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1. Free electron laser generation of x-ray Poincaré beams

Author

Jenny Morgan, Erik Hemsing, Brian W J McNeil, and Alison Yao

Subjects
free electron lasers, fully structured light, Poincaré beams, Science, Physics, QC1-999
Abstract

An optics-free method is proposed to generate x-ray radiation with spatially variant states of polarization via an afterburner extension to a free electron laser. Control of the polarization in the transverse plane is obtained through the overlap of different coherent transverse light distributions radiated from a bunched electron beam in two consecutive orthogonally polarised undulators. Different transverse profiles are obtained by emitting at a higher harmonic in one or both of the undulators. This method enables the generation of beams structured in their intensity, phase, and polarization—so-called Poincaré beams—at high powers with tunable wavelengths. Simulations are used to demonstrate the generation of two different classes of light with spatially inhomogeneous polarization—cylindrical vector beams and full Poincaré beams.

Published
2020
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2. Standardized metadata for human pathogen/vector genomic sequences.

Author

Vivien G Dugan, Scott J Emrich, Gloria I Giraldo-Calderón, Omar S Harb, Ruchi M Newman, Brett E Pickett, Lynn M Schriml, Timothy B Stockwell, Christian J Stoeckert, Dan E Sullivan, Indresh Singh, Doyle V Ward, Alison Yao, Jie Zheng, Tanya Barrett, Bruce Birren, Lauren Brinkac, Vincent M Bruno, Elizabet Caler, Sinéad Chapman, Frank H Collins, Christina A Cuomo, Valentina Di Francesco, Scott Durkin, Mark Eppinger, Michael Feldgarden, Claire Fraser, W Florian Fricke, Maria Giovanni, Matthew R Henn, Erin Hine, Julie Dunning Hotopp, Ilene Karsch-Mizrachi, Jessica C Kissinger, Eun Mi Lee, Punam Mathur, Emmanuel F Mongodin, Cheryl I Murphy, Garry Myers, Daniel E Neafsey, Karen E Nelson, William C Nierman, Julia Puzak, David Rasko, David S Roos, Lisa Sadzewicz, Joana C Silva, Bruno Sobral, R Burke Squires, Rick L Stevens, Luke Tallon, Herve Tettelin, David Wentworth, Owen White, Rebecca Will, Jennifer Wortman, Yun Zhang, and Richard H Scheuermann

Subjects
Medicine, Science
Abstract

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.

Published
2014
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3. Strong chiral optical force for small chiral molecules based on electric-dipole interactions, inspired by the asymmetrical hydrozoan Velella velella

Author

Alison Yao, Duncan McArthur, and Robert P. Cameron

Abstract

Drawing inspiration from a remarkable chiral force found in nature, we show that a static electric field combined with an optical lin-perp-lin polarization standing wave can exert a chiral optical force on a small chiral molecule that is several orders of magnitude stronger than other chiral optical forces proposed to date, being based on leading electric-dipole interactions rather than relying on weak magnetic-dipole and electric-quadrupole interactions. Our chiral optical force applies to most small chiral molecules, including isotopically chiral molecules, and does not require a specific energy-level structure. Potential applications range from chiral molecular matter-wave interferometry for precision metrology and tests of fundamental physics to the resolution of enantiomers for use in chemistry and biology.

Published
2023
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4. Hematopoietic cell types: Prototype for a revised cell ontology.

Author

Alexander D. Diehl, Alison Deckhut Augustine, Judith A. Blake, Lindsay G. Cowell, Elizabeth S. Gold, Timothy A. Gondré-Lewis, Anna Maria Masci, Terrence F. Meehan, Penelope A. Morel, Anastasia Nijnik, Bjoern Peters, Bali Pulendran, Richard H. Scheuermann, Q. Alison Yao, Martin S. Zand, and Christopher J. Mungall

Published
2011
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5. Control of light-atom solitons and atomic transport by optical vortex beams propagating through a Bose-Einstein Condensate

Author

Grant Henderson, Alison Yao, Gordon Robb, and Gian-Luca Oppo

Subjects
Condensed Matter::Quantum Gases, QC350, Quantum Gases (cond-mat.quant-gas), General Physics and Astronomy, FOS: Physical sciences, Pattern Formation and Solitons (nlin.PS), Condensed Matter - Quantum Gases, Nonlinear Sciences - Pattern Formation and Solitons, Nonlinear Sciences::Pattern Formation and Solitons, Physics - Optics, Optics (physics.optics)
Abstract

