Author: "Minx, Patrick" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Minx, Patrick"' showing total 331 results

Start Over Author "Minx, Patrick"

331 results on '"Minx, Patrick"'

1. Author Correction: Elephant shark genome provides unique insights into gnathostome evolution.

Author: Venkatesh, Byrappa, Lee, Alison, Ravi, Vydianathan, Maurya, Ashish, Lian, Michelle, Swann, Jeremy, Ohta, Yuko, Flajnik, Martin, Sutoh, Yoichi, Kasahara, Masanori, Hoon, Shawn, Gangu, Vamshidhar, Roy, Scott, Irimia, Manuel, Korzh, Vladimir, Kondrychyn, Igor, Lim, Zhi, Tay, Boon-Hui, Tohari, Sumanty, Kong, Kiat, Ho, Shufen, Lorente-Galdos, Belen, Quilez, Javier, Marques-Bonet, Tomas, Raney, Brian, Ingham, Philip, Tay, Alice, Hillier, LaDeana, Minx, Patrick, Boehm, Thomas, Wilson, Richard, Brenner, Sydney, and Warren, Wesley
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Published: 2020

2. 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

3. 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

4. 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

5. The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development.

Author: Wagner, Josiah, Singh, Param, Romney, Amie, Riggs, Claire, Minx, Patrick, Woll, Steven, Roush, Jake, Warren, Wesley, Brunet, Anne, and Podrabsky, Jason
Subjects: Annual killifish, Austrofundulus limnaeus, Development, Fish genome, Gene expression, Positive selection, Stress tolerance, Transcriptome, Adaptation, Biological, Animals, Base Composition, Biological Evolution, Chickens, Embryo, Nonmammalian, Embryonic Development, Gene Expression Regulation, Genome, Genome Size, Genomics, Killifishes, Mitochondria, Phylogeny, Repetitive Sequences, Nucleic Acid, Stress, Physiological, Vertebrates, Zebrafish
Abstract: BACKGROUND: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system. RESULTS: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy and was annotated using the NCBI Eukaryotic Annotation Pipeline. We show that the assembled genome has a high degree of completeness in genic regions that is on par with several other teleost genomes. Using RNA-seq and phylogenetic-based approaches, we identify several candidate genes that may be important for embryonic stress tolerance and post-diapause development in A. limnaeus. Several of these genes include heat shock proteins that have unique expression patterns in A. limnaeus embryos and at least one of these may be under positive selection. CONCLUSION: The A. limnaeus genome is the first South American annual killifish genome made publicly available. This genome will be a valuable resource for comparative genomics to determine the genetic and evolutionary mechanisms that support the unique biology of annual killifishes. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and their impacts on vertebrate physiology and evolution.
Published: 2018

6. Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail.

Author: Adema, Coen, Hillier, LaDeana, Jones, Catherine, Loker, Eric, Knight, Matty, Minx, Patrick, Oliveira, Guilherme, Raghavan, Nithya, Shedlock, Andrew, do Amaral, Laurence, Arican-Goktas, Halime, Assis, Juliana, Baba, Elio, Baron, Olga, Bayne, Christopher, Bickham-Wright, Utibe, Biggar, Kyle, Blouin, Michael, Bonning, Bryony, Botka, Chris, Bridger, Joanna, Buckley, Katherine, Buddenborg, Sarah, Lima Caldeira, Roberta, Carleton, Julia, Carvalho, Omar, Castillo, Maria, Chalmers, Iain, Christensens, Mikkel, Clifton, Sandra, Cosseau, Celine, Coustau, Christine, Cripps, Richard, Cuesta-Astroz, Yesid, Cummins, Scott, Di Stefano, Leon, Dinguirard, Nathalie, Duval, David, Emrich, Scott, Feschotte, Cédric, Feyereisen, Rene, FitzGerald, Peter, Fronick, Catrina, Fulton, Lucinda, Galinier, Richard, Gava, Sandra, Geusz, Michael, Geyer, Kathrin, Giraldo-Calderón, Gloria, de Souza Gomes, Matheus, Gordy, Michelle, Gourbal, Benjamin, Grunau, Christoph, Hanington, Patrick, Hoffmann, Karl, Hughes, Daniel, Humphries, Judith, Jackson, Daniel, Jannotti-Passos, Liana, de Jesus Jeremias, Wander, Jobling, Susan, Kamel, Bishoy, Kapusta, Aurélie, Kaur, Satwant, Koene, Joris, Kohn, Andrea, Lawson, Dan, Lawton, Scott, Liang, Di, Limpanont, Yanin, Liu, Sijun, Lockyer, Anne, Lovato, Ty, Ludolf, Fernanda, Magrini, Vince, McManus, Donald, Medina, Monica, Misra, Milind, Mitta, Guillaume, Mkoji, Gerald, Montague, Michael, Montelongo, Cesar, Moroz, Leonid, Munoz-Torres, Monica, Niazi, Umar, Noble, Leslie, Oliveira, Francislon, Pais, Fabiano, Papenfuss, Anthony, Peace, Rob, Pena, Janeth, Pila, Emmanuel, Quelais, Titouan, Raney, Brian, Rast, Jonathan, Rollinson, David, Rosse, Izinara, Rotgans, Bronwyn, Routledge, Edwin, and Ryan, Kathryn
Abstract: This corrects the article DOI: 10.1038/ncomms15451.
Published: 2017

7. 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 Stephano, 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, TyAnna 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, and Ryan, Kathryn M
Subjects: Animals, Schistosoma mansoni, Biomphalaria, Schistosomiasis mansoni, Proteome, DNA Transposable Elements, Pheromones, Sequence Analysis, DNA, Animal Communication, Fresh Water, Evolution, Molecular, Gene Expression Regulation, Genome, Host-Parasite Interactions, Stress, Physiological, Evolution, Molecular, Sequence Analysis, DNA, Stress, Physiological
Abstract: Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis.
Published: 2017

8. 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

9. Opsin Repertoire and Expression Patterns in Horseshoe Crabs: Evidence from the Genome of Limulus polyphemus (Arthropoda: Chelicerata).

Author: Battelle, Barbara-Anne, Ryan, Joseph, Kempler, Karen, Saraf, Spencer, Marten, Catherine, Warren, Wesley, Minx, Patrick, Montague, Michael, Green, Pamela, Schmidt, Skye, Fulton, Lucinda, PATEL, Nipam, Protas, Meredith, Wilson, Richard, and Porter, Megan
Subjects: Limulus polyphemus, evolution, opsin, photoreceptors, xiphosuran, Amino Acid Sequence, Animals, Evolution, Molecular, Eye, Genome, Horseshoe Crabs, Multigene Family, Opsins, Phylogeny
Abstract: Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of genes encoding Limulus opsins, the protein component of the visual pigments, are critical for understanding opsin evolution and diversification among chelicerates, where knowledge of opsins is limited, and more broadly among arthropods. In the present study, we sequenced and assembled a high quality nuclear genomic sequence of L. polyphemus and used these data to annotate the full repertoire of Limulus opsins. We conducted a detailed phylogenetic analysis of Limulus opsins, including using gene structure and synteny information to identify relationships among different opsin classes. We used our phylogeny to identify significant genomic events that shaped opsin evolution and therefore the visual system of Limulus We also describe the tissue expression patterns of the 18 opsins identified and show that transcripts encoding a number, including a peropsin, are present throughout the central nervous system. In addition to significantly extending our understanding of photosensitivity in Limulus and providing critical insight into the genomic evolution of horseshoe crab opsins, this work provides a valuable genomic resource for addressing myriad questions related to xiphosuran physiology and arthropod evolution.
Published: 2016

