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3. Leveraging a new data resource to define the response of Cryptococcus neoformansto environmental signals

Author

Kang, Yu Sung, Jung, Jeffery, Brown, Holly L, Mateusiak, Chase, Doering, Tamara L, and Brent, Michael R

Abstract

Cryptococcus neoformansis an opportunistic fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth under host-like conditions. To understand how individual environmental signals affect capsule size and gene expression, we grew cells in all combinations of 5 signals implicated in capsule size and systematically measured cell and capsule sizes. We also sampled these cultures over time and performed RNA-seq in quadruplicate, yielding 881 RNA-seq samples. Analysis of the resulting data sets showed that capsule induction in tissue culture medium, typically used to represent host-like conditions, requires the presence of either CO2or exogenous cyclic AMP. Surprisingly, adding either of these pushes overall gene expression in the opposite direction from tissue culture media alone, even though both are required for capsule development. Another unexpected finding was that rich medium blocks capsule growth completely. Statistical analysis further revealed many genes whose expression is associated with capsule thickness; deletion of one of these significantly reduced capsule size. Beyond illuminating capsule induction, our massive, uniformly collected data set will be a significant resource for the research community.Cryptococcus neoformans is an opportunistic yeast that kills ~150,000 people each year. One of its key virulence factors is a polysaccharide capsule that expands greatly during infection. To help define capsule synthesis and fungal biology, we provided cells with many different combinations of host-like signals and sampled the cultures over time for transcriptional analysis. The resulting time resolved data set is by far the largest gene expression resource ever produced for C. neoformans, with 881 RNA-seq samples and matching capsule measurements. This landmark data resource will be enormously valuable to the research community as it continues to define the relationships among environmental signals and cryptococcal gene expression, biology, and virulence.

Published
2025
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4. Discovery of genomic and transcriptomic pleiotropy between kidney function and soluble receptor for advanced glycation end products using correlated meta‐analyses: The Long Life Family Study.

Author

Feitosa, Mary F., Lin, Shiow J., Acharya, Sandeep, Thyagarajan, Bharat, Wojczynski, Mary K., Kuipers, Allison L., Kulminski, Alexander, Christensen, Kaare, Zmuda, Joseph M., Brent, Michael R., and Province, Michael A.

Subjects
ADVANCED glycation end-products, KIDNEY tubules, CHRONIC kidney failure, CYSTATIN C, GENE expression
Abstract

Patients with chronic kidney disease (CKD) have increased oxidative stress and chronic inflammation, which may escalate the production of advanced glycation end‐products (AGEs). High soluble receptor for AGE (sRAGE) and low estimated glomerular filtration rate (eGFR) levels are associated with CKD and aging. We evaluated whether eGFR calculated from creatinine and cystatin C share pleiotropic genetic factors with sRAGE. We employed whole‐genome sequencing and correlated meta‐analyses on combined genome‐wide association study (GWAS) p‐values in 4182 individuals (age range: 24–110) from the Long Life Family Study (LLFS). We also conducted transcriptome‐wide association studies (TWAS) on whole blood in a subset of 1209 individuals. We identified 59 pleiotropic GWAS loci (p < 5 × 10−8) and 17 TWAS genes (Bonferroni‐p < 2.73 × 10−6) for eGFR traits and sRAGE. TWAS genes, LSP1 and MIR23AHG, were associated with eGFR and sRAGE located within GWAS loci, lncRNA‐KCNQ1OT1 and CACNA1A/CCDC130, respectively. GWAS variants were eQTLs in the kidney glomeruli and tubules, and GWAS genes predicted kidney carcinoma. TWAS genes harbored eQTLs in the kidney, predicted kidney carcinoma, and connected enhancer‐promoter variants with kidney function‐related phenotypes at p < 5 × 10−8. Additionally, higher allele frequencies of protective variants for eGFR traits were detected in LLFS than in ALFA‐Europeans and TOPMed, suggesting better kidney function in healthy‐aging LLFS than in general populations. Integrating genomic annotation and transcriptional gene activity revealed the enrichment of genetic elements in kidney function and aging‐related processes. The identified pleiotropic loci and gene expressions for eGFR and sRAGE suggest their underlying shared genetic effects and highlight their roles in kidney‐ and aging‐related signaling pathways. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Multi-omics Integration Identifies Genes Influencing Traits Associated with Cardiovascular Risks: The Long Life Family Study