We model propagation of far-red-detuned optical vortex beams through a Bose-Einstein Condensate using nonlinear Schr\"odinger and Gross-Pitaevskii equations. We show the formation of coupled light/atomic solitons that rotate azimuthally before moving off tangentially, carrying angular momentum. The number, and velocity, of solitons, depends on the orbital angular momentum of the optical field. Using a Bessel-Gauss beam increases radial confinement so that solitons can rotate with fixed azimuthal velocity. Our model provides a highly controllable method of channelling a BEC and atomic transport., Comment: 5 pages, 4 figures

Published
2022
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7. Systematic identification of pseudogenes through whole genome expression evidence profiling

Author

Rosane Charlab, Alison Yao, and Peter Li

Subjects
Expressed Sequence Tags, Genetics, Genome evolution, Gene Expression Profiling, Pseudogene, Gene prediction, Computational Biology, Genomics, Genome project, Gene Annotation, Vertebrate and Genome Annotation Project, Biology, Genome, Sequence Analysis, Protein, Data Interpretation, Statistical, Humans, Ensembl, Pseudogenes
Abstract

The identification of pseudogenes is an integral and significant part of the genome annotation because of their abundance and their impact on the experimental analysis of functional genes. Most of the computational annotation systems are not optimized for systematic pseudogene recognition, often annotating pseudogenes as functional genes, and users then propagate these errors to subsequent analyses and interpretations. In order to validate gene annotations and to identify pseudogenes that are potentially mis-annotated, we developed a novel approach based on whole genome profiling of existing transcript and protein sequences. This method has two important features: (i) equally detects both processed and non-processed pseudogenes and (ii) can identify transcribed pseudogenes. Applying this method to the human Ensembl gene predictions, we discovered that 2011 (9% of total) Ensembl genes in the categories of known and novel might be pseudogenes based on expression evidence. Of these, 1200 genes are found to have no existing evidence of transcription, and 811 genes are found with transcription evidence but contain significant translation disruption. Approximately 40% of the 2011 identified pseudogenes presented a multi-exon structure, representing non-processed pseudogenes. We have demonstrated the power of whole genome profiling of expression sequences to improve the accuracy of gene annotations.

Published
2006
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8. The Genome Sequence of the Malaria Mosquito Anopheles gambiae

Author

Mei Wang, Frank H. Collins, Yong Liang, José M. C. Ribeiro, Zhijian Tu, Jason R. Miller, Mark Yandell, Pantelis Topalis, Hongguang Shao, Qi Zhao, Hamilton O. Smith, Ali N Dana, Zhaoxi Ke, J. Craig Venter, Deborah R. Nusskern, Christos Louis, Ivica Letunic, Brian P. Walenz, Granger G. Sutton, Patrick Wincker, Anastasios C. Koutsos, Paul T. Brey, Ewan Birney, Jean Weissenbach, Fotis C. Kafatos, Cheryl A. Evans, Kerry J. Woodford, Dana Thomasova, Eugene W. Myers, Stephen L. Hoffman, Kokoza Eb, Josep F. Abril, Randall Bolanos, Megan A. Regier, Holly Baden, George K. Christophides, Véronique de Berardinis, Jingtao Sun, James R. Hogan, Kabir Chatuverdi, Ron Wides, Emmanuel Mongin, Igor F. Zhimulev, Steven L. Salzberg, Danita Baldwin, Richard J. Mural, Shiaoping C. Zhu, Anibal Cravchik, Jhy-Jhu Lin, G. Mani Subramanian, Young S. Hong, Shuang Cai, Francis Kalush, Rosane Charlab, Martin Wu, Claudia Blass, Mark Raymond Adams, Robert A. Holt, Clark M. Mobarry, Douglas B. Rusch, Michael Flanigan, Jim Biedler, Susanne L. Hladun, Ping Guan, Cynthia Sitter, Joel A. Malek, Mario Coluzzi, Cynthia Pfannkoch, Arthur L. Delcher, Alessandra della Torre, Maria F. Unger, Evgeny M. Zdobnov, Stephan Meister, Karin A. Remington, Peter W. Atkinson, Malcolm J. Gardner, Vladimir Benes, Ian M. Dew, Maria V. Sharakhova, X. Wang, Hongyu Zhang, Jian Wang, Jeffrey Hoover, Cheryl L. Kraft, Charles Roth, Andrew G. Clark, Shaying Zhao, Jyoti Shetty, Tina C. McIntosh, Aihui Wang, Zhiping Gu, Aaron L. Halpern, Anne Grundschober-Freimoser, David A. O'Brochta, Peter Arensburger, Brendan J. Loftus, Lucas Q. Ton, Véronique Anthouard, Mary Barnstead, John Lopez, Peer Bork, Didier Boscus, Michele Clamp, Jennifer R. Wortman, Claire M. Fraser, Lisa Friedli, William H. Majoros, Thomas J. Smith, Olivier Jaillon, Val Curwen, Samuel Broder, Sean D. Murphy, Roderic Guigó, Neil F. Lobo, Mathew A. Chrystal, Alison Yao, Alex Levitsky, Renee Strong, Maureen E. Hillenmeyer, Zhongwu Lai, Chinnappa D. Kodira, Rong Qi, and Zdobnov, Evgeny

