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1. Cytoplasmic control of intranuclear polarity by human cytomegalovirus

Author

Steven T. Kosak, Derek Walsh, Dean J. Procter, Colleen Furey, and Arturo G. Garza-Gongora

Subjects
Cytoplasm, Rotation, Nuclear Envelope, Emerin, Cytomegalovirus, Nerve Tissue Proteins, Virus Replication, Microtubules, Article, Cell Line, Histones, 03 medical and health sciences, 0302 clinical medicine, Tubulin, Microtubule, LINC complex, convolutional neural networks, Cell polarity, medicine, Humans, Inner membrane, 030304 developmental biology, Cell Nucleus, polarization, 0303 health sciences, Multidisciplinary, Chemistry, Microfilament Proteins, Cell Polarity, Dyneins, Membrane Proteins, Nuclear Proteins, Acetylation, Actins, Chromatin, Cell biology, nuclear rotation, Actin Cytoskeleton, Cell nucleus, medicine.anatomical_structure, Viral replication, nuclear actin, DNA, Viral, Neural Networks, Computer, Microtubule-Associated Proteins, Microtubule-Organizing Center, 030217 neurology & neurosurgery
Abstract

Despite its size and rigidity, the cell nucleus can be moved or reorganized by cytoskeletal filaments under various conditions (for example, during viral infection)1-11. Moreover, whereas chromatin organizes into non-random domains12, extensive heterogeneity at the single-cell level13 means that precisely how and why nuclei reorganize remains an area of intense investigation. Here we describe convolutional neural network-based automated cell classification and analysis pipelines, which revealed the extent to which human cytomegalovirus generates nuclear polarity through a virus-assembled microtubule-organizing centre. Acetylation of tubulin enables microtubules emanating from this centre to rotate the nucleus by engaging cytoplasmically exposed dynein-binding domains in the outer nuclear membrane protein nesprin-2G, which polarizes the inner nuclear membrane protein SUN1. This in turn creates intranuclear polarity in emerin, and thereby controls nuclear actin filaments that spatially segregate viral DNA from inactive histones and host DNA, maximizing virus replication. Our findings demonstrate the extent to which viruses can control the nucleus from the cytoplasm.

Published
2020

2. 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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3. The accessible chromatin landscape of the human genome

Author

Thurman, Robert E., Rynes, Eric, Humbert, Richard, Vierstra, Jeff, Maurano, Matthew T., Haugen, Eric, Sheffield, Nathan C., Stergachis, Andrew B., Vernot, Benjamin, Garg, Kavita, John, Sam, Sandstrom, Richard, Bates, Daniel, Boatman, Lisa, Canfield, Theresa K., Diegel, Morgan, Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Giste, Erika, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tanya, Lajoie, Bryan, Lee, Bum-Kyu, Lee, Kristen, London, Darin, Lotakis, Dimitra, Neph, Shane, Neri, Fidencio, Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Safi, Alexias, Sanchez, Minerva E., Sanyal, Amartya, Shafer, Anthony, Simon, Jeremy M., Song, Lingyun, Vong, Shinny, Weaver, Molly, Yan, Yongqi, Zhang, Zhancheng, Zhang, Zhuzhu, Lenhard, Boris, Tewari, Muneesh, Dorschner, Michael O., Hansen, R. Scott, Navas, Patrick A., Stamatoyannopoulos, George, Iyer, Vishwanath R., Lieb, Jason D., Sunyaev, Shamil R., Akey, Joshua M., Sabo, Peter J., Kaul, Rajinder, Furey, Terrence S., Dekker, Job, Crawford, Gregory E., and Stamatoyannopoulos, John A.

Subjects
Chromatin -- Physiological aspects, DNA -- Physiological aspects, Genetic research, Human genome -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify [similar]2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect [similar]580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation., Author(s): Robert E. Thurman [1, 13]; Eric Rynes [1, 13]; Richard Humbert [1, 13]; Jeff Vierstra [1]; Matthew T. Maurano [1]; Eric Haugen [1]; Nathan C. Sheffield [2]; Andrew B. [...]

Published
2012
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4. 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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5. 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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6. The DNA sequence and biology of human chromosome 19

Author

Grimwood, Jane, Gordon, Laurie A., Olsen, Anne, Terry, Astrid, Schmutz, Jeremy, Lamerdin, Jane, Hellsten, Uffe, Goodstein, David, Couronne, Olivier, Tran-Gyamfi, Mary, Aerts, Andrea, Altherr, Michael, Ashworth, Linda, Bajorek, Eva, Black, Stacey, Branscomb, Elbert, Caenepeel, Sean, Carrano, Anthony, Caoile, Chenier, Man Chan, Yee, Christensen, Mari, Cleland, Catherine A., Copeland, Alex, Dalin, Eileen, Dehal, Paramvir, Denys, Mirian, Detter, John C., Escobar, Julio, Flowers, Dave, Fotopulos, Dea, Garcia, Carmen, Georgescu, Anca M., Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Ho, Isaac, Huang, Wayne, Israni, Sanjay, Jett, Jamie, Kadner, Kristen, Kimball, Heather, Kobayashi, Arthur, Larionov, Vladimer, Leem, Sun-Hee, Lopez, Frederick, Lou, Yunian, Lowry, Steve, Malfatti, Stephanie, Martinez, Diego, McCready, Paula, Medina, Catherine, Morgan, Jenna, Nelson, Kathryn, Nolan, Matt, Ovcharenko, Ivan, Pitluck, Sam, Pollard, Martin, Popkie, Anthony P., Predki, Paul, Quan, Glenda, Ramirez, Lucia, Rash, Sam, Retterer, James, Rodriguez, Alex, Rogers, Stephanine, Salamov, Asaf, Salazar, Angelica, She, Xinwei, Smith, Doug, Slezak, Tom, Solovyev, Victor, Thayer, Nina, Tice, Hope, Tsai, Ming, Ustaszewska, Anna, Vo, Nu, Wagner, Mark, Wheeler, Jeremy, Wu, Kevin, Xie, Gary, Yang, Joan, Dubchak, Inna, Furey, Terrence S., DeJong, Pieter, Dickson, Mark, Gordon, David, Eichler, Evan E., Pennacchio, Len A., Richardson, Paul, Stubbs, Lisa, Rokhsar, Daniel S., Myers, Richard M., Rubin, Edward M., and Lucas, Susan M.

