BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data

by Narasimhan, Vagheesh, Danecek, Petr, Scally, Aylwyn, Xue, Yali, Tyler-Smith, Chris, Durbin, Richard
Published in Bioinformatics (Oxford, England)

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

by Zhang, Xiaojun, Sun, Lina, Yuan, Jianbo, Sun, Yamin, Gao, Yi, Zhang, Libin, Li, Shihao, Dai, Hui, Hamel, Jean-François, Liu, Chengzhang, Yu, Yang, Liu, Shilin, Lin, Wenchao, Guo, Kaimin, Jin, Songjun, Xu, Peng, Storey, Kenneth B, Huan, Pin, Zhang, Tao, Zhou, Yi, Zhang, Jiquan, Lin, Chenggang, Li, Xiaoni, Xing, Lili, Huo, Da, Sun, Mingzhe, Wang, Lei, Mercier, Annie, Li, Fuhua, Yang, Hongsheng, Xiang, Jianhai
Published in PLoS biology

Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection

by Kijas, James W, Lenstra, Johannes A, Hayes, Ben, Boitard, Simon, Porto Neto, Laercio R, San Cristobal, Magali, Servin, Bertrand, McCulloch, Russell, Whan, Vicki, Gietzen, Kimberly, Paiva, Samuel, Barendse, William, Ciani, Elena, Raadsma, Herman, McEwan, John, Dalrymple, Brian
Published in PLoS biology

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

by Yoshida, Yuki, Koutsovoulos, Georgios, Laetsch, Dominik R, Stevens, Lewis, Kumar, Sujai, Horikawa, Daiki D, Ishino, Kyoko, Komine, Shiori, Kunieda, Takekazu, Tomita, Masaru, Blaxter, Mark, Arakawa, Kazuharu
Published in PLoS biology

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

by Chipman, Ariel D, Ferrier, David E K, Brena, Carlo, Hughes, Daniel S T, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis J P, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, Richards, Stephen
Published in PLoS biology

The geography of recent genetic ancestry across Europe

by Ralph, Peter, Coop, Graham
Published in PLoS biology

De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture

by Mahajan, Shivani, Wei, Kevin H-C, Nalley, Matthew J, Gibilisco, Lauren, Bachtrog, Doris
Published in PLoS biology

The African Genome Variation Project shapes medical genetics in Africa

by Gurdasani, Deepti, Carstensen, Tommy, Tekola-Ayele, Fasil, Pagani, Luca, Tachmazidou, Ioanna, Hatzikotoulas, Konstantinos, Karthikeyan, Savita, Iles, Louise, Pollard, Martin O, Choudhury, Ananyo, Ritchie, Graham R S, Xue, Yali, Asimit, Jennifer, Nsubuga, Rebecca N, Young, Elizabeth H, Pomilla, Cristina, Kivinen, Katja, Rockett, Kirk, Kamali, Anatoli, Doumatey, Ayo P, Asiki, Gershim, Seeley, Janet, Sisay-Joof, Fatoumatta, Jallow, Muminatou, Tollman, Stephen, Mekonnen, Ephrem, Ekong, Rosemary, Oljira, Tamiru, Bradman, Neil, Bojang, Kalifa, Ramsay, Michele, Adeyemo, Adebowale, Bekele, Endashaw, Motala, Ayesha, Norris, Shane A, Pirie, Fraser, Kaleebu, Pontiano, Kwiatkowski, Dominic, Tyler-Smith, Chris, Rotimi, Charles, Zeggini, Eleftheria, Sandhu, Manjinder S
Published in Nature (London)

Comparative genomics and the nature of placozoan species

by Eitel, Michael, Francis, Warren R, Varoqueaux, Frédérique, Daraspe, Jean, Osigus, Hans-Jürgen, Krebs, Stefan, Vargas, Sergio, Blum, Helmut, Williams, Gray A, Schierwater, Bernd, Wörheide, Gert
Published in PLoS biology

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

by Nowell, Reuben W, Almeida, Pedro, Wilson, Christopher G, Smith, Thomas P, Fontaneto, Diego, Crisp, Alastair, Micklem, Gos, Tunnacliffe, Alan, Boschetti, Chiara, Barraclough, Timothy G
Published in PLoS biology

Iron Age and Anglo-Saxon genomes from East England reveal British migration history

by Schiffels, Stephan, Haak, Wolfgang, Paajanen, Pirita, Llamas, Bastien, Popescu, Elizabeth, Loe, Louise, Clarke, Rachel, Lyons, Alice, Mortimer, Richard, Sayer, Duncan, Tyler-Smith, Chris, Cooper, Alan, Durbin, Richard
Published in Nature communications

Origins and functional impact of copy number variation in the human genome

by Scherer, Stephen W, Hurles, Matthew E, Conrad, Donald F, Pinto, Dalila, Redon, Richard, Feuk, Lars, Gokcumen, Omer, Zhang, Yujun, Aerts, Jan, Andrews, T. Daniel, Barnes, Chris, Campbell, Peter, Fitzgerald, Tomas, Hu, Min, Ihm, Chun Hwa, Kristiansson, Kati, MacArthur, Daniel G, MacDonald, Jeffrey R, Onyiah, Ifejinelo, Pang, Andy Wing Chun, Robson, Sam, Stirrups, Kathy, Valsesia, Armand, Walter, Klaudia, Wei, John, Tyler-Smith, Chris, Carter, Nigel P, Lee, Charles
Published in Nature (London)