10. Reinstatement and expansion of the genus Anatherum (Andropogoneae, Panicoideae, Poaceae)

Author: Vorontsova, Maria S., primary, Petersen, Kurt B., additional, Minx, Patrick, additional, Aubuchon-Elder, Taylor M., additional, Romay, M. Cinta, additional, Buckler, Edward S., additional, and Kellogg, Elizabeth A., additional
Published: 2023
Full Text: View/download PDF

11. Symbiotic organs shaped by distinct modes of genome evolution in cephalopods

Author: Belcaid, Mahdi, Casaburi, Giorgio, McAnulty, Sarah J., Schmidbaur, Hannah, Suria, Andrea M., Moriano-Gutierrez, Silvia, Pankey, M. Sabrina, Oakley, Todd H., Kremer, Natacha, Koch, Eric J., Collins, Andrew J., Nguyen, Hoan, Lek, Sai, Goncharenko-Foster, Irina, Minx, Patrick, Sodergren, Erica, Weinstock, George, Rokhsar, Daniel S., McFall-Ngai, Margaret, Simakov, Oleg, Foster, Jamie S., and Nyholm, Spencer V.
Published: 2019

12. 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

13. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

Author: Montague, Michael J, Li, Gang, Gandolfi, Barbara, Khan, Razib, Aken, Bronwen L, Searle, Steven MJ, Minx, Patrick, Hillier, LaDeana W, Koboldt, Daniel C, Davis, Brian W, Driscoll, Carlos A, Barr, Christina S, Blackistone, Kevin, Quilez, Javier, Lorente-Galdos, Belen, Marques-Bonet, Tomas, Alkan, Can, Thomas, Gregg WC, Hahn, Matthew W, Menotti-Raymond, Marilyn, O'Brien, Stephen J, Wilson, Richard K, Lyons, Leslie A, Murphy, William J, and Warren, Wesley C
Subjects: Human Genome, Genetics, Biotechnology, Adaptation, Physiological, Amino Acid Sequence, Animals, Animals, Domestic, Animals, Wild, Carnivory, Cats, Chromosome Mapping, DNA Copy Number Variations, Dogs, Female, Gene Deletion, Gene Duplication, Genome, Genomics, Male, Membrane Transport Proteins, Molecular Sequence Data, Phylogeny, Selection, Genetic, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Species Specificity, Felis catus, domestication, genome
Abstract: Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.
Published: 2014

14. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Author: Bradley Shaffer, H, Minx, Patrick, Warren, Daniel E, Shedlock, Andrew M, Thomson, Robert C, Valenzuela, Nicole, Abramyan, John, Amemiya, Chris T, Badenhorst, Daleen, Biggar, Kyle K, Borchert, Glen M, Botka, Christopher W, Bowden, Rachel M, Braun, Edward L, Bronikowski, Anne M, Bruneau, Benoit G, Buck, Leslie T, Capel, Blanche, Castoe, Todd A, Czerwinski, Mike, Delehaunty, Kim D, Edwards, Scott V, Fronick, Catrina C, Fujita, Matthew K, Fulton, Lucinda, Graves, Tina A, Green, Richard E, Haerty, Wilfried, Hariharan, Ramkumar, Hernandez, Omar, Hillier, LaDeana W, Holloway, Alisha K, Janes, Daniel, Janzen, Fredric J, Kandoth, Cyriac, Kong, Lesheng, de Koning, AP, Li, Yang, Literman, Robert, McGaugh, Suzanne E, Mork, Lindsey, O'Laughlin, Michelle, Paitz, Ryan T, Pollock, David D, Ponting, Chris P, Radhakrishnan, Srihari, Raney, Brian J, Richman, Joy M, St John, John, Schwartz, Tonia, Sethuraman, Arun, Spinks, Phillip Q, Storey, Kenneth B, Thane, Nay, Vinar, Tomas, Zimmerman, Laura M, Warren, Wesley C, Mardis, Elaine R, and Wilson, Richard K
Abstract: Abstract Background We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. Results Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. Conclusions Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.
Published: 2013

15. A high-resolution map of human evolutionary constraint using 29 mammals.

Author: Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F, Parker, Brian J, Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D, Lowe, Craig B, Holloway, Alisha K, Clamp, Michele, Gnerre, Sante, Alföldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J, Jaffe, David B, Jungreis, Irwin, Kent, W James, Kostka, Dennis, Lara, Marcia, Martins, Andre L, Massingham, Tim, Moltke, Ida, Raney, Brian J, Rasmussen, Matthew D, Robinson, Jim, Stark, Alexander, Vilella, Albert J, Wen, Jiayu, Xie, Xiaohui, Zody, Michael C, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin, Jen, Bloom, Toby, Chin, Chee Whye, Heiman, Dave, Nicol, Robert, Nusbaum, Chad, Young, Sarah, Wilkinson, Jane, Worley, Kim C, Kovar, Christie L, Muzny, Donna M, Gibbs, Richard A, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree, Andrew, Dihn, Huyen H, Fowler, Gerald, Jhangiani, Shalili, Joshi, Vandita, Lee, Sandra, Lewis, Lora R, Nazareth, Lynne V, Okwuonu, Geoffrey, Santibanez, Jireh, Warren, Wesley C, Mardis, Elaine R, Weinstock, George M, Wilson, Richard K, Genome Institute at Washington University, Delehaunty, Kim, Dooling, David, Fronik, Catrina, Fulton, Lucinda, Fulton, Bob, Graves, Tina, Minx, Patrick, Sodergren, Erica, Birney, Ewan, Margulies, Elliott H, Herrero, Javier, Green, Eric D, Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S, Pedersen, Jakob S, Lander, Eric S, and Kellis, Manolis
Subjects: Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Animals, Mammals, Humans, Disease, RNA, Sequence Alignment, Sequence Analysis, DNA, Genomics, Evolution, Molecular, Phylogeny, Genome, Genome, Human, Exons, Health, Selection, Genetic, Molecular Sequence Annotation, Sequence Analysis, DNA, Evolution, Molecular, Human, Selection, Genetic, General Science & Technology
Abstract: The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.
Published: 2011

16. Genome sequence of Cronobacter sakazakii BAA-894 and comparative genomic hybridization analysis with other Cronobacter species.

Author: Kucerova, Eva, Clifton, Sandra W, Xia, Xiao-Qin, Long, Fred, Porwollik, Steffen, Fulton, Lucinda, Fronick, Catrina, Minx, Patrick, Kyung, Kim, Warren, Wesley, Fulton, Robert, Feng, Dongyan, Wollam, Aye, Shah, Neha, Bhonagiri, Veena, Nash, William E, Hallsworth-Pepin, Kymberlie, Wilson, Richard K, McClelland, Michael, and Forsythe, Stephen J
Subjects: CHO Cells, Animals, Humans, Cricetulus, Enterobacteriaceae, Bacteriophages, Enterobacteriaceae Infections, Meningitis, Cluster Analysis, Species Specificity, Genome, Bacterial, Genome, Infant, Newborn, Cricetinae, Comparative Genomic Hybridization, Bacterial, Infant, Newborn, General Science & Technology
Abstract: BackgroundThe genus Cronobacter (formerly called Enterobacter sakazakii) is composed of five species; C. sakazakii, C. malonaticus, C. turicensis, C. muytjensii, and C. dublinensis. The genus includes opportunistic human pathogens, and the first three species have been associated with neonatal infections. The most severe diseases are caused in neonates and include fatal necrotizing enterocolitis and meningitis. The genetic basis of the diversity within the genus is unknown, and few virulence traits have been identified.Methodology/principal findingsWe report here the first sequence of a member of this genus, C. sakazakii strain BAA-894. The genome of Cronobacter sakazakii strain BAA-894 comprises a 4.4 Mb chromosome (57% GC content) and two plasmids; 31 kb (51% GC) and 131 kb (56% GC). The genome was used to construct a 387,000 probe oligonucleotide tiling DNA microarray covering the whole genome. Comparative genomic hybridization (CGH) was undertaken on five other C. sakazakii strains, and representatives of the four other Cronobacter species. Among 4,382 annotated genes inspected in this study, about 55% of genes were common to all C. sakazakii strains and 43% were common to all Cronobacter strains, with 10-17% absence of genes.Conclusions/significanceCGH highlighted 15 clusters of genes in C. sakazakii BAA-894 that were divergent or absent in more than half of the tested strains; six of these are of probable prophage origin. Putative virulence factors were identified in these prophage and in other variable regions. A number of genes unique to Cronobacter species associated with neonatal infections (C. sakazakii, C. malonaticus and C. turicensis) were identified. These included a copper and silver resistance system known to be linked to invasion of the blood-brain barrier by neonatal meningitic strains of Escherichia coli. In addition, genes encoding for multidrug efflux pumps and adhesins were identified that were unique to C. sakazakii strains from outbreaks in neonatal intensive care units.
Published: 2010

17. Sequence and Comparative Analysis of the Maize NB Mitochondrial Genome

Author: Clifton, Sandra W., Minx, Patrick, Gibson, Michael, Sun, Hui, Thompson, Melissa, Barbazuk, W. Brad, Wilson, Richard K., and Newton, Kathleen J.
Published: 2004

18. 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
Full Text: View/download PDF

19. A Pilot Study of High-Throughput, Sequence-Based Mutational Profiling of Primary Human Acute Myeloid Leukemia Cell Genomes

Author: Ley, Timothy J., Minx, Patrick J., Walter, Matthew J., Ries, Rhonda E., Sun, Hui, McLellan, Michael, DiPersio, John F., Link, Daniel C., Tomasson, Michael H., Graubert, Timothy A., McLeod, Howard, Khoury, Hanna, Watson, Mark, Shannon, William, Trinkaus, Kathryn, Heath, Sharon, Vardiman, James W., Caligiuri, Michael A., Bloomfield, Clara D., Milbrandt, Jeffrey D., Mardis, Elaine R., and Wilson, Richard K.
Published: 2003

20. 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
Full Text: View/download PDF

21. Evolution of Symbiotic Bacteria in the Distal Human Intestine

Author: Xu, Jian, Mahowald, Michael A, Ley, Ruth E, Lozupone, Catherine A, Hamady, Micah, Martens, Eric C, Henrissat, Bernard, Coutinho, Pedro M, Minx, Patrick, Latreille, Philippe, Cordum, Holland, Van Brunt, Andrew, Kim, Kyung, Fulton, Robert S, Fulton, Lucinda A, Clifton, Sandra W, Wilson, Richard K, Knight, Robin D, and Gordon, Jeffrey I
Subjects: Microbiology, Biological Sciences, Genetics, Human Genome, Digestive Diseases, Adaptation, Physiological, Bacteriophages, Bacteroides, Conjugation, Genetic, DNA Transposable Elements, Ecosystem, Evolution, Molecular, Gene Duplication, Gene Transfer, Horizontal, Genetic Variation, Genome, Bacterial, Humans, Intestines, Molecular Sequence Data, Phylogeny, Polysaccharides, Bacterial, RNA, Bacterial, RNA, Ribosomal, 16S, Species Specificity, Symbiosis, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract: The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the Bacteroidetes and Firmicutes divisions. To examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, Bacteroides vulgatus and Bacteroides distasonis, and by comparison with the few other sequenced gut and non-gut Bacteroidetes, analyzed their niche and habitat adaptations. The results show that lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine. Our findings show that these processes have been a driving force in the adaptation of Bacteroidetes to the distal gut environment, and emphasize the importance of considering the evolution of humans from an additional perspective, namely the evolution of our microbiomes.
Published: 2007

22. Comparative Genomic Sequence Analysis of the Human and Mouse Cystic Fibrosis Transmembrane Conductance Regulator Genes

Author: Ellsworth, Rachel E., Jamison, D. Curtis, Touchman, Jeffrey W., Chissoe, Stephanie L., Bouffard, Gerard G., Dietrich, Nicole L., Beckstrom-Sternberg, Stephen M., Iyer, Leslie M., Weintraub, Lauren A., Cotton, Marc, Courtney, Laura, Edwards, Jennifer, Maupin, Rachel, Ozersky, Philip, Rohlfing, Theresa, Wohldmann, Patricia, Miner, Tracie, Kemp, Kimberley, Kramer, Jason, Korf, Ian, Pepin, Kimberlie, Antonacci-Fulton, Lucinda, Fulton, Robert S., Minx, Patrick, Hillier, LaDeana W., Wilson, Richard K., Waterston, Robert H., Miller, Webb, and Green, Eric D.
Published: 2000

23. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

Author: Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, Chinwalla, Asif, Clarke, Laura, Clee, Chris, Coghlan, Avril, Coulson, Alan, D'Eustachio, Peter, Fitch, David HA, Fulton, Lucinda A, Fulton, Robert E, Griffiths-Jones, Sam, Harris, Todd W, Hillier, LaDeana W, Kamath, Ravi, Kuwabara, Patricia E, Mardis, Elaine R, Marra, Marco A, Miner, Tracie L, Minx, Patrick, Mullikin, James C, Plumb, Robert W, Rogers, Jane, Schein, Jacqueline E, Sohrmann, Marc, Spieth, John, Stajich, Jason E, Wei, C, Willey, David, Wilson, Richard K, Durbin, Richard, and Waterston, Robert H
Subjects: Chromosomes, Artificial, Bacterial, Animals, Caenorhabditis, Caenorhabditis elegans, Proteins, MicroRNAs, RNA, Codon, RNA, Ribosomal, RNA, Transfer, RNA, Spliced Leader, Cluster Analysis, Models, Statistical, Chromosome Mapping, Physical Chromosome Mapping, Sequence Analysis, DNA, Genomics, Evolution, Molecular, Species Specificity, Interspersed Repetitive Sequences, Conserved Sequence, Protein Structure, Tertiary, Gene Library, Multigene Family, Open Reading Frames, Genome, Introns, Exons, Plasmids, Models, Genetic, Molecular Sequence Data, Biological Evolution, Chromosomes, Artificial, Bacterial, Ribosomal, Transfer, Spliced Leader, Models, Statistical, Sequence Analysis, DNA, Evolution, Molecular, Protein Structure, Tertiary, Genetic, Developmental Biology, Biological Sciences, Medical and Health Sciences, Agricultural and Veterinary Sciences
Abstract: The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.
Published: 2003

24. 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
Full Text: View/download PDF

25. Plant conservation assessment at scale: Rapid triage of extinction risks

Author: AuBuchon‐Elder, Taylor, primary, Minx, Patrick, additional, Bookout, Bess, additional, and Kellogg, Elizabeth A., additional
Published: 2023
Full Text: View/download PDF

26. Phylogenetic Relationships among the Box Turtles, Genus Terrapene

Author: Minx, Patrick
Published: 1996

27. Molecular Systematics of the Genus Clemmys and the Intergeneric Relationships of Emydid Turtles

Author: Bickham, John W., Lamb, Trip, Minx, Patrick, and Patton, John C.
Published: 1996

28. Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

Author: Mesquita, Rafael D., Vionette-Amaral, Raquel J., Lowenberger, Carl, Rivera-Pomar, Rolando, Monteiro, Fernando A., Minx, Patrick, Spieth, John, Carvalho, A. Bernardo, Panzera, Francisco, Lawson, Daniel, Torres, André Q., Ribeiro, Jose M. C., Sorgine, Marcos H. F., Waterhouse, Robert M., Montague, Michael J., Abad-Franch, Fernando, Alves-Bezerra, Michele, Amaral, Laurence R., Araujo, Helena M., Araujo, Ricardo N., Aravind, L., Atella, Georgia C., Azambuja, Patricia, Berni, Mateus, Bittencourt-Cunha, Paula R., Braz, Gloria R. C., Calderón-Fernández, Gustavo, Carareto, Claudia M. A., Christensen, Mikkel B., Costa, Igor R., Costa, Samara G., Dansa, Marilvia, Daumas-Filho, Carlos R. O., De-Paula, Iron F., Dias, Felipe A., Dimopoulos, George, Emrich, Scott J., Esponda-Behrens, Natalia, Fampa, Patricia, Fernandez-Medina, Rita D., da Fonseca, Rodrigo N., Fontenele, Marcio, Fronick, Catrina, Fulton, Lucinda A., Gandara, Ana Caroline, Garcia, Eloi S., Genta, Fernando A., Giraldo-Calderón, Gloria I., Gomes, Bruno, Gondim, Katia C., Granzotto, Adriana, Guarneri, Alessandra A., Guigó, Roderic, Harry, Myriam, Hughes, Daniel S. T., Jablonka, Willy, Jacquin-Joly, Emmanuelle, Juárez, M. Patricia, Koerich, Leonardo B., Lange, Angela B., Latorre-Estivalis, José Manuel, Lavore, Andrés, Lawrence, Gena G., Lazoski, Cristiano, Lazzari, Claudio R., Lopes, Raphael R., Lorenzo, Marcelo G., Lugon, Magda D., Majerowicz, David, Marcet, Paula L., Mariotti, Marco, Masuda, Hatisaburo, Megy, Karine, Melo, Ana C. A., Missirlis, Fanis, Mota, Theo, Noriega, Fernando G., Nouzova, Marcela, Nunes, Rodrigo D., Oliveira, Raquel L. L., Oliveira-Silveira, Gilbert, Ons, Sheila, Orchard, Ian, Pagola, Lucia, Paiva-Silva, Gabriela O., Pascual, Agustina, Pavan, Marcio G., Pedrini, Nicolás, Peixoto, Alexandre A., Pereira, Marcos H., Pike, Andrew, Polycarpo, Carla, Prosdocimi, Francisco, Ribeiro-Rodrigues, Rodrigo, Robertson, Hugh M., Salerno, Ana Paula, Salmon, Didier, Santesmasses, Didac, Schama, Renata, Seabra-Junior, Eloy S., Silva-Cardoso, Livia, Silva-Neto, Mario A. C., Souza-Gomes, Matheus, Sterkel, Marcos, Taracena, Mabel L., Tojo, Marta, Tu, Zhijian Jake, Tubio, Jose M. C., Ursic-Bedoya, Raul, Venancio, Thiago M., Walter-Nuno, Ana Beatriz, Wilson, Derek, Warren, Wesley C., Wilson, Richard K., Huebner, Erwin, Dotson, Ellen M., and Oliveira, Pedro L.
Published: 2015

29. Plant conservation assessment at scale: rapid triage of extinction risks

Author: AuBuchon-Elder, Taylor, primary, Minx, Patrick, additional, Bookout, Bess, additional, and Kellogg, Elizabeth A., additional
Published: 2022
Full Text: View/download PDF

30. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

Author: Castoe, Todd A., de Koning, A. P. Jason, Hall, Kathryn T., Card, Daren C., Schield, Drew R., Fujita, Matthew K., Ruggiero, Robert P., Degner, Jack F., Daza, Juan M., Gu, Wanjun, Reyes-Velasco, Jacobo, Shaney, Kyle J., Castoe, Jill M., Fox, Samuel E., Poole, Alex W., Polanco, Daniel, Dobry, Jason, Vandewege, Michael W., Li, Qing, Schott, Ryan K., Kapusta, Aurélie, Minx, Patrick, Feschotte, Cédric, Uetz, Peter, Ray, David A., Hoffmann, Federico G., Bogden, Robert, Smith, Eric N., Chang, Belinda S. W., Vonk, Freek J., Casewell, Nicholas R., Henkel, Christiaan V., Richardson, Michael K., Mackessy, Stephen P., Bronikowsi, Anne M., Yandell, Mark, Warren, Wesley C., Secor, Stephen M., and Pollock, David D.
Published: 2013

31. 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
Full Text: View/download PDF

32. Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome

Author: Baxter, Laura, Tripathy, Sucheta, Ishaque, Naveed, Boot, Nico, Cabral, Adriana, Kemen, Eric, Thines, Marco, Ah-Fong, Audrey, Anderson, Ryan, Badejoko, Wole, Bittner-Eddy, Peter, Boore, Jeffrey L., Chibucos, Marcus C., Coates, Mary, Dehal, Paramvir, Delehaunty, Kim, Dong, Suomeng, Downton, Polly, Dumas, Bernard, Fabro, Georgina, Fronick, Catrina, Fuerstenberg, Susan I., Fulton, Lucinda, Gaulin, Elodie, Govers, Francine, Hughes, Linda, Humphrey, Sean, Jiang, Rays H. Y., Judelson, Howard, Kamoun, Sophien, Kyung, Kim, Meijer, Harold, Minx, Patrick, Morris, Paul, Nelson, Joanne, Phuntumart, Vipa, Qutob, Dinah, Rehmany, Anne, Rougon-Cardoso, Alejandra, Ryden, Peter, Torto-Alalibo, Trudy, Studholme, David, Wang, Yuanchao, Win, Joe, Wood, Jo, Clifton, Sandra W., Rogers, Jane, Van den Ackerveken, Guido, Jones, Jonathan D. G., McDowell, John M., Beynon, Jim, and Tyler, Brett M.
Published: 2010

33. 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
Full Text: View/download PDF

34. Elephant shark genome provides unique insights into gnathostome evolution

Author: Venkatesh, Byrappa, Lee, Alison P., Ravi, Vydianathan, Maurya, Ashish K., Lian, Michelle M., Swann, Jeremy B., Ohta, Yuko, Flajnik, Martin F., Sutoh, Yoichi, Kasahara, Masanori, Hoon, Shawn, Gangu, Vamshidhar, Roy, Scott W., Irimia, Manuel, Korzh, Vladimir, Kondrychyn, Igor, Lim, Zhi Wei, Tay, Boon-Hui, Tohari, Sumanty, Kong, Kiat Whye, Ho, Shufen, Lorente-Galdos, Belen, Quilez, Javier, Marques-Bonet, Tomas, Raney, Brian J., Ingham, Philip W., Tay, Alice, Hillier, LaDeana W., Minx, Patrick, Boehm, Thomas, Wilson, Richard K., Brenner, Sydney, and Warren, Wesley C.
Subjects: Nucleotide sequencing -- Methods, Immune system -- Genetic aspects, DNA sequencing -- Methods, Genomes -- Identification and classification, Sharks -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged [...]
Published: 2014
Full Text: View/download PDF

35. Variation in Phalangeal Formulae in the Turtle Genus Terrapene

Author: Minx, Patrick
Published: 1992
Full Text: View/download PDF

36. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content

Author: Hughes, Jennifer F., Skaletsky, Helen, Pyntikova, Tatyana, Graves, Tina A., van Daalen, Saskia K.M., Minx, Patrick J., Fulton, Robert S., McGrath, Sean D., Locke, Devin P., Friedman, Cynthia, Trask, Barbara J., Mardis, Elaine R., Warren, Wesley C., Repping, Sjoerd, Rozen, Steve, Wilson, Richard K., and Page, David C.
Subjects: Man -- Genetic aspects -- Research, Chimpanzees -- Research -- Genetic aspects, Human beings -- Genetic aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The human Y chromosome began to evolve from an autosome hundreds of millions of years ago, acquiring a sex-determining function and undergoing a series of inversions that suppressed crossing over with the X chromosome (1,2). Little is known about the recent evolution of the Y chromosome because only the human Y chromosome has been fully sequenced. Prevailing theories hold that Y chromosomes evolve by gene loss, the pace of which slows over time, eventually leading to a paucity of genes, and stasis (3,4). These theories have been buttressed by partial sequence data from newly emergent plant and animal Y chromosomes (5-8), but they have not been tested in older, highly evolved Y chromosomes such as that of humans. Here we finished sequencing of the male-specific region of the Y chromosome (MSY) in our closest living relative, the chimpanzee, achieving levels of accuracy and completion previously reached for the human MSY. By comparing the MSYs of the two species we show that they differ radically in sequence structure and gene content, indicating rapid evolution during the past 6 million years. The chimpanzee MSY contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor. We suggest that the extraordinary divergence of the chimpanzee and human MSYs was driven by four synergistic factors: the prominent role of the MSY in sperm production, 'genetic hitchhiking' effects in the absence of meiotic crossing over, frequent ectopic recombination within the MSY, and species differences in mating behaviour. Although genetic decay may be the principal dynamic in the evolution of newly emergent Y chromosomes, wholesale renovation is the paramount theme in the continuing evolution of chimpanzee, human and perhaps other older MSYs., This study required that we first complete the sequencing of the chimpanzee MSY (9-11) using large-insert bacterial artificial chromosome (BAC) clones and the iterative mapping and sequencing strategy used to [...]
Published: 2010
Full Text: View/download PDF

37. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

Author: Ley, Timothy J., Mardis, Elaine R., Ding, Li, Fulton, Bob, McLellan, Michael D., Chen, Ken, Dooling, David, Dunford-Shore, Brian H., McGrath, Sean, Hickenbotham, Matthew, Cook, Lisa, Abbott, Rachel, Larson, David E., Koboldt, Dan C., Pohl, Craig, Smith, Scott, Hawkins, Amy, Abbott, Scott, Locke, Devin, Hillier, LaDeana W., Miner, Tracie, Fulton, Lucinda, Magrini, Vincent, Wylie, Todd, Glasscock, Jarret, Conyers, Joshua, Sander, Nathan, Shi, Xiaoqi, Osborne, John R., Minx, Patrick, Gordon, David, Chinwalla, Asif, Zhao, Yu, Ries, Rhonda E., Payton, Jacqueline E., Westervelt, Peter, Tomasson, Michael H., Watson, Mark, Baty, Jack, Ivanovich, Jennifer, Heath, Sharon, Shannon, William D., Nagarajan, Rakesh, Walter, Matthew J., Link, Daniel C., Graubert, Timothy A., DiPersio, John F., and Wilson, Richard K.
Subjects: Nucleotide sequencing -- Health aspects -- Genetic aspects, Leukemia -- Care and treatment -- Genetic aspects, DNA sequencing -- Health aspects -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Care and treatment, Genetic aspects, Health aspects
Abstract: Acute myeloid leukaemia is a highly malignant haematopoietic tumour that affects about 13,000 adults in the United States each year. The treatment of this disease has changed little in the [...]
Published: 2008

38. Evolution of genes and genomes on the Drosophila phylogeny

Author: Clark, Andrew G., Eisen, Michael B., Smith, Douglas R., Bergman, Casey M., Oliver, Brian, Markow, Therese A., Kaufman, Thomas C., Kellis, Manolis, Gelbart, William, Iyer, Venky N., Pollard, Daniel A., Sackton, Timothy B., Larracuente, Amanda M., Singh, Nadia D., Abad, Jose P., Abt, Dawn N., Adryan, Boris, Aguade, Montserrat, Akashi, Hiroshi, Anderson, Wyatt W., Aquadro, Charles F., Ardell, David H., Arguello, Roman, Artieri, Carlo G., Barbash, Daniel A., Barker, Daniel, Barsanti, Paolo, Batterham, Phil, Batzoglou, Serafim, Begun, Dave, Bhutkar, Arjun, Blanco, Enrico, Bosak, Stephanie A., Bradley, Robert K., Brand, Adrianne D., Brent, Michael R., Brooks, Angela N., Brown, Randall H., Butlin, Roger K., Caggese, Corrado, Calvi, Brian R., Bernardo de Carvalho, A., Caspi, Anat, Castrezana, Sergio, Celniker, Susan E., Chang, Jean L., Chapple, Charles, Chatterji, Sourav, Chinwalla, Asif, Civetta, Alberto, Clifton, Sandra W., Comeron, Josep M., Costello, James C., Coyne, Jerry A., Daub, Jennifer, David, Robert G., Delcher, Arthur L., Delehaunty, Kim, Do, Chuong B., Ebling, Heather, Edwards, Kevin, Eickbush, Thomas, Evans, Jay D., Filipski, Alan, Findeiß, Sven, Freyhult, Eva, Fulton, Lucinda, Fulton, Robert, Garcia, Ana C. L., Gardiner, Anastasia, Garfield, David A., Garvin, Barry E., Gibson, Greg, Gilbert, Don, Gnerre, Sante, Godfrey, Jennifer, Good, Robert, Gotea, Valer, Gravely, Brenton, Greenberg, Anthony J., Griffiths-Jones, Sam, Gross, Samuel, Guigo, Roderic, Gustafson, Erik A., Haerty, Wilfried, Hahn, Matthew W., Halligan, Daniel L., Halpern, Aaron L., Halter, Gillian M., Han, Mira V., Heger, Andreas, Hillier, LaDeana, Hinrichs, Angie S., Holmes, Ian, Hoskins, Roger A., Hubisz, Melissa J., Hultmark, Dan, Huntley, Melanie A., Jaffe, David B., Jagadeeshan, Santosh, Jeck, William R., Johnson, Justin, Jones, Corbin D., Jordan, William C., Karpen, Gary H., Kataoka, Eiko, Keightley, Peter D., Kheradpour, Pouya, Kirkness, Ewen F., Koerich, Leonardo B., Kristiansen, Karsten, Kudrna, Dave, Kulathinal, Rob J., Kumar, Sudhir, Kwok, Roberta, Lander, Eric, Langley, Charles H., Lapoint, Richard, Lazzaro, Brian P., Lee, So-Jeong, Levesque, Lisa, Li, Ruiqiang, Lin, Chiao-Feng, Lin, Michael F., Lindblad-Toh, Kerstin, Llopart, Ana, Long, Manyuan, Low, Lloyd, Lozovsky, Elena, Lu, Jian, Luo, Meizhong, Machado, Carlos A., Makalowski, Wojciech, Marzo, Mar, Matsuda, Muneo, Matzkin, Luciano, McAllister, Bryant, McBride, Carolyn S., McKernan, Brendan, McKernan, Kevin, Mendez-Lago, Maria, Minx, Patrick, Mollenhauer, Michael U., Montooth, Kristi, Mount, Stephen M., Mu, Xu, Myers, Eugene, Negre, Barbara, Newfeld, Stuart, Nielsen, Rasmus, Noor, Mohamed A. F., O'Grady, Patrick, Pachter, Lior, Papaceit, Montserrat, Parisi, Matthew J., Parisi, Michael, Parts, Leopold, Pedersen, Jakob S., Pesole, Graziano, Phillippy, Adam M., Ponting, Chris P., Pop, Mihai, Porcelli, Damiano, Powell, Jeffrey R., Prohaska, Sonja, Pruitt, Kim, Puig, Marta, Quesneville, Hadi, Ravi Ram, Kristipati, Rand, David, Rasmussen, Matthew D., Reed, Laura K., Reenan, Robert, Reily, Amy, Remington, Karin A., Rieger, Tania T., Ritchie, Michael G., Robin, Charles, Rogers, Yu-Hui, Rohde, Claudia, Rozas, Julio, Rubenfield, Marc J., Ruiz, Alfredo, Russo, Susan, Salzberg, Steven L., Sanchez-Gracia, Alejandro, Saranga, David J., Sato, Hajime, Schaeffer, Stephen W., Schatz, Michael C., Schlenke, Todd, Schwartz, Russell, Segarra, Carmen, Singh, Rama S., Sirot, Laura, Sirota, Marina, Sisneros, Nicholas B., Smith, Chris D., Smith, Temple F., Spieth, John, Stage, Deborah E., Stark, Alexander, Stephan, Wolfgang, Strausberg, Robert L., Strempel, Sebastian, Sturgill, David, Sutton, Granger, Sutton, Granger G., Tao, Wei, Teichmann, Sarah, Tobari, Yoshiko N., Tomimura, Yoshihiko, Tsolas, Jason M., Valente, Vera L. S., Venter, Eli, Craig Venter, J., Vicario, Saverio, Vieira, Filipe G., Vilella, Albert J., Villasante, Alfredo, Walenz, Brian, Wang, Jun, Wasserman, Marvin, Watts, Thomas, Wilson, Derek, Wilson, Richard K., Wing, Rod A., Wolfner, Mariana F., Wong, Alex, Ka-Shu Wong, Gane, Wu, Chung-I, Wu, Gabriel, Yamamoto, Daisuke, Yang, Hsiao-Pei, Yang, Shiaw-Pyng, Yorke, James A., Yoshida, Kiyohito, Zdobnov, Evgeny, Zhang, Peili, Zhang, Yu, Zimin, Aleksey V., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Christophe Acer, St, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Erii Husby, M, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Grabherr, Manfred, Kleber, Michael, Mauceli, Evan, and MacCallum, Iain
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Drosophila 12 Genomes Consortium; Project Leaders; Andrew G. Clark (corresponding author) [1]; Michael B. Eisen (corresponding author) [2, 3]; Douglas R. Smith (corresponding author) [4]; Casey M. Bergman (corresponding [...]
Published: 2007
Full Text: View/download PDF

39. Comparisons among two fertile and three male-sterile mitochondrial genomes of maize

Author: Allen, James O., Fauron, Christiane M., Minx, Patrick, Roark, Leah, Oddiraju, Swetha, Lin, Guan Ning, Meyer, Louis, Sun, Hui, Kim, Kyung, Wang, Chunyan, Du, Feiyu, Xu, Dong, Gibson, Michael, Cifrese, Jill, Clifton, Sandra W., and Newton, Kathleen J.
Subjects: Corn -- Genetic aspects, Corn -- Demographic aspects, Plant mitochondria -- Genetic aspects, Cytoplasmic male sterility -- Genetic aspects, Cytoplasmic male sterility -- Influence, Nucleotide sequence -- Research, Biological sciences
Abstract: We have sequenced five distinct mitochondrial genomes in maize: two fertile cytotypes (NA and the previously reported NB) and three cytoplasmic-male-sterile cytotypes (CMS-C, CMS-S, and CMS-T). Their genome sizes range from 535,895 bp in CMS-T to 739,719 bp in CMS-C. Large duplications (0.5-190 kb) account for most of the size increases. Plastid DNA accounts for 2.3-4.6% of each mitochondrial genome. The genomes share a minimum set of 51 genes for 33 conserved proteins, three ribosomal RNAs, and 15 transfer RNAs. Numbers of duplicate genes and plastid-derived tRNAs vary among cytotypes. A high level of sequence conservation exists both within and outside of genes (1.65-7.04 substitutions/10 kb in pairwise comparisons). However, sequence losses and gains are common: integrated plastid and plasmid sequences, as well as noncoding 'native' mitochondrial sequences, can be lost with no phenotypic consequence. The organization of the different maize mitochondrial genomes varies dramatically; even between the two fertile cytotypes, there are 16 rearrangements. Comparing the finished shotgun sequences of multiple mitochondrial genomes from the same species suggests which genes and open reading frames are potentially functional, including which chimeric ORFs are candidate genes for cytoplasmic male sterility. This method identified the known CMS-associated ORFs in CMS-S and CMS-T, but not in CMS-C.
Published: 2007

40. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid

Author: McClelland, Michael, Sanderson, Kenneth E, Clifton, Sandra W, Latreille, Phil, Porwollik, Steffen, Sabo, Aniko, Meyer, Rekha, Bieri, Tamberlyn, Ozersky, Phil, McLellan, Michael, Harkins, C Richard, Wang, Chunyan, Nguyen, Christine, Berghoff, Amy, Elliott, Glendoria, Kohlberg, Sara, Strong, Cindy, Du, Feiyu, Carter, Jason, Kremizki, Colin, Layman, Dan, Leonard, Shawn, Sun, Hui, Fulton, Lucinda, Nash, William, Miner, Tracie, Minx, Patrick, Delehaunty, Kim, Fronick, Catrina, Magrini, Vincent, Nhan, Michael, Warren, Wesley, Florea, Liliana, Spieth, John, and Wilson, Richard K
Published: 2004
Full Text: View/download PDF

41. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee

Author: Hughes, Jennifer F., Skaletsky, Helen, Pyntikova, Tatyana, Minx, Patrick J., Graves, Tina, Rozen, Steve, Wilson, Richard K., and Page, David C.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Jennifer F. Hughes [1]; Helen Skaletsky [1]; Tatyana Pyntikova [1]; Patrick J. Minx [2]; Tina Graves [2]; Steve Rozen [1]; Richard K. Wilson [2]; David C. Page (corresponding author) [...]
Published: 2005
Full Text: View/download PDF

42. 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
Full Text: View/download PDF

