Search

Your search keyword '"Tuzun, Eray"' showing total 95 results
Start Over Author "Tuzun, Eray"
95 results on '"Tuzun, Eray"'

1. A Fine-grained Data Set and Analysis of Tangling in Bug Fixing Commits

Author

Herbold, Steffen, Trautsch, Alexander, Ledel, Benjamin, Aghamohammadi, Alireza, Ghaleb, Taher Ahmed, Chahal, Kuljit Kaur, Bossenmaier, Tim, Nagaria, Bhaveet, Makedonski, Philip, Ahmadabadi, Matin Nili, Szabados, Kristof, Spieker, Helge, Madeja, Matej, Hoy, Nathaniel, Lenarduzzi, Valentina, Wang, Shangwen, Rodríguez-Pérez, Gema, Colomo-Palacios, Ricardo, Verdecchia, Roberto, Singh, Paramvir, Qin, Yihao, Chakroborti, Debasish, Davis, Willard, Walunj, Vijay, Wu, Hongjun, Marcilio, Diego, Alam, Omar, Aldaeej, Abdullah, Amit, Idan, Turhan, Burak, Eismann, Simon, Wickert, Anna-Katharina, Malavolta, Ivano, Sulir, Matus, Fard, Fatemeh, Henley, Austin Z., Kourtzanidis, Stratos, Tuzun, Eray, Treude, Christoph, Shamasbi, Simin Maleki, Pashchenko, Ivan, Wyrich, Marvin, Davis, James, Serebrenik, Alexander, Albrecht, Ella, Aktas, Ethem Utku, Strüber, Daniel, and Erbel, Johannes

Subjects
Computer Science - Software Engineering
Abstract

Context: Tangled commits are changes to software that address multiple concerns at once. For researchers interested in bugs, tangled commits mean that they actually study not only bugs, but also other concerns irrelevant for the study of bugs. Objective: We want to improve our understanding of the prevalence of tangling and the types of changes that are tangled within bug fixing commits. Methods: We use a crowd sourcing approach for manual labeling to validate which changes contribute to bug fixes for each line in bug fixing commits. Each line is labeled by four participants. If at least three participants agree on the same label, we have consensus. Results: We estimate that between 17% and 32% of all changes in bug fixing commits modify the source code to fix the underlying problem. However, when we only consider changes to the production code files this ratio increases to 66% to 87%. We find that about 11% of lines are hard to label leading to active disagreements between participants. Due to confirmed tangling and the uncertainty in our data, we estimate that 3% to 47% of data is noisy without manual untangling, depending on the use case. Conclusion: Tangled commits have a high prevalence in bug fixes and can lead to a large amount of noise in the data. Prior research indicates that this noise may alter results. As researchers, we should be skeptics and assume that unvalidated data is likely very noisy, until proven otherwise., Comment: Status: Accepted at Empirical Software Engineering

Published
2020

2. Are Computer Science and Engineering Graduates Ready for the Software Industry? Experiences from an Industrial Student Training Program

Author

Tuzun, Eray, Erdogmus, Hakan, and Ozbilgin, Izzet Gokhan

Subjects
Computer Science - Computers and Society, Computer Science - Software Engineering
Abstract

It has been 50 years since the term software engineering was coined in 1968 at a NATO conference. The field should be relatively mature by now, with most established universities covering core software engineering topics in their Computer Science programs and others offering specialized degrees. However, still many practitioners lament a lack of skills in new software engineering hires. With the growing demand for software engineers from the industry, this apparent gap becomes more and more pronounced. One corporate strategy to address this gap is for the industry to develop supplementary training programs before the hiring process, which could also help them screen viable candidates. In this paper, we report on our experiences and lessons learned in conducting a summer school program aimed at screening new graduates, introducing them to core skills relevant to the organization and the industry, and assessing their attitudes toward mastering those skills before the hiring process begins. Our experience suggests that such initiatives can be mutually beneficial for new hires and companies. We support this insight with pre- and post-training data collected from the participants during the first edition of such a summer school and a follow-up questionnaire conducted after a year with the graduates, 50% of whom was hired by the company shortly after the summer school.

