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1. An integrated encyclopedia of DNA elements in the human genome

Author

Dunham, Ian, Kundaje, Anshul, Aldred, Shelley F., Collins, Patrick J., Davis, Carrie A., Doyle, Francis, Epstein, Charles B., Frietze, Seth, Harrow, Jennifer, Kaul, Rajinder, Khatun, Jainab, Lajoie, Bryan R., Landt, Stephen G., Lee, Bum-Kyu, Pauli, Florencia, Rosenbloom, Kate R., Sabo, Peter, Safi, Alexias, Sanyal, Amartya, Shoresh, Noam, Simon, Jeremy M., Song, Lingyun, Trinklein, Nathan D., Altshuler, Robert C., Birney, Ewan, Brown, James B., Cheng, Chao, Djebali, Sarah, Dong, Xianjun, Ernst, Jason, Furey, Terrence S., Gerstein, Mark, Giardine, Belinda, Greven, Melissa, Hardison, Ross C., Harris, Robert S., Herrero, Javier, Hoffman, Michael M., Iyer, Sowmya, Kellis, Manolis, Kheradpour, Pouya, Lassmann, Timo, Li, Qunhua, Lin, Xinying, Marinov, Georgi K., Merkel, Angelika, Mortazavi, Ali, Parker, Stephen C. J., Reddy, Timothy E., Rozowsky, Joel, Schlesinger, Felix, Thurman, Robert E., Wang, Jie, Ward, Lucas D., Whitfield, Troy W., Wilder, Steven P., Wu, Weisheng, Xi, Hualin S., Yip, Kevin Y., Zhuang, Jiali, Bernstein, Bradley E., Green, Eric D., Gunter, Chris, Snyder, Michael, Pazin, Michael J., Lowdon, Rebecca F., Dillon, Laura A. L., Adams, Leslie B., Kelly, Caroline J., Zhang, Julia, Wexler, Judith R., Good, Peter J., Feingold, Elise A., Crawford, Gregory E., Dekker, Job, Elnitski, Laura, Farnham, Peggy J., Giddings, Morgan C., Gingeras, Thomas R., Guigo, Roderic, Hubbard, Timothy J., Kent, W. James, Lieb, Jason D., Margulies, Elliott H., Myers, Richard M., Stamatoyannopoulos, John A., Tenenbaum, Scott A., Weng, Zhiping, White, Kevin P., Wold, Barbara, Yu, Yanbao, Wrobel, John, Risk, Brian A., Gunawardena, Harsha P., Kuiper, Heather C., Maier, Christopher W., Xie, Ling, Chen, Xian, Mikkelsen, Tarjei S., Gillespie, Shawn, Goren, Alon, Ram, Oren, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Eaton, Matthew L., Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Xue, Chenghai, Williams, Brian A., Zaleski, Chris, Roder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Batut, Philippe, Bell, Ian, Bell, Kimberly, Chakrabortty, Sudipto, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jackie, Duttagupta, Radha, Fastuca, Megan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Li, Guoliang, Luo, Oscar J., Park, Eddie, Preall, Jonathan B., Presaud, Kimberly, Ribeca, Paolo, Robyr, Daniel, Ruan, Xiaoan, Sammeth, Michael, Sandhu, Kuljeet Singh, Schaeffer, Lorain, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Hayashizaki, Yoshihide, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory J., Ruan, Yijun, Carninci, Piero, Sloan, Cricket A., Learned, Katrina, Malladi, Venkat S., Wong, Matthew C., Barber, Galt P., Cline, Melissa S., Dreszer, Timothy R., Heitner, Steven G., Karolchik, Donna, Kirkup, Vanessa M., Meyer, Laurence R., Long, Jeffrey C., Maddren, Morgan, Raney, Brian J., Grasfeder, Linda L., Giresi, Paul G., Battenhouse, Anna, Sheffield, Nathan C., Showers, Kimberly A., London, Darin, Bhinge, Akshay A., Shestak, Christopher, Schaner, Matthew R., Ki Kim, Seul, Zhang, Zhuzhu Z., Mieczkowski, Piotr A., Mieczkowska, Joanna O., Liu, Zheng, McDaniell, Ryan M., Ni, Yunyun, Rashid, Naim U., Kim, Min Jae, Adar, Sheera, Zhang, Zhancheng, Wang, Tianyuan, Winter, Deborah, Keefe, Damian, Iyer, Vishwanath R., Zheng, Meizhen, Wang, Ping, Gertz, Jason, Vielmetter, Jost, Partridge, E., Varley, Katherine E., Gasper, Clarke, Bansal, Anita, Pepke, Shirley, Jain, Preti, Amrhein, Henry, Bowling, Kevin M., Anaya, Michael, Cross, Marie K., Muratet, Michael A., Newberry, Kimberly M., McCue, Kenneth, Nesmith, Amy S., Fisher-Aylor, Katherine I., Pusey, Barbara, DeSalvo, Gilberto, Parker, Stephanie L., Balasubramanian, Sreeram, Davis, Nicholas S., Meadows, Sarah K., Eggleston, Tracy, Newberry, J. Scott, Levy, Shawn E., Absher, Devin M., Wong, Wing H., Blow, Matthew J., Visel, Axel, Pennachio, Len A., Petrykowska, Hanna M., Abyzov, Alexej, Aken, Bronwen, Barrell, Daniel, Barson, Gemma, Berry, Andrew, Bignell, Alexandra, Boychenko, Veronika, Bussotti, Giovanni, Davidson, Claire, Despacio-Reyes, Gloria, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Gilbert, James, Gonzalez, Jose Manuel, Griffiths, Ed, Harte, Rachel, Hendrix, David A., Hunt, Toby, Jungreis, Irwin, Kay, Mike, Khurana, Ekta, Leng, Jing, Lin, Michael F., Loveland, Jane, Lu, Zhi, Manthravadi, Deepa, Mariotti, Marco, Mudge, Jonathan, Mukherjee, Gaurab, Notredame, Cedric, Pei, Baikang, Rodriguez, Jose Manuel, Saunders, Gary, Sboner, Andrea, Searle, Stephen, Sisu, Cristina, Snow, Catherine, Steward, Charlie, Tapanari, Electra, Tress, Michael L., van Baren, Marijke J., Washietl, Stefan, Wilming, Laurens, Zadissa, Amonida, Zhang, Zhengdong, Brent, Michael, Haussler, David, Valencia, Alfonso, Addleman, Nick, Alexander, Roger P., Auerbach, Raymond K., Balasubramanian, Suganthi, Bettinger, Keith, Bhardwaj, Nitin, Boyle, Alan P., Cao, Alina R., Cayting, Philip, Charos, Alexandra, Cheng, Yong, Eastman, Catharine, Euskirchen, Ghia, Fleming, Joseph D., Grubert, Fabian, Habegger, Lukas, Hariharan, Manoj, Harmanci, Arif, Iyengar, Sushma, Jin, Victor X., Karczewski, Konrad J., Kasowski, Maya, Lacroute, Phil, Lam, Hugo, Lamarre-Vincent, Nathan, Lian, Jin, Lindahl-Allen, Marianne, Min, Renqiang, Miotto, Benoit, Monahan, Hannah, Moqtaderi, Zarmik, Mu, Xinmeng J., Ouyang, Zhengqing, Patacsil, Dorrelyn, Raha, Debasish, Ramirez, Lucia, Reed, Brian, Shi, Minyi, Slifer, Teri, Witt, Heather, Wu, Linfeng, Xu, Xiaoqin, Yan, Koon-Kiu, Yang, Xinqiong, Struhl, Kevin, Weissman, Sherman M., Penalva, Luiz O., Karmakar, Subhradip, Bhanvadia, Raj R., Choudhury, Alina, Domanus, Marc, Ma, Lijia, Moran, Jennifer, Victorsen, Alec, Auer, Thomas, Centanin, Lazaro, Eichenlaub, Michael, Gruhl, Franziska, Heermann, Stephan, Hoeckendorf, Burkhard, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Mueller, Claudia, Reinhardt, Robert, Schertel, Lea, Schneider, Stephanie, Sinn, Rebecca, Wittbrodt, Beate, Wittbrodt, Jochen, Partridge, E. Christopher, Jain, Gaurav, Balasundaram, Gayathri, Bates, Daniel L., Byron, Rachel, Canfield, Theresa K., Diegel, Morgan J., Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Garg, Kavita, Gist, Erica, Hansen, R. Scott, Boatman, Lisa, Haugen, Eric, Humbert, Richard, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tattyana V., Lee, Kristen, Lotakis, Dimitra, Maurano, Matthew T., Neph, Shane J., Neri, Fiedencio V., Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Rynes, Eric, Sanchez, Minerva E., Sandstrom, Richard S., Shafer, Anthony O., Stergachis, Andrew B., Thomas, Sean, Vernot, Benjamin, Vierstra, Jeff, Vong, Shinny, Weaver, Molly A., Yan, Yongqi, Zhang, Miaohua, Akey, Joshua M., Bender, Michael, Dorschner, Michael O., Groudine, Mark, MacCoss, Michael J., Navas, Patrick, Stamatoyannopoulos, George, Beal, Kathryn, Brazma, Alvis, Flicek, Paul, Johnson, Nathan, Lukk, Margus, Luscombe, Nicholas M., Sobral, Daniel, Vaquerizas, Juan M., Batzoglou, Serafim, Sidow, Arend, Hussami, Nadine, Kyriazopoulou-Panagiotopoulou, Sofia, Libbrecht, Max W., Schaub, Marc A., Miller, Webb, Bickel, Peter J., Banfai, Balazs, Boley, Nathan P., Huang, Haiyan, Li, Jingyi Jessica, Noble, William Stafford, Bilmes, Jeffrey A., Buske, Orion J., Sahu, Avinash D., Kharchenko, Peter V., Park, Peter J., Baker, Dannon, Taylor, James, and Lochovsky, Lucas