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

Author(s): Jane Grimwood (corresponding author) [1]; Laurie A. Gordon [2, 3]; Anne Olsen [2, 3]; Astrid Terry [2]; Jeremy Schmutz [1]; Jane Lamerdin [2, 3]; Uffe Hellsten [2]; David Goodstein [...]

Published
2004
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7. The DNA sequence of human chromosome 7

Author

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

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

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

Published
2003
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8. 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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9. 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
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10. Integration of cytogenetic landmarks into the draft sequence of the human genome

Author

BAC Resource Consortium, The, Cheung, V. G., Nowak, N., Jang, W., Kirsch, I. R., Zhao, S., Chen, X.-N., Furey, T. S., Kim, U.-J., Kuo, W.-L., Olivier, M., Conroy, J., Kasprzyk, A., Massa, H., Yonescu, R., Sait, S., Thoreen, C., Snijders, A., Lemyre, E., Bailey, J. A., Bruzel, A., Burrill, W. D., Clegg, S. M., Collins, S., Dhami, P., Friedman, C., Han, C. S., Herrick, S., Lee, J., Ligon, A. H., Lowry, S., Morley, M., Narasimhan, S., Osoegawa, K., Peng, Z., Plajzer-Frick, I., Quade, B. J., Scott, D., Sirotkin, K., Thorpe, A. A., Gray, J. W., Hudson, J., Pinkel, D., Ried, T., Rowen, L., Shen-Ong, G. L., Strausberg, R. L., Birney, E., Callen, D. F., Cheng, J.-F., Cox, D. R., Doggett, N. A., Carter, N. P., Eichler, E. E., Haussler, D., Korenberg, J. R., Morton, C. C., Albertson, D., Schuler, G., de Jong, P. J., and Trask, B. J.

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

Author(s): The BAC Resource Consortium; V. G. Cheung [1]; N. Nowak [2]; W. Jang [3]; I. R. Kirsch [4]; S. Zhao [5]; X.-N. Chen [6]; T. S. Furey [7]; U.-J. [...]

Published
2001

11. A physical map of the human genome

Author

McPherson, John D., Marra, Marco, Hillier, LaDeana, Waterston, Robert H., Chinwalla, Asif, Wallis, John, Sekhon, Mandeep, Wylie, Kristine, Mardis, Elaine R., Wilson, Richard K., Fulton, Robert, Kucaba, Tamara A., Wagner-McPherson, Caryn, Barbazuk, William B., Gregory, Simon G., Humphray, Sean J., French, Lisa, Evans, Richard S., Bethel, Graeme, Whittaker, Adam, Holden, Jane L., McCann, Owen T., Dunham, Andrew, Soderlund, Carol, Scott, Carol E., Bentley, David R., Schuler, Gregory, Chen, Hsiu-Chuan, Jang, Wonhee, Green, Eric D., Idol, Jacquelyn R., Maduro, Valerie V. Braden, Montgomery, Kate T., Lee, Eunice, Miller, Ashley, Emerling, Suzanne, Kucherlapati, Raju, Gibbs, Richard, Scherer, Steve, Gorrell, J. Harley, Sodergren, Erica, Clerc-Blankenburg, Kerstin, Tabor, Paul, Naylor, Susan, Garcia, Dawn, de Jong, Pieter J., Catanese, Joseph J., Nowak, Norma, Osoegawa, Kazutoyo, Qin, Shizhen, Rowen, Lee, Madan, Anuradha, Dors, Monica, Hood, Leroy, Trask, Barbara, Friedman, Cynthia, Massa, Hillary, Cheung, Vivian G., Kirsch, Ilan R., Reid, Thomas, Yonescu, Raluca, Weissenbach, Jean, Bruls, Thomas, Heilig, Roland, Branscomb, Elbert, Olsen, Anne, Doggett, Norman, Cheng, Jan-Fang, Hawkins, Trevor, Myers, Richard M., Shang, Jin, Ramirez, Lucia, Schmutz, Jeremy, Velasquez, Olivia, Dixon, Kami, Stone, Nancy E., Cox, David R., Haussler, David, Kent, W. James, Furey, Terrence, Rogic, Sanja, Kennedy, Scot, Jones, Steven, Rosenthal, Andre, Wen, Gaiping, Schilhabel, Markus, Gloeckner, Gernot, Nyakatura, Gerald, Siebert, Reiner, Schlegelberger, Brigitte, Korenberg, Julie, Chen, Xiao-Ning, Fujiyama, Asao, Hattori, Masahira, Toyoda, Atsushi, Yada, Tetsushi, Park, Hong-Seok, Sakaki, Yoshiyuki, Shimizu, Nobuyoshi, Asakawa, Shuichi, Kawasaki, Kazuhiko, Sasaki, Takashi, Shintani, Ai, Shimizu, Atsushi, Shibuya, Kazunori, Kudoh, Jun, Minoshima, Shinsei, Ramser, Juliane, Seranski, Peter, Hoff, Celine, Poustka, Annemarie, Reinhardt, Richard, and Lehrach, Hans

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

Author(s): The International Human Genome Mapping Consortium ; Washington University School of Medicine, Genome Sequencing Center: ; John D. McPherson (corresponding author) [1]; Marco Marra [1]; LaDeana Hillier [1]; Robert [...]