Subjects
Chromosomes, Artificial, Bacterial, Drosophila melanogaster/genetics, Mosquito Control, Proteome, Enzymes/chemistry/genetics/metabolism, Anopheles gambiae, Genes, Insect, Genome, Plasmodium falciparum/growth & development, Malaria, Falciparum, Expressed Sequence Tags, Genetics, Expressed sequence tag, Multidisciplinary, Physical Chromosome Mapping, Biological Evolution, Enzymes, Blood, Drosophila melanogaster, Insect Proteins, Digestion, Sequence analysis, Molecular Sequence Data, Plasmodium falciparum, Biology, Polymorphism, Single Nucleotide, Species Specificity, Anopheles, Genetic variation, Transcription Factors/chemistry/genetics/physiology, Animals, Humans, Insect Proteins/chemistry/genetics/physiology, Malaria, Falciparum/transmission, Gene, Anopheles/classification/genetics/parasitology/physiology, Whole genome sequencing, Haplotype, Computational Biology, Genetic Variation, Feeding Behavior, Sequence Analysis, DNA, biology.organism_classification, Insect Vectors, Gene Expression Regulation, Haplotypes, Chromosome Inversion, DNA Transposable Elements, Insect Vectors/genetics/parasitology/physiology, Transcription Factors
Abstract

Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency (“dual haplotypes”) in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.

Published
2002
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9. Standardized metadata for human pathogen/vector genomic sequences

Author

Daniel E. Neafsey, Luke J. Tallon, David A. Rasko, Rick Stevens, Lisa Sadzewicz, Eun Mi Lee, Jie Zheng, Maria Y. Giovanni, Alison Yao, Scott J. Emrich, Doyle V. Ward, Ilene Karsch-Mizrachi, Timothy B. Stockwell, Gloria I. Giraldo-Calderón, Elizabet Caler, Erin Hine, Mark Eppinger, Michael Feldgarden, Christian J. Stoeckert, Emmanuel F. Mongodin, Vincent M. Bruno, David E. Wentworth, Jessica C. Kissinger, W. Florian Fricke, Yun Zhang, R. Burke Squires, Cheryl I. Murphy, Frank H. Collins, Julia Puzak, Scott Durkin, Omar S. Harb, Brett E. Pickett, Christina A. Cuomo, David S. Roos, Hervé Tettelin, Indresh Singh, Rebecca Will, Matthew R. Henn, Bruce W. Birren, William C. Nierman, Valentina Di Francesco, Lynn M. Schriml, Lauren M. Brinkac, Vivien G. Dugan, Sinéad B. Chapman, Richard H. Scheuermann, Jennifer R. Wortman, Claire M. Fraser, Punam Mathur, Joana C. Silva, Garry S. A. Myers, Tanya Barrett, Julie C. Dunning Hotopp, Karen E. Nelson, Daniel E. Sullivan, Ruchi M. Newman, Owen White, and Bruno W. S. Sobral

Subjects
Epigenomics, Text Mining, Datasets as Topic, lcsh:Medicine, Disease Vectors, Ontology (information science), Genome, 0302 clinical medicine, Databases, Genetic, Medicine and Health Sciences, Technology Regulations, Genome Sequencing, lcsh:Science, Data Management, Genetics, 0303 health sciences, Multidisciplinary, Virulence, Metadata standard, Genomics, Reference Standards, Genomic Databases, Bioontologies, 3. Good health, Infectious Diseases, Ontology and Logic, Information Technology, Research Article, Biotechnology, Computer and Information Sciences, Science Policy, General Science & Technology, Biological Data Management, Computational biology, Biology, Microbiology, Communicable Diseases, Databases, 03 medical and health sciences, Animals, Humans, Molecular Biology Techniques, Sequencing Techniques, Molecular Biology, 030304 developmental biology, Comparative genomics, Ontology for Biomedical Investigations, Evolutionary Biology, lcsh:R, Biology and Life Sciences, Computational Biology, Sequence Analysis, DNA, Comparative Genomics, Genome Analysis, Metadata, Gene Ontology, Infectious disease (medical specialty), Genetic Polymorphism, lcsh:Q, Zoology, Entomology, Population Genetics, 030217 neurology & neurosurgery
Abstract

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.

Published
2014

10. More on the sequencing of the human genome

Author

J. Craig Venter, Mark D. Adams, Eugene W. Myers, Peter W. Li, Richard J. Mural, Granger G. Sutton, Hamilton O. Smith, Mark Yandell, Cheryl A. Evans, Robert A. Holt, Jeannine D. Gocayne, Peter Amanatides, Richard M. Ballew, Daniel H. Huson, Jennifer Russo Wortman, Qing Zhang, Chinnappa D. Kodira, Xiangqun H. Zheng, Lin Chen, Marian Skupski, Gangadharan Subramanian, Paul D. Thomas, Jinghui Zhang, George L. Gabor Miklos, Catherine Nelson, Samuel Broder, Andrew G. Clark, Joe Nadeau, Victor A. McKusick, Norton Zinder, Arnold J. Levine, Richard J. Roberts, Mel Simon, Carolyn Slayman, Michael Hunkapiller, Randall Bolanos, Arthur Delcher, Ian Dew, Daniel Fasulo, Michael Flanigan, Liliana Florea, Aaron Halpern, Sridhar Hannenhalli, Saul Kravitz, Samuel Levy, Clark Mobarry, Knut Reinert, Karin Remington, Jane Abu-Threideh, Ellen Beasley, Kendra Biddick, Vivien Bonazzi, Rhonda Brandon, Michele Cargill, Ishwar Chandramouliswaran, Rosane Charlab, Kabir Chaturvedi, Zuoming Deng, Valentina Di Francesco, Patrick Dunn, Karen Eilbeck, Carlos Evangelista, Andrei E. Gabrielian, Weiniu Gan, Wangmao Ge, Fangcheng Gong, Zhiping Gu, Ping Guan, Thomas J. Heiman, Maureen E. Higgins, Rui-Ru Ji, Zhaoxi Ke, Karen A. Ketchum, Zhongwu Lai, Yiding Lei, Zhenya Li, Jiayin Li, Yong Liang, Xiaoying Lin, Fu Lu, Gennady V. Merkulov, Natalia Milshina, Helen M. Moore, Ashwinikumar K Naik, Vaibhav A. Narayan, Beena Neelam, Deborah Nusskern, Douglas B. Rusch, Steven Salzberg, Wei Shao, Bixiong Shue, Jingtao Sun, Zhen Yuan Wang, Aihui Wang, Xin Wang, Jian Wang, Ming-Hui Wei, Ron Wides, Chunlin Xiao, Chunhua Yan, Alison Yao, Jane Ye, Ming Zhan, Weiqing Zhang, Hongyu Zhang, Qi Zhao, Liansheng Zheng, Fei Zhong, Wenyan Zhong, Shiaoping C. Zhu, Shaying Zhao, Dennis Gilbert, Suzanna Baumhueter, Gene Spier, Christine Carter, Anibal Cravchik, Trevor Woodage, Feroze Ali, Huijin An, Aderonke Awe, Danita Baldwin, Holly Baden, Mary Barnstead, Ian Barrow, Karen Beeson, Dana Busam, Amy Carver, Angela Center, Ming Lai Cheng, Liz Curry, Steve Danaher, Lionel Davenport, Raymond Desilets, Susanne Dietz, Kristina Dodson, Lisa Doup, Steven Ferriera, Neha Garg, Andres Gluecksmann, Brit Hart, Jason Haynes, Charles Haynes, Cheryl Heiner, Suzanne Hladun, Damon Hostin, Jarrett Houck, Timothy Howland, Chinyere Ibegwam, Jeffery Johnson, Francis Kalush, Lesley Kline, Shashi Koduru, Amy Love, Felecia Mann, David May, Steven McCawley, Tina McIntosh, Ivy McMullen, Mee Moy, Linda Moy, Brian Murphy, Keith Nelson, Cynthia Pfannkoch, Eric Pratts, Vinita Puri, Hina Qureshi, Matthew Reardon, Robert Rodriguez, Yu-Hui Rogers, Deanna Romblad, Bob Ruhfel, Richard Scott, Cynthia Sitter, Michelle Smallwood, Erin Stewart, Renee Strong, Ellen Suh, Reginald Thomas, Ni Ni Tint, Sukyee Tse, Claire Vech, Gary Wang, Jeremy Wetter, Sherita Williams, Monica Williams, Sandra Windsor, Emily Winn-Deen, Keriellen Wolfe, Jayshree Zaveri, Karena Zaveri, Josep F. Abril, Roderic Guigó, Michael J. Campbell, Kimmen V. Sjolander, Brian Karlak, Anish Kejariwal, Huaiyu Mi, Betty Lazareva, Thomas Hatton, Apurva Narechania, Karen Diemer, Anushya Muruganujan, Nan Guo, Shinji Sato, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz, Brian Walenz, Shibu Yooseph, David Allen, Anand Basu, James Baxendale, Louis Blick, Marcelo Caminha, John Carnes-Stine, Parris Caulk, Yen-Hui Chiang, My Coyne, Carl Dahlke, Anne Deslattes Mays, Maria Dombroski, Michael Donnelly, Dale Ely, Shiva Esparham, Carl Fosler, Harold Gire, Stephen Glanowski, Kenneth Glasser, Anna Glodek, Mark Gorokhov, Ken Graham, Barry Gropman, Michael Harris, Jeremy Heil, Scott Henderson, Jeffrey Hoover, Donald Jennings, Catherine Jordan, James Jordan, John Kasha, Leonid Kagan, Cheryl Kraft, Alexander Levitsky, Mark Lewis, Xiangjun Liu, John Lopez, Daniel Ma, William Majoros, Joe McDaniel, Sean Murphy, Matthew Newman, Trung Nguyen, Ngoc Nguyen, Marc Nodell, Sue Pan, Jim Peck, Marshall Peterson, William Rowe, Robert Sanders, John Scott, Michael Simpson, Thomas Smith, Arlan Sprague, Timothy Stockwell, Russell Turner, Eli Venter, Mei Wang, Meiyuan Wen, David Wu, Mitchell Wu, Ashley Xia, Ali Zandieh, and Xiaohong Zhu

Subjects
Male, Cancer genome sequencing, Chromosomes, Artificial, Bacterial, Databases, Factual, Clinical Biochemistry, Genome, Gene Duplication, Databases, Genetic, Human Genome Project, Genetics, Multidisciplinary, Chromosome Mapping, Exons, Genomics, Genome project, Physical Chromosome Mapping, Phenotype, Genetic Techniques, Perspective, DNA, Intergenic, Female, Algorithms, Pseudogenes, Personal genomics, Genome evolution, Retroelements, Hybrid genome assembly, Biology, ENCODE, Polymorphism, Single Nucleotide, Evolution, Molecular, Sequence-tagged site, Species Specificity, Gene density, Consensus Sequence, Animals, Humans, Genome size, Repetitive Sequences, Nucleic Acid, Whole genome sequencing, Comparative genomics, Genome, Human, Biochemistry (medical), Computational Biology, Genetic Variation, Proteins, Sequence Analysis, DNA, Introns, Chromosome Banding, Genes, CpG Islands, Reference genome
Abstract

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies—a whole-genome assembly and a regional chromosome assembly—were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional ∼12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Published
2003
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11. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology

Author

Alexander Diehl, Alison Augustine, Judith Blake, Lindsay Cowell, Elizabeth Gold, Timothy Gondré-Lewis, Anna Maria Masci, Terrence Meehan, Penelope Morel, Anastasia Nijnik, Bjoern Peters, Bali Pulendran, Richard Scheuermann, Q. Alison Yao, Martin Zand, and Christopher Mungall

Subjects
General Materials Science
Published
2009
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12. Gene and alternative splicing annotation with AIR

Author

Jason R. Miller, Liliana Florea, Granger G. Sutton, Brian P. Walenz, Russell Turner, Gennady V. Merkulov, Sorin Istrail, Alison Yao, Michael Harris, Rosane Charlab, Ian M. Dew, Clark M. Mobarry, Peter W. Li, Zuoming Deng, and Valentina Di Francesco

Subjects
Pan troglodytes, Swine, Genomics, Computational biology, Vertebrate and Genome Annotation Project, Biology, Synteny, Evolution, Molecular, Annotation, Exon, Mice, Dogs, Predictive Value of Tests, Genetics, Methods, Animals, Genetics (clinical), Zebrafish, Genome, Models, Genetic, Alternative splicing, Intron, Computational Biology, Gene Annotation, Genome project, Rats, Takifugu, Alternative Splicing, Genes, Cats, Cattle, Chickens, Software, Papio
Abstract

Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced mRNA transcripts based on existing cDNA and protein sequence evidence from the same species or projected from a related species using syntenic mapping information. At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced isoforms. The putative transcripts are enumerated from the graph and assigned confidence scores based on the strength of sequence evidence, and a subset of the high-scoring candidates are selected and promoted into the annotation. The method is highly selective, eliminating the unlikely candidates while retaining 98% of the high-quality mRNA evidence in well-formed transcripts, and produces annotation that is measurably more accurate than some evidence-based gene sets. The process is fast, accurate, and fully automated, and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and systematic way, thus considerably aiding in the ensuing manual curation efforts.

Published
2005

13. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome

Author

Richard J, Mural, Mark D, Adams, Eugene W, Myers, Hamilton O, Smith, George L Gabor, Miklos, Ron, Wides, Aaron, Halpern, Peter W, Li, Granger G, Sutton, Joe, Nadeau, Steven L, Salzberg, Robert A, Holt, Chinnappa D, Kodira, Fu, Lu, Lin, Chen, Zuoming, Deng, Carlos C, Evangelista, Weiniu, Gan, Thomas J, Heiman, Jiayin, Li, Zhenya, Li, Gennady V, Merkulov, Natalia V, Milshina, Ashwinikumar K, Naik, Rong, Qi, Bixiong Chris, Shue, Aihui, Wang, Jian, Wang, Xin, Wang, Xianghe, Yan, Jane, Ye, Shibu, Yooseph, Qi, Zhao, Liansheng, Zheng, Shiaoping C, Zhu, Kendra, Biddick, Randall, Bolanos, Arthur L, Delcher, Ian M, Dew, Daniel, Fasulo, Michael J, Flanigan, Daniel H, Huson, Saul A, Kravitz, Jason R, Miller, Clark M, Mobarry, Knut, Reinert, Karin A, Remington, Qing, Zhang, Xiangqun H, Zheng, Deborah R, Nusskern, Zhongwu, Lai, Yiding, Lei, Wenyan, Zhong, Alison, Yao, Ping, Guan, Rui-Ru, Ji, Zhiping, Gu, Zhen-Yuan, Wang, Fei, Zhong, Chunlin, Xiao, Chia-Chien, Chiang, Mark, Yandell, Jennifer R, Wortman, Peter G, Amanatides, Suzanne L, Hladun, Eric C, Pratts, Jeffery E, Johnson, Kristina L, Dodson, Kerry J, Woodford, Cheryl A, Evans, Barry, Gropman, Douglas B, Rusch, Eli, Venter, Mei, Wang, Thomas J, Smith, Jarrett T, Houck, Donald E, Tompkins, Charles, Haynes, Debbie, Jacob, Soo H, Chin, David R, Allen, Carl E, Dahlke, Robert, Sanders, Kelvin, Li, Xiangjun, Liu, Alexander A, Levitsky, William H, Majoros, Quan, Chen, Ashley C, Xia, John R, Lopez, Michael T, Donnelly, Matthew H, Newman, Anna, Glodek, Cheryl L, Kraft, Marc, Nodell, Feroze, Ali, Hui-Jin, An, Danita, Baldwin-Pitts, Karen Y, Beeson, Shuang, Cai, Mark, Carnes, Amy, Carver, Parris M, Caulk, Angela, Center, Yen-Hui, Chen, Ming-Lai, Cheng, My D, Coyne, Michelle, Crowder, Steven, Danaher, Lionel B, Davenport, Raymond, Desilets, Susanne M, Dietz, Lisa, Doup, Patrick, Dullaghan, Steven, Ferriera, Carl R, Fosler, Harold C, Gire, Andres, Gluecksmann, Jeannine D, Gocayne, Jonathan, Gray, Brit, Hart, Jason, Haynes, Jeffery, Hoover, Tim, Howland, Chinyere, Ibegwam, Mena, Jalali, David, Johns, Leslie, Kline, Daniel S, Ma, Steven, MacCawley, Anand, Magoon, Felecia, Mann, David, May, Tina C, McIntosh, Somil, Mehta, Linda, Moy, Mee C, Moy, Brian J, Murphy, Sean D, Murphy, Keith A, Nelson, Zubeda, Nuri, Kimberly A, Parker, Alexandre C, Prudhomme, Vinita N, Puri, Hina, Qureshi, John C, Raley, Matthew S, Reardon, Megan A, Regier, Yu-Hui C, Rogers, Deanna L, Romblad, Jakob, Schutz, John L, Scott, Richard, Scott, Cynthia D, Sitter, Michella, Smallwood, Arlan C, Sprague, Erin, Stewart, Renee V, Strong, Ellen, Suh, Karena, Sylvester, Reginald, Thomas, Ni Ni, Tint, Christopher, Tsonis, Gary, Wang, George, Wang, Monica S, Williams, Sherita M, Williams, Sandra M, Windsor, Keriellen, Wolfe, Mitchell M, Wu, Jayshree, Zaveri, Kabir, Chaturvedi, Andrei E, Gabrielian, Zhaoxi, Ke, Jingtao, Sun, Gangadharan, Subramanian, J Craig, Venter, Cynthia M, Pfannkoch, Mary, Barnstead, and Lisa D, Stephenson

Subjects
Genetic Markers, Genome evolution, Mice, Inbred A, Molecular Sequence Data, Genomics, Mice, Inbred Strains, Biology, Genome, Synteny, Chromosomes, Evolution, Molecular, Mice, Species Specificity, Gene density, Animals, Chromosomes, Human, Humans, Conserved Sequence, Genetics, Base Composition, Multidisciplinary, Shotgun sequencing, Genome, Human, Computational Biology, Proteins, Genome project, Sequence Analysis, DNA, Physical Chromosome Mapping, Genes, Mice, Inbred DBA, Human genome, Databases, Nucleic Acid, Sequence Alignment, Reference genome
Abstract

The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.

Published
2002

14. The genome sequence of Drosophila melanogaster

Author

Mark D. Adams, Susan E. Celniker, Robert A. Holt, Cheryl A. Evans, Jeannine D. Gocayne, Peter G. Amanatides, Steven E. Scherer, Peter W. Li, Roger A. Hoskins, Richard F. Galle, Reed A. George, Suzanna E. Lewis, Stephen Richards, Michael Ashburner, Scott N. Henderson, Granger G. Sutton, Jennifer R. Wortman, Mark D. Yandell, Qing Zhang, Lin X. Chen, Rhonda C. Brandon, Yu-Hui C. Rogers, Robert G. Blazej, Mark Champe, Barret D. Pfeiffer, Kenneth H. Wan, Clare Doyle, Evan G. Baxter, Gregg Helt, Catherine R. Nelson, George L. Gabor, null Miklos, Josep F. Abril, Anna Agbayani, Hui-Jin An, Cynthia Andrews-Pfannkoch, Danita Baldwin, Richard M. Ballew, Anand Basu, James Baxendale, Leyla Bayraktaroglu, Ellen M. Beasley, Karen Y. Beeson, P. V. Benos, Benjamin P. Berman, Deepali Bhandari, Slava Bolshakov, Dana Borkova, Michael R. Botchan, John Bouck, Peter Brokstein, Phillipe Brottier, Kenneth C. Burtis, Dana A. Busam, Heather Butler, Edouard Cadieu, Angela Center, Ishwar Chandra, J. Michael Cherry, Simon Cawley, Carl Dahlke, Lionel B. Davenport, Peter Davies, Beatriz de Pablos, Arthur Delcher, Zuoming Deng, Anne Deslattes Mays, Ian Dew, Suzanne M. Dietz, Kristina Dodson, Lisa E. Doup, Michael Downes, Shannon Dugan-Rocha, Boris C. Dunkov, Patrick Dunn, Kenneth J. Durbin, Carlos C. Evangelista, Concepcion Ferraz, Steven Ferriera, Wolfgang Fleischmann, Carl Fosler, Andrei E. Gabrielian, Neha S. Garg, William M. Gelbart, Ken Glasser, Anna Glodek, Fangcheng Gong, J. Harley Gorrell, Zhiping Gu, Ping Guan, Michael Harris, Nomi L. Harris, Damon Harvey, Thomas J. Heiman, Judith R. Hernandez, Jarrett Houck, Damon Hostin, Kathryn A. Houston, Timothy J. Howland, Ming-Hui Wei, Chinyere Ibegwam, Mena Jalali, Francis Kalush, Gary H. Karpen, Zhaoxi Ke, James A. Kennison, Karen A. Ketchum, Bruce E. Kimmel, Chinnappa D. Kodira, Cheryl Kraft, Saul Kravitz, David Kulp, Zhongwu Lai, Paul Lasko, Yiding Lei, Alexander A. Levitsky, Jiayin Li, Zhenya Li, Yong Liang, Xiaoying Lin, Xiangjun Liu, Bettina Mattei, Tina C. McIntosh, Michael P. McLeod, Duncan McPherson, Gennady Merkulov, Natalia V. Milshina, Clark Mobarry, Joe Morris, Ali Moshrefi, Stephen M. Mount, Mee Moy, Brian Murphy, Lee Murphy, Donna M. Muzny, David L. Nelson, David R. Nelson, Keith A. Nelson, Katherine Nixon, Deborah R. Nusskern, Joanne M. Pacleb, Michael Palazzolo, Gjange S. Pittman, Sue Pan, John Pollard, Vinita Puri, Martin G. Reese, Knut Reinert, Karin Remington, Robert D. C. Saunders, Frederick Scheeler, Hua Shen, Bixiang Christopher Shue, Inga Sidén-Kiamos, Michael Simpson, Marian P. Skupski, Tom Smith, Eugene Spier, Allan C. Spradling, Mark Stapleton, Renee Strong, Eric Sun, Robert Svirskas, Cyndee Tector, Russell Turner, Eli Venter, Aihui H. Wang, Xin Wang, Zhen-Yuan Wang, David A. Wassarman, George M. Weinstock, Jean Weissenbach, Sherita M. Williams, Trevor Woodage, Kim C. Worley, David Wu, Song Yang, Q. Alison Yao, Jane Ye, Ru-Fang Yeh, Jayshree S. Zaveri, Ming Zhan, Guangren Zhang, Qi Zhao, Liansheng Zheng, Xiangqun H. Zheng, Fei N. Zhong, Wenyan Zhong, Xiaojun Zhou, Shiaoping Zhu, Xiaohong Zhu, Hamilton O. Smith, Richard A. Gibbs, Eugene W. Myers, Gerald M. Rubin, and J. Craig Venter

Subjects
DNA Replication, Genome evolution, DNA Repair, Transcription, Genetic, Genes, Insect, Computational biology, Biology, Genome, Euchromatin, Contig Mapping, Cytochrome P-450 Enzyme System, Gene density, Heterochromatin, Animals, Cloning, Molecular, Genome size, Gene Library, Whole genome sequencing, Genetics, Bacterial artificial chromosome, Multidisciplinary, Shotgun sequencing, Computational Biology, Nuclear Proteins, Biological Transport, Genome project, Sequence Analysis, DNA, Chromatin, Drosophila melanogaster, Protein Biosynthesis, Insect Proteins
Abstract

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the ∼120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes ∼13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

Published
2000

15. Microrheology with optical tweezersPart of a Lab on a Chipthemed issue on fundamental principles and techniques in microfluidics, edited by Juan Santiago and Chuan-Hua Chen.

Author

Alison Yao, Manlio Tassieri, Miles Padgett, and Jonathan Cooper

Subjects
*RHEOLOGY, *INTEGRATED circuits, *MICROTECHNOLOGY, *MICROFLUIDICS, *VISCOELASTICITY, *FLUID dynamics
Abstract

Microrheology is the study of the flow of materials over small scales. It is of particular interest to those involved with investigations of fluid properties within Lab-on-a-Chip structures or within other micron-scale environments. The article briefly reviews existing active and passive methods used in the study of fluids. It then explores in greater detail the use of optical tweezers as an emerging method to investigate rheological phenomena, including, for example, viscosity and viscoelasticity, as well as the related topic of flow. The article also describes, briefly, potential future applications of this topic, in the fields of biological measurement, in general, and Lab-on-a-Chip, in particular. [ABSTRACT FROM AUTHOR]

Published
2009
Full Text
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16. Multipoint viscosity measurements in microfluidic channels using optical tweezers.

Author

Stephen Keen, Alison Yao, Jonathan Leach, Roberto Di Leonardo, Chris Saunter, Gordon Love, Jonathan Cooper, and Miles Padgett

Subjects
*VISCOSITY, *PHYSICAL measurements, *MICROFLUIDIC devices, *OPTICAL instruments, *CALIBRATION, *MICROSTRUCTURE
Abstract

We demonstrate the technique of multipoint viscosity measurements incorporating the accurate calibration of micron sized particles. We describe the use of a high-speed camera to measure the residual motion of particles trapped in holographic optical tweezers, enabling us to calculate the fluid viscosity at multiple points across the field-of-view of the microscope within a microfluidic system. [ABSTRACT FROM AUTHOR]

Published
2009
Full Text
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