Publications
More recent publications are listed first. Links to the following are provided:
Preprint: preprint web version
DOI: peer-reviewed web version (via its DOI)
PDF: PDF of most recent version (preprint/peer-reviewed)
FigShare/Zenodo: associated large data sets
GitHub: computer code/scripts
Protocols: wet lab protocols
Twitter: explanatory Twitter thread
Gàlvez-Morante A, Guéguen L, Natsidis P, Telford MJ, Richter DJ. Dollo parsimony overestimates ancestral gene content reconstructions. Genome Biology and Evolution 16, evae062 (2024). Preprint | DOI | PDF | GitHub | Twitter
Llopis Monferrer N, Romac S, Laget M, Biard T, Sandín MM. Gelatinous matrix, an original convergent evolution to cope with oligotrophy in Nassellaria (Radiolaria). bioRxiv 2024.01.22.576765 (2024). Preprint | PDF
del Campo J, Carlos-Oliveira M, Čepička I, Hehenberger E, Horák A, Karnkowska A, Kolisko M, Lara E, Lukeš J, Pánek T, Piwosz K, Richter DJ, Škaloud P, Sutak R, Tachezy J, Hampl V. The protist cultural renaissance. Trends in Microbiology 32, 128-131 (2024). DOI | PDF | Twitter
Zavadska D, Henry N, Auladell A, Berney C, Richter DJ. On the relationship between protist metabarcoding and protist metagenome-assembled genomes. bioRxiv 2023.10.09.561583 (2023). Preprint | PDF | GitHub | Twitter
Mitsi K, Richter DJ, Arroyo AS, López-Escardó D, Antó M, Guillén A, Ruiz-Trillo I. Taxonomic composition, community structure and molecular novelty of microeukaryotes in a temperate oligomesotrophic lake as revealed by metabarcoding. Scientific Reports, 13 (2023). Preprint | DOI | PDF
Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C. EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotic life. Peer Community Journal 2, e56 (2022). Preprint | DOI | PDF | FigShare | GitHub | Twitter
Recommended in: Douglas G. EukProt enables reproducible Eukaryota-wide protein sequence analyses. Peer Community in Genomics, 100021 (2022). DOI
Richter DJ*, Watteaux R*, Vannier T*, Leconte J, Frémont P, Reygondeau G, Maillet N, Henry N, Benoit G, Da Silva O, Delmont TO, Fernàndez-Guerra A, Suweis S, Narci R, Berney C, Eveillard D, Gavory F, Guidi L, Labadie K, Mahieu E, Poulain J, Romac S, Roux S, Dimier C, Kandels S, Picheral M, Searson S, Tara Oceans Coordinators, Pesant S, Aury JM, Brum JR, Lemaitre C, Pelletier E, Bork P, Sunagawa S, Lombard F, Karp-Boss L, Bowler C, Sullivan MB, Karsenti E, Mariadassou M, Probert I, Peterlongo P, Wincker P, de Vargas C, Ribera d'Alcalà M, Iudicone D, Jaillon O. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife 11, e78129 (2022). Preprint | DOI | PDF | FigShare | Twitter
Berney C, Henry N, Mahé F, Richter DJ, de Vargas C. EukRibo: a manually curated eukaryotic 18S rDNA reference database to facilitate identification of new diversity. bioRxiv 2022.11.03.515105 (2022). Preprint | PDF | Zenodo
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 | Twitter
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 | Twitter
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). PDF