Published
2001
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13. Accurate whole human genome sequencing using reversible terminator chemistry

Author

Bentley, David R., Balasubramanian, Shankar, Swerdlow, Harold P., Smith, Geoffrey P., Milton, John, Brown, Clive G., Hall, Kevin P., Evers, Dirk J., Barnes, Colin L., Bignell, Helen R., Boutell, Jonathan M., Bryant, Jason, Carter, Richard J., Cheetham, R. Keira, Cox, Anthony J., Ellis, Darren J., Flatbush, Michael R., Gormley, Niall A., Humphray, Sean J., Irving, Leslie J., Karbelashvili, Mirian S., Kirk, Scott M., Li, Heng, Liu, Xiaohai, Maisinger, Klaus S., Murray, Lisa J., Obradovic, Bojan, Ost, Tobias, Parkinson, Michael L., Pratt, Mark R., Rasolonjatovo, Isabelle M. J., Reed, Mark T., Rigatti, Roberto, Rodighiero, Chiara, Ross, Mark T., Sabot, Andrea, Sankar, Subramanian V., Scally, Aylwyn, Schroth, Gary P., Smith, Mark E., Smith, Vincent P., Spiridou, Anastassia, Torrance, Peta E., Tzonev, Svilen S., Vermaas, Eric H., Walter, Klaudia, Wu, Xiaolin, Zhang, Lu, Alam, Mohammed D., Anastasi, Carole, Aniebo, Ify C., Bailey, David M. D., Bancarz, Iain R., Banerjee, Saibal, Barbour, Selena G., Baybayan, Primo A., Benoit, Vincent A., Benson, Kevin F., Bevis, Claire, Black, Phillip J., Boodhun, Asha, Brennan, Joe S., Bridgham, John A., Brown, Rob C., Brown, Andrew A., Buermann, Dale H., Bundu, Abass A., Burrows, James C., Carter, Nigel P., Castillo, Nestor, Catenazzi, Maria Chiara E., Chang, Simon, Cooley, R. Neil, Crake, Natasha R., Dada, Olubunmi O., Diakoumakos, Konstantinos D., Dominguez-Fernandez, Belen, Earnshaw, David J., Egbujor, Ugonna C., Elmore, David W., Etchin, Sergey S, Ewan, Mark R., Fedurco, Milan, Fraser, Louise J., Fuentes Fajardo, Karin V., Furey, W. Scott, George, David, Gietzen, Kimberley J., Goddard, Colin P., Golda, George S., Granieri, Philip A., Green, David E., Gustafson, David L., Hansen, Nancy F., Harnish, Kevin, Haudenschild, Christian D., Heyer, Narinder I, Hims, Matthew M., Ho, Johnny T., Horgan, Adrian M., Hoschler, Katya, Hurwitz, Steve, Ivanov, Denis V., Johnson, Maria Q., James, Terena, Huw Jones, T. A., Kang, Gyoung-Dong, Kerelska, Tzvetana H., Kersey, Alan D., Khrebtukova, Irina, Kindwall, Alex P., Kingsbury, Zoya, Kokko-Gonzales, Paula I., Kumar, Anil, Laurent, Marc A., Lawley, Cynthia T., Lee, Sarah E., Lee, Xavier, Liao, Arnold K., Loch, Jennifer A., Lok, Mitch, Luo, Shujun, Mammen, Radhika M., Martin, John W., McCauley, Patrick G., McNitt, Paul, Mehta, Parul, Moon, Keith W., Mullens, Joe W., Newington, Taksina, Ning, Zemin, Ling Ng, Bee, Novo, Sonia M., O'Neill, Michael J., Osborne, Mark A., Osnowski, Andrew, Ostadan, Omead, Paraschos, Lambros L., Pickering, Lea, Pike, Andrew C., Pike, Alger C., Pinkard, D. Chris, Pliskin, Daniel P., Podhasky, Joe, Quijano, Victor J., Raczy, Come, Rae, Vicki H., Rawlings, Stephen R., Rodriguez, Ana Chiva, Roe, Phyllida M., Rogers, John, Rogert Bacigalupo, Maria C., Romanov, Nikolai, Romieu, Anthony, Roth, Rithy K., Rourke, Natalie J., Ruediger, Silke T., Rusman, Eli, Sanches-Kuiper, Raquel M., Schenker, Martin R., Seoane, Josefina M., Shaw, Richard J., Shiver, Mitch K., Short, Steven W., Sizto, Ning L., Sluis, Johannes P., Smith, Melanie A., Sohna Sohna, Jean Ernest, Spence, Eric J., Stevens, Kim, Sutton, Neil, Szajkowski, Lukasz, Tregidgo, Carolyn L., Turcatti, Gerardo, vandeVondele, Stephanie, Verhovsky, Yuli, Virk, Selene M., Wakelin, Suzanne, Walcott, Gregory C., Wang, Jingwen, Worsley, Graham J., Yan, Juying, Yau, Ling, Zuerlein, Mike, Rogers, Jane, Mullikin, James C., Hurles, Matthew E., McCooke, Nick J., West, John S., Oaks, Frank L., Lundberg, Peter L., Klenerman, David, Durbin, Richard, and Smith, Anthony J.

Published
2008
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14. Crystal structure of staphylococcal enterotoxin B, a superantigen

Author

Swaminathan, S., Furey, William, Pletcher, James, and Sax, Martin

Subjects
Enterotoxins -- Research, Staphylococcus aureus -- Health aspects, Antigens -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The staphylococcal enterotoxin B consists of a three-dimensional structure with main-chain folding of two domains which appears to characterize the morphology of all enterotoxins produced by Staphylococcus aureus. These enterotoxins are both toxins that trigger food poisoning symptoms and superantigens whose main immunological effect is to initiate the release of T cells. Enterotoxin B's binding sites for the T cell receptors and the major histocompatability complex have been identified.

Published
1992

15. The accessible chromatin landscape of the human genome

Author

Vishwanath R. Iyer, Lingyun Song, Michael O. Dorschner, Joshua M. Akey, Andrew B. Stergachis, Kristen Lee, Anthony Shafer, Shinny Vong, Amartya Sanyal, Hongzhu Qu, Audra K. Johnson, Ericka M. Johnson, Kavita Garg, Minerva E. Sanchez, Daniel Bates, Benjamin Vernot, George Stamatoyannopoulos, Tanya Kutyavin, Robert E. Thurman, Patrick A. Navas, Douglas Dunn, Eric Rynes, Bryan R. Lajoie, Matthew T. Maurano, Jeff Vierstra, Molly Weaver, Jason D. Lieb, Sam John, Alexias Safi, Lisa Boatman, Shane Neph, Zhancheng Zhang, Yongqi Yan, Bum Kyu Lee, Dimitra Lotakis, Zhuzhu Zhang, Gregory E. Crawford, Tristan Frum, Abigail K. Ebersol, Richard Sandstrom, Theresa K. Canfield, Eric Haugen, Erika Giste, Job Dekker, Muneesh Tewari, Alex Reynolds, Eric D. Nguyen, Fidencio Neri, Richard Humbert, Peter J. Sabo, Morgan Diegel, John A. Stamatoyannopoulos, Vaughn Roach, Hao Wang, Rajinder Kaul, Terrence S. Furey, Nathan C. Sheffield, R. Scott Hansen, Jeremy M. Simon, Shamil R. Sunyaev, Boris Lenhard, and Darin London

Subjects
Encyclopedias as Topic, Transcription, Genetic, DNA Footprinting, ATAC-seq, Computational biology, Regulatory Sequences, Nucleic Acid, Biology, DNase-Seq, Article, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Mutation Rate, Deoxyribonuclease I, Humans, Promoter Regions, Genetic, Enhancer, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Genome, Human, Molecular Sequence Annotation, Promoter, DNA, Genomics, DNA Methylation, Chromatin, DNA-Binding Proteins, DNA methylation, Human genome, DNase I hypersensitive site, Transcription Initiation Site, 030217 neurology & neurosurgery, Transcription Factors
Abstract

DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation. An extensive map of human DNase I hypersensitive sites, markers of regulatory DNA, in 125 diverse cell and tissue types is described; integration of this information with other ENCODE-generated data sets identifies new relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. This paper describes the first extensive map of human DNaseI hypersensitive sites — markers of regulatory DNA — in 125 diverse cell and tissue types. Integration of this information with other data sets generated by ENCODE (Encyclopedia of DNA Elements) identified new relationships between chromatin accessibility, transcription, DNA methylation and regulatory-factor occupancy patterns. Evolutionary-conservation analysis revealed signatures of recent functional constraint within DNaseI hypersensitive sites.

Published
2012

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

Author

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

Subjects
Expressed Sequence Tags, Genetics, Base Composition, Multidisciplinary, Transcription, Genetic, Euchromatin, Genome, Human, Centromere, Chromosome, DNA, Biology, Exon shuffling, Evolution, Molecular, Molecular evolution, Gene Duplication, Chromosome regions, Animals, Humans, Human genome, RNA, Messenger, Genomic organization
Abstract

An understanding of how centromeric transition regions are organized is a critical aspect of chromosome structure and function; however, the sequence context of these regions has been difficult to resolve on the basis of the draft genome sequence. We present a detailed analysis of the structure and assembly of all human pericentromeric regions (5 megabases). Most chromosome arms (35 out of 43) show a gradient of dwindling transcriptional diversity accompanied by an increasing number of interchromosomal duplications in proximity to the centromere. At least 30% of the centromeric transition region structure originates from euchromatic gene-containing segments of DNA that were duplicatively transposed towards pericentromeric regions at a rate of six-seven events per million years during primate evolution. This process has led to the formation of a minimum of 28 new transcripts by exon exaptation and exon shuffling, many of which are primarily expressed in the testis. The distribution of these duplicated segments is nonrandom among pericentromeric regions, suggesting that some regions have served as preferential acceptors of euchromatic DNA.

Published
2004

17. The DNA sequence of human chromosome 7

Author

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

Subjects
Williams Syndrome, Chromosome 7 (human), Genetics, RNA, Untranslated, Multidisciplinary, Base Sequence, Sequence analysis, Pseudogene, Molecular Sequence Data, Proteins, Sequence Analysis, DNA, Genome project, Biology, Physical Chromosome Mapping, Conserved sequence, Sequence-tagged site, Mice, Sequence logo, Species Specificity, Gene Duplication, Consensus sequence, Animals, Humans, Chromosomes, Human, Pair 7, Pseudogenes
Abstract

Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.

Published
2003

18. A physical map of the human genome

Author

Anuradha Madan, S. Naylor, Kami Dixon, Wonhee Jang, John Douglas Mcpherson, Asao Fujiyama, Simon G. Gregory, Jacquelyn R. Idol, Takashi Sasaki, David Haussler, Hong Seok Park, Jun Kudoh, Ai Shintani, Erica Sodergren, Barbara J. Trask, Norma J. Nowak, Gerald Nyakatura, Gregory D. Schuler, Shinsei Minoshima, Raluca Yonescu, J. Harley Gorrell, Roland Heilig, Vivian G. Cheung, Steve Scherer, Kazunori Shibuya, Hsiu Chuan Chen, Olivia Velasquez, Scot Kennedy, Leroy Hood, Richard Reinhardt, Lucía Ramírez, Richard M. Myers, Atsushi Toyoda, Tetsushi Yada, Nobuyoshi Shimizu, Eric D. Green, Dawn Garcia, Owen T. McCann, Kate Montgomery, Asif T. Chinwalla, Elaine R. Mardis, Peter Seranski, Valerie Maduro, W. James Kent, Cynthia Friedman, Kazutoyo Osoegawa, Carol Scott, Juliane Ramser, Marco A. Marra, Caryn Wagner-McPherson, William B. Barbazuk, Thomas Reid, Mandeep Sekhon, Lee Rowen, Nancy E. Stone, Richard A. Gibbs, Lisa French, Trevor Hawkins, J. de Jong, Jin Shang, Tamara A. Kucaba, Robert H. Waterston, Adam Whittaker, Jeremy Schmutz, Richard K. Wilson, Kristine M. Wylie, Masahira Hattori, Atsushi Shimizu, Ilan R. Kirsch, Jean Weissenbach, Céline Hoff, Julie R. Korenberg, Markus Schilhabel, Sanja Rogic, David R. Bentley, Shuichi Asakawa, Paul E. Tabor, Terrence S. Furey, Kerstin P. Clerc-Blankenburg, Raju Kucherlapati, Joseph J. Catanese, Shizhen Qin, Annemarie Poustka, Suzanne Emerling, Reiner Siebert, Brigitte Schlegelberger, Hans Lehrach, Monica Dors, Thomas Brüls, Hillary Massa, R Evans, Steven J.M. Jones, Gernot Gloeckner, Elbert Branscomb, Andrew Dunham, Jane L. Holden, Xiao Ning Chen, Ashley Miller, Jan Fang Cheng, André Rosenthal, John W. Wallis, Eunice Lee, Gaiping Wen, Sean Humphray, Carol Soderlund, Robert S. Fulton, Yoshiyuki Sakaki, David R. Cox, Norman A. Doggett, Kazuhiko Kawasaki, Anne S. Olsen, Graeme Bethel, and LaDeana W. Hillier

Subjects
Genetics, Cancer genome sequencing, Whole genome sequencing, Chromosomes, Artificial, Bacterial, Multidisciplinary, Contig, Genome, Human, Computational biology, Genome project, Biology, ENCODE, DNA Fingerprinting, Genome, Chimpanzee genome project, Contig Mapping, Gene Duplication, Humans, Cloning, Molecular, In Situ Hybridization, Fluorescence, Repetitive Sequences, Nucleic Acid, Reference genome
Abstract

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

Published
2001

19. Crystal structure of staphylococcal enterotoxin B, a superantigen

Author

S. Swaminathan, J. Pletcher, William Furey, and M. Sax

Subjects
Models, Molecular, Antigens, Bacterial, Staphylococcus aureus, Binding Sites, Multidisciplinary, Protein Conformation, Toxin, Stereochemistry, Antigen presentation, T-cell receptor, Receptors, Antigen, T-Cell, Biological activity, Enterotoxin, Biology, medicine.disease_cause, Protein Structure, Secondary, Enterotoxins, Protein structure, X-Ray Diffraction, medicine, Superantigen, Animals, Binding site
Abstract

The three-dimensional structure of staphylococcal enterotoxin B, which is both a toxin and a super-antigen, has been determined to a resolution of 2.5 A. The unusual main-chain fold containing two domains may represent a general motif adopted by all staphylococcal enterotoxins. The T-cell receptor binding site encompasses a shallow cavity formed by both domains. The MHCII molecule binds to an adjacent site. Another cavity with possible biological activity was also identified.

Published
1992

20. Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Author

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

Subjects
Primates, RNA, Untranslated, Centromere, Molecular Sequence Data, Biology, Euchromatin, Chromosome 16, Chromosome 19, Gene Duplication, Animals, Humans, RNA, Messenger, Conserved Sequence, Genetics, Expressed Sequence Tags, Recombination, Genetic, Base Composition, Multidisciplinary, Polymorphism, Genetic, Base Sequence, Genetic Variation, Proteins, Genomics, Sequence Analysis, DNA, Physical Chromosome Mapping, Chromosome 17 (human), Chromosome 4, Chromosome 3, Chromosomes, Human, Pair 2, CpG Islands, Chromosome 20, Chromosomes, Human, Pair 4, Chromosome 21, Chromosome 22, Pseudogenes
Abstract

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.