Subjects
Genetic research, Human genome -- Research, Genetic transcription -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research., Author(s): The ENCODE Project Consortium; Overall coordination (data analysis coordination); Ian Dunham [2]; Anshul Kundaje [3, 82]; Data production leads (data production); Shelley F. Aldred [4]; Patrick J. Collins [4]; [...]

Published
2012
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2. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

Author

Lindqvist, Charlotte, Schuster, Stephan C., Sun, Yazhou, Talbot, Sandra L., Qi, Ji, Ratan, Aakrosh, Tomsho, Lynn P., Kasson, Lindsay, Zeyl, Eve, Aars, Jon, Miller, Webb, Ingolfsson, Olafur, Bachmann, Lutz, and Wiig, Oystein

Subjects
Mitochondrial DNA -- Research, Molecular evolution -- Research, Polar bear -- Natural history, Polar bear -- Genetic aspects, Polar bear -- Research, Science and technology
Abstract

The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage. ancient DNA | Arctic | mammal evolution | next-generation sequencing | Svalbard doi/ 10.1073/pnas.094266107

Published
2010

3. Sequencing the nuclear genome of the extinct woolly mammoth

Author

Miller, Webb, Drautz, Daniela I., Ratan, Aakrosh, Pusey, Barbara, Qi, Ji, Lesk, Arthur M., Tomsho, Lynn P., Packard, Michael D., Zhao, Fangqing, Sher, Andrei, Tikhonov, Alexei, Raney, Brian, Patterson, Nick, Lindblad-Toh, Kerstin, Lander, Eric S., Knight, James R., Irzyk, Gerard P., Fredrikson, Karin M., Harkins, Timothy T., Sheridan, Sharon, Pringle, Tom, and Schuster, Stephan C.

Subjects
Population biology -- Research -- Genetic aspects -- Usage, Extinct mammals -- Genetic aspects -- Usage -- Research, Mammoths -- Genetic aspects -- Research -- Usage, Chromosome mapping -- Usage -- Research -- Genetic aspects, African elephant -- Genetic aspects -- Usage -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation, Usage, Research, Genetic aspects
Abstract

In 1994, two independent groups extracted DNA from several Pleistocene epoch mammoths and noted differences among individual Specimens (1,2). Subsequently, DNA sequences have been published for a number of extinct [...]

Published
2008

4. The infinite sites model of genome evolution

Author

Ma, Jian, Ratan, Aakrosh, Raney, Brian J., Suh, Bernard B., Miller, Webb, and Haussler, David

Subjects
Gene expression -- Research, Genomes -- Identification and classification, Evolution -- Genetic aspects, Science and technology
Abstract

We formalize the problem of recovering the evolutionary history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement of segments of bases. The problem is examined in the limit as the number of bases in each genome goes to infinity. In this limit, the chromosomes are represented by continuous circles or line segments. For such an infinite-sites model, we present a polynomial-time algorithm to find the most parsimonious evolutionary history of any set of related present-day genomes. ancestral reconstruction | gene duplication | genome rearrangements

Published
2008

5. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

Author

Gilbert, M. Thomas P., Drautz, Daniela I., Lesk, Arthur M., Ho, Simon Y.W., Qi, Ji, Ratan, Aakrosh, Hsu, Chih-Hao, Sher, Andrei, Dalen, Love, Gotherstrom, Anders, Tomsho, Lynn P., Rendulic, Snjezana, Packard, Michael, Campos, Paula F., Kuznetsova, Tatyana V., Shidlovskiy, Fyodor, Tikhonov, Alexei, Willerslev, Eske, Iacumink, Paola, Buigues, Bernard, Ericson, Per G.P., Germonpre, Mietje, Kosintsev, Pavel, Nikolaev, Vladimir, Nowak-Kemp, Malgosia, Knight, James R., Irzyk, Gerard P., Perbost, Clotilde S., Fredrikson, Karin M., Harkins, Timothy T., Sheridan, Sharon, Miller, Webb, and Schuster, Stephan C.