Published
2018

3. A fine-grained data set and analysis of tangling in bug fixing commits

Author

Herbold, Steffen, Trautsch, Alexander, Ledel, Benjamin, Aghamohammadi, Alireza, Ghaleb, Taher A., Chahal, Kuljit Kaur, Bossenmaier, Tim, Nagaria, Bhaveet, Makedonski, Philip, Ahmadabadi, Matin Nili, Szabados, Kristof, Spieker, Helge, Madeja, Matej, Hoy, Nathaniel, Lenarduzzi, Valentina, Wang, Shangwen, Rodríguez-Pérez, Gema, Colomo-Palacios, Ricardo, Verdecchia, Roberto, Singh, Paramvir, Qin, Yihao, Chakroborti, Debasish, Davis, Willard, Walunj, Vijay, Wu, Hongjun, Marcilio, Diego, Alam, Omar, Aldaeej, Abdullah, Amit, Idan, Turhan, Burak, Eismann, Simon, Wickert, Anna-Katharina, Malavolta, Ivano, Sulír, Matúš, Fard, Fatemeh, Henley, Austin Z., Kourtzanidis, Stratos, Tuzun, Eray, Treude, Christoph, Shamasbi, Simin Maleki, Pashchenko, Ivan, Wyrich, Marvin, Davis, James, Serebrenik, Alexander, Albrecht, Ella, Aktas, Ethem Utku, Strüber, Daniel, and Erbel, Johannes

Published
2022
Full Text
View/download PDF

4. Applying Blockchain to Improve the Integrity of the Software Development Process

Author

Yilmaz, Murat, Tasel, Serdar, Tuzun, Eray, Gulec, Ulas, O’Connor, Rory V., Clarke, Paul M., Barbosa, Simone Diniz Junqueira, Editorial Board Member, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Yuan, Junsong, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Walker, Alastair, editor, O'Connor, Rory V., editor, and Messnarz, Richard, editor

Published
2019
Full Text
View/download PDF

5. Adopting Augmented Reality for the Purpose of Software Development Process Training and Improvement: An Exploration

Author

Ohri, İpek, Öge, İrem, Orkun, Bora, Yilmaz, Murat, Tuzun, Eray, Clarke, Paul, O’Connor, Rory V., Barbosa, Simone Diniz Junqueira, Series Editor, Filipe, Joaquim, Series Editor, Kotenko, Igor, Series Editor, Sivalingam, Krishna M., Series Editor, Washio, Takashi, Series Editor, Yuan, Junsong, Series Editor, Zhou, Lizhu, Series Editor, Larrucea, Xabier, editor, Santamaria, Izaskun, editor, O'Connor, Rory V., editor, and Messnarz, Richard, editor

Published
2018
Full Text
View/download PDF

6. Examining Reward Mechanisms for Effective Usage of Application Lifecycle Management Tools

Author

Üsfekes, Çağdaş, Yilmaz, Murat, Tuzun, Eray, Clarke, Paul M., O’Connor, Rory V., Diniz Junqueira Barbosa, Simone, Series editor, Chen, Phoebe, Series editor, Du, Xiaoyong, Series editor, Filipe, Joaquim, Series editor, Kotenko, Igor, Series editor, Liu, Ting, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Stolfa, Jakub, editor, Stolfa, Svatopluk, editor, O'Connor, Rory V., editor, and Messnarz, Richard, editor

Published
2017
Full Text
View/download PDF

7. Characterizing duplicate bugs: Perceptions of practitioners and an empirical analysis.

Author

Kucuk, Berfin, Hanhan, Idil, and Tuzun, Eray

Subjects
COMPUTER software industry, COMPUTER software development, INDUSTRIAL surveys, MAINTENANCE costs
Abstract

Bug handling is an essential part of the software development process. Ideally, in a bug‐tracking system, bugs are reported, fixed, verified, and closed. In some cases, bugs have to be reopened mostly due to an incorrect fix. However, instead of reopening the existing bug report, users may submit a new report for a previously reported bug, which results in duplicate bug reports. Users might report duplicate bugs if they miss the previous bug report or if the previous bug is unresolved (i.e., in progress) and therefore cannot be reopened. These duplicate bug reports may cost extra maintenance efforts in triaging and bug fixing. There have been several studies on characterizing reopened bugs and duplicate bug reports; however, to the best of our knowledge, there has been no prior work on understanding the dynamics of their interaction, which is missed reopen bugs. Our study is based on analyzing the difference between duplicate and nonduplicate bugs and further categorizing the duplicate bugs. In this regard, we categorize duplicate bugs according to the original bug's resolution status at the duplicate's creation time as Master‐Unresolved bugs and Master‐Resolved (Missed Reopen) bugs to distinguish their properties. We compare these two types of bugs in terms of their relationship to their master bug, bug surface time, bug fix time, bug's severity, and the number of users involved. We perform case studies using the Eclipse and Mozilla projects' bug repositories that include more than 165,500 and 394,000 bug reports, respectively. Additionally, we investigate the perceived importance, impact, and causes of duplicate bugs, as well as the difference between nonduplicate and duplicate bugs and its categories for practitioners in the software industry by conducting a survey. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

10. Editorial : Best papers of the 14th International Conference on Software and System Processes (ICSSP 2020) and 15th International Conference on Global Software Engineering (ICGSE 2020)

Author

Steinmacher, Igor, Clarke, Paul, Tuzun, Eray, Britto, Ricardo, Steinmacher, Igor, Clarke, Paul, Tuzun, Eray, and Britto, Ricardo

Abstract

Today's software industry is global, virtual, and depending more than ever on strong and reliable processes. Stakeholders and infrastructure are distributed across the globe, posing challenges that go beyond those with co-located teams and servers. Software Engineering continues to be a complex undertaking, with projects challenged to meet expectations, especially regarding costs. We know that Software Engineering is an ever-changing discipline, with the result that firms and their employees must regularly embrace new methods, tools, technologies, and processes. In 2020, the International Conference on Global Software Engineering (ICGSE) and the International Conference on Systems and Software Processes (ICSSP) joined forces aiming to create a holistic understanding of the software landscape both from the perspective of human and infrastructure distribution and also the processes to support software development. Unfortunately, these challenges have become even more personal to many more in 2020 due to the disruption introduced by the COVID-19 pandemic, which forced both conferences to be held virtually. As an outcome of the joint event, we selected a set of the best papers from the two conferences, which were invited to submit extended versions to this Special Issue in the Journal of Software: Maintenance and Evolution. Dedicated committees were established to identify the best papers. Eight papers were invited and ultimately, seven of these invited papers have made it into this Special Issue. © 2023 John Wiley & Sons, Ltd.

Published
2023
Full Text
View/download PDF

11. Editorial : Machine learning, software process, and global software engineering

Author

Steinmacher, Igor, Clarke, Paul, Tuzun, Eray, Britto, Ricardo, Steinmacher, Igor, Clarke, Paul, Tuzun, Eray, and Britto, Ricardo

Abstract

On June 26–28, 2020, the International Conference on Software and Systems Processes (ICSSP 2020) and the International Conference on Global Software Engineering (ICGSE 2020) were held in virtual settings during the first year of the COVID pandemic. Several submissions to the joint event have been selected for inclusion in this special issue, focusing on impactful and timely contributions to machine learning (ML). At present, many in our field are enthusiastic about the potential of ML, yet some risks should not be casually overlooked or summarily dismissed. Each ML implementation is subtly different from any other implementation, and the risk profile varies greatly based on the approach adopted and the implementation context. The ICSSP/ICGSE 2020 Program Committees have encouraged submissions that explore the risks and benefits associated with ML so that the important discussion regarding ML efficacy and advocacy can be further elaborated. Four contributions have been included in this special issue. © 2023 John Wiley & Sons, Ltd.

Published
2023
Full Text
View/download PDF

13. What Makes Agile Software Development Agile?

Author

Kuhrmann, Marco, primary, Tell, Paolo, additional, Hebig, Regina, additional, Klunder, Jil, additional, Munch, Jurgen, additional, Linssen, Oliver, additional, Pfahl, Dietmar, additional, Felderer, Michael, additional, Prause, Christian R., additional, MacDonell, Stephen G., additional, Nakatumba-Nabende, Joyce, additional, Raffo, David, additional, Beecham, Sarah, additional, Tuzun, Eray, additional, Lopez, Gustavo, additional, Paez, Nicolas, additional, Fontdevila, Diego, additional, Licorish, Sherlock A., additional, Kupper, Steffen, additional, Ruhe, Gunther, additional, Knauss, Eric, additional, Ozcan-Top, Ozden, additional, Clarke, Paul, additional, McCaffery, Fergal, additional, Genero, Marcela, additional, Vizcaino, Aurora, additional, Piattini, Mario, additional, Kalinowski, Marcos, additional, Conte, Tayana, additional, Prikladnicki, Rafael, additional, Krusche, Stephan, additional, Coskuncay, Ahmet, additional, Scott, Ezequiel, additional, Calefato, Fabio, additional, Pimonova, Svetlana, additional, Pfeiffer, Rolf-Helge, additional, Schultz, Ulrik Pagh, additional, Heldal, Rogardt, additional, Fazal-Baqaie, Masud, additional, Anslow, Craig, additional, Nayebi, Maleknaz, additional, Schneider, Kurt, additional, Sauer, Stefan, additional, Winkler, Dietmar, additional, Biffl, Stefan, additional, Bastarrica, Maria Cecilia, additional, and Richardson, Ita, additional