Author

Acharya, Sandeep, primary, Liao, Shu, additional, Jung, Wooseok J., additional, Kang, Yu S., additional, Moghaddam, Vaha A., additional, Feitosa, Mary, additional, Wojczynski, Mary, additional, Lin, Shiow, additional, Anema, Jason A., additional, Schwander, Karen, additional, Connell, Jeff O, additional, Province, Mike, additional, and Brent, Michael R., additional

Published
2024
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6. Whole Genome Linkage and Association Analyses Identify DLG Associated Protein-1 as a Novel Positional and Biological Candidate Gene for Muscle Strength: The Long Life Family Study.

Author

Santanasto, Adam J, Acharya, Sandeep, Wojczynski, Mary K, Cvejkus, Ryan K, Lin, Shiow, Brent, Michael R, Anema, Jason A, Wang, Lihua, Thyagarajan, Bharat, Christensen, Kaare, Daw, E Warwick, and Zmuda, Joseph M

Subjects
GRIP strength, GENETIC variation, MUSCLE strength, WHOLE genome sequencing, ERYTHROCYTE membranes
Abstract

Background Grip strength is a robust indicator of overall health, is moderately heritable, and predicts longevity in older adults. Methods Using genome-wide linkage analysis, we identified a novel locus on chromosome 18p (mega-basepair region: 3.4–4.0) linked to grip strength in 3 755 individuals from 582 families aged 64 ± 12 years (range 30–110 years; 55% women). There were 26 families that contributed to the linkage peak (cumulative logarithm of the odds [LOD] score = 10.94), with 6 families (119 individuals) accounting for most of the linkage signal (LOD = 6.4). In these 6 families, using whole genome sequencing data, we performed association analyses between the 7 312 single nucleotide (SNVs) and insertion deletion (INDELs) variants in the linkage region and grip strength. Models were adjusted for age, age2, sex, height, field center, and population substructure. Results We found significant associations between genetic variants (8 SNVs and 4 INDELs, p  < 5 × 10−5) in the Disks Large-associated Protein 1 (DLGAP1) gene and grip strength. Haplotypes constructed using these variants explained up to 98.1% of the LOD score. Finally, RNAseq data showed that these variants were significantly associated with the expression of nearby Myosin Light Chain 12A (MYL12A), Structural Maintenance of Chromosomes Flexible Hinge Domain Containing 1 (SMCHD1), Erythrocyte Membrane Protein Band 4.1 Like 3 (EPB41L3) genes (p  < .0004). Conclusions The DLGAP1 gene plays an important role in the postsynaptic density of neurons; thus, it is both a novel positional and biological candidate gene for follow-up studies aimed at uncovering genetic determinants of muscle strength. [ABSTRACT FROM AUTHOR]

Published
2024
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7. The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus neoformans

Author

Loftus, Brendan J., Fung, Eula, Roncaglia, Paola, Rowley, Don, Amedeo, Paolo, Bruno, Dan, Vamathevan, Jessica, Miranda, Molly, Anderson, Iain J., Fraser, James A., Allen, Jonathan E., Bosdet, Ian E., Brent, Michael R., Chiu, Readman, Doering, Tamara L., Donlin, Maureen J., D'Souza, Cletus A., Fox, Deborah S., Grinberg, Viktoriya, Fu, Jianmin, Fukushima, Marilyn, Haas, Brian J., Huang, James C., Janbon, Guilhem, Koo, Hean L., Krzywinski, Martin I., Kwon-Chung, June K., Lengeler, Klaus B., Maiti, Rama, Marra, Marco A., Marra, Robert E., Mathewson, Carrie A., Mitchell, Thomas G., Pertea, Mihaela, Riggs, Florenta R., Salzberg, Steven L., Schein, Jacqueline E., Shvartsbeyn, Alla, Shin, Heesun, Shumway, Martin, Specht, Charles A., Suh, Bernard B., Tenney, Aaron, Utterback, Terry R., Wickes, Brian L., Wortman, Jennifer R., Wye, Natasja H., Kronstad, James W., Lodge, Jennifer K., Heitman, Joseph, Davis, Ronald W., Fraser, Claire M., and Hyman, Richard W.