Subjects
Mitochondrial DNA -- Usage, Mitochondrial DNA -- Research, Phylogeny -- Research, Mammoths -- Physiological aspects, Mammoths -- Genetic aspects, Mammoths -- Research, Science and technology
Abstract

We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, [approximately equal to]1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the [sup.14]C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep. mtDNA genome | phylogeny | ancient DNA | next-generation sequencing

Published
2008

6. Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

Author

Gilbert, M. Thomas P., Tomsho, Lynn P., Rendulic, Snjezana, Packard, Michael, Drautz, Daniela I., Sher, Andrei, Tikhonov, Alexei, Dalen, Love, Kuznetsova, Tatyana, Kosintsev, Pavel, Campos, Paula F., Higham, Thomas, Collins, Matthew J., Wilson, Andrew S., Shidlovskiy, Fyodor, Buigues, Bernard, Ericson, Per G.P., Germonpre, Mietje, Gotherstrom, Anders, Iacumin, Paola, Nikolaev, Vladimir, Nowak-Kemp, Malgosia, Willerslev, Eske, Knight, James R., Irzyk, Gerard P. Perbost, Clotilde S., Fredrikson, Karin M., Harkins, Timothy T., Sheridan, Sharon, Miller, Webb, and Schuster, Stephan C.

Subjects
Mammoths -- Physiological aspects, Mammoths -- Genetic aspects, Mitochondria -- Genetic aspects, Nucleotide sequencing -- Methods, Hair -- Genetic aspects
Published
2007

7. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Author

Birney, Ewan, Stamatoyannopoulos, John A., Dutta, Anindya, Guigo, Roderic, Gingeras, Thomas R., Margulies, Elliott H., Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T., Thurman, Robert E., Kuehn, Michael S., Taylor, Christopher M., Neph, Shane, Koch, Christoph M., Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A., Andrews, Robert M., Flicek, Paul, Boyle, Patrick J., Cao, Hua, Carter, Nigel P., Clelland, Gayle K., Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C., Dorschner, Michael O., Fiegler, Heike, Giresi, Paul G., Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D., Johnson, Brett E., Johnson, Ericka M., Frum, Tristan T., Rosenzweig, Elizabeth R., Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C., Navas, Patrick A., Neri, Fidencio, Parker, Stephen C. J., Sabo, Peter J., Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu1, Man, Collins, Francis S., Dekker, Job, Lieb, Jason D., Tullius, Thomas D., Crawford, Gregory E., Sunyaev, Shamil, Noble, William S., Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L., Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A., Sekinger, Edward A., Lagarde, Julien, Abril, Josep F., Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermuller, Jorg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S., Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C., Thomas, Daryl J., Weirauch, Matthew T., Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K.G., Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L., Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G., Brown, James B., Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N., Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S., Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M., Rogers, Jane, Stadler, Peter F., Lowe, Todd M., Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E., Fu, Yutao, Green, Eric D., Karaoz, Ulaş, Siepel, Adam, Taylor, James, Liefer, Laura A., Wetterstrand, Kris A., Good, Peter J., Feingold, Elise A., Guyer, Mark S., Cooper, Gregory M., Asimenos, George, Dewey, Colin N., Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I., Loytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R., Holmes, Ian, Mullikin, James C., Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W. James, Stone, Eric A., Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C., Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D., Zhang, Zhengdong D., Barrera, Leah, Stuart, Rhona, King, David C., Ameur, Adam, Enroth, Stefan, Bieda, Mark C., Kim, Jonghwan, Bhinge, Akshay A., Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B., Lee, Charlie W.H., Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J., Inman, David, Singer, Michael A., Richmond, Todd A., Munn, Kyle J., Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C., Couttet, Phillippe, Bruce, Alexander W., Dovey, Oliver M., Ellis, Peter D., Langford, Cordelia F., Nix, David A., Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E., Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Hoon Kim, Tae, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K., Rosenfeld, M. Geoff, Aldred, Shelley Force, Cooper, Sara J., Halees, Anason, Lin, Jane M., Shulha, Hennady P., Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N. S., Yu, Yong, Birney*, Ewan, Iyer, Vishwanath R., Green, Roland D., Wadelius, Claes, Farnham, Peggy J., Ren, Bing, Harte, Rachel A., Hinrichs, Angie S., Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S., Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M., Karolchik, Donna, Armengol, Lluis, Bird, Christine P., de Bakker, Paul I. W., Kern, Andrew D., Lopez-Bigas, Nuria, Martin, Joel D., Stranger, Barbara E., Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrimsdottir, Ingileif B., Huppert, Julian, Zody, Michael C., Abecasis, Goncalo R., Estivill, Xavier, Bouffard, Gerard G., Guan, Xiaobin, Hansen, Nancy F., Idol, Jacquelyn R., Maduro, Valerie V.B., Maskeri, Baishali, McDowell, Jennifer C., Park, Morgan, Thomas, Pamela J., Young, Alice C., Blakesley, Robert W., Baylor College of Medicine, Human Genome Sequencing Center, Muzny, Donna M., Sodergren, Erica, Wheeler, David A., Worley, Kim C., Jiang, Huaiyang, Weinstock, George M., Gibbs, Richard A., Graves, Tina, Fulton, Robert, Mardis, Elaine R., Wilson, Richard K., Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B., Chang, Jean L., Lindblad-Toh, Kerstin, Lander, Eric S., Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, and de Jong, Pieter J.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): The ENCODE Project Consortium; Analysis Coordination; Ewan Birney (corresponding author) [1]; John A. Stamatoyannopoulos (corresponding author) [2]; Anindya Dutta (corresponding author) [3]; Roderic Guigó (corresponding author) [4, 5]; Thomas [...]

Published
2007
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8. Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Author

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

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): LaDeana W. Hillier [1]; Tina A. Graves [1]; Robert S. Fulton [1]; Lucinda A. Fulton [1]; Kymberlie H. Pepin [1]; Patrick Minx [1]; Caryn Wagner-McPherson [1]; Dan Layman [1]; [...]

Published
2005
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9. An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing

Author

Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., Green, Eric D., Lander, Eric S., Mullikin, James C., and Clamp, Michele

Subjects
Genomics -- Research, Human genome -- Research, Science and technology
Abstract

With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful approach for finding such elements by identifying sequences that have been highly conserved during evolution. Here, we propose an initial strategy for detecting such regions by generating low-redundancy sequence from a collection of 16 eutherian mammals, beyond the 7 for which genome sequence data are already available. We show that such sequence can be accurately aligned to the human genome and used to identify most of the highly conserved regions. Although not a long-term substitute for generating high-quality genomic sequences from many mammalian species, this strategy represents a practical initial approach for rapidly annotating the most evolutionarily conserved sequences in the human genome, providing a key resource for the systematic study of human genome function. comparative genomics | genome sequencing | genome analysis | phylogenetics | mammalian evolution

Published
2005

10. The structure and evolution of centromeric transition regions within the human genome

Author

She, Xinwei, Horvath, Julie E., Jiang, Zhaoshi, Liu, Ge, Furey, Terrence S., Christ, Laurie, Clark, Royden, Graves, Tina, Gulden, Cassy L., Alkan, Can, Bailey, Jeff A., Sahinalp, Cenk, Rocchi, Mariano, Haussler, David, Wilson, Richard K., Miller, Webb, Schwartz, Stuart, and Eichler, Evan E.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Xinwei She [1, 2, 8]; Julie E. Horvath [1, 8]; Zhaoshi Jiang [1, 2]; Ge Liu [1]; Terrence S. Furey [3]; Laurie Christ [1]; Royden Clark [1]; Tina Graves [...]

