Publications

More recent publications are listed first. Links to the following are provided:

Preprint: preprint web version

DOI: final published web version (via its DOI)

PDF: PDF of most recent version (preprint/final)

FigShare: associated large data sets

GitHub: computer code/scripts

Protocols: wet lab protocols

  • Hake K, West PT, McDonald KL, Laundon D, Feng C, Burkhardt P, Richter DJ, Banfield J, King N. Colonial choanoflagellate isolated from Mono Lake harbors a microbiome. bioRxiv 2021.03.30.437421 (2021). Preprint | PDF | FigShare | Protocols

  • Richter DJ, Berney C, Strassert JFH, Burki F, de Vargas C. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotic life. bioRxiv 2020.06.30.180687 (2020). Preprint | PDF | FigShare | GitHub

  • Richter DJ*, Watteaux R*, Vannier T*, Leconte J, Frémont P, Reygondeau G, Maillet N, Henry N et al. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. bioRxiv 867739 (2020). Preprint | PDF | FigShare

  • Richter DJ, Levin TC. The origin and evolution of cell-intrinsic antibacterial defenses in eukaryotes. Current Opinion in Genetics and Development 59, 111-122 (2019). DOI | PDF

  • Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q. Revisions to the classification, nomenclature and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66, 4-119 (2019). DOI | PDF

  • Richter DJ, Fozouni P, Eisen MB, King N. Gene family innovation, conservation and loss on the animal stem lineage. eLife 7, e34226 (2018). Preprint | DOI | PDF | FigShare | Protocols

    • Featured in: Lewis ZR, Dunn CW. Genome Evolution: We are not so special. eLife 7, e38726 (2018). DOI

    • Featured in: Galupa R. Which set of genes distinguishes animals from other organisms? Work from the King lab suggests we need to rewrite textbooks. preLights (2018). Link

  • Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui M-A, Méheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P. A global ocean atlas of eukaryotic genes. Nature Communications 9, 373 (2018). DOI | PDF

  • Richter DJ, Nitsche F. Choanoflagellatea. In: Handbook of the Protists, Archibald et al., eds. (2017). DOI | PDF

  • Nitsche F, Thomsen HA, Richter DJ. Bridging the gap between morphological species and molecular barcodes - exemplified by loricate choanoflagellates. European Journal of Protistology 57, 26-37 (2017). DOI | PDF

  • Carr M*, Richter DJ*, Fozouni P, Smith TJ, Jeuck A, Leadbeater BSC, Nitsche F. A six-gene phylogeny provides new insights into choanoflagellate evolution. Molecular Phylogenetics and Evolution 107, 166-178 (2017). DOI | PDF

  • Ereskovsky A, Richter DJ, Lavrov DV, Schippers KJ, Nichols SA. Transcriptome sequencing and delimitation of sympatric Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA. PloS ONE 12, e0183002 (2017). DOI | PDF

  • Dorrell RG, Gile G, McCallum G, Méheust R, Bapteste EP, Klinger CM, Brillet-Guéguen L, Freeman KD, Richter DJ, Bowler C. Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. eLife 6, e23717 (2017). DOI | PDF

  • Simion P, Philippe H, Baurain D, Jager M, Richter DJ, Di Franco A, Roure B, Satoh N, Quéinnec É, Ereskovsky A, Lapébie P, Corre E, Delsuc F, King N, Wörheide G, Manuel M. A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals. Current Biology 27, 958-967 (2017). DOI | PDF

  • Marron AO, Ratcliffe S, Wheeler GL, Goldstein RE, King N, Not F, de Vargas C, Richter DJ. The evolution of silicon transport in eukaryotes. Molecular Biology and Evolution 33, 3226-3248 (2016). DOI | PDF

  • Thomsen HA, Nitsche F, Richter DJ. Seasonal occurrence of loricate choanoflagellates in Danish inner waters. Protist 167, 622-638 (2016). DOI | PDF | Color Figures

  • Peña JF, Alié A, Richter DJ, Wang L, Funayama N, Nichols SA. Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges. EvoDevo 7 (2016). DOI | PDF

  • Mordret S, Romac S, Henry N, Colin S, Carmichael M, Berney C, Audic S, Richter DJ, Pochon X, de Vargas C, Decelle J. The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.). The ISME Journal 10, 1424-1436 (2016). DOI | PDF

  • Richter DJ, King N. The genomic and cellular foundations of animal origins. Annual Review of Genetics 47, 509-537 (2013). DOI | PDF

  • Fairclough SR, Chen Z, Kramer E, Zeng Q, Young S, Robertson HM, Begovic E, Richter DJ, Russ C, Westbrook MJ, Manning G, Lang BF, Haas B, Nusbaum C, King N. Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta. Genome Biology 14, R15 (2013). DOI | PDF

  • Nichols SA, Roberts BW, Richter DJ, Fairclough SR, King N. Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/β-catenin complex. PNAS 109, 13046-13051 (2012). DOI | PDF

  • Gerhold AR, Richter DJ, Yu AS, Hariharan IK. Identification and characterization of genes required for compensatory growth in Drosophila. Genetics 189, 1309-1326 (2011). DOI | PDF

  • Caswell JL, Mallick S, Richter DJ, Neubauer J, Schirmer C, Gnerre S, Reich D. Analysis of chimpanzee history based on genome sequence alignments. PLoS Genetics 4, e1000057 (2008). DOI | PDF

  • Liu M, Duke JL, Richter DJ, Vinuesa CG, Goodnow CC, Kleinstein SH, Schatz DG. Two levels of protection for the B cell genome during somatic hypermutation. Nature 451, 841-845 (2008). DOI | PDF

  • King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV, Rokhsar D. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451, 783-788 (2008). DOI | PDF

  • Dutt A, Salvesen HB, Chen TH, Ramos AH, Onofrio RC, Hatton C, Nicoletti R, Winckler W, Grewal R, Hanna M, Wyhs N, Ziaugra L, Richter DJ, Trovik J, Engelsen IB, Stefansson IM, Fennell T, Cibulskis K, Zody MC, Akslen LA, Gabriel S, Wong KK, Sellers WR, Meyerson M, Greulich H. Drug-sensitive FGFR2 mutations in endometrial carcinoma. PNAS 105, 8713-8717 (2008). DOI | PDF

  • Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, International HapMap Consortium. Genome-wide detection and characterization of positive selection in human populations. Nature 449, 913-918 (2007). DOI | PDF

  • International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861 (2007). DOI | PDF

  • Dennis JH, Fan HY, Reynolds SM, Yuan G, Meldrim JC, Richter DJ, Peterson DG, Rando OJ, Noble WS, Kingston RE. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Research 17, 928-939 (2007). DOI | PDF

  • Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D. Genetic evidence for complex speciation of humans and chimpanzees. Nature 441, 1103-1108 (2006). DOI | PDF

  • Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, Bontrop RE, McVean GA, Gabriel SB, Reich D, Donnelly P, Altshuler D. Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308, 107-111 (2005). DOI | PDF

  • International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320 (2005). DOI | PDF

  • Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87 (2005). DOI | PDF

  • Paez JG, Lin M, Beroukhim R, Lee JC, Zhao X, Richter DJ, Gabriel S, Herman P, Sasaki H, Altshuler D, Li C, Meyerson M, Sellers WR. Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Research 32, e71 (2004). DOI | PDF

  • Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837 (2002). DOI | PDF

  • Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, Higgins JM, Richter DJ, Lander ES, Altshuler D. Human genome sequence variation and the influence of gene history, mutation and recombination. Nature Genetics 32, 135-142 (2002). DOI | PDF

  • Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES. Linkage disequilibrium in the human genome. Nature 411, 199-204 (2001). DOI | PDF

  • Balazs ME, Richter D. A genetic algorithm with dynamic population: experimental results. Late Breaking Papers at GECCO-99, 25-30 (1999).