43. The DNA sequence of the human X chromosome

Author: Ross, Mark T., Grafham, Darren V., Coffey, Alison J., Scherer, Steven, McLay, Kirsten, Muzny, Donna, Platzer, Matthias, Howell, Gareth R., Burrows, Christine, Bird, Christine P., Frankish, Adam, Lovell, Frances L., Howe, Kevin L., Ashurst, Jennifer L., Fulton, Robert S., Sudbrak, Ralf, Wen, Gaiping, Jones, Matthew C., Hurles, Matthew E., Andrews, T. Daniel, Scott, Carol E., Searle, Stephen, Ramser, Juliane, Whittaker, Adam, Deadman, Rebecca, Carter, Nigel P., Hunt, Sarah E., Chen, Rui, Cree, Andrew, Gunaratne, Preethi, Havlak, Paul, Hodgson, Anne, Metzker, Michael L., Richards, Stephen, Scott, Graham, Steffen, David, Sodergren, Erica, Wheeler, David A., Worley, Kim C., Ainscough, Rachael, Ambrose, Kerrie D., Ansari-Lari, M. Ali, Aradhya, Swaroop, Ashwell, Robert I. S., Babbage, Anne K., Bagguley, Claire L., Ballabio, Andrea, Banerjee, Ruby, Barker, Gary E., Barlow, Karen F., Barrett, Ian P., Bates, Karen N., Beare, David M., Beasley, Helen, Beasley, Oliver, Beck, Alfred, Bethel, Graeme, Blechschmidt, Karin, Brady, Nicola, Bray-Allen, Sarah, Bridgeman, Anne M., Brown, Andrew J., Brown, Mary J., Bonnin, David, Bruford, Elspeth A., Buhay, Christian, Burch, Paula, Burford, Deborah, Burgess, Joanne, Burrill, Wayne, Burton, John, Bye, Jackie M., Carder, Carol, Carrel, Laura, Chako, Joseph, Chapman, Joanne C., Chavez, Dean, Chen, Ellson, Chen, Guan, Chen, Yuan, Chen, Zhijian, Chinault, Craig, Ciccodicola, Alfredo, Clark, Sue Y., Clarke, Graham, Clee, Chris M., Clegg, Sheila, Clerc-Blankenburg, Kerstin, Clifford, Karen, Cobley, Vicky, Cole, Charlotte G., Conquer, Jen S., Corby, Nicole, Connor, Richard E., David, Robert, Davies, Joy, Davis, Clay, Davis, John, Delgado, Oliver, DeShazo, Denise, Dhami, Pawandeep, Ding, Yan, Dinh, Huyen, Dodsworth, Steve, Draper, Heather, Dugan-Rocha, Shannon, Dunham, Andrew, Dunn, Matthew, Durbin, K. James, Dutta, Ireena, Eades, Tamsin, Ellwood, Matthew, Emery-Cohen, Alexandra, Errington, Helen, Evans, Kathryn L., Faulkner, Louisa, Francis, Fiona, Frankland, John, Fraser, Audrey E., Galgoczy, Petra, Gilbert, James, Gill, Rachel, Glockner, Gernot, Gregory, Simon G., Gribble, Susan, Griffiths, Coline, Grocock, Russell, Gu, Yanghong, Gwilliam, Rhian, Hamilton, Cerissa, Hart, Elizabeth A., Hawes, Alicia, Heath, Paul D., Heitmann, Katja, Hennig, Steffen, Hernandez, Judith, Hinzmann, Bernd, Ho, Sarah, Hoffs, Michael, Howden, Phillip J., Huckle, Elizabeth J., Hume, Jennifer, Hunt, Paul J., Hunt, Adrienne R., Isherwood, Judith, Jacob, Leni, Johnson, David, Jones, Sally, de Jong, Pieter J., Joseph, Shirin S., Keenan, Stephen, Kelly, Susan, Kershaw, Joanne K., Khan, Ziad, Kioschis, Petra, Klages, Sven, Knights, Andrew J., Kosiura, Anna, Kovar-Smith, Christie, Laird, Gavin K., Langford, Cordelia, Lawlor, Stephanie, Leversha, Margaret, Lewis, Lora, Liu, Wen, Lloyd, Christine, Lloyd, David M., Loulseged, Hermela, Loveland, Jane E., Lovell, Jamieson D., Lozado, Ryan, Lu, Jing, Lyne, Rachael, Ma, Jie, Maheshwari, Manjula, Matthews, Lucy H., McDowall, Jennifer, McLaren, Stuart, McMurray, Amanda, Meidl, Patrick, Meitinger, Thomas, Milne, Sarah, Miner, George, Mistry, Shailesh L., Morgan, Margaret, Morris, Sidney, Muller, Ines, Mullikin, James C., Nguyen, Ngoc, Nordsiek, Gabriele, Nyakatura, Gerald, O'Dell, Christopher N., Okwuonu, Geoffery, Palmer, Sophie, Pandian, Richard, Parker, David, Parrish, Julia, Pasternak, Shiran, Patel, Dina, Pearce, Alex V., Pearson, Danita M., Pelan, Sarah E., Perez, Lesette, Porter, Keith M., Ramsey, Yvonne, Reichwald, Kathrin, Rhodes, Susan, Ridler, Kerry A., Schlessinger, David, Schueler, Mary G., Sehra, Harminder K., Shaw-Smith, Charles, Shen, Hua, Sheridan, Elizabeth M., Shownkeen, Ratna, Skuce, Carl D., Smith, Michelle L., Sotheran, Elizabeth C., Steingruber, Helen E., Steward, Charles A., Storey, Roy, Swann, R. Mark, Swarbreck, David, Tabor, Paul E., Taudien, Stefan, Taylor, Tineace, Teague, Brian, Thomas, Karen, Thorpe, Andrea, Timms, Kirsten, Tracey, Alan, Trevanion, Steve, Tromans, Anthony C., d'Urso, Michele, Verduzco, Daniel, Villasana, Donna, Waldron, Lenee, Wall, Melanie, Wang, Qiaoyan, Warren, James, Warry, Georgina L., Wei, Xuehong, West, Anthony, Whitehead, Siobhan L., Whiteley, Mathew N., Wilkinson, Jane E., Willey, David L., Williams, Gabrielle, Williams, Leanne, Williamson, Angela, Williamson, Helen, Wilming, Laurens, Woodmansey, Rebecca L., Wray, Paul W., Yen, Jennifer, Zhang, Jingkun, Zhou, Jianling, Zoghbi, Huda, Zorilla, Sara, Buck, David, Reinhardt, Richard, Poustka, Annemarie, Rosenthal, Andre, Lehrach, Hans, Meindl, Alfons, Minx, Patrick J., Hillier, LaDeana W., Willard, Huntington F., Wilson, Richard K., Waterston, Robert H., Rice, Catherine M., Vaudin, Mark, Coulson, Alan, Nelson, David L., Weinstock, George, Sulston, John E., Durbin, Richard, Hubbard, Tim, Gibbs, Richard A., Beck, Stephan, Rogers, Jane, and Bentley, David R.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Mark T. Ross (corresponding author) [1]; Darren V. Grafham [1]; Alison J. Coffey [1]; Steven Scherer [2]; Kirsten McLay [1]; Donna Muzny [2]; Matthias Platzer [3]; Gareth R. Howell [...]
Published: 2005
Full Text: View/download PDF

44. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes

Author: Rozen, Steve, Skaletsky, Helen, Marszalek, Janet D., Minx, Patrick J., Cordum, Holland S., Waterston, Robert H., Wilson, Richard K., and Page, David C.
Published: 2003
Full Text: View/download PDF

45. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes

Author: Skaletsky, Helen, Kuroda-Kawaguchi, Tomoko, Minx, Patrick J., Cordum, Holland S., Hillier, LaDeana, Brown, Laura G., Repping, Sjoerd, Pyntikova, Tatyana, Ali, Johar, Bieri, Tamberlyn, Chinwalla, Asif, Delehaunty, Andrew, Delehaunty, Kim, Du, Hui, Fewell, Ginger, Fulton, Lucinda, Fulton, Robert, Graves, Tina, Hou, Shun-Fang, Latrielle, Philip, Leonard, Shawn, Mardis, Elaine, Maupin, Rachel, McPherson, John, Miner, Tracie, Nash, William, Nguyen, Christine, Ozersky, Philip, Pepin, Kymberlie, Rock, Susan, Rohlfing, Tracy, Scott, Kelsi, Schultz, Brian, Strong, Cindy, Tin-Wollam, Aye, Yang, Shiaw-Pyng, Waterston, Robert H., Wilson, Richard K., Rozen, Steve, and Page, David C.
Published: 2003
Full Text: View/download PDF

46. 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
Full Text: View/download PDF

47. 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
Full Text: View/download PDF

48. 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
Full Text: View/download PDF

49. Graph accordance of next-generation sequence assemblies

Author: Yao, Guohui, Ye, Liang, Gao, Hongyu, Minx, Patrick, Warren, Wesley C., and Weinstock, George M.
Published: 2012
Full Text: View/download PDF

50. Initial sequencing and analysis of the human genome

Author: Lander, Eric S., Linton, Lauren M., Birren, Bruce, Nusbaum, Chad, Zody, Michael C., Baldwin, Jennifer, Devon, Keri, Dewar, Ken, Doyle, Michael, FitzHugh, William, Funke, Roel, Gage, Diane, Harris, Katrina, Heaford, Andrew, Howland, John, Kann, Lisa, Lehoczky, Jessica, LeVine, Rosie, McEwan, Paul, McKernan, Kevin, Meldrim, James, Mesirov, Jill P., Miranda, Cher, Morris, William, Naylor, Jerome, Raymond, Christina, Rosetti, Mark, Santos, Ralph, Sheridan, Andrew, Sougnez, Carrie, Stange-Thomann, Nicole, Stojanovic, Nikola, Subramanian, Aravind, Wyman, Dudley, Rogers, Jane, Sulston, John, Ainscough, Rachael, Beck, Stephan, Bentley, David, Burton, John, Clee, Christopher, Carter, Nigel, Coulson, Alan, Deadman, Rebecca, Deloukas, Panos, Dunham, Andrew, Dunham, Ian, Durbin, Richard, French, Lisa, Grafham, Darren, Gregory, Simon, Hubbard, Tim, Humphray, Sean, Hunt, Adrienne, Jones, Matthew, Lloyd, Christine, McMurray, Amanda, Matthews, Lucy, Mercer, Simon, Milne, Sarah, Mullikin, James C., Mungall, Andrew, Plumb, Robert, Ross, Mark, Shownkeen, Ratna, Sims, Sarah, Waterston, Robert H., Wilson, Richard K., Hillier, LaDeana W., McPherson, John D., Marra, Marco A., Mardis, Elaine R., Fulton, Lucinda A., Chinwalla, Asif T., Pepin, Kymberlie H., Gish, Warren R., Chissoe, Stephanie L., Wendl, Michael C., Delehaunty, Kim D., Miner, Tracie L., Delehaunty, Andrew, Kramer, Jason B., Cook, Lisa L., Fulton, Robert S., Johnson, Douglas L., Minx, Patrick J., Clifton, Sandra W., Hawkins, Trevor, Branscomb, Elbert, Predki, Paul, Richardson, Paul, Wenning, Sarah, Slezak, Tom, Doggett, Norman, Cheng, Jan-Fang, Olsen, Anne, Lucas, Susan, Elkin, Christopher, Uberbacher, Edward, Frazier, Marvin, Gibbs, Richard A., Muzny, Donna M., Scherer, Steven E., Bouck, John B., Sodergren, Erica J., Worley, Kim C., Rives, Catherine M., Gorrell, James H., Metzker, Michael L., Naylor, Susan L., Kucherlapati, Raju S., Nelson, David L., Weinstock, George M., Sakaki, Yoshiyuki, Fujiyama, Asao, Hattori, Masahira, Yada, Tetsushi, Toyoda, Atsushi, Itoh, Takehiko, Kawagoe, Chiharu, Watanabe, Hidemi, Totoki, Yasushi, Taylor, Todd, Weissenbach, Jean, Heilig, Roland, Saurin, William, Artiguenave, Francois, Brottier, Philippe, Bruls, Thomas, Pelletier, Eric, Robert, Catherine, Wincker, Patrick, Rosenthal, Andre, Platzer, Matthias, Nyakatura, Gerald, Taudien, Stefan, Rump, Andreas, Smith, Douglas R., Doucette-Stamm, Lynn, Rubenfield, Marc, Weinstock, Keith, Lee, Hong Mei, Dubois, JoAnn, Yang, Huanming, Yu, Jun, Wang, Jian, Huang, Guyang, Gu, Jun, Hood, Leroy, Rowen, Lee, Madan, Anup, Qin, Shizen, Davis, Ronald W., Federspiel, Nancy A., Abola, A. Pia, Proctor, Michael J., Roe, Bruce A., Chen, Feng, Pan, Huaqin, Ramser, Juliane, Lehrach, Hans, Reinhardt, Richard, McCombie, W. Richard, de la Bastide, Melissa, Dedhia, Neilay, Blocker, Helmut, Hornischer, Klaus, Nordsiek, Gabriele, Agarwala, Richa, Aravind, L., Bailey, Jeffrey A., Bateman, Alex, Batzoglou, Serafim, Birney, Ewan, Bork, Peer, Brown, Daniel G., Burge, Christopher B., Cerutti, Lorenzo, Chen, Hsiu-Chuan, Church, Deanna, Clamp, Michele, Copley, Richard R., Doerks, Tobias, Eddy, Sean R., Eichler, Evan E., Furey, Terrence S., Galagan, James, Gilbert, James G. R., Harmon, Cyrus, Hayashizaki, Yoshihide, Haussler, David, Hermjakob, Henning, Hokamp, Karsten, Jang, Wonhee, Johnson, L. Steven, Jones, Thomas A., Kasif, Simon, Kaspryzk, Arek, Kennedy, Scot, Kent, W. James, Kitts, Paul, Koonin, Eugene V., Korf, Ian, Kulp, David, Lancet, Doron, Lowe, Todd M., McLysaght, Aoife, Mikkelsen, Tarjei, Moran, John V., Mulder, Nicola, Pollara, Victor J., Ponting, Chris P., Schuler, Greg, Schultz, Jorg, Slater, Guy, Smit, Arian F. A., Stupka, Elia, Szustakowki, Joseph, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Wagner, Lukas, Wallis, John, Wheeler, Raymond, Williams, Alan, Wolf, Yuri I., Wolfe, Kenneth H., Yang, Shiaw-Pyng, Yeh, Ru-Fang, Collins, Francis, Guyer, Mark S., Peterson, Jane, Felsenfeld, Adam, Wetterstrand, Kris A., Myers, Richard M., Schmutz, Jeremy, Dickson, Mark, Grimwood, Jane, Cox, David R., Olson, Maynard V., Kaul, Rajinder, Raymond, Christopher, Shimizu, Nobuyoshi, Kawasaki, Kazuhiko, Minoshima, Shinsei, Evans, Glen A., Athanasiou, Maria, Schultz, Roger, Patrinos, Aristides, and Morgan, Michael J.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): International Human Genome Sequencing Consortium; Whitehead Institute for Biomedical Research, Center for Genome Research:; Eric S. Lander [1]; Lauren M. Linton [1]; Bruce Birren [1]; Chad Nusbaum [1]; Michael [...]
Published: 2001
Full Text: View/download PDF

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

331 results on '"Minx, Patrick"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources