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28 results on '"John Stalker"'

1. On almost Ehlers–Geren–Sachs theorems

Author

Ho Lee, Ernesto Nungesser, and John Stalker

Subjects
High Energy Physics - Theory, General Relativity and Quantum Cosmology, High Energy Physics - Theory (hep-th), Physics and Astronomy (miscellaneous), FOS: Physical sciences, General Relativity and Quantum Cosmology (gr-qc), Mathematical Physics (math-ph), Mathematical Physics
Abstract

We show assuming small data that massless solutions to the reflection symmetric Einstein-Vlasov system with Bianchi VII$_0$ symmetry which are not locally rotational symmetric, can be arbitrarily close to and will remain close to isotropy as regards {to} the shear. However in general the shear will not tend to zero and the Hubble normalised Weyl curvature will blow up. This generalises the work \cite{NHW,WHU}, which considered a non-tilted radiation fluid to the massless Vlasov case. This represents another example of the fact that almost Ehlers-Geren-Sachs theorems do not hold in general and that collisionless matter behaves differently than a perfect fluid., 26 pages, 1 figure; matches accepted version in CQG; presentation improved, minor typos corrected

Published
2022
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2. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Author

Frances Letendre, Vasilia Magnisalis, Helen Vassiliev, Rebecca Reyes, Maura Costello, St Christophe Acer, Pen MacDonald, Geneva Young, Katherine Thompson, Iain MacCallum, Tarjei S. Mikkelsen, Andy Vo, Eva Markiewicz, Yeshi Lokyitsang, Sharon Stavropoulos, Rachel Mittelman, Xiaohui Xie, Diallo Ferguson, James Cuff, Terence P. Speed, Catherine Stone, Tanya Mihova, Janine E. Deakin, Aaron M. Berlin, David A. Ray, David D. Pollock, Ben Kanga, Kunsang Gyaltsen, Scott Anderson, Gary Gearin, Nabil Hafez, Lisa Chuda, Marco A. Marra, David B. Jaffe, Leonid Boguslavskiy, Asha Kamat, Jonathan Butler, Alicia Franke, Lynne Aftuck, Sheridon Channer, Rosie Levine, Kerstin Lindblad-Toh, Birhane Hagos, Imane Bourzgui, Monika D. Huard, Tamrat Negash, Jamal Abdulkadir, Tsering Wangchuk, Georgius De Haan, Sheila Fisher, Justin Abreu, Abderrahim Farina, Kebede Maru, M. Erii Husby, Peter Kisner, Kunsang Dorjee, Jacob L. Glass, Tashi Lokyitsang, Nyima Norbu, Jennifer Baldwin, Christina R. Gearin, Otero L. Oyono, Atanas Mihalev, Yama Thoulutsang, Katie D'Aco, Choe Norbu, Christopher Strader, Edda Koina, Allen Alexander, Barry O'Neill, William Brockman, Wanjun Gu, Richard Elong, Keenan Ross, Shailendra Yadav, Alan Dupes, Seva Kashin, James Meldrim, Dmitry Khazanovich, Passang Dorje, Adal Abebe, April Cook, Matthew Breen, Randy L. Jirtle, Shangtao Liu, Jean L. Chang, Patrick Cahill, Claire M. Wade, Chee Whye Chin, Dennis C. Friedrich, Tina Goode, Cecil Rise, Robert D. Nicholls, Peter Rogov, Adam Brown, Oana Mihai, Sujaa Raghuraman, Adam Wilson, Marcia Lara, Chelsea D. Foley, Susan Faro, Sampath Settipalli, Thu Nguyen, Matthew Wakefield, Xiaohong Liu, Anna Montmayeur, Jerzy Jurka, Ngawang Sherpa, Riza M. Daza, Evan Mauceli, Senait Tesfaye, Sharleen Grewal, Susan McDonough, Leo Goodstadt, Manuel Garber, John M. Greally, Valentine Mlenga, Manfred Grabherr, Charles Matthews, Andrew Zimmer, Teena Mehta, Harindra Arachi, Mark A. Batzer, Rakela Lubonja, Margaret Priest, Diana Shih, Joseph Graham, Panayiotis V. Benos, Lance S. Davidow, Alex Lipovsky, Stephen M. J. Searle, Andreas Heger, Timothy A. Hore, Patrick Cooke, Leonidas Mulrain, Tsering Wangdi, Jennifer A. Marshall Graves, Sante Gnerre, Michelle L. Baker, Jacqueline E. Schein, Michael Weiand, Jessica Spaulding, Charlotte Henson, Jane Wilkinson, Terry Shea, Shannon E. Duke, William McCusker, Kerri Topham, Jerome Naylor, Lu Shi, Fritz Pierre, Claude Bonnet, Shaun Mahony, Michele Clamp, Katherine Belov, John L. VandeBerg, Nicole Stange-Thomann, Annie Lui, Radhika Das, Pema Phunkhang, Andrew J. Gentles, Elizabeth P. Ryan, Erica Anderson, Jill Falk, Bronwen Aken, Robert Nicol, Ted Sharpe, Sahal Osman, Missole Doricent, Michael Kleber, Jeannie T. Lee, Paul D. Waters, Melissa Fazzari, Jinlei Liu, Loryn Gadbois, Lisa Zembek, Daniel Bessette, Pasang Bachantsang, Adam Navidi, Caleb Webber, Tashi Bayul, Brikti Abera, Mayumi Oda, Gavin A. Huttley, Jennifer L. Hall, Chris P. Ponting, Michael Kamal, Kimberly Dooley, Mieke Citroen, Tsamla Tsamla, Ira Topping, Eric S. Lander, Edward Grandbois, Christopher Patti, Louis Meneus, Tracey Honan, Zuly E. Parra, Nga Nguyen, Todd Sparrow, Dawa Thoulutsang, Leanne Hughes, Yama Cheshatsang, Qing Yu, Niall J. Lennon, Nathaniel Novod, Christina Demaso, Anthony T. Papenfuss, Paul B. Samollow, Toby Bloom, Andrew Hollinger, Boris Boukhgalter, Talene Thomson, Zac Zwirko, Georgia Giannoukos, Michael C. Zody, Danni Zhong, Jason Blye, Stuart DeGray, Marc Azer, Robert D. Miller, Amr Abdouelleil, Brian Hurhula, Filip Rege, John Stalker, Andrew Barry, Pablo Alvarez, Norbu Dhargay, Krista Lance, Chris T. Amemiya, Jerilyn A. Walker, Jennifer R. Weidman, Peter An, Erin E. Dooley, William Lee, and Alville Collymore

Subjects
Genetics, Base Composition, Genome evolution, Genome, Multidisciplinary, Genomics, Opossums, Biology, biology.organism_classification, Polymorphism, Single Nucleotide, Synteny, Monodelphis domestica, Evolution, Molecular, X Chromosome Inactivation, Opossum, Molecular evolution, Protein Biosynthesis, DNA Transposable Elements, Animals, Humans, Gene family, Gene conversion, Conserved Sequence
Abstract

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

Published
2007
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3. Strichartz estimates for the wave and Schroedinger equations with potentials of critical decay

Author

A. Shadi Tahvildar-Zadeh, Nicolas Burq, John Stalker, and Fabrice Planchon

Subjects
Elliptic operator, symbols.namesake, Partial differential equation, General Mathematics, symbols, Strichartz estimate, Wave equation, Schrödinger's cat, Mathematical physics, Schrödinger equation, Mathematics, Resolvent
Abstract

We prove weighted L 2 estimates for the solutions of linear Schrodinger and wave equation with potentials that decay like |x| -2 for large x, by deducing them from estimates on the resolvent of the associated elliptic operator. We then deduce Strichartz estimates for these equations.

Published
2004
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4. Dispersive estimate for the wave equation with the inverse-square potential

Author

Fabrice Planchon, A. Shadi Tahvildar-Zadeh, and John Stalker

Subjects
Laplace's equation, Partial differential equation, Helmholtz equation, Eikonal equation, Applied Mathematics, Wave packet, Mathematical analysis, Mathematics::Analysis of PDEs, Wave equation, Schrödinger equation, Dispersive partial differential equation, symbols.namesake, symbols, Discrete Mathematics and Combinatorics, Analysis, Mathematics
Abstract

We prove that spherically symmetric solutions of the Cauchy problem for the linear wave equation with the inverse-square potential satisfy a modified dispersive inequality that bounds the $L^\infty$ norm of the solution in terms of certain Besov norms of the data, with a factor that decays in $t$ for positive potentials. When the potential is negative we show that the decay is split between $t$ and $r$, and the estimate blows up at $r=0$. We also provide a counterexample showing that the use of Besov norms in dispersive inequalities for the wave equation are in general unavoidable.

Published
2003
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5. $L^p$ Estimates for the wave equation with the inverse-square potential

Author

A. Shadi Tahvildar-Zadeh, John Stalker, and Fabrice Planchon

Subjects
Laplace's equation, Electromagnetic wave equation, Partial differential equation, Helmholtz equation, Eikonal equation, Applied Mathematics, Wave packet, Mathematical analysis, Mathematics::Analysis of PDEs, Wave equation, Discrete Mathematics and Combinatorics, Acoustic wave equation, Analysis, Mathematics
Abstract

We prove that Strichartz-type $L^p$ estimates hold for solutions of the linear wave equation with the inverse square potential, under the additional assumption that the Cauchy data are spherically symmetric. The estimates are then applied to prove global well-posedness in the critical norm for a nonlinear wave equation.

Published
2002
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6. On Hubbell's rectangular source integral

Author

John Stalker

Subjects
Physics, Radiation, Series expansion, Mathematical physics
Abstract

The integral H(a,b)= ∫ 0 b ∫ 0 a d x d y/(1+x 2 +y 2 ) arises naturally in the study of radiation from a rectangular source and has been studied by many authors. This paper introduces a new series expansion which is rapidly convergent for large a and b.

Published
2001
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7. An Essentially Singular Classical Limit

Author

John Stalker

Subjects
Essential singularity, Mathematics(all), General Mathematics, Mathematical analysis, Particle in a box, Simple variant, Classical limit, Mathematics, Mathematical physics
Abstract

A simple variant of the problem of a particle in a box is shown to have an essential singularity in the classical limith→0.

Published
1999
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8. A Convergence Speeding Algorithm with Applications to Numerical Integration

Author

John Stalker

Subjects
symbols.namesake, Convergence acceleration, Riemann sum, Applied Mathematics, Convergence (routing), symbols, Asymptotic expansion, Algorithm, Time complexity, Mathematics, Numerical integration, Interpolation
Abstract

A new algorithm is presented for accelerating the convergence of sequences possessing an asymptotic expansion. This method is compared to methods already shown. Explicit error estimates are given and the algorithm is shown to be nearly optimal. The algorithm is applied to the problem of numerical integration, and is shown to give good results for real analytic integrands.

Published
1999
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9. A lower bound for the amplitude of traveling waves of suspension bridges

Author

John Stalker and Paschalis Karageorgis

Subjects
Mathematics::Dynamical Systems, Applied Mathematics, Mathematical analysis, Zero (complex analysis), Upper and lower bounds, Amplitude, Mathematics - Analysis of PDEs, FOS: Mathematics, Traveling wave, Homoclinic orbit, Suspension (vehicle), Analysis, Analysis of PDEs (math.AP), Mathematics
Abstract

We obtain a lower bound for the amplitude of nonzero homoclinic traveling wave solutions of the McKenna–Walter suspension bridge model. As a consequence of our lower bound, all nonzero homoclinic traveling waves become unbounded as their speed of propagation goes to zero (in accordance with numerical observations).

Published
2012

10. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

Author

Frank Juhn, Jillian Nolan, Chad Nusbaum, Robert Nicol, Alexander Allen, Geneva Young, Aaron M. Berlin, Andrew Barry, John Stalker, Sean M. Sykes, Jon Thompson, John Jarlath Walsh, Andrew Zimmer, Toni Delorey, Justin Abreu, Ramy Shammas, Sheila Fisher, Brian Minie, Lauren Ambrogio, Kristian Cibulskis, Zac Zwirko, Ryan Johnson, Dennis C. Friedrich, Brendan Blumenstiel, Timothy Fennell, Brian Reilly, and Stacey Gabriel

Subjects
Quality Control, Process (engineering), Method, Biology, Genome, 03 medical and health sciences, 0302 clinical medicine, Humans, Exome, Protocol (object-oriented programming), Throughput (business), 030304 developmental biology, Gene Library, Oligonucleotide Array Sequence Analysis, Genetics, Automation, Laboratory, 0303 health sciences, business.industry, Genome, Human, High-Throughput Nucleotide Sequencing, Nucleic Acid Hybridization, Automation, Computer architecture, 030220 oncology & carcinogenesis, Scalability, Human genome, business
Abstract

Genome targeting methods enable cost-effective capture of specific subsets of the genome for sequencing. We present here an automated, highly scalable method for carrying out the Solution Hybrid Selection capture approach that provides a dramatic increase in scale and throughput of sequence-ready libraries produced. Significant process improvements and a series of in-process quality control checkpoints are also added. These process improvements can also be used in a manual version of the protocol.

Published
2010

11. Evolution of genes and genomes on the Drosophila phylogeny

Author

Adam M. Phillippy, Edward Grandbois, Pen MacDonald, Iain MacCallum, Laura K. Reed, Wojciech Makalowski, Tracey Honan, Tania Tassinari Rieger, Melissa J. Hubisz, Josep M. Comeron, Douglas Smith, Jennifer Godfrey, Sebastian Strempel, Amr Abdouelleil, Brenton Gravely, Harindra Arachi, Albert J. Vilella, Marc Azer, Sarah A. Teichmann, Roger A. Hoskins, Corbin D. Jones, Keenan Ross, Derek Wilson, Stuart J. Newfeld, John Stalker, Thomas D. Watts, Dennis C. Friedrich, Therese A. Markow, Michael U. Mollenhauer, Tina Goode, Geneva Young, Terry Shea, Krista Lance, Karin A. Remington, Kevin A. Edwards, Lynne Aftuck, Cecil Rise, Sheridon Channer, Matthew D. Rasmussen, Nicole Stange-Thomann, Annie Lui, Robert A. Reenan, Todd Sparrow, Dave Begun, Tamrat Negash, Laura K. Sirot, Adrianne Brand, Adam Brown, Daisuke Yamamoto, Pema Phunkhang, Justin Abreu, Russell Schwartz, Ana Llopart, Abderrahim Farina, Kebede Maru, Chung-I Wu, Allen Alexander, Scott Anderson, So Jeong Lee, Jason Blye, Gary H. Karpen, Wilfried Haerty, Daniel A. Barbash, Peter Rogov, Barry O'Neill, Rachel Mittelman, Jakob Skou Pedersen, Leanne Hughes, Robert K. Bradley, Graziano Pesole, Wyatt W. Anderson, Anthony J. Greenberg, Alejandro Sánchez-Gracia, Julio Rozas, Stephen W. Schaeffer, Yama Thoulutsang, Roger K. Butlin, David H. Ardell, Stuart DeGray, Chris P. Ponting, Deborah E. Stage, Corrado Caggese, Montserrat Aguadé, Casey M. Bergman, Diallo Ferguson, Peili Zhang, Jeffrey R. Powell, Hajime Sato, Xiaohong Liu, Marta Sabariego Puig, Michael Parisi, Passang Dorje, Yoshihiko Tomimura, Adal Abebe, Carlo G. Artieri, Brian Hurhula, Filip Rege, Peter D. Keightley, Andrew Barry, Pablo Alvarez, Tsamla Tsamla, Marvin Wasserman, Santosh Jagadeeshan, Daniel L. Halligan, Chelsea D. Foley, Kim D. Delehaunty, Manfred Grabherr, Sourav Chatterji, Angela N. Brooks, James C. Costello, Mieke Citroen, James A. Yorke, Hsiao Pei Yang, Charles Chapple, Jian Lu, Carlos A. Machado, Norbu Dhargay, Tsering Wangchuk, Anat Caspi, Patrick Cahill, Tashi Bayul, Lisa Levesque, Otero L. Oyono, Atanas Mihalev, Dawa Thoulutsang, Dawn N. Abt, Sujaa Raghuraman, Manyuan Long, Maria Mendez-Lago, Charles Matthews, Kimberly Dooley, Alex Wong, Melanie A. Huntley, William R. Jeck, Ira Topping, Ben Kanga, José P. Abad, Ana Cristina Lauer Garcia, Brikti Abera, Kunsang Gyaltsen, Jonathan Butler, Alicia Franke, Michael C. Schatz, Cheewhye Chin, Charles F. Aquadro, Justin Johnson, Bryant F. McAllister, Georgia Giannoukos, M. Erii Husby, Rod A. Wing, Shangtao Liu, Jean L. Chang, Jennifer Daub, Eiko Kataoka, Leopold Parts, Rakela Lubonja, Margaret Priest, Yoshiko N. Tobari, Teena Mehta, Evgeny M. Zdobnov, Yeshi Lokyitsang, Richard Elong, Matthew J. Parisi, Louis Meneus, Eric S. Lander, Alan Filipski, Gary Gearin, Nabil Hafez, Nicholas Sisneros, David B. Jaffe, Ian Holmes, Marina Sirota, Leonid Boguslavskiy, Lisa Chuda, LaDeana W. Hillier, Meizhong Luo, Phil Batterham, Michael Kleber, Richard K. Wilson, Yama Cheshatsang, Qing Yu, Rebecca Reyes, Matthew W. Hahn, Andreas Heger, Mar Marzo, Patrick Minx, Kerstin Lindblad-Toh, Vera L. S. Valente, Adam Wilson, William C. Jordan, Mohamed A. F. Noor, Chiao-Feng Lin, Asha Kamat, Heather Ebling, Mihai Pop, Frances Letendre, Mariana F. Wolfner, Don Gilbert, Ngawang Sherpa, Riza M. Daza, Oana Mihai, Gabriel C. Wu, Aaron M. Berlin, Ewen F. Kirkness, Monika D. Huard, Robert S. Fulton, Randall H. Brown, Danni Zhong, Sharon Stavropoulos, Venky N. Iyer, Xu Mu, Christina R. Gearin, David M. Rand, Jerry A. Coyne, Dan Hultmark, Jill Falk, Christopher Patti, Montserrat Papaceit, James Meldrim, Valentine Mlenga, Muneo Matsuda, Sven Findeiß, Todd A. Schlenke, Kevin McKernan, Brian P. Walenz, Timothy B. Sackton, Leonardo Koerich, Peter An, Robert Nicol, Chuong B. Do, Dmitry Khazanovich, Carmen Segarra, Maura Costello, St Christophe Acer, Claudia Rohde, Serafim Batzoglou, Hadi Quesneville, Evan Mauceli, Andy Vo, Luciano M. Matzkin, Susan E. Celniker, Patrick M. O’Grady, William M. Gelbart, Lloyd Low, Jamal Abdulkadir, Jessica Spaulding, Brian R. Calvi, Charlotte Henson, Robert David, Jennifer L. Hall, Andrew G. Clark, Anastasia Gardiner, Susan M. Russo, Birhane Hagos, Kerri Topham, Amy Denise Reily, Eli Venter, Jerome Naylor, Sandra W. Clifton, Valer Gotea, Samuel R. Gross, Manolis Kellis, Claude Bonnet, Christopher Strader, Tashi Lokyitsang, Nyima Norbu, Jennifer Baldwin, Stephen M. Mount, Robert L. Strausberg, Shailendra Yadav, Kristipati Ravi Ram, Steven L. Salzberg, Erik Gustafson, David A. Garfield, Eva Freyhult, Arthur L. Delcher, Enrico Blanco, Granger G. Sutton, Jason M. Tsolas, Charles Robin, Angie S. Hinrichs, Christopher D. Smith, Jane Wilkinson, Brendan McKernan, Fritz Pierre, William McCusker, Brian Oliver, Barry E. Garvin, Sudhir Kumar, Peter Kisner, Kunsang Dorjee, A. Bernardo Carvalho, Anna Montmayeur, Andrew Zimmer, Diana Shih, Wei Tao, Shiaw Pyng Yang, Sante Gnerre, Sampath Settipalli, Thu Nguyen, Paolo Barsanti, Brian P. Lazzaro, Sonja J. Prohaska, J. Craig Venter, Senait Tesfaye, Susan McDonough, Kim D. Pruitt, Alexander Stark, Sergio Castrezana, Lucinda Fulton, Richard T. Lapoint, Greg Gibson, John Spieth, Boris Adryan, Georgius De Haan, Sheila Fisher, Daniel A. Pollard, Seva Kashin, Rob J. Kulathinal, Michael B. Eisen, Nathaniel Novod, Christina Demaso, Alan Dupes, Amanda M. Larracuente, Toby Bloom, Alfredo Villasante, Charles H. Langley, Rama S. Singh, Niall J. Lennon, Kristi L. Montooth, Daniel Barker, Wolfgang Stephan, David Sturgill, Ruiqiang Li, Andrew Hollinger, Boris Boukhgalter, Talene Thomson, Patrick Cooke, Zac Zwirko, Nadia D. Singh, Michael Weiand, Lior Pachter, Roderic Guigó, Yu Zhang, Jay D. Evans, Stephanie Bosak, Rosie Levine, Lu Shi, Kiyohito Yoshida, Carolyn S. McBride, Pouya Kheradpour, William Brockman, Alberto Civetta, Hiroshi Akashi, Marcia Lara, Susan Faro, Sam Griffiths-Jones, Michael R. Brent, Thomas H. Eickbush, Gane Ka-Shu Wong, Elizabeth P. Ryan, Erica Anderson, Roberta Kwok, Asif T. Chinwalla, Sahal Osman, Nga Nguyen, Damiano Porcelli, Missole Doricent, Saverio Vicario, Marc Rubenfield, Bárbara Negre, Gillian M. Halter, Erin E. Dooley, Elena R. Lozovsky, William Lee, Alville Collymore, Catherine Stone, Tanya Mihova, Jun Wang, Karsten Kristiansen, Imane Bourzgui, Michael F. Lin, Katie D'Aco, Filipe G. Vieira, Choe Norbu, Yu-Hui Rogers, Aaron L. Halpern, Eugene W. Myers, Sharleen Grewal, Robert T. Good, Alfredo Ruiz, Dave Kudrna, Joseph Graham, Alex Lipovsky, Leonidas Mulrain, Tsering Wangdi, Roman Arguello, Mira V. Han, Arjun Bhutkar, Rasmus Nielsen, David J. Saranga, Aleksey V. Zimin, Vasilia Magnisalis, Helen Vassiliev, Thomas C. Kaufman, Eva Markiewicz, Temple F. Smith, Jinlei Liu, Loryn Gadbois, Michael G. Ritchie, Lisa Zembek, Daniel Bessette, Pasang Bachantsang, Adam Navidi, Department of Molecular Biology and Genetics, Cornell University [New York], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), University of California [Berkeley], University of California, Agencourt Bioscience Corporation, Partenaires INRAE, Faculty of Life Science, University of Manchester [Manchester], Laboratory of Cellular and Developmental Biology (LCDB), NIDDK, NIH, Department of Ecology and Evolutionary Biology, University of Arizona, Department of Biology, Indiana University [Bloomington], Indiana University System-Indiana University System, Massachusetts Institute of Technology (MIT), Harvard University [Cambridge], Centro de Biología Molecular Severo Ochoa [Madrid] (CBMSO), Universidad Autonoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Brown University, Laboratory of Molecular Biology, Medical Research Council, Departament de Genetica, Universitat de Barcelona (UB), Pennsylvania State University (Penn State), Penn State System-Penn State System, Department of Genetics, University of Georgia [USA], Uppsala University, Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), McMaster University, School of Biology, IE University, Università degli Studi di Bari Aldo Moro, University of Melbourne, Stanford University, University of California [Davis] (UC Davis), Boston University [Boston] (BU), Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Washington University in Saint Louis (WUSTL), University of Sheffield, Syracuse University, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Department of Bioengineering, Beihang University (BUAA), Tucson Stock Center, Genome Center, University of California-University of California, Genome Sequencing Center, University of Washington School of Medicine, University of Winnipeg, Iowa State University (ISU), Indiana University System, The Wellcome Trust Sanger Institute [Cambridge], Center for Bioinformatics and Computational Biology, University of Delaware [Newark], Illinois State University, University of Rochester [USA], United States Department of Agriculture (USDA), Arizona State University [Tempe] (ASU), Leipzig University, Universidade Federal do Rio Grande do Sul (UFRGS), Duke University, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), University of Connecticut (UCONN), Computer Science Département, Université Saint-Esprit de Kaslik (USEK), Mc Master University, Indiana University, Institute of Evolutionary Biology, University of Edinburgh, J. Craig Venter Institute [La Jolla, USA] (JCVI), University of Oxford [Oxford], Center for Biomolecular Science and Engineering, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), and Zdobnov, Evgeny

Subjects
melanogaster genome, 0106 biological sciences, RNA, Untranslated, [SDV]Life Sciences [q-bio], Genome, Insect, RNA, Untranslated/genetics, Genes, Insect, 01 natural sciences, Genome, Genome, Insect/ genetics, Gene Order, Genome, Mitochondrial/genetics, Drosophila Proteins, Phylogeny, ddc:616, Genetics, 0303 health sciences, Multidisciplinary, biology, Reproduction, Genomics, Multigene Family/genetics, Reproduction/genetics, DNA Transposable Elements/genetics, Genes, Insect/ genetics, Multigene Family, dosage compensation, Drosophila, amino-acid substitution, Drosophila Protein, Drosophila Proteins/genetics, Synteny/genetics, fruit-fly, 010603 evolutionary biology, Synteny, Drosophila sechellia, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Molecular evolution, Codon/genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Animals, adaptive protein evolution, Codon, 030304 developmental biology, Gene Order/genetics, molecular evolution, fungi, Immunity, synonymous codon usage, Sequence Analysis, DNA, Immunity/genetics, biology.organism_classification, Drosophila mojavensis, Evolutionary biology, Genome, Mitochondrial, DNA Transposable Elements, maximum-likelihood, noncoding dna, Drosophila/ classification/ genetics/immunology/metabolism, Sequence Alignment, natural-selection, Drosophila yakuba
Abstract

Affiliations des auteurs : cf page 216 de l'article; International audience; Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Published
2007
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12. Genome sequence, comparative analysis and haplotype structure of the domestic dog

Author

Tsering Wangchuk, Mayank Kumar, Sharon Stavropoulos, James Cuff, Mostafa Benamara, David DeCaprio, Birhane Hagos, Nathaniel Novod, Tashi Lokyitsang, Nyima Norbu, Jennifer Baldwin, Sabrina M. Stone, Catherine Stone, Geneva Young, Osebhajajeme Egbiremolen, Dawa Thoulutsang, Tanya Mihova, Lisa Kim, Julie Sahalie, Jan Macdonald, Amr Abouelleil, Toby Bloom, Yama Cheshatsang, Carolyne Bardeleben, Qing Yu, Berta Blitshteyn, Tuyen T. Nguyen, Tarjei S. Mikkelsen, Edward Grandbois, Claire M. Wade, John E. Major, Filip Rege, Cindy Nguyen, Andrew Barry, Tracey Honan, Pablo Alvarez, Andy Vo, Manuel Garber, Cristyn Kells, Rachel Mittelman, Lucien Oyono, Norbu Dhargay, Sean M. Sykes, Diallo Ferguson, Tyler Aldredge, Tenchoe Nyima, Todd Sparrow, Daniel S. Hagopian, Christophe Hitte, Andreas Heger, Jane E. Wilkinson, Verneda Ray, Peter Rogov, Ewen F. Kirkness, Jill Falk, Robert Nicol, Christopher Patti, Danielle Perrin, Ted Sharpe, Douglas Smith, Peter Olandt, Matthew Breen, Ali Aslam, Cherylyn Smith, Tara Biagi, Diane Gage, Jean L. Chang, Karen Hughes Miller, Valentine Mlenga, Andrea Horn, Jessie Sloan, Claire M. Healy, Adam Wilson, Ngawang Sherpa, Riza M. Daza, David B. Jaffe, Leonid Boguslavskiy, Jody Camarata, Peter Kisner, William H. Lee, Kunsang Dorjee, M. Husby, Sante Gnerre, Kunsang Gyaltsen, Asha Kamat, Jonathan Butler, Terrance Shea, Alicia Franke, Patrick Cooke, Rayale Rameau, Andrew Zimmer, Gary Gearin, Nabil Hafez, Kerri Topham, Kebede Maru, Chris P. Ponting, Jerome Naylor, Yama Thoulutsang, Keith O'Neill, Jinlei Liu, Manolis Kellis, Claude Bonnet, Claudel Antoine, Passang Dorje, Adal Abebe, Tsamla Tsamla, Michael Kleber, Michael Weiand, Audra Goyette, Rachael Thomas, Lisa Zembek, Atanas Mihalev, Daniel Bessette, Helen Vassiliev, Pasang Bachantsang, Adam Navidi, Kathleen Dooley, Caleb Webber, Pierre Tchuinga, Tashi Bayul, Michael Kamal, Heidi G. Parker, Ben Kanga, Kimberly Dooley, Nadia Calixte, Mostafa Ait-zahra, Niall J. Lennon, Ira Topping, Eric S. Lander, Pieter J. deJong, Nicole R. Allen, Peter An, Boris Boukhgalter, Richard Elong, Thomas E. Landers, Anthony Rachupka, Michael Fitzgerald, Lisa Leuper, William Brockman, Marcia Lara, Susan Faro, Elaine A. Ostrander, Joanne Zainoun, Leigh Anne Hunnicutt, Mark J. Daly, Leanne Hughes, April Cook, Patrick Cahill, Sujaa Raghuraman, Manfred Grabherr, Robert K. Wayne, Adam Brown, Xiaohong Liu, Charles Matthews, Scott Anderson, Margaret Priest, Shailendra Yadav, Evan Mauceli, Kerstin Lindblad-Toh, Patricia Ferreira, Yeshi Lokyitsang, Harindra Arachchi, Alexandre Melnikov, Christina Raymond, James Meldrim, Dmitry Khazanovich, Mieke Citroen, Aaron M. Berlin, Alix Chinh Kieu, John Stalker, Francis Galibert, Noah Duffey, Krista Lance, Louis Meneus, Jennifer Ruth Sadler Hall, Choe Norbu, Pema Tenzing, Richard Marabella, Chee-Wye Chin, Karen Foley, Xiaoping Yang, Nga Nguyen, Tenzin Dawoe, Ryan Hegarty, Julie Rogers, Joseph Graham, Chelsea D. Foley, Leonidas Mulrain, Tsering Wangdi, Karin Decktor, Sarah LeVine, Shuli Yang, Dennis C. Friedrich, Tina Goode, Cecil Rise, Teena Mehta, Laura Ayotte, Michele Clamp, Nicole Stange-Thomann, Annie Lui, Edward J. Kulbokas, Pema Phunkhang, Alan Dupes, Elinor K. Karlsson, Lynne Aftuck, Sahal Osman, Abderrahim Farina, Barry O'Neill, Diana M. Shih, Xiaohui Xie, Lester Dorris, Vijay Venkataraman, Benjamin Jester, Sampath Settipalli, Thu Nguyen, Alville Collymore, Klaus-Peter Koepfli, Senait Tesfaye, Nathan Houde, Susan McDonough, Leo Goodstadt, Glen Munson, Georgia Giannoukos, Jeffrey Chu, Nathan B. Sutter, Sheila A. Fisher, Charlien Jones, Michael C. Zody, Jianying Shi, John P. Pollinger, Mechele Sheehan, Stephen M. J. Searle, Fritz Pierre, Jason Blye, Jean-Pierre Leger, and Stuart DeGray

Subjects
Male, Genomics, Single-nucleotide polymorphism, Biology, Genome, Polymorphism, Single Nucleotide, Synteny, Conserved sequence, Evolution, Molecular, Mice, Dogs, Molecular evolution, Animals, Humans, Dog Diseases, Conserved Sequence, Short Interspersed Nucleotide Elements, Genetics, Whole genome sequencing, Multidisciplinary, Dog leukocyte antigen, Haplotype, Rats, Haplotypes, Mutagenesis, biology.protein, Hybridization, Genetic, Female
Abstract

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Published
2005

13. A Compactness Criterion for Real Plane Algebraic Curves

Author

John Stalker

Subjects
Polynomial, Pure mathematics, Applied Mathematics, General Mathematics, Newton polygon, Algebraic geometry, Real plane, Mathematics - Algebraic Geometry, Compact space, TheoryofComputation_ANALYSISOFALGORITHMSANDPROBLEMCOMPLEXITY, ComputingMethodologies_SYMBOLICANDALGEBRAICMANIPULATION, FOS: Mathematics, Algebraic curve, Algebraic Geometry (math.AG), Mathematics
Abstract

Two sets of conditions are presented for the compactness of a real plane algebraic curve, one sufficient and one necessary, in terms of the Newton polygon of the defining polynomial., 7 pages, 0 figures

Published
2004

14. Scalar waves on a naked-singularity background

Author

John Stalker and A. Shadi Tahvildar-Zadeh

Subjects
Physics, Physics and Astronomy (miscellaneous), 010308 nuclear & particles physics, Function space, Scalar (mathematics), Friedrichs extension, Mathematics::Analysis of PDEs, FOS: Physical sciences, Naked singularity, General Relativity and Quantum Cosmology (gr-qc), Wave equation, 01 natural sciences, General Relativity and Quantum Cosmology, 0103 physical sciences, Minkowski space, Initial value problem, 010306 general physics, Scalar field, Mathematical physics
Abstract

We obtain global space-time weighted-L^2 (Morawetz) and L^4 (Strichartz) estimates for a massless chargeless scalar field propagating on a super-extremal (overcharged) Reissner-Nordstrom background. We begin by discussing the question of well-posedness of the Cauchy problem for scalar fields on non-globally hyperbolic manifolds and the role played by the Friedrichs extension, go over the construction of the function spaces involved, show how to transform the problem to one about the wave equation on the Minkowski space with a singular potential, and finally prove that the potential thus obtained satisfies the various conditions needed in order for the estimates to hold., 20 pages, 2 figures. final version, to appear in Classical and Quantum Gravity. Includes minor corrections, additional footnotes and references

Published
2004

15. Complex Analysis : Fundamentals of the Classical Theory of Functions

Author

John Stalker and John Stalker

Subjects
Functions of complex variables, Mathematical analysis
Abstract

All modem introductions to complex analysis follow, more or less explicitly, the pattern laid down in Whittaker and Watson [75]. In'part I''we find the foundational material, the basic definitions and theorems. In'part II'we find the examples and applications. Slowly we begin to understand why we read part I. Historically this is an anachronism. Pedagogically it is a disaster. Part II in fact predates part I, so clearly it can be taught first. Why should the student have to wade through hundreds of pages before finding out what the subject is good for? In teaching complex analysis this way, we risk more than just boredom. Beginning with a series of unmotivated definitions gives a misleading impression of complex analy­ sis in particular and of mathematics in general. The classical theory of analytic functions did not arise from the idle speculation of bored mathematicians on the possible conse­ quences of an arbitrary set of definitions; it was the natural, even inevitable, consequence of the practical need to answer questions about specific examples. In standard texts, after hundreds of pages of theorems about generic analytic functions with only the rational and trigonometric functions as examples, students inevitably begin to believe that the purpose of complex analysis is to produce more such theorems. We require introductory com­ plex analysis courses of our undergraduates and graduates because it is useful both within mathematics and beyond.

Published
2009

18. Elliptic and Modular Functions

Author

John Stalker

Subjects
Pure mathematics, business.industry, Computer science, Theta function, Modular design, business
Abstract

In the chapter we will examine theta functions, elliptic, and modular functions. We will study theta functions in great detail. Since the elliptic and modular functions are simply rational expressions in theta functions, they can be disposed of quite quickly.

Published
1998
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19. A Quick Review of Real Analysis

Author

John Stalker

Subjects
Generality, Real analysis, Computer science, Elegance, media_common.quotation_subject, Calculus, Remainder, media_common
Abstract

The purpose of this appendix is to provide the reader with exactly enough real analysis to read the remainder of the text. It is intended as a reference rather than as a substitute for a real analysis course. No attempt has been made at either elegance or generality.

Published
1998
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21. Sharp bounds on 2 m / r for static spherical objects

Author

John Stalker and Paschalis Karageorgis

Subjects
Physics, Physics and Astronomy (miscellaneous), FOS: Physical sciences, General Relativity and Quantum Cosmology (gr-qc), Radius, General Relativity and Quantum Cosmology, Einstein tensor, symbols.namesake, Hawking, symbols, Variety (universal algebra), Eigenvalues and eigenvectors, Mathematical physics
Abstract

Sharp bounds are obtained, under a variety of assumptions on the eigenvalues of the Einstein tensor, for the ratio of the Hawking mass to the areal radius in static, spherically symmetric space-times., We changed a footnote in which an earlier result of H\aa{}kan Andr\'{e}asson was not described correctly

Published
2008
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22. GRAVE LIES The inside story of a dirty war.

Author

JOHN STALKER EXCERPTED FROM THE STALKER AFFAIR, WRITTEN BY JOHN STALKER (c) 1988 JOHN STALKER LTD., TO BE PUBLISHED BY VIKING PENGUIN INC

Subjects
STALKER Affair, The (Book), STALKER, John, 1939-2019, IRISH Republican Army
Published
1988

23. Singular Perturbation Series in Quantum Mechanics

Author

John Stalker

Subjects
Power series, Mathematics(all), Singular perturbation, General Mathematics, Anharmonicity, Transition of state, Dyson series, symbols.namesake, Quantum mechanics, Path integral formulation, symbols, Feynman diagram, Series expansion, Mathematics
Abstract

This is the first in a series of articles on singular perturbation series in quantum mechanics. In these papers we will compute transition amplitudes non-perturbatively for several simple quantum mechanical systems. This paper treats the behavior of a harmonic oscillator as a function of the spring constant. All the systems to be considered exhibit the same phenomenon: there is, in general, no power series expansion, even of an asymptotic nature, in powers of the perturbation parameter. For reasonable initial and final states there are, however, expansions of a more complicated type. In the case of the harmonic oscillator there is a log-power series expansion. This example is sufficiently simple and explicit that one can see how the logarithmic terms arise mathematically. How they arise physically is rather more mysterious. One point however is clear; the standard techniques of perturbation theory, whether expressed in terms of Dyson series, Feynman diagrams, successive approximation, or path integrals, are all structured so as to produce only power series and thus fail to detect logarithmic terms.

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24. Strichartz estimates for the wave and Schrödinger equations with the inverse-square potential

Author

A. Shadi Tahvildar-Zadeh, John Stalker, Nicolas Burq, Fabrice Planchon, Laboratoire de Mathématiques d'Orsay (LM-Orsay), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), Laboratoire Analyse, Géométrie et Applications (LAGA), Université Paris 8 Vincennes-Saint-Denis (UP8)-Centre National de la Recherche Scientifique (CNRS)-Institut Galilée-Université Paris 13 (UP13), and Burq, Nicolas

Subjects
Mathematics::Analysis of PDEs, Inverse, Schrödinger equation, 01 natural sciences, Square (algebra), Strichartz estimate, symbols.namesake, Mathematics - Analysis of PDEs, FOS: Mathematics, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], Morawetz estimate, [MATH.MATH-AP] Mathematics [math]/Analysis of PDEs [math.AP], 0101 mathematics, Smoothing estimate, Mathematics, Mathematical physics, Spacetime, 010102 general mathematics, Mathematical analysis, Wave equation, 010101 applied mathematics, Inverse-square potential, symbols, Schrödinger's cat, Analysis, Analysis of PDEs (math.AP)
Abstract

We prove spacetime weighted-L^2 estimates for the Schrodinger and wave equation with an inverse-square potential. We then deduce Strichartz estimates for these equations., 30 pages v2: added references v3: corrected remark on dispersion (remark 1 section 3.1) v4: final version, to appear in JFA

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27. Stalker

Author

Steven Greer and John Stalker

Subjects
Sociology and Political Science, Law
Published
1988
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28. A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454

Author

Andrew Barry, Pablo Alvarez, Danielle Perrin, Matthew R. Henn, William Brockman, Georgia Giannoukos, Chad Nusbaum, Andrew Hollinger, Scott Anderson, Dana Robbins, Michael Weiand, Robert Nicol, Todd Sparrow, Taryn L Powers, David B. Jaffe, Scott Steelman, Frank Juhn, Cindi A. Hoover, Carsten Russ, Kamran Rizzolo, Andrew Zimmer, Danielle McCarthy, Robert E. Lintner, Elizabeth M. Ryan, John Stalker, Niall J. Lennon, Lisa Green, Riza M. Daza, Rachel L. Erlich, and Karen Ponchner

Subjects
Sample handling, Genetics, Electronic Data Processing, Sequence, Process (engineering), business.industry, Method, Sequence Analysis, DNA, Biology, Microspheres, High-Throughput Screening Assays, Fully automated, Embedded system, Magnetic bead, Scalability, Humans, Sources of error, business, Throughput (business), Algorithms, Gene Library
Abstract

An automated method for constructing libraries for 454 sequencing significantly reduces the cost and time required., We present an automated, high throughput library construction process for 454 technology. Sample handling errors and cross-contamination are minimized via end-to-end barcoding of plasticware, along with molecular DNA barcoding of constructs. Automation-friendly magnetic bead-based size selection and cleanup steps have been devised, eliminating major bottlenecks and significant sources of error. Using this methodology, one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method.

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