Published
2005

8. An Efficient, Probabilistically Sound Algorithm for Segmentation and Word Discovery

Author

Brent, Michael R.

Subjects
Computer Science - Computation and Language, Computer Science - Learning, I.2.0, I.2.6, I.2.7
Abstract

This paper presents a model-based, unsupervised algorithm for recovering word boundaries in a natural-language text from which they have been deleted. The algorithm is derived from a probability model of the source that generated the text. The fundamental structure of the model is specified abstractly so that the detailed component models of phonology, word-order, and word frequency can be replaced in a modular fashion. The model yields a language-independent, prior probability distribution on all possible sequences of all possible words over a given alphabet, based on the assumption that the input was generated by concatenating words from a fixed but unknown lexicon. The model is unusual in that it treats the generation of a complete corpus, regardless of length, as a single event in the probability space. Accordingly, the algorithm does not estimate a probability distribution on words; instead, it attempts to calculate the prior probabilities of various word sequences that could underlie the observed text. Experiments on phonemic transcripts of spontaneous speech by parents to young children suggest that this algorithm is more effective than other proposed algorithms, at least when utterance boundaries are given and the text includes a substantial number of short utterances. Keywords: Bayesian grammar induction, probability models, minimum description length (MDL), unsupervised learning, cognitive modeling, language acquisition, segmentation, Comment: 65 double-spaced ms. pages including 3 figures

Published
1999

11. Segmenting speech without a lexicon: The roles of phonotactics and speech source

Author

Cartwright, Timothy Andrew and Brent, Michael R.

Subjects
Computer Science - Computation and Language
Abstract

Infants face the difficult problem of segmenting continuous speech into words without the benefit of a fully developed lexicon. Several sources of information in speech might help infants solve this problem, including prosody, semantic correlations and phonotactics. Research to date has focused on determining to which of these sources infants might be sensitive, but little work has been done to determine the potential usefulness of each source. The computer simulations reported here are a first attempt to measure the usefulness of distributional and phonotactic information in segmenting phoneme sequences. The algorithms hypothesize different segmentations of the input into words and select the best hypothesis according to the Minimum Description Length principle. Our results indicate that while there is some useful information in both phoneme distributions and phonotactic rules, the combination of both sources is most useful., Comment: Uses wsuipa font package and latex-acl.sty

Published
1994

12. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

Author

Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, Chinwalla, Asif, Clarke, Laura, Clee, Chris, Coghlan, Avril, Coulson, Alan, D'Eustachio, Peter, Fitch, David HA, Fulton, Lucinda A, Fulton, Robert E, Griffiths-Jones, Sam, Harris, Todd W, Hillier, LaDeana W, Kamath, Ravi, Kuwabara, Patricia E, Mardis, Elaine R, Marra, Marco A, Miner, Tracie L, Minx, Patrick, Mullikin, James C, Plumb, Robert W, Rogers, Jane, Schein, Jacqueline E, Sohrmann, Marc, Spieth, John, Stajich, Jason E, Wei, C, Willey, David, Wilson, Richard K, Durbin, Richard, and Waterston, Robert H

Subjects
Chromosomes, Artificial, Bacterial, Animals, Caenorhabditis, Caenorhabditis elegans, Proteins, MicroRNAs, RNA, Codon, RNA, Ribosomal, RNA, Transfer, RNA, