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1. A draft human pangenome reference

Author: Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K, Monlong, Jean, Abel, Haley J, Buonaiuto, Silvia, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M, Feng, Xiaowen, Fischer, Christian, Fulton, Robert S, Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T, Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J, Mitchell, Matthew W, Munson, Katherine M, Mwaniki, Moses Njagi, Novak, Adam M, Olsen, Hugh E, Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A, Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R, Antonacci-Fulton, Lucinda L, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Korbel, Jan O, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D, Popejoy, Alice B, Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A, Rhie, Arang, Sacco, Samuel, Sanders, Ashley D, Schneider, Valerie A, Schultz, Baergen I, Shafin, Kishwar, Smith, Michael W, Sofia, Heidi J, Abou Tayoun, Ahmad N, Thibaud-Nissen, Françoise, and Tricomi, Francesca Floriana
Subjects: Biological Sciences, Genetics, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Humans, Diploidy, Genome, Human, Haplotypes, Sequence Analysis, DNA, Genomics, Reference Standards, Cohort Studies, Alleles, Genetic Variation, General Science & Technology
Abstract: Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.
Published: 2023

2. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author: Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Lee, HoJoon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Olson, Nathan D., Puiu, Daniela, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sirén, Jouni, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M.D., Zimin, Aleksey V., Popejoy, Alice B., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Jarvis, Erich D., Miga, Karen H., Wang, Ting, Garrison, Erik, Marschall, Tobias, Hall, Ira, Li, Heng, Paten, Benedict, Greer, Stephanie U., Pavlichin, Dmitri S., Zhou, Bo, Urban, Alexander E., and Weissman, Tsachy
Published: 2023
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3. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

Author: Warren, Wesley C, Harris, R Alan, Haukness, Marina, Fiddes, Ian T, Murali, Shwetha C, Fernandes, Jason, Dishuck, Philip C, Storer, Jessica M, Raveendran, Muthuswamy, Hillier, LaDeana W, Porubsky, David, Mao, Yafei, Gordon, David, Vollger, Mitchell R, Lewis, Alexandra P, Munson, Katherine M, DeVogelaere, Elizabeth, Armstrong, Joel, Diekhans, Mark, Walker, Jerilyn A, Tomlinson, Chad, Graves-Lindsay, Tina A, Kremitzki, Milinn, Salama, Sofie R, Audano, Peter A, Escalona, Merly, Maurer, Nicholas W, Antonacci, Francesca, Mercuri, Ludovica, Maggiolini, Flavia AM, Catacchio, Claudia Rita, Underwood, Jason G, O'Connor, David H, Sanders, Ashley D, Korbel, Jan O, Ferguson, Betsy, Kubisch, H Michael, Picker, Louis, Kalin, Ned H, Rosene, Douglas, Levine, Jon, Abbott, David H, Gray, Stanton B, Sanchez, Mar M, Kovacs-Balint, Zsofia A, Kemnitz, Joseph W, Thomasy, Sara M, Roberts, Jeffrey A, Kinnally, Erin L, Capitanio, John P, Skene, JH Pate, Platt, Michael, Cole, Shelley A, Green, Richard E, Ventura, Mario, Wiseman, Roger W, Paten, Benedict, Batzer, Mark A, Rogers, Jeffrey, and Eichler, Evan E
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, HIV/AIDS, Biotechnology, Animals, Genetic Predisposition to Disease, Genetic Variation, Genome, Humans, Macaca mulatta, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Whole Genome Sequencing, General Science & Technology
Abstract: The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.
Published: 2020

4. A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism.

Author: Buckley, Reuben M, Davis, Brian W, Brashear, Wesley A, Farias, Fabiana HG, Kuroki, Kei, Graves, Tina, Hillier, LaDeana W, Kremitzki, Milinn, Li, Gang, Middleton, Rondo P, Minx, Patrick, Tomlinson, Chad, Lyons, Leslie A, Murphy, William J, and Warren, Wesley C
Subjects: Genetics, Developmental Biology
Abstract: The domestic cat (Felis catus) numbers over 94 million in the USA alone, occupies households as a companion animal, and, like humans, suffers from cancer and common and rare diseases. However, genome-wide sequence variant information is limited for this species. To empower trait analyses, a new cat genome reference assembly was developed from PacBio long sequence reads that significantly improve sequence representation and assembly contiguity. The whole genome sequences of 54 domestic cats were aligned to the reference to identify single nucleotide variants (SNVs) and structural variants (SVs). Across all cats, 16 SNVs predicted to have deleterious impacts and in a singleton state were identified as high priority candidates for causative mutations. One candidate was a stop gain in the tumor suppressor FBXW7. The SNV is found in cats segregating for feline mediastinal lymphoma and is a candidate for inherited cancer susceptibility. SV analysis revealed a complex deletion coupled with a nearby potential duplication event that was shared privately across three unrelated cats with dwarfism and is found within a known dwarfism associated region on cat chromosome B1. This SV interrupted UDP-glucose 6-dehydrogenase (UGDH), a gene involved in the biosynthesis of glycosaminoglycans. Importantly, UGDH has not yet been associated with human dwarfism and should be screened in undiagnosed patients. The new high-quality cat genome reference and the compilation of sequence variation demonstrate the importance of these resources when searching for disease causative alleles in the domestic cat and for identification of feline biomedical models.
Published: 2020

5. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Author: Attardo, Geoffrey M, Abd-Alla, Adly MM, Acosta-Serrano, Alvaro, Allen, James E, Bateta, Rosemary, Benoit, Joshua B, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel B, Farrow, David W, Friedrich, Markus, Hua-Van, Aurélie, Jennings, Emily C, Larkin, Denis M, Lawson, Daniel, Lehane, Michael J, Lenis, Vasileios P, Lowy-Gallego, Ernesto, Macharia, Rosaline W, Malacrida, Anna R, Marco, Heather G, Masiga, Daniel, Maslen, Gareth L, Matetovici, Irina, Meisel, Richard P, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang J, Minx, Patrick, Mireji, Paul O, Ometto, Lino, Parker, Andrew G, Rio, Rita, Rose, Clair, Rosendale, Andrew J, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin T, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Van Den Abbeele, Jan, Vigneron, Aurelien, Wang, Jingwen, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Weiss, Brian L, Wilson, Richard K, Zhao, Xin, and Aksoy, Serap
Subjects: Biological Sciences, Genetics, Vector-Borne Diseases, Biotechnology, Infectious Diseases, Infection, Good Health and Well Being, Animals, DNA Transposable Elements, Drosophila melanogaster, Female, Gene Expression Regulation, Genes, Insect, Genes, X-Linked, Genome, Insect, Genomics, Geography, Insect Proteins, Insect Vectors, Male, Mutagenesis, Insertional, Phylogeny, Repetitive Sequences, Nucleic Acid, Sequence Homology, Amino Acid, Synteny, Trypanosoma, Tsetse Flies, Wolbachia, Tsetse, Trypanosomiasis, Hematophagy, Lactation, Disease, Neglected, Symbiosis, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract: BackgroundTsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity.ResultsGenomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges.ConclusionsExpanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
Published: 2019

6. The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes

Author: Attardo, Geoffrey M, Abd-Alla, Adly MM, Acosta-Serrano, Alvaro, Allen, James E, Bateta, Rosemary, Benoit, Joshua B, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel B, Farrow, David W, Friedrich, Markus, Hua-Van, Aurélie, Jennings, Emily C, Larkin, Denis M, Lawson, Daniel, Lehane, Michael J, Lenis, Vasileios P, Lowy-Gallego, Ernesto, Macharia, Rosaline W, Malacrida, Anna R, Marco, Heather G, Masiga, Daniel, Maslen, Gareth L, Matetovici, Irina, Meisel, Richard P, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang J, Minx, Patrick, Mireji, Paul O, Ometto, Lino, Parker, Andrew G, Rio, Rita, Rose, Clair, Rosendale, Andrew J, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin T, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Van Den Abbeele, Jan, Vigneron, Aurelien, Wang, Jingwen, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Weiss, Brian L, Wilson, Richard K, Zhao, Xin, and Aksoy, Serap
Subjects: Biological Sciences, Genetics, Infectious Diseases, Vector-Borne Diseases, Biotechnology, Infection, Good Health and Well Being
Abstract: Background: Tsetse flies (Glossina sp.) are the sole vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood specific diet by both sexes and obligate bacterial symbiosis. This work describes comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans (G.m. morsitans), G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes) and Fusca (G. brevipalpis) which represent different habitats, host preferences and vectorial capacity. Results: Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex linked scaffolds show increased rates of female specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse specific genes are enriched in protease, odorant binding and helicase activities. Lactation associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other characterized insects. Vision associated Rhodopsin genes show conservation of motion detection/tracking functions and significant variance in the Rhodopsin detecting colors in the blue wavelength ranges. Conclusions: Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
Published: 2019