Published
2004

21. Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Author

Rui Chen, George M. Weinstock, Cynthia Pfannkoch, Chris P. Ponting, Mark S. Guyer, Manuel L. Gonzalez-Garay, James Taylor, Yixin Chen, Eric D. Green, Simon Cawley, Jo Gullings-Handley, Granger G. Sutton, Jose M. Duarte, Stephen M. J. Searle, Laura Elnitski, Aleksandar Milosavljevic, Alicia Hawes, Stephen C. Mockrin, Oliver Delgado, Shannon Dugan-Rocha, Christine Deramo, Dean Pasko, Marina Alexandersson, Eitan E. Winter, Robert W. Blakesley, Donna Karolchik, Huajun Wang, David Shteynberg, Diane M. Dunn, Carlos López-Otín, Abel Ureta-Vidal, Jia Qian Wu, A. Glodek, Shan Yang, Natasja Wye, Sue Daniels, Keita Geer, Arian F.A. Smit, Jozef Lazar, Pallavi Eswara, Carl Fosler, Douglas Smith, Martin Krzywinski, Uma Mudunuri, George Miner, Herbert Schulz, Angie S. Hinrichs, Manimozhiyan Arumugam, Josep F. Abril, Ursula Vitt, Andrei Volkov, Peter J. Tonellato, Von Bing Yap, Bingshan Li, Jyoti Shetty, Ian Bosdet, Evgeny M. Zdobnov, San Diego Glenn Tesler, Chris Fjell, Yi Zhang, Francis S. Collins, Serafim Batzoglou, Robert Baertsch, Laura Clarke, David Neil Cooper, Carrie Mathewson, Diana L. Kolbe, Kate R. Rosenbloom, Valerie Curwen, Bret A. Payseur, Gerard G. Bouffard, Michael R. Brent, Barbara J. Trask, Scott A. Beatson, Sourav Chatterji, Francisco Camara, Detlev Ganten, Andrew R. Jackson, Claire M. Fraser, Klaus Lindpaintner, Yue Liu, Mark Raymond Adams, Robert A. Holt, Erik Gustafson, Hiram Clawson, Michael L. Metzker, John Douglas Mcpherson, Gregory M. Cooper, Martin S. Taylor, Scott Schwartz, Hui Huang, Darryl Gietzen, Patrick Cahill, Geoffrey Okwuonu, Sandra Hines, J. Craig Venter, Jan Monti, David Steffen, Marco A. Marra, Arnold Kana, Richard D. Emes, Asim Sarosh Siddiqui, Erica Sodergren, Mario Caccamo, Jim Wingrove, Richard R. Copley, Leo Goodstadt, Francesca Chiaromonte, Davinder Virk, Kirt Martin, Colin N. Dewey, Xiang Qin, T. Dan Andrews, K. James Durbin, Michael P. McLeod, Susan Bromberg, Pavel A. Pevzner, Petra Brandt, Austin J. Cooney, Don Jennings, Baoli Zhu, Lynn Doucette-Stamm, Heather Trumbower, Eray Tüzün, Kristian Stevens, Norbert Hubner, Young-Ae Lee, Zhiping Gu, Harold Riethman, Xose S. Puente, Cynthia Sitter, Michael Brudno, Gerald Nyakatura, Oliver Hummel, Caleb Webber, Olivier Couronne, Kim Fechtel, W. J. Kent, Zhengdong D. Zhang, Xing Zhi Song, Matt Weirauch, Ewan Birney, Richard A. Gibbs, William C. Nierman, Anne E. Kwitek, Alexander Poliakov, Mary Barnstead, Jeanette Schmidt, Yanru Ren, Howard J. Jacob, Kateryna D. Makova, Edward M. Rubin, Susan Old, Trixie Nguyen, Arend Sidow, Nicolas Bray, Hong Mei Lee, Lisa M. D'Souza, Heinz Himmelbauer, Cara Woodwark, Peter G. Amanatides, Paul Havlak, Janet M. Young, Eduardo Eyras, Thomas Kreitler, Heming Xing, Sofiya Shatsman, Kushal Chakrabarti, Stephen Rice, Cheryl A. Evans, Kim C. Worley, Peter D. Stenson, Rachel Gill, Pieter J. de Jong, Jacqueline E. Schein, Lior Pachter, Steve Ferriera, Santa Cruz David Haussler, Ross C. Hardison, Holly Baden-Tillson, Margaret Adetobi, Krishna M. Roskin, Guillaume Bourque, Eric A. Stone, Emmanuel Mongin, Michele Clamp, Margaret Morgan, Richard Durbin, Cathy Riemer, Anton Nekrutenko, Mikita Suyama, Soo H. Chin, Kenneth J. Kalafus, Anat Caspi, Donna M. Muzny, Inna Dubchak, Shaying Zhao, Sofyia Abramzon, Michael I. Jensen-Seaman, Steven E. Scherer, Lora Lewis, M. Mar Albà, Terrence S. Furey, Peer Bork, Trevor Woodage, David A. Wheeler, Hans Lehrach, Graham R. Scott, Bin Ma, Paula E. Burch, Robert B. Weiss, Kazutoyo Osoegawa, Evan E. Eichler, Amy Egan, Webb Miller, Cheryl L. Kraft, Steven J.M. Jones, Jeffrey A. Bailey, Roderic Guigó, David Torrents, Heike Zimdahl, Adam Felsenfeld, Jane Peterson, Simon N. Twigger, Claudia Goesele, Keith Weinstock, Minmei Hou, and Zdobnov, Evgeny

Subjects
Male, Models, Molecular, Mammalian Genetics, RNA, Untranslated, Retroelements, Sequence analysis, Gene prediction, Centromere, Genomics, Biology, Regulatory Sequences, Nucleic Acid, Genome, DNA, Mitochondrial, Polymorphism, Single Nucleotide, Rat Genome Database, Evolution, Molecular, Mice, Gene Duplication, Rats, Inbred BN, Animals, Humans, ddc:576.5, Gene, Whole genome sequencing, Genetics, Base Composition, Multidisciplinary, Sequence Analysis, DNA, Telomere, Chromosomes, Mammalian, Introns, Rats, Evolutionary biology, Mutagenesis, DNA Transposable Elements, CpG Islands, RNA Splice Sites
Abstract

