;16:445. doi: 10.1186/s12864-015-1565-6.


Changes in the Mitogenome Announcement manuscript category.

DeSalle R, Kolokotronis SO.

Mitochondrial DNA. 2015 Feb;26(1):1. doi: 10.3109/19401736.2015.1013392. Epub 2015 Feb 19. No abstract available.


We can't all be supermodels: the value of comparative transcriptomics to the study of non-model insects.

Oppenheim SJ, Baker RH, Simon S, DeSalle R.

Insect Mol Biol. 2015 Apr;24(2):139-54. doi: 10.1111/imb.12154. Epub 2014 Dec 19. Review.


Evolutionary dynamics of Polynucelotide phosphorylases.

Sokhi UK, DeSalle R, Bacolod MD, Das SK, Dasgupta S, Sarkar D, Fisher PB.

Mol Phylogenet Evol. 2014 Apr;73:77-86. doi: 10.1016/j.ympev.2014.01.020. Epub 2014 Feb 3.


Generation of divergent uroplakin tetraspanins and their partners during vertebrate evolution: identification of novel uroplakins.

Desalle R, Chicote JU, Sun TT, Garcia-España A.

BMC Evol Biol. 2014 Jan 23;14:13. doi: 10.1186/1471-2148-14-13.


Mitogenomics and metazoan evolution.

Schierwater B, Stadler P, Desalle R, Podsiadlowski L.

Mol Phylogenet Evol. 2013 Nov;69(2):311-2. doi: 10.1016/j.ympev.2013.08.009. No abstract available.


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