Published
2004
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11. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes

Author

Kent, W. James, Baertsch, Robert, Hinrichs, Angie, Miller, Webb, and Haussler, David

Subjects
Chromosomes -- Research, Genomics -- Research, Science and technology
Abstract

This study examines genomic duplications, deletions, and rearrangements that have happened at scales ranging from a single base to complete chromosomes by comparing the mouse and human genomes. From whole-genome sequence alignments, 344 large (>100-kb) blocks of conserved synteny are evident, but these are further fragmented by smaller-scale evolutionary events. Excluding transposon insertions, on average in each megabase of genomic alignment we observe two inversions, 17 duplications (five tandem or nearly tandem), seven transpositions, and 200 deletions of 100 bases or more. This includes 160 inversions and 75 duplications or transpositions of length > 100 kb. The frequencies of these smaller events are not substantially higher in finished portions in the assembly. Many of the smaller transpositions are processed pseudogenes; we define a 'syntenic' subset of the alignments that excludes these and other small-scale transpositions. These alignments provide evidence that [approximately equal to] 2% of the genes in the human/mouse common ancestor have been deleted or partially deleted in the mouse. There also appears to be slightly less nontransposon-induced genome duplication in the mouse than in the human lineage. Although some of the events we detect are possibly due to misassemblies or missing data in the current genome sequence or to the limitations of our methods, most are likely to represent genuine evolutionary events. To make these observations, we developed new alignment techniques that can handle large gaps in a robust fashion and discriminate between orthologous and paralogous alignments. comparative genomics | cross-species alignments | synteny | chromosomal inversion | breakpoints

Published
2003

12. Initial sequencing and comparative analysis of the mouse genome

Author

Chinwalla, Asif T., Cook, Lisa L., Delehaunty, Kimberly D., Fewell, Ginger A., Fulton, Lucinda A., Fulton, Robert S., Graves, Tina A., Hillier, LaDeana W., Mardis, Elaine R., McPherson, John D., Miner, Tracie L., Nash, William E., Nelson, Joanne O., Nhan, Michael N., Pepin, Kymberlie H., Pohl, Craig S., Ponce, Tracy C., Schultz, Brian, Thompson, Johanna, Trevaskis, Evanne, Waterston, Robert H., Wendl, Michael C., Wilson, Richard K., Yang, Shiaw-Pyng, An, Peter, Berry, Eric, Birren, Bruce, Bloom, Toby, Brown, Daniel G., Butler, Jonathan, Daly, Mark, David, Robert, Deri, Justin, Dodge, Sheila, Foley, Karen, Gage, Diane, Gnerre, Sante, Holzer, Timothy, Jaffe, David B., Kamal, Michael, Karlsson, Elinor K., Kells, Cristyn, Kirby, Andrew, Kulbokas, III, Edward J., Lander, Eric S., Landers, Tom, Leger, J. P., Levine, Rosie, Lindblad-Toh, Kerstin, Mauceli, Evan, Mayer, John H., McCarthy, Megan, Meldrim, Jim, Mesirov, Jill P., Nicol, Robert, Nusbaum, Chad, Seaman, Steven, Sharpe, Ted, Sheridan, Andrew, Singer, Jonathan B., Santos, Ralph, Spencer, Brian, Stange-Thomann, Nicole, Vinson, Jade P., Wade, Claire M., Wierzbowski, Jamey, Wyman, Dudley, Zody, Michael C., Birney, Ewan, Goldman, Nick, Kasprzyk, Arkadiusz, Mongin, Emmanuel, Rust, Alistair G., Slater, Guy, Stabenau, Arne, Ureta-Vidal, Abel, Whelan, Simon, Ainscough, Rachel, Attwood, John, Bailey, Jonathon, Barlow, Karen, Beck, Stephan, Burton, John, Clamp, Michele, Clee, Christopher, Coulson, Alan, Cuff, James, Curwen, Val, Cutts, Tim, Davies, Joy, Eyras, Eduardo, Grafham, Darren, Gregory, Simon, Hubbard, Tim, Hunt, Adrienne, Jones, Matthew, Joy, Ann, Leonard, Steven, Lloyd, Christine, Matthews, Lucy, McLaren, Stuart, McLay, Kirsten, Meredith, Beverley, Mullikin, James C., Ning, Zemin, Oliver, Karen, Overton-Larty, Emma, Plumb, Robert, Potter, Simon, Quail, Michael, Rogers, Jane, Scott, Carol, Searle, Steve, Shownkeen, Ratna, Sims, Sarah, Wall, Melanie, West, Anthony P., Willey, David, Williams, Sophie, Abril, Josep F., Guigo, Roderic, Parra, Genis, Agarwal, Pankaj, Agarwala, Richa, Church, Deanna M., Hlavina, Wratko, Maglott, Donna R., Sapojnikov, Victor, Alexandersson, Marina, Pachter, Lior, Antonarakis, Stylianos E., Dermitzakis, Emmanouil T., Reymond, Alexandre, Ucla, Catherine, Baertsch, Robert, Diekhans, Mark, Furey, Terrence S., Hinrichs, Angela, Hsu, Fan, Karolchik, Donna, Kent, W. James, Roskin, Krishna M., Schwartz, Matthias S., Sugnet, Charles, Weber, Ryan J., Bork, Peer, Letunic, Ivica, Suyama, Mikita, Torrents, David, Zdobnov, Evgeny M., Botcherby, Marc, Brown, Stephen D., Campbell, Robert D., Jackson, Ian, Bray, Nicolas, Couronne, Olivier, Dubchak, Inna, Poliakov, Alex, Rubin, Edward M., Brent, Michael R., Flicek, Paul, Keibler, Evan, Korf, Ian, Batalov, S., Bult, Carol, Frankel, Wayne N., Carninci, Piero, Hayashizaki, Yoshihide, Kawai, Jun, Okazaki, Yasushi, Cawley, Simon, Kulp, David, Wheeler, Raymond, Chiaromonte, Francesca, Collins, Francis S., Felsenfeld, Adam, Guyer, Mark, Peterson, Jane, Wetterstrand, Kris, Copley, Richard R., Mott, Richard, Dewey, Colin, Dickens, Nicholas J., Emes, Richard D., Goodstadt, Leo, Ponting, Chris P., Winter, Eitan, Dunn, Diane M., von Niederhausern, Andrew C., Weiss, Robert B., Eddy, Sean R., Johnson, L. Steven, Jones, Thomas A., Elnitski, Laura, Kolbe, Diana L., Eswara, Pallavi, Miller, Webb, O'Connor, Michael J., Schwartz, Scott, Muzny, Donna M., Glusman, Gustavo, Smit, Arian, Green, Eric D., Hardison, Ross C., Yang, Shan, Haussler, David, Hua, Axin, Roe, Bruce A., Kucherlapati, Raju S., Montgomery, Kate T., Li, Jia, Li, Ming, Lucas, Susan, Ma, Bin, McCombie, W. Richard, Morgan, Michael, Pevzner, Pavel, Tesler, Glenn, Schultz, Jorg, Smith, Douglas R., Tromp, John, and Worley, Kim C.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Mouse Genome Sequencing Consortium ; Genome Sequencing Center: ; Asif T. Chinwalla [1, 47]; Lisa L. Cook [1]; Kimberly D. Delehaunty [1]; Ginger A. Fewell [1]; Lucinda A. Fulton [...]

Published
2002
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14. Genomic structure and functional control of the Dlx3-7 bigene cluster

Author

Sumiyama, Kenta, Irvine, Steven Q., Stock, David W., Weiss, Kenneth M., Kawasaki, Kazuhiko, Shimizu, Nobuyoshi, Shashikant, Cooduvalli S., Miller, Webb, and Ruddle, Frank H.

Subjects
Genomes -- Physiological aspects, Vertebrates -- Genetic aspects, Genetic transcription -- Physiological aspects, Proteins -- Physiological aspects, Microbiological research -- Analysis, Science and technology
Abstract

The Dlx genes are involved in early vertebrate morphogenesis, notably of the head. The six Dlx genes of mammals are arranged in three convergently transcribed bigene clusters. In this study, we examine the regulation of the Dlx3-7 cluster of the mouse. We obtained and sequenced human and mouse P1 clones covering the entire Dlx3-7 cluster. Comparative analysis of the human and mouse sequences revealed several highly conserved noncoding regions within 30 kb of the Dlx3-7-coding regions. These conserved elements were located both 5' of the coding exons of each gene and in the intergenic region 3' of the exons, suggesting that some enhancers might be shared between genes. We also found that the protein sequence of Dlx7 is evolving more rapidly than that of Dlx3. We conducted a functional study of the 79-kb mouse genomic clone to locate cis-element activity able to reproduce the endogenous expression pattern by using transgenic mice. We inserted a lacZ reporter gene into the first exon of the Dlx3 gene by using homologous recombination in yeast. Strong lacZ expression in embryonic (E) stage E9.5 and E10.5 mouse embryos was found in the limb buds and first and second visceral arches, consistent with the endogenous Dlx3 expression pattern. This result shows that the 79-kb region contains the major cis-elements required to direct the endogenous expression of Dlx3 at stage E10.5. To test for enhancer location, we divided the construct in the mid-intergenic region and injected the Dlx3 gene portion. This shortened fragment lacking Dlx7-flanking sequences is able to drive expression in the limb buds but not in the visceral arches. This observation is consistent with a cis-regulatory enhancer-sharing model within the Dlx bigene cluster.

Published
2002

15. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA

Author

Chiaromonte, Francesca, Yang, Shan, Elnitski, Laura, Yap, Von Bing, Miller, Webb, and Hardison, Ross C.

Subjects
DNA -- Physiological aspects, Genetic research -- Analysis, Rodents -- Genetic aspects, Mammals -- Genetic aspects, Science and technology
Abstract

The amount of noncoding genomic DNA sequence that aligns between human and mouse varies substantially in different regions of their genomes, and the amount of repetitive DNA also varies. In this report, we show that divergence in noncoding nonrepetitive DNA is strongly correlated with the amount of repetitive DNA in a region. We investigated aligned DNA in four large genomic regions with finished human sequence and almost or completely finished mouse sequence. These regions, totaling 5.89 Mb of DNA, are on different chromosomes and vary in their base composition. An analysis based on sliding windows of 10 kb shows that the fraction of aligned noncoding nonrepetitive DNA and the fraction of repetitive DNA are negatively correlated, both at the level of an entire region and locally within it. This conclusion is strongly supported by a randomization study, in which repetitive elements are removed and randomly relocated along the sequences. Thus, regions of noncoding genomic DNA that accumulated fewer point mutations since the primate-rodent divergence also suffered fewer retrotransposition events. These results indicate that some regions of the genome are more 'flexible' over the time scale of mammalian evolution, being able to accommodate many point mutations and insertions, whereas other regions are more 'rigid' and accumulate fewer changes. Stronger conservation is generally interpreted as indicating more extensive or more important function. The evidence presented here of correlated variation in the rates of different evolutionary processes across noncoding DNA must be considered in assessing such conservation for evidence of selection.

Published
2001

16. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2

Author

McClelland, Michael, Sanderson, Kenneth E., Spieth, John, Clifton, Sandra W., Latreille, Phil, Courtney, Laura, Porwollik, Steffen, Ali, Johar, Dante, Mike, Du, Feiyu, Hou, Shunfang, Layman, Dan, Leonard, Shawn, Nguyen, Christine, Scott, Kelsi, Holmes, Andrea, Grewal, Neenu, Mulvaney, Elizabeth, Ryan, Ellen, Sun, Hui, Florea, Liliana, Miller, Webb, Stoneking, Tamberlyn, Nhan, Michael, Waterston, Robert, and Wilson, Richard K.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Michael McClelland (corresponding author) [1]; Kenneth E. Sanderson [2]; John Spieth [3]; Sandra W. Clifton [3]; Phil Latreille [3]; Laura Courtney [3]; Steffen Porwollik [1]; Johar Ali [3]; Mike [...]

Published
2001
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17. Galaxy: A platform for interactive large-scale genome analysis

Author

Giardine, Belinda, Hardison, Ross C., Elnitski, Laura, Albert, Istvan, Kent, W. James, Riemer, Cathy, Burhans, Richard, Shah, Prachi, Yi Zhang, Blakenberg, Daniel, Taylor, James, Nekrutenko, Anton, and Miller, Webb

Subjects
Interactive computer systems -- Evaluation, Interactive media -- Evaluation, Electronic publishing -- Evaluation, Interactive technology, Electronic publication, Electronic publishing, Health
Abstract

An interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries and visualize the results, is presented. The heart of Galaxy is a flexible history system that stores the queries from each user, performs operations such as intersections unions and subtractions and links to other computational tools.

Published
2005

18. Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Author

Ovcharenko, Ivan, Giardine, Belinda M., Jian Ma, Minmei Hou, Loots, Gabriela G., Hardison, Ross C., Stubbs, Lisa, and Miller, Webb

Subjects
Birds -- Genetic aspects, Online information services -- Analysis, Information services -- Analysis, Online services -- Analysis, Online information service, Health
Abstract

Mulan, a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time, is introduced. The uses and applications of Mulan tool through multispecies comparisons of the GATA3 gene locus and the identification of elements that are conserved in a different way in avians than in other genomes, allowing speculation on the evolution of birds are illustrated.

Published
2005

19. Evolutional and functional classification of vertebrate gene deserts

Author

Ovcharenko, Ivan, Loots, Gabriela G., Nobrega, Marcelo A., Hardison, Ross C., Miller, Webb, and Stubbs, Lisa

Subjects
Chickens -- Genetic aspects, Vertebrates -- Genetic aspects, Genetic research, Health
Abstract

The sequence comparisons with the chicken genome, an organism strategically positioned between rodents and fish in the vertebrate evolutionary tree are focused to investigate the possibility that the differences in the rate of neutral evolution reflect the existence of distinct categories of gene deserts. Various analyses have enabled to classify the gene deserts into two functionally different groups and to provide new insights regarding the functions of these intervals in the human genome.