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

Published
2003

22. The DNA sequence and biology of human chromosome 19

Author

Mary Bao Tran-Gyamfi, Ivan Ovcharenko, Trevor Hawkins, Maria Gomez, Mirian Denys, Victor V. Solovyev, Terrence S. Furey, Jamie Jett, Jeremy Schmutz, Dea Fotopulos, David Gordon, Tom Slezak, Kevin Wu, Heather Kimball, Pieter J. deJong, Catherine Medina, Vladimer Larionov, Paula McCready, Stephanine Rogers, James Retterer, John C. Detter, Diego Martinez, Richard M. Myers, Paul Predki, Stacey Black, Eva Bajorek, Chenier Caoile, Alex Rodriguez, Isaac Ho, Arthur Kobayashi, Jane Lamerdin, Xinwei She, Yunian Lou, Jane Grimwood, Kristen Kadner, Alex Copeland, Wayne Huang, Sanjay Israni, Carmen Rosa Albacete García, Gary Xie, Doug Smith, Anthony V. Carrano, Matthew Groza, Catherine A. Cleland, Matt Nolan, Paul G. Richardson, Eidelyn Gonzales, Nina Thayer, Anna Ustaszewska, Eileen Dalin, Olivier Couronne, Evan E. Eichler, Tijana Glavina, Astrid Terry, Sun-Hee Leem, Steve Lowry, Anne S. Olsen, Lucía Ramírez, Ming Tsai, Stephanie Malfatti, Hope Tice, Uffe Hellsten, David Goodstein, Martin Pollard, Daniel S. Rokhsar, Nancy Hammon, Angelica Salazar, Jenna Morgan, Yee Man Chan, Michael R. Altherr, Paramvir S. Dehal, Nu Vo, Linda K. Ashworth, Elbert Branscomb, Laurie Gordon, Julio Escobar, Anthony P. Popkie, Dave Flowers, Anca M. Georgescu, Len A. Pennacchio, Sam Pitluck, Sam Rash, Edward M. Rubin, Sean Caenepeel, Glenda Quan, Asaf Salamov, Inna Dubchak, Lisa Stubbs, Andrea Aerts, Mark Dickson, Kathryn Nelson, Mari Christensen, Lauren Haydu, Frederick Lopez, Mark C. Wagner, Jeremy Wheeler, Joan Yang, and Susan Lucas

Subjects
Genetics, Medical, Molecular Sequence Data, Biology, Evolution, Molecular, Chromosome 15, Mice, Chromosome 16, Chromosome 19, Gene Duplication, Animals, Humans, Conserved Sequence, Genetics, Base Composition, Multidisciplinary, Sequence Analysis, DNA, Physical Chromosome Mapping, Chromosome 17 (human), Alternative Splicing, Chromosome 4, Chromosome 3, Genes, Multigene Family, CpG Islands, Chromosome 21, Chromosome 22, Chromosomes, Human, Pair 19, Pseudogenes
Abstract

Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.

Published
2003

23. Initial sequencing and comparative analysis of the mouse genome

Author

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

Subjects
RNA, Untranslated, Proteome, Untranslated/genetics, Genome, Transgenic, Repetitive Sequences, Mice, Models, Neoplasms, Conserved Sequence, ddc:616, Genetics, Mice, Knockout, Base Composition, Multidisciplinary, Sex Chromosomes, Pseudogenes/genetics, Genomics, Multigene Family/genetics, Physical Chromosome Mapping, Neoplasms/genetics, CpG Islands/genetics, Proteome/genetics, Genetic Variation/genetics, Multigene Family, Mice/classification/ genetics, Models, Animal, Conserved Sequence/genetics, Sequence Analysis, Pseudogenes, Human, Genome evolution, Evolution, Sequence analysis, Knockout, Quantitative Trait Loci, Mice, Transgenic, Sex Chromosomes/genetics, Computational biology, Biology, Synteny, Chromosomes, Evolution, Molecular, Nucleic Acid/genetics, Genetic, Species Specificity, Mammalian/ genetics, Animals, Humans, Genes/genetics, Selection, Genetic, Selection, Repetitive Sequences, Nucleic Acid, Comparative genomics, Animal, Genome, Human, Molecular, Genetic Variation, DNA, Sequence Analysis, DNA, Chromosomes, Mammalian, Gene Expression Regulation, Genes, Mutagenesis, RNA, Human genome, CpG Islands, Quantitative Trait Loci/genetics, Reference genome
Abstract

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

Published
2002

24. Correction: Initial sequencing and analysis of the human genome

Author

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

Subjects
Multidisciplinary, Correction, Human genome, Computational biology, Biology
Published
2001