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

by Xue, Yali, Prado-Martinez, Javier, Sudmant, Peter H., Narasimhan, Vagheesh, Ayub, Qasim, Szpak, Michal, Frandsen, Peter, Chen, Yuan, Yngvadottir, Bryndis, Cooper, David N., de Manuel, Marc, Hernandez-Rodriguez, Jessica, Lobon, Irene, Siegismund, Hans R., Pagani, Luca, Quail, Michael A., Hvilsom, Christina, Mudakikwa, Antoine, Eichler, Evan E., Cranfield, Michael R., Marques-Bonet, Tomas, Tyler-Smith, Chris, Scally, Aylwyn
Published in Science (American Association for the Advancement of Science)

Genetic variation and population structure in native Americans

by Wang, Sijia, Lewis, Cecil M, Jakobsson, Mattias, Ramachandran, Sohini, Ray, Nicolas, Bedoya, Gabriel, Rojas, Winston, Parra, Maria V, Molina, Julio A, Gallo, Carla, Mazzotti, Guido, Poletti, Giovanni, Hill, Kim, Hurtado, Ana M, Labuda, Damian, Klitz, William, Barrantes, Ramiro, Bortolini, Maria Cátira, Salzano, Francisco M, Petzl-Erler, Maria Luiza, Tsuneto, Luiza T, Llop, Elena, Rothhammer, Francisco, Excoffier, Laurent, Feldman, Marcus W, Rosenberg, Noah A, Ruiz-Linares, Andrés
Published in PLoS genetics

Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

by Pagani, Luca, Schiffels, Stephan, Gurdasani, Deepti, Danecek, Petr, Scally, Aylwyn, Chen, Yuan, Xue, Yali, Haber, Marc, Ekong, Rosemary, Oljira, Tamiru, Mekonnen, Ephrem, Luiselli, Donata, Bradman, Neil, Bekele, Endashaw, Zalloua, Pierre, Durbin, Richard, Kivisild, Toomas, Tyler-Smith, Chris
Published in American journal of human genetics

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

by Smith, Oliver, Dunshea, Glenn, Sinding, Mikkel-Holger S, Fedorov, Sergey, Germonpre, Mietje, Bocherens, Hervé, Gilbert, M T P
Published in PLoS biology

A scan for positively selected genes in the genomes of humans and chimpanzees

by Nielsen, Rasmus, Bustamante, Carlos, Clark, Andrew G, Glanowski, Stephen, Sackton, Timothy B, Hubisz, Melissa J, Fledel-Alon, Adi, Tanenbaum, David M, Civello, Daniel, White, Thomas J, J Sninsky, John, Adams, Mark D, Cargill, Michele
Published in PLoS biology

Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders

by Pinotti, Thomaz, Bergström, Anders, Geppert, Maria, Bawn, Matt, Ohasi, Dominique, Shi, Wentao, Lacerda, Daniela R., Solli, Arne, Norstedt, Jakob, Reed, Kate, Dawtry, Kim, González-Andrade, Fabricio, Paz-y-Miño, Cesar, Revollo, Susana, Cuellar, Cinthia, Jota, Marilza S., Santos, José E., Ayub, Qasim, Kivisild, Toomas, Sandoval, José R., Fujita, Ricardo, Xue, Yali, Roewer, Lutz, Santos, Fabrício R., Tyler-Smith, Chris
Published in Current biology

Health and population effects of rare gene knockouts in adult humans with related parents

by Narasimhan, Vagheesh M., Hunt, Karen A., Mason, Dan, Baker, Christopher L., Karczewski, Konrad J., Barnes, Michael R., Barnett, Anthony H., Bates, Chris, Bellary, Srikanth, Bockett, Nicholas A., Giorda, Kristina, Griffiths, Christopher J., Hemingway, Harry, Jia, Zhilong, Kelly, M. Ann, Khawaja, Hajrah A., Lek, Monkol, McCarthy, Shane, McEachan, Rosie, O'Donnell-Luria, Anne, Paigen, Kenneth, Parisinos, Constantinos A., Sheridan, Eamonn, Southgate, Laura, Tee, Louise, Thomas, Mark, Xue, Yali, Schnall-Levin, Michael, Petkov, Petko M., Tyler-Smith, Chris, Maher, Eamonn R., Trembath, Richard C., MacArthur, Daniel G., Wright, John, Durbin, Richard, van Heel, David A.
Published in Science (American Association for the Advancement of Science)

Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes

by Stranger, Barbara E, Forrest, Matthew S, Dunning, Mark, Ingle, Catherine E, Beazley, Claude, Thorne, Natalie, Redon, Richard, Bird, Christine P, de Grassi, Anna, Lee, Charles, Tyler-Smith, Chris, Carter, Nigel, Scherer, Stephen W, Tavaré, Simon, Deloukas, Panagiotis, Hurles, Matthew E, Dermitzakis, Emmanouil T
Published in Science (American Association for the Advancement of Science)