Published
2022
Full Text
View/download PDF

14. Bus Factor in Practice

Author

Jabrayilzade, Elgun, primary, Evtikhiev, Mikhail, additional, Tuzun, Eray, additional, and Kovalenko, Vladimir, additional

Published
2022
Full Text
View/download PDF

16. Ground-Truth Deficiencies in Software Engineering : When Codifying the Past Can Be Counterproductive

Author

Tuzun, Eray, Erdogmus, Hakan, Baldassarre, Maria Teresa, Felderer, Michael, Feldt, Robert, Turhan, Burak, Tuzun, Eray, Erdogmus, Hakan, Baldassarre, Maria Teresa, Felderer, Michael, Feldt, Robert, and Turhan, Burak

Abstract

In software engineering, the objective function of human decision makers might be influenced by many factors. Relying on historical data as the ground truth may give rise to systems that automate software engineering decisions by mimicking past suboptimal behavior. We describe the problem and offer some strategies. ©IEEE.

Published
2022
Full Text
View/download PDF

22. Closing the Gap Between Software Engineering Education and Industrial Needs

Author

Garousi, Vahid, Giray, Görkem, Tuzun, Eray, Catal, Cagatay, Felderer, Michael, Garousi, Vahid, Giray, Görkem, Tuzun, Eray, Catal, Cagatay, and Felderer, Michael

Abstract

According to different reports, many recent software engineering graduates often face difficulties when beginning their professional careers, due to misalignment of the skills learnt in their university education with what is needed in industry. To address that need, many studies have been conducted to align software engineering education with industry needs. To synthesize that body of knowledge, we present in this paper a systematic literature review (SLR) which summarizes the findings of 33 studies in this area. By doing a meta-analysis of all those studies and using data from 12 countries and over 4,000 data points, this study will enable educators and hiring managers to adapt their education / hiring efforts to best prepare the software engineering workforce. IEEE, open access

Published
2020
Full Text
View/download PDF

26. Shotgun sequence assembly and recent segmental duplications within the human genome

Author

She, Xinwei, Jiang, Zhaoshi, Clark, Royden A., Liu, Ge, Cheng, Ze, Tuzun, Eray, Church, Deanna M., Sutton, Granger, Halpern, Aaron L., and Eichler, Evan E.

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

Author(s): Xinwei She [1]; Zhaoshi Jiang [1]; Royden A. Clark [2]; Ge Liu [2]; Ze Cheng [1]; Eray Tuzun [1]; Deanna M. Church [3]; Granger Sutton [4]; Aaron L. Halpern [...]

Published
2004
Full Text
View/download PDF

30. A genome-wide survey of structural variation between human and chimpanzee

Author

Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., Rocchi, Mariano, and Eichler, Evan E.

Subjects
Nucleotide sequence -- Research, Chimpanzees -- Genetic aspects, Genetic research, Health
Abstract

An analysis is performed in which a library of chimpanzee fosmid end sequences is used to compare the genome of a single chimpanzee individual against the human reference sequence. A resource for interrogating functional differences between humans and chimpanzees is provided.

Published
2005

33. Catching up with Method and Process Practice: An Industry-Informed Baseline for Researchers

Author

Klunder, Jil, primary, Hebig, Regina, additional, Tell, Paolo, additional, Kuhrmann, Marco, additional, Nakatumba-Nabende, Joyce, additional, Heldal, Rogardt, additional, Krusche, Stephan, additional, Fazal-Baqaie, Masud, additional, Felderer, Michael, additional, Genero Bocco, Marcela Fabiana, additional, Kupper, Steffen, additional, Licorish, Sherlock A., additional, Lopez, Gustavo, additional, McCaffery, Fergal, additional, Ozcan Top, Ozden, additional, Prause, Christian R., additional, Prikladnicki, Rafael, additional, Tuzun, Eray, additional, Pfahl, Dietmar, additional, Schneider, Kurt, additional, and MacDonell, Stephen G., additional

Published
2019
Full Text
View/download PDF

35. Trade Secrets: A Moyers Report

Author

Tuzun, Eray, Bailey, Jeffrey A., and Eicher, Evan E.

Subjects
Mice as laboratory animals -- Genetic aspects, Mice as laboratory animals -- Analysis, Nucleotide sequence -- Analysis, Genetic research, Health
Abstract

Genome-wide analysis of the segmental duplication content of the rat is given. The results reveal that overall fraction of duplicated sequence within the rat assembly is greater than that of the mouse but significantly less than that of human.

Published
2004

36. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome

Author

Liu, Ge, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, Tuzun, Eray, Green, Eric D., and Eichler, Evan E.

Subjects
Genomes -- Research, Genomes -- Comparative analysis, Genetic research -- Analysis, Primates -- Genetic aspects, Nucleotides -- Genetic aspects, Health
Abstract

Research has been conducted on genomic sequence from primate species. The authors have compared these sequences to those of human genome, and the results demonstrate that the nonhuman genomic sequencies diverge from human at three different time points.

Published
2003

37. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Author

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

Subjects
RNA, Untranslated, olfactory receptor, [SDV]Life Sciences [q-bio], mouse genome, QH75, Genome, 0302 clinical medicine, Gene Duplication, Coding region, ddc:576.5, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Short Interspersed Nucleotide Elements, Genetics, 0303 health sciences, Multidisciplinary, CHICKENS, recent segmental duplications, Untranslated, GENOME SEQUENCE, International Chicken Genome Sequencing Consortium, Genomics, Physical Chromosome Mapping, major histocompatibility complex, mammalian evolution, [SDV] Life Sciences [q-bio], Multigene Family, Vertebrates, SEQUENCE DU GENOME, Sequence Analysis, Pseudogenes, Biotechnology, brown-norway rat, animal structures, Evolution, General Science & Technology, Sequence analysis, Biology, Animal Breeding and Genomics, Synteny, Evolution, Molecular, Avian Proteins, 03 medical and health sciences, non-ltr retrotransposons, Animals, Humans, alcohol-dehydrogenase, Fokkerij en Genomica, SF, QP506, Gene, QH426, 030304 developmental biology, Whole genome sequencing, QL, phylogenetic analysis, QH, Human Genome, Molecular, Sequence Analysis, DNA, DNA, tissue-specific genes, EVOLUTION, Retroviridae, Long Interspersed Nucleotide Elements, Genes, Mutagenesis, Evolutionary biology, DNA Transposable Elements, Microchromosome, WIAS, RNA, Chickens, 030217 neurology & neurosurgery
Abstract

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Published
2004

38. Initial sequence of the chimpanzee genome and comparison with the human genome

Author

Mikkelsen, Tarjei, Hillier, LaDeana, Eichler, Evan, Zody, Michael, Jaffe, David, Yang, Shiaw-Pyng, Enard, Wolfgang, Hellmann, Ines, Lindblad-Toh, Kerstin, Altheide, Tasha, Archidiacono, Nicoletta, Bork, Peer, Butler, Jonathan, Chang, Jean, Cheng, Ze, Chinwalla, Asif, de Jong, Pieter, Delehaunty, Kimberley, Fronick, Catrina, Fulton, Lucinda, Gilad, Yoav, Glusman, Gustavo, Gnerre, Sante, Graves, Tina, Hayakawa, Toshiyuki, Hayden, Karen, Huang, Xiaoqiu, Ji, Hongkai, Kent, W., King, Mary-Claire, Kulbokas, Edward, Lee, Ming, Liu, Ge, Lopez-Otin, Carlos, Makova, Kateryna, Man, Orna, Mardis, Elaine, Mauceli, Evan, Miner, Tracie, Nash, illiam, Nelson, Joanne, Pääbo, Svante, Patterson, Nick, Pohl, Craig, Pollard, Katherine, Prüfer, Kay, Puente, Xose, Reich, David, Rocchi, Mariano, Rosenbloom, Kate, Ruvolo, Maryellen, Richter, Daniel, Schaffner, Stephen, Smit, Arian, Smith, Scott, Suyama, Mikita, Taylor, James, Torrents, David, Tuzun, Eray, Varki, Ajit, Velasco, Gloria, Ventura, Mario, Wallis, John, Wendl, Michael, Wilson, Richard, Lander, Eric, Waterston, Robert, Mikkelsen, Tarjei, Hillier, LaDeana, Eichler, Evan, Zody, Michael, Jaffe, David, Yang, Shiaw-Pyng, Enard, Wolfgang, Hellmann, Ines, Lindblad-Toh, Kerstin, Altheide, Tasha, Archidiacono, Nicoletta, Bork, Peer, Butler, Jonathan, Chang, Jean, Cheng, Ze, Chinwalla, Asif, de Jong, Pieter, Delehaunty, Kimberley, Fronick, Catrina, Fulton, Lucinda, Gilad, Yoav, Glusman, Gustavo, Gnerre, Sante, Graves, Tina, Hayakawa, Toshiyuki, Hayden, Karen, Huang, Xiaoqiu, Ji, Hongkai, Kent, W., King, Mary-Claire, Kulbokas, Edward, Lee, Ming, Liu, Ge, Lopez-Otin, Carlos, Makova, Kateryna, Man, Orna, Mardis, Elaine, Mauceli, Evan, Miner, Tracie, Nash, illiam, Nelson, Joanne, Pääbo, Svante, Patterson, Nick, Pohl, Craig, Pollard, Katherine, Prüfer, Kay, Puente, Xose, Reich, David, Rocchi, Mariano, Rosenbloom, Kate, Ruvolo, Maryellen, Richter, Daniel, Schaffner, Stephen, Smit, Arian, Smith, Scott, Suyama, Mikita, Taylor, James, Torrents, David, Tuzun, Eray, Varki, Ajit, Velasco, Gloria, Ventura, Mario, Wallis, John, Wendl, Michael, Wilson, Richard, Lander, Eric, and Waterston, Robert

Abstract

Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.

Published
2005
Full Text
View/download PDF

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

Author

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

Abstract

International Chicken Genome Sequencing Consortium. The Original Article was published on 09 December 2004. Nature432, 695–716 (2004). In Table 5 of this Article, the last four values listed in the ‘Copy number’ column were incorrect. These should be: LTR elements, 30,000; DNA transposons, 20,000; simple repeats, 140,000; and satellites, 4,000. These errors do not affect any of the conclusions in our paper. Additional information. The online version of the original article can be found at 10.1038/nature03154

Published
2005

42. Closing gaps in the human genome with fosmid resources generated from multiple individuals

Author

Bovee, Donald, primary, Zhou, Yang, additional, Haugen, Eric, additional, Wu, Zaining, additional, Hayden, Hillary S, additional, Gillett, Will, additional, Tuzun, Eray, additional, Cooper, Gregory M, additional, Sampas, Nick, additional, Phelps, Karen, additional, Levy, Ruth, additional, Morrison, V Anne, additional, Sprague, James, additional, Jewett, Donald, additional, Buckley, Danielle, additional, Subramaniam, Sandhya, additional, Chang, Jean, additional, Smith, Douglas R, additional, Olson, Maynard V, additional, Eichler, Evan E, additional, and Kaul, Rajinder, additional

Published
2007
Full Text
View/download PDF

44. Molecular refinement of gibbon genome rearrangements

Author

Roberto, Roberta, primary, Capozzi, Oronzo, additional, Wilson, Richard K., additional, Mardis, Elaine R., additional, Lomiento, Mariana, additional, Tuzun, Eray, additional, Cheng, Ze, additional, Mootnick, Alan R., additional, Archidiacono, Nicoletta, additional, Rocchi, Mariano, additional, and Eichler, Evan E., additional

Published
2006
Full Text
View/download PDF

45. Fine-scale structural variation of the human genome

Author

Tuzun, Eray, primary, Sharp, Andrew J, additional, Bailey, Jeffrey A, additional, Kaul, Rajinder, additional, Morrison, V Anne, additional, Pertz, Lisa M, additional, Haugen, Eric, additional, Hayden, Hillary, additional, Albertson, Donna, additional, Pinkel, Daniel, additional, Olson, Maynard V, additional, and Eichler, Evan E, additional

Published
2005
Full Text
View/download PDF

47. Closing gaps in the human genome with fosmid resources generated from multiple individuals.

Author

Bovee, Donald, Yang Zhou, Haugen, Eric, Wu, Zaining, Hayden, Hillary S., Gillett, Will, Tuzun, Eray, Cooper, Gregory M., Sampas, Nick, Phelps, Karen, Levy, Ruth, Morrison, V. Anne, Sprague, James, Jewett, Donald, Buckley, Danielle, Subramaniam, Sandhya, Chang, Jean, Smith, Douglas R., Olson, Maynard V., and Eichler, Evan E.

Subjects
HUMAN genome, CHROMOSOMES, GENOMES, HUMAN gene mapping, GENETICS
Abstract

The human genome sequence has been finished to very high standards; however, more than 340 gaps remained when the finished genome was published by the International Human Genome Sequencing Consortium in 2004. Using fosmid resources generated from multiple individuals, we targeted gaps in the euchromatic part of the human genome. Here we report 2,488,842 bp of previously unknown euchromatic sequence, 363,114 bp of which close 26 of 250 euchromatic gaps, or 10%, including two remaining euchromatic gaps on chromosome 19. Eight (30.7%) of the closed gaps were found to be polymorphic. These sequences allow complete annotation of several human genes as well as the assignment of mRNAs. The gap sequences are 2.3-fold enriched in segmentally duplicated sequences compared to the whole genome. Our analysis confirms that not all gaps within 'finished' genomes are recalcitrant to subcloning and suggests that the paired-end-sequenced fosmid libraries could prove to be a rich resource for completion of the human euchromatic genome. [ABSTRACT FROM AUTHOR]

Published
2008
Full Text
View/download PDF

48. Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome.

Author

Ge Liu, Shaying Zhao, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, Tuzun, Eray, Green, Eric D., and Eichler, Evan E.

Subjects
*NUCLEOTIDES, *GENOMICS, *LEMUR (Genus), *BABOONS
Abstract

Analyzes the single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to human. Use of human genomic reference and optimal global alignments; Measurement of the single-nucleotide substitution rates; Variation in the rates of retrotransposition.

Published
2003
Full Text
View/download PDF

49. Molecular refinement of gibbon genome rearrangements.

Author

Roberto, Roberta, Capozzi, Oronzo, Wilson, Richard K., Mardis, Elaine R., Lomiento, Mariana, Tuzun, Eray, Ze Cheng, Mootnick, Alan R., Archidiacono, Nicoletta, Rocchi, Mariano, and Eichler, Evan E.

Subjects
*GIBBONS, *KARYOTYPES, *BIOINFORMATICS, *CYTOGENETICS, *HUMAN genome, *GENOMICS, *NUCLEOTIDE sequence
Abstract

The gibbon karyotype is known to be extensively rearranged when compared to the human and to the ancestral primate karyotype. By combining a bioinformatics (paired-end sequence analysis) approach and a molecular cytogenetics approach, we have refined the synteny block arrangement of the white-cheeked gibbon (Nomascus leucogenys, NLE) with respect to the human genome. We provide the first detailed clone framework map of the gibbon genome and refine the location of 86 evolutionary breakpoints to <1 Mb resolution. An additional 12 breakpoints, mapping primarily to centromeric and telomeric regions, were mapped to ∼5 Mb resolution. Our combined FISH and BES analysis indicates that we have effectively subcloned 49 of these breakpoints within NLE gibbon BAC clones, mapped to a median resolution of 79.7 kb. Interestingly, many of the intervals associated with translocations were gene-rich, including some genes associated with normal skeletal development. Comparisons of NLE breakpoints with those of other gibbon species reveal variability in the position, suggesting that chromosomal rearrangement has been a longstanding property of this particular ape lineage. Our data emphasize the synergistic effect of combining computational genomics and cytogenetics and provide a framework for ultimate sequence and assembly of the gibbon genome. [ABSTRACT FROM AUTHOR]

Published
2007
Full Text
View/download PDF

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

Author

Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, and Collins F

Subjects
Animals, Base Composition, Centromere genetics, Chromosomes, Mammalian genetics, CpG Islands genetics, DNA Transposable Elements genetics, DNA, Mitochondrial genetics, Gene Duplication, Humans, Introns genetics, Male, Mice, Models, Molecular, Mutagenesis, Polymorphism, Single Nucleotide genetics, RNA Splice Sites genetics, RNA, Untranslated genetics, Rats, Regulatory Sequences, Nucleic Acid genetics, Retroelements genetics, Sequence Analysis, DNA, Telomere genetics, Evolution, Molecular, Genome, Genomics, Rats, Inbred BN genetics
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
2004
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results