25. Correction: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Author

Lindsay Robertson, Christian von Mering, David Torrents, Paul E. Boardman, Erik Axelsson, Pieter J. deJong, Darren K. Griffin, Ivan Ovcharenko, James K. Bonfield, Tina Graves, Hidetoshi Inoko, Cheryll Tickle, Tracie L. Miner, Kevin J. Beattie, Leo Goodstadt, David W. Burt, John W. Wallis, Richard P. M. A. Crooijmans, Marcia M. Miller, Zissimos Mourelatos, David Speed, Dan Layman, Robert L. Davies, Laura Elnitski, Michael N Romanov, Michael R. Brent, Francesca Chiaromonte, Svitlana Tyekucheva, Jun Wang, Susanne Kerje, Wesley C. Warren, J. J. Emerson, Sergi Castellano, Catrina Fronick, Mary E. Delany, Stuart McLaren, Eduardo Eyras, Kimberly D. Delehaunty, Takashi Shiina, Lucinda Fulton, Michael N. Nhan, Elaine R. Mardis, Mikael Brandström, Patrick Minx, LaDeana W. Hillier, Pavel A. Pevzner, John Douglas Mcpherson, Adam Siepel, David C. King, Lisa Stubbs, Ivica Letunic, Niclas Backström, Hiroshi Arakawa, Maxim Koriabine, Stephen M. J. Searle, Valerie Fillon, Gill Bejerano, Bob Paton, Glenn Tesler, Jessica Severin, Ze Cheng, Leif C. Andersson, Zhirong Bao, David Haussler, Roderic Guigó, Francisco Camara, Sandra W. Clifton, Robert Ivarie, Rick K. Wilson, James C. Kaufman, Mikhail Nefedov, Scott M. Smith, David Shteynberg, Anton Nekrutenko, Mikita Suyama, Jacqueline Smith, Susan Lucas, Arian F.A. Smit, Robert Castelo, Martien A. M. Groenen, Ewan Birney, William Brown, Shiaw-Pyng Yang, Karsten Skjoedt, Lina Jacobbson, Carol Scott, Paul Flicek, Webb Miller, Andrzej M. Kierzek, Yuri Bezzubov, Catherine M. Rondelli, David Morrice, Olivier Pourquié, Stylianos E. Antonarakis, Michael D. R. Croning, Catherine Ucla, Brian J. Raney, Jan Aerts, Jian Wang, Lachlan G. Oddy, Simon J. Hubbard, Peer Bork, Asif T. Chinwalla, Anusha Radakrishnan, Evgeny M. Zdobnov, Artemis G. Hatzigeorgiou, Hans Ellegren, Alain Vignal, Jean-Marie Buerstedde, Matthew T. Webster, Robert S. Harris, Lior Pachter, Henrik Kaessmann, Manyuan Long, Bin Liu, Colin Kremitzki, Pallavi Eswara, Jane Rogers, Evan E. Eichler, Darren Grafham, Jianbin He, D. Waddington, Laurie Gordon, Caleb Webber, W. James Kent, Sam Griffiths-Jones, Gane Ka-Shu Wong, Esther Betrán, Andrew H. Paterson, Sourav Chatterji, Jan J. van der Poel, Nicholas J. Dickens, Terrence S. Furey, Genís Parra, Ian M. Overton, Chris P. Ponting, Randolph B. Caldwell, Sofia Berlin, Isabelle Dupanloup, Rachel A. Harte, Eray Tuzun, Julio S. Masabanda, Matthew D. Francis, Elizabeth J. Huckle, Andy Law, Robert S. Fulton, Kateryna D. Makova, Jan Salomonsen, William E. Nash, Helen G. Tempest, Ross C. Hardison, Sean Humphray, Jerry B. Dodgson, James E. Taylor, Paul F. Cliften, Guillaume Bourque, Monique Rijnkels, Angie S. Hinrichs, Joanne O. Nelson, Josep F. Abril, Colin N. Dewey, Alexandre Reymond, Andrei Kouranov, Craig Pohl, Michael M. Hoffman, Jun Yu, Vincent Magrini, Jacqueline M. Bye, Huanming Yang, Abel Ureta-Vidal, Ruth Taylor, Laura M. Daniels, Shan Yang, Stuart A. Wilson, and Jennifer Randall-Maher

Subjects
Multidisciplinary, biology, Evolutionary biology, biology.animal, Perspective (graphical), Vertebrate, Erratum, Genome, Sequence (medicine)
Published
2005

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

Author

Xinwei She, Horvath, Julie E., Zhaoshi Jiang, Ge Liu, 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
HUMAN genome, GENES, HUMAN gene mapping, GENETICS, DNA, MOLECULAR genetics
Abstract

An understanding of how centromeric transition regions are organized is a critical aspect of chromosome structure and function; however, the sequence context of these regions has been difficult to resolve on the basis of the draft genome sequence. We present a detailed analysis of the structure and assembly of all human pericentromeric regions (5 megabases). Most chromosome arms (35 out of 43) show a gradient of dwindling transcriptional diversity accompanied by an increasing number of interchromosomal duplications in proximity to the centromere. At least 30% of the centromeric transition region structure originates from euchromatic gene-containing segments of DNA that were duplicatively transposed towards pericentromeric regions at a rate of six-seven events per million years during primate evolution. This process has led to the formation of a minimum of 28 new transcripts by exon exaptation and exon shuffling, many of which are primarily expressed in the testis. The distribution of these duplicated segments is nonrandom among pericentromeric regions, suggesting that some regions have served as preferential acceptors of euchromatic DNA. [ABSTRACT FROM AUTHOR]

Published
2004
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27. Integration of cytogenetic landmarks into the draft sequence of the human genome.

Author

Cheung, V.G., Nowak, N., Jang, W., Kirsch, I.R., Zhao, S., Chen, X.-N., Furey, T.S., Kim, U.-J., Kuo, W.-L., Olivier, M., Conroy, J., Kasprzyk, A., Massa, H., Yonescu, R., Sait, S., Thoreen, C., Snijders, A., Lemyre, E., Bailey, J.A., and Bruzel, A.

Subjects
CHROMOSOME abnormalities, MEDICAL genetics, CHROMOSOME banding, FLUORESCENCE in situ hybridization
Abstract

Reports the placement of 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks, which are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization; Structural and functional analyses of the genome which the landmarks provide; Implications for the understanding of the molecular bases of human disease and cancer.

Published
2001

28. Iodine as a boundary lubricant: a contrary view

Author

Michael J. Furey

Subjects
Multidisciplinary, Materials science, chemistry, Inorganic chemistry, Metallurgy, Lubrication, Boundary (topology), chemistry.chemical_element, Iodine, Boundary lubrication, Titanium
Abstract

Roberts and Owens reported1 that charge-transfer complexes of iodine and n-butylbenzene were effective boundary lubricants for titanium sliding on titanium. The discovery is interesting because titanium and its alloys are being used more widely and are difficult to machine and lubricate.

Published
1969

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