Published
2005

20. Reconstructing large regions of an ancestral mammalian genome in silico

Author

Blanchette, Mathieu, Green, Eric D., Miller, Webb, and Haussler, David

Subjects
Nucleotide sequence -- Research, Mammals -- Genetic aspects, Transposons -- Research, Genetic research, Health
Abstract

An ancient genome sequence of 1.1 Mb is reconstructed around the CFTR locus using actual genomic sequences form 19 extant mammals. The reconstruction is accurate and allows the identification of the features in modern species, such as remnants of ancient transposon insertions that were not identified by direct analysis.

Published
2004

22. Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome

Author

Han, Kyudong, Konkel, Miriam K., Xing, Jinchuan, Wang, Hui, Lee, Jungnam, Meyer, Thomas J., Huang, Charles T., Sandifer, Erin, Hebert, Kristi, Barnes, Erin W., Hubley, Robert, Miller, Webb, Smit, Arian F.A., Ullmer, Brygg, and Batzer, Mark A.

Subjects
Rhesus monkey -- Genetic aspects, Old-World monkeys -- Genetic aspects, DNA -- Properties
Published
2007

23. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA

Author

Poinar, Hendrik N., Schwarz, Carsten, Qi, Ji, Shapiro, Beth, MacPhee, Ross D.E., Buigues, Bernard, Tikhonov, Alexei, Huson, Daniel H., Tomsho, Lynn P., Auch, Alexander, Rampp, Markus, Miller, Webb, and Schuster, Stephan C.

Subjects
DNA -- Research, DNA -- Analysis, Extinct animals -- Research, Genomes -- Research, Genomes -- Analysis, Mammoths -- Research, Molecular evolution -- Research, Molecular evolution -- Analysis
Published
2006

24. Sequence conservation at human and mouse orthologous common fragile regions, FRA3B/FHIT and Fra 14A2/Fhit

Author

Shiraishi, Takeshi, Druck, Teresa, Mimori, Koshi, Flomenberg, Jacob, Berk, Lori, Alder, Hansjuerg, Miller, Webb, Huebner, Kay, and Croce, Carlo M.

Subjects
Chromosome deletion -- Analysis, Linkage (Genetics) -- Research, Nucleotide sequence -- Analysis, Science and technology
Abstract

It has been suggested that delayed DNA replication underlies fragility at common human fragile sites, but specific sequences responsible for expression of these inducible fragile sites have not been identified. One approach to identify such cis-acting sequences within the large nonexonic regions of fragile sites would be to identify conserved functional elements within orthologous fragile sites by interspecies sequence comparison. This study describes a comparison of orthologous fragile regions, the human FRA3B/FHIT and the murine Fra14A2/Fhit locus. We sequenced over 600 kbp of the mouse Fra14A2, covering the region orthologous to the fragile epicenter of FRA3B, and determined the Fhit deletion break points in a mouse kidney cancer cell line (RENCA). The murine Fra14A2 locus, like the human FRA3B, was characterized by a high AT content. Alignment of the two sequences showed that this fragile region was stable in evolution despite its susceptibility to mitotic recombination on inhibition of DNA replication. There were also several unusual highly conserved regions (HCRs). The positions of predicted matrix attachment regions (MARs), possibly related to replication origins, were not conserved. Of known fragile region landmarks, five cancer cell break points, one viral integration site, and one aphidicolin break cluster were located within or near HCRs. Thus, comparison of orthologous fragile regions has identified highly conserved sequences with possible functional roles in maintenance of fragility.

Published
2001

25. Hox cluster genomics in the horn shark, Heterodontus francisci

Author

Kim, Chang-Bae, Amemiya, Chris, Bailey, Wendy, Kawasaki, Kazuhiko, Mezey, Jason, Miller, Webb, Minoshima, Shinsei, Shimizu, Nobuyoshi, Wagner, Gunter, and Ruddle, Frank

Subjects
Sharks -- Genetic aspects, Genotype -- Research, Science and technology
Abstract

Reconstructing the evolutionary history of Hox cluster origins will lead to insights into the developmental and evolutionary significance of Hox gene clusters in vertebrate phylogeny and to their role in the origins of various vertebrate body plans. We have isolated two Hox clusters from the horn shark, Heterodontus francisci. These have been sequenced and compared with one another and with other chordate Hox clusters. The results show that one of the horn shark clusters (HoxM) is orthologous to the mammalian HoxA cluster and shows a structural similarity to the amphioxus cluster, whereas the other shark cluster (HoxN) is orthologous to the mammalian HoxD cluster based on cluster organization and a comparison with noncoding and Hox gene-coding sequences. The persistence of an identifiable HoxA cluster over an 800-million-year divergence time demonstrates that the Hox gene clusters are highly integrated and structured genetic entities. The data presented herein identify many noncoding sequence motifs conserved over 800 million years that may function as genetic control motifs essential to the developmental process.

Published
2000

26. 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., Maduro, Valerie V. Branden, 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.

Subjects
Cystic fibrosis -- Causes of, Proteins -- Research, Gene expression -- Research, Cloning -- Research, DNA -- Research, Mice -- Physiological aspects, Science and technology
Abstract

The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous advances in elucidating the function of the encoded protein and the physiological basis of cystic fibrosis. However, numerous areas of cystic fibrosis biology require additional investigation, some of which would be facilitated by information about the long-range sequence context of the CFTR gene. For example, the latter might provide clues about the sequence elements responsible for the temporal and spatial regulation of CFTR expression. We thus sought to establish the sequence of the chromosomal segments encompassing the human CFTR and mouse Cftr genes, with the hope of identifying conserved regions of biologic interest by sequence comparison. Bacterial clone-based physical maps of the relevant human and mouse genomic regions were constructed, and minimally overlapping sets of clones were selected and sequenced, eventually yielding [approximately equals] 1.6 Mb and [approximately equals] 358 kb of contiguous human and mouse sequence, respectively. These efforts have produced the complete sequence of the [approximately equals] 189-kb and [approximately equals] 152-kb segments containing the human CFTR and mouse Cftr genes, respectively, as well as significant amounts of flanking DNA. Analyses of the resulting data provide insights about the organization of the CFTR/Cftr genes and potential sequence elements regulating their expression. Furthermore, the generated sequence reveals the precise architecture of genes residing near CFTR/Cftr, including one known gene (WNT2/Wnt2) and two previously unknown genes that immediately flank CFTR/Cftr.

Published
2000

27. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

Author

Yong Cheng, Weisheng Wu, Kumar, Swathi Ashok, Duonan Yu, Deng, Wulan, Tripic, Tamara, King, David C., Kuan-Bei Chen, Ying Zhang, Drautz, Daniela, Giardine, Belinda, Schuster, Stephan C., Miller,Webb, Chiaromonte, Francesca, Yu Zhang, Blobel, Gerd A., Weiss, Mitchell J., and Hardison, Ross C.

Subjects
Histones -- Structure, Gene expression -- Analysis, Genetic transcription -- Research, Binding proteins -- Research, Health
Published
2009

28. The mitochondrial genome sequence of the Tasmanian tiger(Thylacinus cynocephalus)

Author

Miller, Webb, Drautz, Daniela I., Janecka, Jan E., Lesk, Arthur M., Ratan, Aakrosh, Tomsho, Lynn P., Packard, Mike, Zhang, Yeting, McClellan, Lindsay R., Ji Qi, Zhao, Fangqing, Gilbert, M. Thomas P., Dalen, Love, Arsuaga, Juan Luis, Ericson, Per G.P., Huson, Daniel H., Helgen, Kristofer M., Murphy, William J., Gotherstrom, Anders, and Schuster, Stephan C.

Subjects
Nucleotide sequence -- Research, Biological diversity -- Research, Mitochondrial DNA -- Research, Thylacine -- Genetic aspects, Health
Published
2009

29. Transciptional enhancement by GATA1-occupaied DNA segments is strongly associated with evolutionary constraint on the binding site motif

Author

Yong Cheng, King, David C., Dore, Louis C., Xinmin Zhang, Yuepin Zhou, Ying Zhang, Dorman, Christine, Abebe, Demesew, Kumar, Swathi A., Chiaromonte, Francesca, Miller, Webb, Green, Ronald D., Weiss, Mitchell J., and Hardison, Ross C.

Subjects
Genetic transcription -- Research, Chromatin -- Usage, Chromatin -- Genetic aspects, DNA replication -- Research, Health
Published
2008

30. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser

Author

Miller, Webb, Rosenbloom, Kate, Hardison, Ross C., Minmei Hou, Taylor, James, Raney, Brian, Burhans, Richard, King, David C., Baertsch, Robert, Blankenberg, Daniel, Pond, Sergei L. Kosakovsky, Nekrutenko, Anton, Giardine, Belinda, Harris, Robert S., Tyekucheva, Svitlana, Diekhans, Mark, Pringle, Thomas H., Murphy, William J., Lesk, Arthur, Weinstock, George M., Lindblad-Toh, Kerstin, Gibbs, Richard A., Lander, Eric S., Siepel, Adam, Haussler, David, and Kent, W. James

Subjects
Evolution -- Research, Human genome -- Research, Human genome -- Information management, Mutation (Biology) -- Research, Company systems management, Health
Abstract

A set of alignments of 28 vertebrate genome sequences observed on the UCSC Human Genome Browser is described. The data source could be used to explore vertebrate and mammalian evolution.

Published
2007

31. A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

Author

Blankenberg, Daniel, Taylor, James, Schenck, Ian, Jianbin He, Yi Zhang, Ghent, Matthew, Veeraraghavan, Narayanan, Istvan, Albert, Miller, Webb, Makova, Kateryna D., Hardison, Ross C., and Nekrutenko, Anton

Subjects
Gene banks -- Usage, Human genome -- Research, Genetic research -- Technology application, Technology application, Health
Abstract

The analyses of huge ENCODE data are carried out using a web application called [Galaxy2.sup.ENCODE] which is quick, user friendly and can be easily updated with new applications.

Published
2007

32. Analyses of deep mammalian sequence alignment and constraint predictions for 1% of the human genome

Author

Margulies, Elliott H., Schwartz, Ariel S., Loytynoja, Ari, Whelan, Simon, Pardi, Fabio, Taylor, James, Nikolaev, Sergey, Montoya-Burgos, Juan I., Minmei Hou, Dewey, Colin N., Siepel, Adam, Birney, Ewan, Keefe, Damian, Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Massingham, Tim, Ureta-Vidal, Abel, Paten, Benedict; Stone, Eric A., Bickel, Peter, Mullikin, James C., Holmes, Ian, Rosenbloom, Kate R., Brown, James B., Goldman, Nick, Hardison, Ross, Miller, Webb, Haussler, David, Antonarakis, Stylianos E., Batzoglou, Serafim, Kent, W.James, Pachter, Lior, Green, Eric D., and Sidow, Arend

Subjects
Mammals -- Genetic aspects, Nucleotide sequence -- Analysis, Biological diversity -- Analysis, Health
Abstract

The sequence analyses of functional elements involving sequence generation, alignment and evolutionary constraint of 23 mammalian species are carried out using quantitative and qualitative methods. The constraint regions and the elements are found to be nonoverlapping.

Published
2007

33. Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data

Author

King, David C., Martin, Joel, Chiaromonte, Francesca, Miller, Webb, Taylor, James, Ying Zhang Yong Cheng, and Lawson, Heather A.

Subjects
Genetic code -- Analysis, Genetic regulation -- Analysis, Health
Abstract

The evolutionary roles of some recognized transcriptional regulatory sequences defined by the human genome project-ENCODE are studied. The comparative genomics tools reveal that these regulatory regions are associated with genes that play a role in selection.

Published
2007

34. Using genomic data to unravel the root of the placental mammal phylogeny

Author

Murphy, William J., Pringle, Thomas H., Crider, Tess A., Springer, Mark S., and Miller, Webb

Subjects
Eutherians -- Genetic aspects, Eutherians -- Research, Genomes -- Research, Phylogeny -- Research, Health
Abstract

The evolution of placental mammal phylogeny is studied by analyzing genome sequence assemblies of humans, elephant, armadillo and opossum to identify relevant coding sequences. A revised molecular timescale for the evolution of placental mammal phylogeny of the Afrotheria and Xenarthra groups is suggested.

Published
2007

35. Experimental validation of predicted mammalian erythroid cis-regulatory modules

Author

Hao Wang; Ying Zhang; Yong Cheng and Gibb, Brian; Dorman, Christine; Miller, Webb

Subjects
Mammals -- Genetic aspects, Mammals -- Physiological aspects, Genetic transcription -- Research, Genetic research, Health
Abstract

The cis-regulatory modules (CRMs) are predicted for mammalian genes expressed in red blood cells by combining two properties obtained from aligned, noncoding genome sequences, such as a positive regulatory potential (RP) score and conservation of a binding site motif for the essential erythroid transcription factor GATA-1. The results have shown that high RP in combination with another feature of a CRM, such as a conserved transcription factor-binding site, is a good predictor of functional CRMs.

Published
2006

36. ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements

Author

Chiaromonte, Francesca, Miller, Webb, and King, David C.; Hardison, Ross C.

Subjects
Nucleotide sequence -- Research, Genetic code -- Research, Genetic research, Health
Abstract

A computational method ESPERR (evolutionary and sequence pattern extraction through reduced representations) is developed, which uses training examples to learn encoding of multispecies alignments into reduced forms tailored for the prediction of chosen classes of functional elements. The results have shown that ESPERR could greatly improve the effectiveness of the strategy used to select regions to be tested for developmental enhancer activity.

Published
2006

37. Reconstructing contiguous regions of an ancestral genome

Author

Burhans, Richard C., Ma, Jian, Haussler, David, Blanchette, Mathieu, Kent, W. James, Zhang, Louxin, and Miller, Webb

Subjects
Genetic research -- Forecasts and trends, Nucleotide sequence -- Chemical properties, Eutherians -- Genetic aspects, Market trend/market analysis, Health
Abstract

Mammalian genome rearrangements are analyzed at higher resolution and a new method is described for predicting ancestral order and orientation of those intervals from their observed adjacencies in modern species. These methods are developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs and most other placental mammals.

Published
2006

38. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genome

Author

Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, Clawson, Hiram, Spieth, John, Hiller, LaDeana W., Richards, Stephen, Weinstock, George M., Wilson, Richard K., Gibbs, Richard A., Kent, W.James, Miller, Webb, and Haussler, David

Subjects
Vertebrates -- Genetic aspects, Genomes -- Research, Nucleotide sequence -- Research, Health
Abstract

A comprehensive search for conserved elements in vertebrate genomes using genome-wide multiple alignments of five vertebrate species and four insect species is done. It is found that in all species groups, the most highly conserved elements (HCEs) are hundreds or thousands of bases long and show extreme levels of conservation.

Published
2005

39. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

Author

King, David C., Taylor, James, Elnitski, Laura, Chiaromonte, Francesca, Miller, Webb, and Hardison, Ross C.

Subjects
Nucleotide sequence -- Research, Mammals -- Genetic aspects, Genomes -- Research, Health
Abstract

Different analytical methods score distinctive features of whole-genome alignments among human, mouse, and rat to predict functional regions. Three of the methods used for their ability to identify the positions of known regulatory regions in the well-studied 'HBB' gene complex are evaluated.

Published
2005

40. Aligning multiple genomic sequences with the threaded blockset aligner

Author

Blanchette, Mathieu, Riemer, Cathy, Kent, W. James, Elnitski, Laura;, Roskin, Krishna M., Smit, Arian F.A., Baertsch, Robert, Rosenbloom, Kate, Clawson, Hiram, Green, Eric D., Haussler, David, and Miller, Webb

Subjects
Genomics -- Analysis, Nucleotide sequence -- Analysis, Mammals -- Genetic aspects, Mammals -- Analysis, Health
Abstract

Threaded blockset, a novel generalization of the classic notion of a multiple alignment, is defined. A new computer program called threaded blockset aligner(TBA) builds a threaded blockset and is designed to be appropriate for aligning many megabase-sized regions of multiple mammalian genomes.

Published
2004

41. Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

Author

Kolbe, Diana;, Taylor, James, Elnitski, Laura, Eswara, Pallavi, Li, Jia, Miller, Webb, and Chiaromonte, Francesca

Subjects
Genomics -- Analysis, Mice -- Genetic aspects, Mice -- Analysis, Human genetics -- Analysis, Chromosome mapping -- Analysis, Health
Abstract

A computational method for identifying regulatory regions within three-way DNA alignments of human, mouse, and rat is developed. The resulting Regulatory Potential(RP) score is generalized.

Published
2004

42. zPicture: dynamic alignment and visualization tool for analyzing conservation profiles

Author

Ovcharenko, Ivan, Loots, Gabriela G., Hardison, Ross C, Miller, Webb, and Stubbs, Lisa

Subjects
Phylogeny -- Research, Nucleotide sequence -- Research, Genetic research, Health
Abstract

zPicture, an interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionary conserved regions (ECRs) is introduced. zPicture is highly flexible, because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates.

Published
2004

43. Gene length and proximity to neighbors affect genome-wide expression levels

Author

Chiaromonte, Francesca, Miller, Webb, and Bouhassira, Eric E.

Subjects
Chromatin -- Genetic aspects, Gene expression -- Physiological aspects, Genetic research -- Analysis, Genetic transcription -- Physiological aspects, Genomes -- Physiological aspects, Genomes -- Research, Messenger RNA -- Genetic aspects, Health
Abstract

Research has been conducted on gene length and proximity to neighbors. The results have demonstrated that on genome-wide scale highly expressed genes are smaller and produce shorter mRNA.

Published
2003

44. GALA, a database for genomic sequence alignments and annotations

Author

Giardine, Belinda, Elnitski, Laura, Riemer, Cathy, Makalowska, Izabela, Schwartz, Scott, Miller, Webb, and Hardison, Ross C.

Subjects
Genetic research -- Analysis, Genetic research -- Methods, Genomes -- Research, Gene expression -- Physiological aspects, DNA -- Genetic aspects, Methodology -- Analysis, Health
Abstract

The authors discuss the development of a relational database, GALA. They report that this database contains whole genome sequence alignments between human and mouse, and that it is useful in searching across data tracks supplied by databases, alignment resources and current browsers.

Published
2003

45. Human-mouse alignments with BLASTZ

Author

Schwartz, Scott, Kent, W. James, Smit, Arian, Zhang, Zheng, Baertsch, Robert, Hardison, Ross C., Haussler, David, and Miller, Webb

Subjects
Genomes -- Research, Genetic research -- Analysis, Methodology -- Analysis, Gene mutations -- Physiological aspects, Genetic algorithms -- Analysis, Genetic algorithms -- Usage, Health
Abstract

Research has been conducted on genome evolution. The use of program BLASTZ, an algorithm designed for aligning long genomic sequences, the modifications of the program and the hardware environment on which it runs are described.

Published
2003

46. Distinguishing regulatory DNA from neutral sites

Author

Elnitski, Laura, Hardison, Ross C., Li, Jia, Yang, Shan, Kolbe, Diana, Eswara, Pallavi, O'Connor, Michael J., Schwartz, Scott, Miller, Webb, and Chiaromonte, Francesca

Subjects
Genetic research -- Analysis, Genomes -- Research, Genetic regulation -- Analysis, DNA -- Genetic aspects, Nucleotides -- Genetic aspects, Health
Abstract

Research has been conducted on genome discrimination. Results demonstrate that discrimination based on individual nucleotide pair frequencies are partially successful.

Published
2003

47. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

Author

Hardison, Ross C., Roskin, Krishna M., Yang, Shan, Diekhans, Mark, Kent, W. James, Weber, Ryan, Elnitski, Laura, Li, Jia, O'Connor, Michael, Kolbe, Diana, Schwartz, Scott, Furey, Terrence S., Whelan, Simon, Goldman, Nick, Smit, Arian, Miller, Webb, Chiaromonte, Francesca, and Haussler, David

Subjects
Genomes -- Research, Genetic research -- Analysis, DNA -- Genetic aspects, Gene mutations -- Physiological aspects, Health
Abstract

Research has been conducted on human genome evolution. Results demonstrate that some regions of genome are changed slowly by the same processes that alter DNA, and some are changed faster.

Published
2003

48. Generation and comparative analysis of ~3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7qll.23 implicated in Williams syndrome

Author

DeSilva, Udaya, Elnitski, Laura, Idol, Jacquelyn R., Doyle, Johannah L., Gan, Weiniu; ., Green, Eric D., Miller, Webb, Touchman, Jeffrey W., Thomas, Pamela J., Bouffard, Gerard G., Blakesley, Robert W., McDowell, Jennifer C., Beckstrom-Sternberg, Stephen M., Dietriich, Nicole L, Schwartz, Scott;, and Thomas, James W.

Subjects
Developmental disabilities -- Research, Child development deviations -- Research, Human chromosomes -- Research, Williams syndrome -- Research, Genetic research, Health
Abstract

Williams syndrome is a complex developmental disorder that results from the heterozygous deletion of a ~1.6-Mb segment of human chromosome 7qll.23. The results from a study in this context provided an important comparative sequence resource to develop mouse models of the disorder.

Published
2002

49. Row replacement algorithms for screen editors

Author

Myers, Eugene W. and Miller, Webb

Subjects
Technology, Algorithm Analysis, Software Complexity, Nonnumerical Algorithms, Discrete Mathematics, Dynamic Programming, Screen Editors, Efficiency
Published
1989

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