7. A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

Author: Warren, Wesley C, Hillier, LaDeana W, Tomlinson, Chad, Minx, Patrick, Kremitzki, Milinn, Graves, Tina, Markovic, Chris, Bouk, Nathan, Pruitt, Kim D, Thibaud-Nissen, Francoise, Schneider, Valerie, Mansour, Tamer A, Brown, C Titus, Zimin, Aleksey, Hawken, Rachel, Abrahamsen, Mitch, Pyrkosz, Alexis B, Morisson, Mireille, Fillon, Valerie, Vignal, Alain, Chow, William, Howe, Kerstin, Fulton, Janet E, Miller, Marcia M, Lovell, Peter, Mello, Claudio V, Wirthlin, Morgan, Mason, Andrew S, Kuo, Richard, Burt, David W, Dodgson, Jerry B, and Cheng, Hans H
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Animals, Chickens, Chromosomes, Artificial, Bacterial, Computational Biology, Contig Mapping, Genome, Molecular Sequence Annotation, Sequence Analysis, DNA, Gallus gallus, genome assembly, MHC, Biochemistry and cell biology, Statistics
Abstract: The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb, including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized. Of the 1.21 Gb genome, we include three previously missing autosomes, GGA30, 31, and 33, and improve sequence contig length 10-fold over the previous Gallus_gallus-4.0. Despite the significant base representation improvements made, 138 Mb of sequence is not yet located to chromosomes. When annotated for gene content, Gallus_gallus-5.0 shows an increase of 4679 annotated genes (2768 noncoding and 1911 protein-coding) over those in Gallus_gallus-4.0. We also revisited the question of what genes are missing in the avian lineage, as assessed by the highest quality avian genome assembly to date, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species. Finally, our new data support a detailed map of MHC-B, encompassing two segments: one with a highly stable gene copy number and another in which the gene copy number is highly variable. The chicken model has been a critical resource for many other fields of study, and this new reference assembly will substantially further these efforts.
Published: 2017

8. Whole Genome Analysis of SNV and Indel Polymorphism in Common Marmosets (Callithrix jacchus)

Author: Harris, R. Alan, primary, Raveendran, Muthuswamy, additional, Warren, Wes, additional, LaDeana, Hillier W., additional, Tomlinson, Chad, additional, Graves-Lindsay, Tina, additional, Green, Richard E., additional, Schmidt, Jenna K., additional, Colwell, Julia C., additional, Makulec, Allison T., additional, Cole, Shelley A., additional, Cheeseman, Ian H., additional, Ross, Corinna N., additional, Capuano, Saverio, additional, Eichler, Evan E., additional, Levine, Jon E., additional, and Rogers, Jeffrey, additional
Published: 2023
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9. The genome of the vervet (Chlorocebus aethiops sabaeus)

Author: Warren, Wesley C, Jasinska, Anna J, García-Pérez, Raquel, Svardal, Hannes, Tomlinson, Chad, Rocchi, Mariano, Archidiacono, Nicoletta, Capozzi, Oronzo, Minx, Patrick, Montague, Michael J, Kyung, Kim, Hillier, LaDeana W, Kremitzki, Milinn, Graves, Tina, Chiang, Colby, Hughes, Jennifer, Tran, Nam, Huang, Yu, Ramensky, Vasily, Choi, Oi-wa, Jung, Yoon J, Schmitt, Christopher A, Juretic, Nikoleta, Wasserscheid, Jessica, Turner, Trudy R, Wiseman, Roger W, Tuscher, Jennifer J, Karl, Julie A, Schmitz, Jörn E, Zahn, Roland, O'Connor, David H, Redmond, Eugene, Nisbett, Alex, Jacquelin, Béatrice, Müller-Trutwin, Michaela C, Brenchley, Jason M, Dione, Michel, Antonio, Martin, Schroth, Gary P, Kaplan, Jay R, Jorgensen, Matthew J, Thomas, Gregg WC, Hahn, Matthew W, Raney, Brian J, Aken, Bronwen, Nag, Rishi, Schmitz, Juergen, Churakov, Gennady, Noll, Angela, Stanyon, Roscoe, Webb, David, Thibaud-Nissen, Francoise, Nordborg, Magnus, Marques-Bonet, Tomas, Dewar, Ken, Weinstock, George M, Wilson, Richard K, and Freimer, Nelson B
Subjects: Human Genome, Biotechnology, Genetics, Infection, Animals, Chlorocebus aethiops, Chromosome Painting, Computational Biology, Evolution, Molecular, Gene Rearrangement, Genetic Variation, Genome, Genomics, Karyotype, Major Histocompatibility Complex, Molecular Sequence Annotation, Phylogeny, Phylogeography, Biological Sciences, Medical and Health Sciences, Bioinformatics
Abstract: We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations.
Published: 2015

10. A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution

Author: Warren, Wesley C., Boggs, Tyler E., Borowsky, Richard, Carlson, Brian M., Ferrufino, Estephany, Gross, Joshua B., Hillier, LaDeana, Hu, Zhilian, Keene, Alex C., Kenzior, Alexander, Kowalko, Johanna E., Tomlinson, Chad, Kremitzki, Milinn, Lemieux, Madeleine E., Graves-Lindsay, Tina, McGaugh, Suzanne E., Miller, Jeffrey T., Mommersteeg, Mathilda T. M., Moran, Rachel L., Peuß, Robert, Rice, Edward S., Riddle, Misty R., Sifuentes-Romero, Itzel, Stanhope, Bethany A., Tabin, Clifford J., Thakur, Sunishka, Yamamoto, Yoshiyuki, and Rohner, Nicolas
Published: 2021
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11. A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference.

Author: Puritz, Jonathan B., Guo, Ximing, Hare, Matthew, He, Yan, Hillier, LaDeana W., Jin, Shubo, Liu, Ming, Lotterhos, Katie E., Minx, Pat, Modak, Tejashree, Proestou, Dina, Rice, Edward S., Tomlinson, Chad, Warren, Wesley C., Witkop, Erin, Zhao, Honggang, and Gomez‐Chiarri, Marta
Subjects: AMERICAN oyster, GENOME size, GENOMES, HETEROZYGOSITY, OUTLIER detection, AUDITORY masking, AQUACULTURE industry, FISH breeding
Abstract: Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis‐assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome‐level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome. [ABSTRACT FROM AUTHOR]
Published: 2024
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12. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author: Lee, HoJoon, primary, Greer, Stephanie U., additional, Pavlichin, Dmitri S., additional, Zhou, Bo, additional, Urban, Alexander E., additional, Weissman, Tsachy, additional, Ji, Hanlee P., additional, Liao, Wen-Wei, additional, Asri, Mobin, additional, Ebler, Jana, additional, Doerr, Daniel, additional, Haukness, Marina, additional, Hickey, Glenn, additional, Lu, Shuangjia, additional, Lucas, Julian K., additional, Monlong, Jean, additional, Abel, Haley J., additional, Buonaiuto, Silvia, additional, Chang, Xian H., additional, Cheng, Haoyu, additional, Chu, Justin, additional, Colonna, Vincenza, additional, Eizenga, Jordan M., additional, Feng, Xiaowen, additional, Fischer, Christian, additional, Fulton, Robert S., additional, Garg, Shilpa, additional, Groza, Cristian, additional, Guarracino, Andrea, additional, Harvey, William T., additional, Heumos, Simon, additional, Howe, Kerstin, additional, Jain, Miten, additional, Lu, Tsung-Yu, additional, Markello, Charles, additional, Martin, Fergal J., additional, Mitchell, Matthew W., additional, Munson, Katherine M., additional, Mwaniki, Moses Njagi, additional, Novak, Adam M., additional, Olsen, Hugh E., additional, Pesout, Trevor, additional, Porubsky, David, additional, Prins, Pjotr, additional, Sibbesen, Jonas A., additional, Tomlinson, Chad, additional, Villani, Flavia, additional, Vollger, Mitchell R., additional, Antonacci-Fulton, Lucinda L., additional, Baid, Gunjan, additional, Baker, Carl A., additional, Belyaeva, Anastasiya, additional, Billis, Konstantinos, additional, Carroll, Andrew, additional, Chang, Pi-Chuan, additional, Cody, Sarah, additional, Cook, Daniel E., additional, Cornejo, Omar E., additional, Diekhans, Mark, additional, Ebert, Peter, additional, Fairley, Susan, additional, Fedrigo, Olivier, additional, Felsenfeld, Adam L., additional, Formenti, Giulio, additional, Frankish, Adam, additional, Gao, Yan, additional, Giron, Carlos Garcia, additional, Green, Richard E., additional, Haggerty, Leanne, additional, Hoekzema, Kendra, additional, Hourlier, Thibaut, additional, Kolesnikov, Alexey, additional, Korbel, Jan O., additional, Kordosky, Jennifer, additional, Lee, HoJoon, additional, Lewis, Alexandra P., additional, Magalhães, Hugo, additional, Marco-Sola, Santiago, additional, Marijon, Pierre, additional, McDaniel, Jennifer, additional, Mountcastle, Jacquelyn, additional, Nattestad, Maria, additional, Olson, Nathan D., additional, Puiu, Daniela, additional, Regier, Allison A., additional, Rhie, Arang, additional, Sacco, Samuel, additional, Sanders, Ashley D., additional, Schneider, Valerie A., additional, Schultz, Baergen I., additional, Shafin, Kishwar, additional, Sirén, Jouni, additional, Smith, Michael W., additional, Sofia, Heidi J., additional, Abou Tayoun, Ahmad N., additional, Thibaud-Nissen, Françoise, additional, Tricomi, Francesca Floriana, additional, Wagner, Justin, additional, Wood, Jonathan M.D., additional, Zimin, Aleksey V., additional, Popejoy, Alice B., additional, Bourque, Guillaume, additional, Chaisson, Mark J.P., additional, Flicek, Paul, additional, Phillippy, Adam M., additional, Zook, Justin M., additional, Eichler, Evan E., additional, Haussler, David, additional, Jarvis, Erich D., additional, Miga, Karen H., additional, Wang, Ting, additional, Garrison, Erik, additional, Marschall, Tobias, additional, Hall, Ira, additional, Li, Heng, additional, and Paten, Benedict, additional
Published: 2023
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13. A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference

Author: Puritz, Jonathan B., primary, Guo, Ximing, additional, Hare, Matthew, additional, He, Yan, additional, Hillier, LaDeana W., additional, Jin, Shubo, additional, Liu, Ming, additional, Lotterhos, Katie E., additional, Minx, Pat, additional, Modak, Tejashree, additional, Proestou, Dina, additional, Rice, Edward S., additional, Tomlinson, Chad, additional, Warren, Wesley C., additional, Witkop, Erin, additional, Zhao, Honggang, additional, and Gomez‐Chiarri, Marta, additional
Published: 2023
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14. Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World

Author: Labbé, Frédéric, primary, Abdeladhim, Maha, additional, Abrudan, Jenica, additional, Araki, Alejandra Saori, additional, Araujo, Ricardo N., additional, Arensburger, Peter, additional, Benoit, Joshua B., additional, Brazil, Reginaldo Pecanha, additional, Bruno, Rafaela V., additional, Bueno da Silva Rivas, Gustavo, additional, Carvalho de Abreu, Vinicius, additional, Charamis, Jason, additional, Coutinho-Abreu, Iliano V., additional, da Costa-Latgé, Samara G., additional, Darby, Alistair, additional, Dillon, Viv M., additional, Emrich, Scott J., additional, Fernandez-Medina, Daniela, additional, Figueiredo Gontijo, Nelder, additional, Flanley, Catherine M., additional, Gatherer, Derek, additional, Genta, Fernando A., additional, Gesing, Sandra, additional, Giraldo-Calderón, Gloria I., additional, Gomes, Bruno, additional, Aguiar, Eric Roberto Guimaraes Rocha, additional, Hamilton, James G. C., additional, Hamarsheh, Omar, additional, Hawksworth, Mallory, additional, Hendershot, Jacob M., additional, Hickner, Paul V., additional, Imler, Jean-Luc, additional, Ioannidis, Panagiotis, additional, Jennings, Emily C., additional, Kamhawi, Shaden, additional, Karageorgiou, Charikleia, additional, Kennedy, Ryan C., additional, Krueger, Andreas, additional, Latorre-Estivalis, José M., additional, Ligoxygakis, Petros, additional, Meireles-Filho, Antonio Carlos A., additional, Minx, Patrick, additional, Miranda, Jose Carlos, additional, Montague, Michael J., additional, Nowling, Ronald J., additional, Oliveira, Fabiano, additional, Ortigão-Farias, João, additional, Pavan, Marcio G., additional, Horacio Pereira, Marcos, additional, Nobrega Pitaluga, Andre, additional, Proveti Olmo, Roenick, additional, Ramalho-Ortigao, Marcelo, additional, Ribeiro, José M. C., additional, Rosendale, Andrew J., additional, Sant’Anna, Mauricio R. V., additional, Scherer, Steven E., additional, Secundino, Nágila F. C., additional, Shoue, Douglas A., additional, da Silva Moraes, Caroline, additional, Gesto, João Silveira Moledo, additional, Souza, Nataly Araujo, additional, Syed, Zainulabueddin, additional, Tadros, Samuel, additional, Teles-de-Freitas, Rayane, additional, Telleria, Erich L., additional, Tomlinson, Chad, additional, Traub-Csekö, Yara M., additional, Marques, João Trindade, additional, Tu, Zhijian, additional, Unger, Maria F., additional, Valenzuela, Jesus, additional, Ferreira, Flávia V., additional, de Oliveira, Karla P. V., additional, Vigoder, Felipe M., additional, Vontas, John, additional, Wang, Lihui, additional, Weedall, Gareth D., additional, Zhioua, Elyes, additional, Richards, Stephen, additional, Warren, Wesley C., additional, Waterhouse, Robert M., additional, Dillon, Rod J., additional, and McDowell, Mary Ann, additional
Published: 2023
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15. High resolution genomes of multipleXiphophorusspecies provide new insights into microevolution, hybrid incompatibility, and epistasis

Author: Lu, Yuan, primary, Rice, Edward, additional, Du, Kang, additional, Kneitz, Susanne, additional, Naville, Magali, additional, Dechaud, Corentin, additional, Volff, Jean-Nicolas, additional, Boswell, Mikki, additional, Boswell, William, additional, Hillier, LaDeana, additional, Tomlinson, Chad, additional, Milin, Kremitzki, additional, Walter, Ronald B., additional, Schartl, Manfred, additional, and Warren, Wesley C., additional
Published: 2023
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16. The quail genome: insights into social behaviour, seasonal biology and infectious disease response

Author: Morris, Katrina M., Hindle, Matthew M., Boitard, Simon, Burt, David W., Danner, Angela F., Eory, Lel, Forrest, Heather L., Gourichon, David, Gros, Jerome, Hillier, LaDeana W., Jaffredo, Thierry, Khoury, Hanane, Lansford, Rusty, Leterrier, Christine, Loudon, Andrew, Mason, Andrew S., Meddle, Simone L., Minvielle, Francis, Minx, Patrick, Pitel, Frédérique, Seiler, J. Patrick, Shimmura, Tsuyoshi, Tomlinson, Chad, Vignal, Alain, Webster, Robert G., Yoshimura, Takashi, Warren, Wesley C., and Smith, Jacqueline
Published: 2020
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17. Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly

Author: Warren, Wesley C., García-Pérez, Raquel, Xu, Sen, Lampert, Kathrin P., Chalopin, Domitille, Stöck, Matthias, Loewe, Laurence, Lu, Yuan, Kuderna, Lukas, Minx, Patrick, Montague, Michael J., Tomlinson, Chad, Hillier, LaDeana W., Murphy, Daniel N., Wang, John, Wang, Zhongwei, Garcia, Constantino Macias, Thomas, Gregg C. W., Volff, Jean-Nicolas, Farias, Fabiana, Aken, Bronwen, Walter, Ronald B., Pruitt, Kim D., Marques-Bonet, Tomas, Hahn, Matthew W., Kneitz, Susanne, Lynch, Michael, and Schartl, Manfred
Published: 2018
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18. Genomic Analysis of Two Phlebotomine Sand Fly Vectors ofLeishmaniafrom the New and Old World

Author: Labbé, Frédéric, primary, Abdeladhim, Maha, additional, Abrudan, Jenica, additional, Araki, Alejandra Saori, additional, Araujo, Ricardo N., additional, Arensburger, Peter, additional, Benoit, Joshua B., additional, Brazil, Reginaldo Pecanha, additional, Bruno, Rafaela V., additional, da Silva Rivas, Gustavo Bueno, additional, de Abreu, Vinicius Carvalho, additional, Charamis, Jason, additional, Coutinho-Abreu, Iliano V., additional, da Costa-Latgé, Samara G., additional, Darby, Alistair, additional, Dillon, Viv M., additional, Emrich, Scott, additional, Fernandez-Medina, Daniela, additional, Gontijo, Nelder Figueiredo, additional, Flannley, Catherine M., additional, Gatherer, Derek, additional, Genta, Fernando A., additional, Gesing, Sandra, additional, Giraldo-Calderón, Gloria I., additional, Gomes, Bruno, additional, Rocha Aguiar, Eric Roberto Guimaraes, additional, Hamarsheh, Omar, additional, Hawksworth, Mallory, additional, Hendershot, Jacob M., additional, Hickner, Paul V., additional, Imler, Jean-Luc, additional, Ioannidis, Panagiotis, additional, Jennings, Emily C., additional, Kamhawi, Shaden, additional, Karageorgiou, Charikleia, additional, Kennedy, Ryan C., additional, Krueger, Andreas, additional, Latorre-Estivalis, José M, additional, Ligoxgakis, Petros, additional, Meireles-Filho, Antonio Carlos A., additional, Miranda, Jose Carlos, additional, Montague, Michael, additional, Nowling, Ronald J., additional, Oliveira, Fabiano, additional, Ortigão-Farias, João, additional, Pavan, Marcio G., additional, Pereira, Marcos Horacio, additional, Pitaluga, Andre Nobrega, additional, Olmo, Roenick Proveti, additional, Ramalho-Ortigao, Marcelo, additional, Ribeiro, Jose Marcos, additional, Rosendale, Andrew J., additional, Sant’Anna, Mauricio R.V., additional, Scherer, Steven E., additional, Secundino, Nagila F. C., additional, Shoue, Douglas A., additional, da Silva Moraes, Caroline, additional, Moledo Gesto, João Silveira, additional, Souza, Nataly Araujo, additional, Syed, Zainulabueddin, additional, Tadros, Samuel, additional, Teles-de-Freitas, Rayane, additional, Telleria, Erich L., additional, Tomlinson, Chad, additional, Traub-Cseko, Yara, additional, Marques, João Trindade, additional, Tu, Zhijian, additional, Unger, Maria F, additional, Valenzuela, Jesus, additional, Ferreira, Flavia Viana, additional, de Oliveira, Karla Pollyanna Vieira, additional, Vigoder, Felipe M, additional, Vontas, John, additional, Wang, Lihui, additional, Weedel, Gareth, additional, Zhioua, Elyes, additional, Richards, Stephen, additional, Warren, Wesley C, additional, Waterhouse, Robert M., additional, Dillon, Rod J., additional, and McDowell, Mary Ann, additional
Published: 2022
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19. A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference

Author: Puritz, Jonathan B., primary, Guo, Ximing, additional, Hare, Matt, additional, He, Yan, additional, Hillier, LaDeana, additional, Jin, Shubo, additional, Liu, Ming, additional, Lotterhos, Katie, additional, Minx, Pat, additional, Modak, Tejashree, additional, Proestou, Dina, additional, Rice, Edward S., additional, Tomlinson, Chad, additional, Warren, Wes, additional, Witkop, Erin, additional, Zhao, Honggang, additional, and Gomez-Chiarri, Marta, additional
Published: 2022
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20. Correction: Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail

Author: Adema, Coen M., Hillier, LaDeana W., Jones, Catherine S., Loker, Eric S., Knight, Matty, Minx, Patrick, Oliveira, Guilherme, Raghavan, Nithya, Shedlock, Andrew, do Amaral, Laurence Rodrigues, Arican-Goktas, Halime D., Assis, Juliana G., Baba, Elio Hideo, Baron, Olga L., Bayne, Christopher J., Bickham-Wright, Utibe, Biggar, Kyle K., Blouin, Michael, Bonning, Bryony C., Botka, Chris, Bridger, Joanna M., Buckley, Katherine M., Buddenborg, Sarah K., Lima Caldeira, Roberta, Carleton, Julia, Carvalho, Omar S., Castillo, Maria G., Chalmers, Iain W., Christensens, Mikkel, Clifton, Sandra, Cosseau, Celine, Coustau, Christine, Cripps, Richard M., Cuesta-Astroz, Yesid, Cummins, Scott F., Di Stefano, Leon, Dinguirard, Nathalie, Duval, David, Emrich, Scott, Feschotte, Cédric, Feyereisen, Rene, FitzGerald, Peter, Fronick, Catrina, Fulton, Lucinda, Galinier, Richard, Gava, Sandra G., Geusz, Michael, Geyer, Kathrin K., Giraldo-Calderón, Gloria I., de Souza Gomes, Matheus, Gordy, Michelle A., Gourbal, Benjamin, Grunau, Christoph, Hanington, Patrick C., Hoffmann, Karl F., Hughes, Daniel, Humphries, Judith, Jackson, Daniel J., Jannotti-Passos, Liana K., de Jesus Jeremias, Wander, Jobling, Susan, Kamel, Bishoy, Kapusta, Aurélie, Kaur, Satwant, Koene, Joris M., Kohn, Andrea B., Lawson, Dan, Lawton, Scott P., Liang, Di, Limpanont, Yanin, Liu, Sijun, Lockyer, Anne E., Lovato, Ty Anna L., Ludolf, Fernanda, Magrini, Vince, McManus, Donald P., Medina, Monica, Misra, Milind, Mitta, Guillaume, Mkoji, Gerald M., Montague, Michael J., Montelongo, Cesar, Moroz, Leonid L., Munoz-Torres, Monica C., Niazi, Umar, Noble, Leslie R., Oliveira, Francislon S., Pais, Fabiano S., Papenfuss, Anthony T., Peace, Rob, Pena, Janeth J., Pila, Emmanuel A., Quelais, Titouan, Raney, Brian J., Rast, Jonathan P., Rollinson, David, Rosse, Izinara C., Rotgans, Bronwyn, Routledge, Edwin J., Ryan, Kathryn M., Scholte, Larissa L. S., Storey, Kenneth B., Swain, Martin, Tennessen, Jacob A., Tomlinson, Chad, Trujillo, Damian L., Volpi, Emanuela V., Walker, Anthony J., Wang, Tianfang, Wannaporn, Ittiprasert, Warren, Wesley C., Wu, Xiao-Jun, Yoshino, Timothy P., Yusuf, Mohammed, Zhang, Si-Ming, Zhao, Min, and Wilson, Richard K.
Published: 2017
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21. The B73 Maize Genome: Complexity, Diversity, and Dynamics

Author: Schnable, Patrick S., Ware, Doreen, Fulton, Robert S., Stein, Joshua C., Wei, Fusheng, Pasternak, Shiran, Liang, Chengzhi, Zhang, Jianwei, Fulton, Lucinda, Graves, Tina A., Minx, Patrick, Reily, Amy Denise, Courtney, Laura, Kruchowski, Scott S., Tomlinson, Chad, Strong, Cindy, Delehaunty, Kim, Fronick, Catrina, Courtney, Bill, Rock, Susan M., Belter, Eddie, Du, Feiyu, Kim, Kyung, Abbott, Rachel M., Cotton, Marc, Levy, Andy, Marchetto, Pamela, Ochoa, Kerri, Jackson, Stephanie M., Gillam, Barbara, Chen, Weizu, Yan, Le, Higginbotham, Jamey, Cardenas, Marco, Waligorski, Jason, Applebaum, Elizabeth, Phelps, Lindsey, Falcone, Jason, Kanchi, Krishna, Thane, Thynn, Scimone, Adam, Thane, Nay, Henke, Jessica, Wang, Tom, Ruppert, Jessica, Shah, Neha, Rotter, Kelsi, Hodges, Jennifer, Ingenthron, Elizabeth, Cordes, Matt, Kohlberg, Sara, Sgro, Jennifer, Delgado, Brandon, Mead, Kelly, Chinwalla, Asif, Leonard, Shawn, Crouse, Kevin, Collura, Kristi, Kudrna, Dave, Currie, Jennifer, He, Ruifeng, Angelova, Angelina, Rajasekar, Shanmugam, Mueller, Teri, Lomeli, Rene, Scara, Gabriel, Ko, Ara, Delaney, Krista, Wissotski, Marina, Lopez, Georgina, Campos, David, Braidotti, Michele, Ashley, Elizabeth, Golser, Wolfgang, Kim, HyeRan, Lee, Seunghee, Lin, Jinke, Dujmic, Zeljko, Kim, Woojin, Talag, Jayson, Zuccolo, Andrea, Fan, Chuanzhu, Sebastian, Aswathy, Kramer, Melissa, Spiegel, Lori, Nascimento, Lidia, Zutavern, Theresa, Miller, Beth, Ambroise, Claude, Muller, Stephanie, Spooner, Will, Narechania, Apurva, Ren, Liya, Wei, Sharon, Kumari, Sunita, Faga, Ben, Levy, Michael J., McMahan, Linda, Van Buren, Peter, Vaughn, Matthew W., Ying, Kai, Yeh, Cheng-Ting, Emrich, Scott J., Jia, Yi, Kalyanaraman, Ananth, Hsia, An-Ping, Barbazuk, W. Brad, Baucom, Regina S., Brutnell, Thomas P., Carpita, Nicholas C., Chaparro, Cristian, Chia, Jer-Ming, Deragon, Jean-Marc, Estill, James C., Fu, Yan, Jeddeloh, Jeffrey A., Han, Yujun, Lee, Hyeran, Li, Pinghua, Lisch, Damon R., Liu, Sanzhen, Liu, Zhijie, Nagel, Dawn Holligan, McCann, Maureen C., SanMiguel, Phillip, Myers, Alan M., Nettleton, Dan, Nguyen, John, Penning, Bryan W., Ponnala, Lalit, Schneider, Kevin L., Schwartz, David C., Sharma, Anupma, Soderlund, Carol, Springer, Nathan M., Sun, Qi, Wang, Hao, Waterman, Michael, Westerman, Richard, Wolfgruber, Thomas K., Yang, Lixing, Yu, Yeisoo, Zhang, Lifang, Zhou, Shiguo, Zhu, Qihui, Bennetzen, Jeffrey L., Dawe, R. Kelly, Jiang, Jiming, Jiang, Ning, Presting, Gernot G., Wessler, Susan R., Aluru, Srinivas, Martienssen, Robert A., Clifton, Sandra W., McCombie, W. Richard, Wing, Rod A., and Wilson, Richard K.
Published: 2009
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22. Genome Assemblies across the Diverse Evolutionary Spectrum of Leishmania Protozoan Parasites

Author: Warren, Wesley C., primary, Akopyants, Natalia S., additional, Dobson, Deborah E., additional, Hertz-Fowler, Christiane, additional, Lye, Lon-Fye, additional, Myler, Peter J., additional, Ramasamy, Gowthaman, additional, Shanmugasundram, Achchuthan, additional, Silva-Franco, Fatima, additional, Steinbiss, Sascha, additional, Tomlinson, Chad, additional, Wilson, Richard K., additional, and Beverley, Stephen M., additional
Published: 2021
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23. High resolution genomes of multiple Xiphophorusspecies provide new insights into microevolution, hybrid incompatibility, and epistasis

Author: Lu, Yuan, Rice, Edward, Du, Kang, Kneitz, Susanne, Naville, Magali, Dechaud, Corentin, Volff, Jean-Nicolas, Boswell, Mikki, Boswell, William, Hillier, LaDeana, Tomlinson, Chad, Milin, Kremitzki, Walter, Ronald B., Schartl, Manfred, and Warren, Wesley C.
Abstract: Because of diverged adaptative phenotypes, fish species of the genus Xiphophorushave contributed to a wide range of research for a century. Existing Xiphophorusgenome assemblies are not at the chromosomal level and are prone to sequence gaps, thus hindering advancement of the intra- and inter-species differences for evolutionary, comparative, and translational biomedical studies. Herein, we assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorusspecies, namely, X. maculatus, X. couchianus, and X. hellerii. Our overall goal is to precisely assess microevolutionary processes in the clade to ascertain molecular events that led to the divergence of the Xiphophorusspecies and to progress understanding of genetic incompatibility to disease. In particular, we measured intra- and inter-species divergence and assessed gene expression dysregulation in reciprocal interspecies hybrids among the three species. We found expanded gene families and positively selected genes associated with live bearing, a special mode of reproduction. We also found positively selected gene families are significantly enriched in nonpolymorphic transposable elements, suggesting the dispersal of these nonpolymorphic transposable elements has accompanied the evolution of the genes, possibly by incorporating new regulatory elements in support of the Britten–Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans.
Published: 2023
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24. Draft Genome Sequences of Two Polycyclic Tetramate Macrolactam Producers, Streptomyces sp. Strains JV180 and SP18CM02

Author: Qi, Yunci, primary, Nepal, Keshav K., additional, Greif, Jennifer, additional, Martini, Cole, additional, Tomlinson, Chad, additional, Markovic, Christopher, additional, Fronick, Catrina, additional, and Blodgett, Joshua A. V., additional
Published: 2020
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25. Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Author: Hillier, LaDeana W., Graves, Tina A., Fulton, Robert S., Fulton, Lucinda A., Pepin, Kymberlie H., Minx, Patrick, Wagner-McPherson, Caryn, Layman, Dan, Wylie, Kristine, Sekhon, Mandeep, Becker, Michael C., Fewell, Ginger A., Delehaunty, Kimberly D., Miner, Tracie L., Nash, William E., Kremitzki, Colin, Oddy, Lachlan, Du, Hui, Sun, Hui, Bradshaw-Cordum, Holland, Ali, Johar, Carter, Jason, Cordes, Matt, Harris, Anthony, Isak, Amber, van Brunt, Andrew, Nguyen, Christine, Du, Feiyu, Courtney, Laura, Kalicki, Joelle, Ozersky, Philip, Abbott, Scott, Armstrong, Jon, Belter, Edward A., Caruso, Lauren, Cedroni, Maria, Cotton, Marc, Davidson, Teresa, Desai, Anu, Elliott, Glendoria, Erb, Thomas, Fronick, Catrina, Gaige, Tony, Haakenson, William, Haglund, Krista, Holmes, Andrea, Harkins, Richard, Kim, Kyung, Kruchowski, Scott S., Strong, Cynthia Madsen, Grewal, Neenu, Goyea, Ernest, Hou, Shunfang, Levy, Andrew, Martinka, Scott, Mead, Kelly, McLellan, Michael D., Meyer, Rick, Randall-Maher, Jennifer, Tomlinson, Chad, Dauphin-Kohlberg, Sara, Kozlowicz-Reilly, Amy, Shah, Neha, Swearengen-Shahid, Sharhonda, Snider, Jacqueline, Strong, Joseph T., Thompson, Johanna, Yoakum, Martin, Leonard, Shawn, Pearman, Charlene, Trani, Lee, Radionenko, Maxim, Waligorski, Jason E., Wang, Chunyan, Rock, Susan M., Tin-Wollam, Aye-Mon, Maupin, Rachel, Latreille, Phil, Wendl, Michael C., Yang, Shiaw-Pyng, Pohl, Craig, Wallis, John W., Spieth, John, Bieri, Tamberlyn A., Berkowicz, Nicolas, Nelson, Joanne O., Osborne, John, Ding, Li, Meyer, Rekha, Sabo, Aniko, Shotland, Yoram, Sinha, Prashant, Wohldmann, Patricia E., Cook, Lisa L., Hickenbotham, Matthew T., Eldred, James, Williams, Donald, Jones, Thomas A., She, Xinwei, Ciccarelli, Francesca D., Izaurralde, Elisa, Taylor, James, Schmutz, Jeremy, Myers, Richard M., Cox, David R., Huang, Xiaoqiu, McPherson, John D., Mardis, Elaine R., Clifton, Sandra W., Warren, Wesley C., Chinwalla, Asif T., Eddy, Sean R., Marra, Marco A., Ovcharenko, Ivan, Furey, Terrence S., Miller, Webb, Eichler, Evan E., Bork, Peer, Suyama, Mikita, Torrents, David, Waterston, Robert H., and Wilson, Richard K.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): LaDeana W. Hillier [1]; Tina A. Graves [1]; Robert S. Fulton [1]; Lucinda A. Fulton [1]; Kymberlie H. Pepin [1]; Patrick Minx [1]; Caryn Wagner-McPherson [1]; Dan Layman [1]; [...]
Published: 2005
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26. The DNA sequence of human chromosome 7

Author: Hillier, LaDeana W., Fulton, Robert S., Fulton, Lucinda A., Graves, Tina A., Pepin, Kymberlie H., Wagner-McPherson, Caryn, Layman, Dan, Maas, Jason, Jaeger, Sara, Walker, Rebecca, Wylie, Kristine, Sekhon, Mandeep, Becker, Michael C., O'Laughlin, Michelle D., Schaller, Mark E., Fewell, Ginger A., Delehaunty, Kimberly D., Miner, Tracie L., Nash, William E., Cordes, Matt, Du, Hui, Sun, Hui, Edwards, Jennifer, Bradshaw-Cordum, Holland, Ali, Johar, Andrews, Stephanie, Isak, Amber, VanBrunt, Andrew, Nguyen, Christine, Du, Feiyu, Lamar, Betty, Courtney, Laura, Kalicki, Joelle, Ozersky, Philip, Bielicki, Lauren, Scott, Kelsi, Holmes, Andrea, Harkins, Richard, Harris, Anthony, Strong, Cynthia Madsen, Hou, Shunfang, Tomlinson, Chad, Dauphin-Kohlberg, Sara, Kozlowicz-Reilly, Amy, Leonard, Shawn, Rohlfing, Theresa, Rock, Susan M., Tin-Wollam, Aye-Mon, Abbott, Amanda, Minx, Patrick, Maupin, Rachel, Strowmatt, Catrina, Latreille, Phil, Miller, Nancy, Johnson, Doug, Murray, Jennifer, Woessner, Jeffrey P., Wendl, Michael C., Yang, Shiaw-Pyng, Schultz, Brian R., Wallis, John W., Spieth, John, Bieri, Tamberlyn A., Nelson, Joanne O., Berkowicz, Nicolas, Wohldmann, Patricia E., Cook, Lisa L., Hickenbotham, Matthew T., Eldred, James, Williams, Donald, Bedell, Joseph A., Mardis, Elaine R., Clifton, Sandra W., Chissoe, Stephanie L., Marra, Marco A., Raymond, Christopher, Haugen, Eric, Gillett, Will, Zhou, Yang, James, Rose, Phelps, Karen, Iadanoto, Shawn, Bubb, Kerry, Simms, Elizabeth, Levy, Ruth, Clendenning, James, Kaul, Rajinder, Kent, W. James, Furey, Terrence S., Baertsch, Robert A., Brent, Michael R., Keibler, Evan, Flicek, Paul, Bork, Peer, Suyama, Mikita, Bailey, Jeffrey A., Portnoy, Matthew E., Torrents, David, Chinwalla, Asif T., Gish, Warren R., Eddy, Sean R., McPherson, John D., Olson, Maynard V., Eichler, Evan E., Green, Eric D., Waterston, Robert H., and Wilson, Richard K.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): LaDeana W. Hillier [1]; Robert S. Fulton [1]; Lucinda A. Fulton [1]; Tina A. Graves [1]; Kymberlie H. Pepin [1]; Caryn Wagner-McPherson [1]; Dan Layman [1]; Jason Maas [1]; [...]
Published: 2003
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27. A framework for human microbiome research

Author: Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen
Published: 2012
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28. Structure, function and diversity of the healthy human microbiome

Author: Huttenhower, Curtis, Gevers, Dirk, Knight, Rob, Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Creasy, Heather H., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Giglio, Michelle G., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien, Brooks, Paul J., Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S. G., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm Michael, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry J., Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haake, Susan Kinder, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, King, Nicholas B., Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavromatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Pop, Mihai, Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Christopher S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, YuanQing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Methé, Barbara A., Nelson, Karen E., Petrosino, Joseph F., Weinstock, George M., Wilson, Richard K., and White, Owen
Published: 2012
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29. A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution.

Author: Warren, Wesley, primary, Boggs, Tyler, additional, Borowsky, Richard, additional, Carlson, Brian, additional, Ferrufino, Estephany, additional, Gross, Joshua, additional, Hillier, LaDeana, additional, Hu, Zhilian, additional, Keene, Alex, additional, Kenzior, Alexander, additional, Kowalko, Johanna, additional, Tomlinson, Chad, additional, Kremitzki, Milinn, additional, Lemieux, Madeleine, additional, Graves-Lindsay, Tina, additional, McGaugh, Suzanne, additional, Miller, Jeffrey, additional, Mommersteeg, Mathilda, additional, Moran, Rachel, additional, Peuß, Robert, additional, Rice, Edward, additional, Riddle, Misty, additional, Sifuentes-Romero, Itzel, additional, Stanhope, Bethany, additional, Tabin, Clifford, additional, Thakur, Sunishka, additional, Yamamoto, Yoshiyuki, additional, and Rohner, Nicolas, additional
Published: 2020
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30. A chromosome level genome ofAstyanax mexicanussurface fish for comparing population-specific genetic differences contributing to trait evolution

Author: Warren, Wesley C., primary, Boggs, Tyler E., additional, Borowsky, Richard, additional, Carlson, Brian M., additional, Ferrufino, Estephany, additional, Gross, Joshua B., additional, Hillier, LaDeana, additional, Hu, Zhilian, additional, Keene, Alex C., additional, Kenzior, Alexander, additional, Kowalko, Johanna E., additional, Tomlinson, Chad, additional, Kremitzki, Milinn, additional, Lemieux, Madeleine E., additional, Graves-Lindsay, Tina, additional, McGaugh, Suzanne E., additional, Miller, Jeff T., additional, Mommersteeg, Mathilda, additional, Moran, Rachel L., additional, Peuß, Robert, additional, Rice, Edward, additional, Riddle, Misty R., additional, Sifuentes-Romero, Itzel, additional, Stanhope, Bethany A., additional, Tabin, Clifford J., additional, Thakur, Sunishka, additional, Yoshiyuki, Yamamoto, additional, and Rohner, Nicolas, additional
Published: 2020
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31. The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

Author: Du, Kang, primary, Stöck, Matthias, additional, Kneitz, Susanne, additional, Klopp, Christophe, additional, Woltering, Joost M., additional, Adolfi, Mateus Contar, additional, Feron, Romain, additional, Prokopov, Dmitry, additional, Makunin, Alexey, additional, Kichigin, Ilya, additional, Schmidt, Cornelia, additional, Fischer, Petra, additional, Kuhl, Heiner, additional, Wuertz, Sven, additional, Gessner, Jörn, additional, Kloas, Werner, additional, Cabau, Cédric, additional, Iampietro, Carole, additional, Parrinello, Hugues, additional, Tomlinson, Chad, additional, Journot, Laurent, additional, Postlethwait, John H., additional, Braasch, Ingo, additional, Trifonov, Vladimir, additional, Warren, Wesley C., additional, Meyer, Axel, additional, Guiguen, Yann, additional, and Schartl, Manfred, additional
Published: 2020
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32. A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

Author: Buckley, Reuben M., primary, Davis, Brian W., additional, Brashear, Wesley A., additional, Farias, Fabiana H. G., additional, Kuroki, Kei, additional, Graves, Tina, additional, Hillier, LaDeana W., additional, Kremitzki, Milinn, additional, Li, Gang, additional, Middleton, Rondo, additional, Minx, Patrick, additional, Tomlinson, Chad, additional, Lyons, Leslie A., additional, Murphy, William J., additional, and Warren, Wesley C., additional
Published: 2020
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33. Additional file 13: of Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Author: Attardo, Geoffrey, Adly Abd-Alla, Acosta-Serrano, Alvaro, Allen, James, Bateta, Rosemary, Benoit, Joshua, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel, Farrow, David, Friedrich, Markus, AurĂŠlie Hua-Van, Jennings, Emily, Larkin, Denis, Lawson, Daniel, Lehane, Michael, Lenis, Vasileios, Lowy-Gallego, Ernesto, Macharia, Rosaline, Malacrida, Anna, Marco, Heather, Masiga, Daniel, Maslen, Gareth, Matetovici, Irina, Meisel, Richard, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang, Minx, Patrick, Mireji, Paul, Ometto, Lino, Parker, Andrew, Rio, Rita, Rose, Clair, Rosendale, Andrew, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin, TakĂĄÄ, Peter, Tomlinson, Chad, Tsiamis, George, Abbeele, Jan, Vigneron, Aurelien, Jingwen Wang, Warren, Wesley, Waterhouse, Robert, Weirauch, Matthew, Weiss, Brian, Wilson, Richard, Zhao, Xin, and Aksoy, Serap
Abstract: Review history. (DOCX 31 kb)
Published: 2019
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34. The piranha genome provides molecular insight associated to its unique feeding behavior

Author: Schartl, Manfred, Kneitz, Susanne, Volkoff, Helene, Adolfi, Mateus, Schmidt, Cornelia, Fischer, Petra, Minx, Patrick, Tomlinson, Chad, Meyer, Axel, and Warren, Wesley C.
Subjects: ddc:570
Abstract: The piranha enjoys notoriety due to its infamous predatory behavior but much is still not understood about its evolutionary origins and the underlying molecular mechanisms for its unusual feeding biology. We sequenced and assembled the red-bellied piranha (Pygocentrus nattereri) genome to aid future phenotypic and genetic investigations. The assembled draft genome is similar to other related fishes in repeat composition and gene count. Our evaluation of genes under positive selection suggests candidates for adaptations of piranhas’ feeding behavior in neural functions, behavior, and regulation of energy metabolism. In the fasted brain, we find genes differentially expressed that are involved in lipid metabolism and appetite regulation as well as genes that may control the aggression/boldness behavior of hungry piranhas. Our first analysis of the piranha genome offers new insight and resources for the study of piranha biology and for feeding motivation and starvation in other organisms.
Published: 2019

35. Dramatic changes in gene expression in different forms of Crithidia fasciculata reveal potential mechanisms for insect-specific adhesion in kinetoplastid parasites

Author: Filosa, John N., primary, Berry, Corbett T., additional, Ruthel, Gordon, additional, Beverley, Stephen M., additional, Warren, Wesley C., additional, Tomlinson, Chad, additional, Myler, Peter J., additional, Dudkin, Elizabeth A., additional, Povelones, Megan L., additional, and Povelones, Michael, additional
Published: 2019
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36. The Piranha Genome Provides Molecular Insight Associated to Its Unique Feeding Behavior

Author: Schartl, Manfred, primary, Kneitz, Susanne, additional, Volkoff, Helene, additional, Adolfi, Mateus, additional, Schmidt, Cornelia, additional, Fischer, Petra, additional, Minx, Patrick, additional, Tomlinson, Chad, additional, Meyer, Axel, additional, and Warren, Wesley C, additional
Published: 2019
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37. The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response

Author: Morris, Katrina M, primary, Hindle, Matthew M, additional, Boitard, Simon, additional, Burt, David W, additional, Danner, Angela F, additional, Eory, Lel, additional, Forrest, Heather L, additional, Gourichon, David, additional, Gros, Jerome, additional, Hillier, LaDeana, additional, Jaffredo, Thierry, additional, Khoury, Hanane, additional, Lansford, Rusty, additional, Leterrier, Christine, additional, Loudon, Andrew, additional, Mason, Andrew S, additional, Meddle, Simone L, additional, Minvielle, Francis, additional, Minx, Patrick, additional, Pitel, Frédérique, additional, Seiler, J Patrick, additional, Shimmura, Tsuyoshi, additional, Tomlinson, Chad, additional, Vignal, Alain, additional, Webster, Robert G, additional, Yoshimura, Takashi, additional, Warren, Wesley C, additional, and Smith, Jacqueline, additional
Published: 2019
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38. The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes

Author: Attardo, Geoffrey Michael, primary, Abd-Alla, Adly M.M., additional, Acosta-Serrano, Alvaro, additional, Allen, James E, additional, Bateta, Rosemary, additional, Benoit, Joshua, additional, Bourtzis, Kostas, additional, Caers, Jelle, additional, Caljon, Guy, additional, Christensen, Mikkel B., additional, Farrow, David W., additional, Friedrich, Markus, additional, Hua-Van, Aurélie, additional, Jennings, Emily C., additional, Larkin, Denis M, additional, Lawson, Daniel, additional, Lehane, Michael J., additional, Lenis, Vasileios P., additional, Lowy-Gallego, Ernesto, additional, Macharia, Rosaline W., additional, Malacrida, Anna R., additional, Marco, Heather G., additional, Masiga, Daniel, additional, Maslen, Gareth L., additional, Matetovici, Irina, additional, Meisel, Richard P., additional, Meki, Irene, additional, Michalkova, Veronika, additional, Miller, Wolfgang J., additional, Minx, Patrick, additional, Mireji, Paul O., additional, Ometto, Lino, additional, Parker, Andrew G., additional, Rio, Rita, additional, Rose, Clair, additional, Rosendale, Andrew J., additional, Rota Stabelli, Omar, additional, Savini, Grazia, additional, Schoofs, Liliane, additional, Scolari, Francesca, additional, Swain, Martin T., additional, Takáč, Peter, additional, Tomlinson, Chad, additional, Tsiamis, George, additional, Van Den Abbeele, Jan, additional, Vigneron, Aurélien, additional, Wang, Jingwen, additional, Warren, Wesley C., additional, Waterhouse, Robert M., additional, Weirauch, Matthew T., additional, Weiss, Brian L., additional, Wilson, Richard K., additional, Zhao, Xin, additional, and Aksoy, Serap, additional
Published: 2019
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39. The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni

Author: Geyer, Kathrin, Niazi, Umar, Duval, David, Cosseau, Céline, Tomlinson, Chad, Chalmers, Iain, Swain, Martin, Cutress, David, Bickham-Wright, Utibe, Munshi, Sabrina, Grunau, Christoph, Yoshino, Timothy, Hoffmann, Karl, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Interactions Hôtes-Pathogènes-Environnements (IHPE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Genome Sequencing Center, University of Washington School of Medicine, Department of Pathobiological Sciences, and University of Wisconsin-Madison
Subjects: [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, lcsh:Arctic medicine. Tropical medicine, lcsh:RC955-962, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], lcsh:Public aspects of medicine, parasitic diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, lcsh:RA1-1270
Abstract: Background The debilitating human disease schistosomiasis is caused by infection with schistosome parasites that maintain a complex lifecycle alternating between definitive (human) and intermediate (snail) hosts. While much is known about how the definitive host responds to schistosome infection, there is comparably less information available describing the snail's response to infection. Methodology/Principle findings Here, using information recently revealed by sequencing of the Biomphalaria glabrata intermediate host genome, we provide evidence that the predicted core snail DNA methylation machinery components are associated with both intra-species reproduction processes and inter-species interactions. Firstly, methyl-CpG binding domain protein (Bgmbd2/3) and DNA methyltransferase 1 (Bgdnmt1) genes are transcriptionally enriched in gonadal compared to somatic tissues with 5-azacytidine (5-AzaC) treatment significantly inhibiting oviposition. Secondly, elevated levels of 5-methyl cytosine (5mC), DNA methyltransferase activity and 5mC binding in pigmented hybrid-compared to inbred (NMRI)-B. glabrata populations indicate a role for the snail's DNA methylation machinery in maintaining hybrid vigour or heterosis. Thirdly, locus-specific detection of 5mC by bisulfite (BS)-PCR revealed 5mC within an exonic region of a housekeeping protein-coding gene (Bg14-3-3), supporting previous in silico predictions and whole genome BS-Seq analysis of this species' genome. Finally, we provide preliminary evidence for parasite-mediated host epigenetic reprogramming in the schistosome/snail system, as demonstrated by the increase in Bgdnmt1 and Bgmbd2/3 transcript abundance following Bge (B. glabrata embryonic cell line) exposure to parasite larval transformation products (LTP). Conclusions/Significance The presence of a functional DNA methylation machinery in B. glabrata as well as the modulation of these gene products in response to schistosome products, suggests a vital role for DNA methylation during snail development/oviposition and parasite interactions. Further deciphering the role of this epigenetic process during Biomphalaria/Schistosoma co-evolutionary biology may reveal key factors associated with disease transmission and, moreover, enable the discovery of novel lifecycle intervention strategies.
Published: 2017

40. Additional file 1: of The practical use of genome sequencing data in the management of a feline colony pedigree

Author: Farias, Fabiana, Tomlinson, Chad, Labuda, Jeffrey, Perez-Camargo, Gerardo, Rondo Middleton, and Warren, Wesley
Abstract: Additional tables. Table S1. Validation primer sequences and PCR annealing temperatures; Table S2. Heterozygous SNPs selected from SNPchip data for cross validation; Table S3. Variants associated with diseases in cats with a commercial DNA test available; Table S4. LoF variants identified in genes associated with disease; Table S5. Inbreeding coefficient calculated with SNPchip data of only 3 cats and with SNPchip data of 297 cats ; Table S6. RoH identified with SNPchip data on the three cats; Table S7. RoH identified with WGS data on the three cats. The last column has the overlap with SNPchip RoH number. (DOCX 42Â kb)
Published: 2017
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41. The Genome and Adult Somatic Transcriptome of the Mormyrid Electric Fish Paramormyrops kingsleyae

Author: Gallant, Jason R, primary, Losilla, Mauricio, additional, Tomlinson, Chad, additional, and Warren, Wesley C, additional
Published: 2017
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42. A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)

Author: Kuderna, Lukas F K, primary, Tomlinson, Chad, additional, Hillier, LaDeana W, additional, Tran, Annabel, additional, Fiddes, Ian T, additional, Armstrong, Joel, additional, Laayouni, Hafid, additional, Gordon, David, additional, Huddleston, John, additional, Garcia Perez, Raquel, additional, Povolotskaya, Inna, additional, Serres Armero, Aitor, additional, Gómez Garrido, Jèssica, additional, Ho, Daniel, additional, Ribeca, Paolo, additional, Alioto, Tyler, additional, Green, Richard E, additional, Paten, Benedict, additional, Navarro, Arcadi, additional, Betranpetit, Jaume, additional, Herrero, Javier, additional, Eichler, Evan E, additional, Sharp, Andrew J, additional, Feuk, Lars, additional, Warren, Wesley C, additional, and Marques-Bonet, Tomas, additional
Published: 2017
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43. The Novel Evolution of the Sperm Whale Genome

Author: Warren, Wesley C, primary, Kuderna, Lukas, additional, Alexander, Alana, additional, Catchen, Julian, additional, Pérez-Silva, José G, additional, López-Otín, Carlos, additional, Quesada, Víctor, additional, Minx, Patrick, additional, Tomlinson, Chad, additional, Montague, Michael J, additional, Farias, Fabiana H G, additional, Walter, Ronald B, additional, Marques-Bonet, Tomas, additional, Glenn, Travis, additional, Kieran, Troy J, additional, Wise, Sandra S, additional, Wise, John Pierce, additional, and Waterhouse, Robert M, additional
Published: 2017
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44. The practical use of genome sequencing data in the management of a feline colony pedigree

Author: Farias, Fabiana H. G., primary, Tomlinson, Chad, additional, Labuda, Jeffrey, additional, Perez-Camargo, Gerardo, additional, Middleton, Rondo, additional, and Warren, Wesley C., additional
Published: 2017
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45. Whole genome analysis of a schistosomiasis-transmitting freshwater snail

Author: Adema, Coen M., primary, Hillier, LaDeana W., additional, Jones, Catherine S., additional, Loker, Eric S., additional, Knight, Matty, additional, Minx, Patrick, additional, Oliveira, Guilherme, additional, Raghavan, Nithya, additional, Shedlock, Andrew, additional, do Amaral, Laurence Rodrigues, additional, Arican-Goktas, Halime D., additional, Assis, Juliana G., additional, Baba, Elio Hideo, additional, Baron, Olga L., additional, Bayne, Christopher J., additional, Bickham-Wright, Utibe, additional, Biggar, Kyle K., additional, Blouin, Michael, additional, Bonning, Bryony C., additional, Botka, Chris, additional, Bridger, Joanna M., additional, Buckley, Katherine M., additional, Buddenborg, Sarah K., additional, Lima Caldeira, Roberta, additional, Carleton, Julia, additional, Carvalho, Omar S., additional, Castillo, Maria G., additional, Chalmers, Iain W., additional, Christensens, Mikkel, additional, Clifton, Sandra, additional, Cosseau, Celine, additional, Coustau, Christine, additional, Cripps, Richard M., additional, Cuesta-Astroz, Yesid, additional, Cummins, Scott F., additional, di Stefano, Leon, additional, Dinguirard, Nathalie, additional, Duval, David, additional, Emrich, Scott, additional, Feschotte, Cédric, additional, Feyereisen, Rene, additional, FitzGerald, Peter, additional, Fronick, Catrina, additional, Fulton, Lucinda, additional, Galinier, Richard, additional, Gava, Sandra G., additional, Geusz, Michael, additional, Geyer, Kathrin K., additional, Giraldo-Calderón, Gloria I., additional, de Souza Gomes, Matheus, additional, Gordy, Michelle A., additional, Gourbal, Benjamin, additional, Grunau, Christoph, additional, Hanington, Patrick C., additional, Hoffmann, Karl F., additional, Hughes, Daniel, additional, Humphries, Judith, additional, Jackson, Daniel J., additional, Jannotti-Passos, Liana K., additional, de Jesus Jeremias, Wander, additional, Jobling, Susan, additional, Kamel, Bishoy, additional, Kapusta, Aurélie, additional, Kaur, Satwant, additional, Koene, Joris M., additional, Kohn, Andrea B., additional, Lawson, Dan, additional, Lawton, Scott P, additional, Liang, Di, additional, Limpanont, Yanin, additional, Liu, Sijun, additional, Lockyer, Anne E., additional, Lovato, TyAnna L., additional, Ludolf, Fernanda, additional, Magrini, Vince, additional, McManus, Donald P., additional, Medina, Monica, additional, Misra, Milind, additional, Mitta, Guillaume, additional, Mkoji, Gerald M., additional, Montague, Michael J., additional, Montelongo, Cesar, additional, Moroz, Leonid L., additional, Munoz-Torres, Monica C., additional, Niazi, Umar, additional, Noble, Leslie R., additional, Oliveira, Francislon S., additional, Pais, Fabiano S., additional, Papenfuss, Anthony T., additional, Peace, Rob, additional, Pena, Janeth J., additional, Pila, Emmanuel A., additional, Quelais, Titouan, additional, Raney, Brian J., additional, Rast, Jonathan P., additional, Rollinson, David, additional, Rosse, Izinara C., additional, Rotgans, Bronwyn, additional, Routledge, Edwin J., additional, Ryan, Kathryn M., additional, Scholte, Larissa L. S., additional, Storey, Kenneth B., additional, Swain, Martin, additional, Tennessen, Jacob A., additional, Tomlinson, Chad, additional, Trujillo, Damian L., additional, Volpi, Emanuela V., additional, Walker, Anthony J., additional, Wang, Tianfang, additional, Wannaporn, Ittiprasert, additional, Warren, Wesley C., additional, Wu, Xiao-Jun, additional, Yoshino, Timothy P., additional, Yusuf, Mohammed, additional, Zhang, Si-Ming, additional, Zhao, Min, additional, and Wilson, Richard K., additional
Published: 2017
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46. An upgrade and revision of the chimpanzee reference genome

Author: Kuderna, Lukas F. K., Tomlinson, Chad, Sharp, Andrew J., Feuk, Lars, Green, Richard E., Warren, Wesley C., and Marqués-Bonet, Tomàs
Abstract: Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), celebrada en Viena del 12 al 16 de julio de 2015., Comparative and evolutionary genomics currently highly rely on genome reference assemblies in order to detect variation between different organisms or species. However, the vast majority of current assemblies are based on whole genome shotgun (WGS) sequencing, a technique known to systematically underrepresent certain complex, and potentially biologically relevant, regions of the genome. Furthermore, these assemblies are highly fragmented in terms of contig and scaffold continuity, leading to fragmented or fully missing gene models and a general loss of information. The genome of our closest living evolutionary relative, the chimpanzee, is of key importance to study the evolutionary trajectories of our own species. Nevertheless, its current reference assembly is also based on a WGS and therefore only a draft and a highly fragmented representation of the genome with still over 25,000 scaffolds and 100,000 gaps. Here, we will present our efforts to apply and integrate different 3rd generation sequencing technologies as well as novel genome assembly strategies to resolve most of the complex and missing sequences of the current chimpanzee genome reference, trying to bring its quality closer to the human reference.
Published: 2015

47. Comparative genomic analysis of six Glossinagenomes, vectors of African trypanosomes

Author: Attardo, Geoffrey, Abd-Alla, Adly, Acosta-Serrano, Alvaro, Allen, James, Bateta, Rosemary, Benoit, Joshua, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel, Farrow, David, Friedrich, Markus, Hua-Van, Aurélie, Jennings, Emily, Larkin, Denis, Lawson, Daniel, Lehane, Michael, Lenis, Vasileios, Lowy-Gallego, Ernesto, Macharia, Rosaline, Malacrida, Anna, Marco, Heather, Masiga, Daniel, Maslen, Gareth, Matetovici, Irina, Meisel, Richard, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang, Minx, Patrick, Mireji, Paul, Ometto, Lino, Parker, Andrew, Rio, Rita, Rose, Clair, Rosendale, Andrew, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Abbeele, Jan, Vigneron, Aurelien, Wang, Jingwen, Warren, Wesley, Waterhouse, Robert, Weirauch, Matthew, Weiss, Brian, Wilson, Richard, Zhao, Xin, and Aksoy, Serap
Abstract: Tsetse flies (Glossinasp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossinagenomes representing three sub-genera: Morsitans(G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis(G. palpalis, G. fuscipes), and Fusca(G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity. Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossinarelative to Drosophila melanogastershows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossinaspecies while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges. Expanded genomic discoveries reveal the genetics underlying Glossinabiology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
Published: 2019
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48. High-Quality Assembly of an Individual of Yoruban Descent

Author: Steinberg, Karyn Meltz, primary, Lindsay, Tina Graves, additional, Schneider, Valerie A., additional, Chaisson, Mark J.P., additional, Tomlinson, Chad, additional, Huddleston, John, additional, Minx, Patrick, additional, Kremitzki, Milinn, additional, Albrecht, Derek, additional, Magrini, Vincent, additional, McGrath, Sean, additional, Raja, Archana, additional, Baker, Carl, additional, Harshman, Lana, additional, Hillier, LaDeana W., additional, Thibaud-Nissen, Françoise, additional, Bouk, Nathan, additional, Ly, Amy, additional, Amemiya, Chris, additional, Tang, Joyce, additional, Eichler, Evan E., additional, Fulton, Robert S., additional, Warren, Wesley C., additional, Church, Deanna M., additional, and Wilson, Richard K., additional
Published: 2016
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49. Whole Body Melanoma Transcriptome Response in Medaka

Author: Schartl, Manfred, primary, Shen, Yingjia, additional, Maurus, Katja, additional, Walter, Ron, additional, Tomlinson, Chad, additional, Wilson, Richard K., additional, Postlethwait, John, additional, and Warren, Wesley C., additional
Published: 2015
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50. ThePhysarum polycephalumGenome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling

Author: Schaap, Pauline, primary, Barrantes, Israel, additional, Minx, Pat, additional, Sasaki, Narie, additional, Anderson, Roger W., additional, Bénard, Marianne, additional, Biggar, Kyle K., additional, Buchler, Nicolas E., additional, Bundschuh, Ralf, additional, Chen, Xiao, additional, Fronick, Catrina, additional, Fulton, Lucinda, additional, Golderer, Georg, additional, Jahn, Niels, additional, Knoop, Volker, additional, Landweber, Laura F., additional, Maric, Chrystelle, additional, Miller, Dennis, additional, Noegel, Angelika A., additional, Peace, Rob, additional, Pierron, Gérard, additional, Sasaki, Taeko, additional, Schallenberg-Rüdinger, Mareike, additional, Schleicher, Michael, additional, Singh, Reema, additional, Spaller, Thomas, additional, Storey, Kenneth B., additional, Suzuki, Takamasa, additional, Tomlinson, Chad, additional, Tyson, John J., additional, Warren, Wesley C., additional, Werner, Ernst R., additional, Werner-Felmayer, Gabriele, additional, Wilson, Richard K., additional, Winckler, Thomas, additional, Gott, Jonatha M., additional, Glöckner, Gernot, additional, and Marwan, Wolfgang, additional
Published: 2015
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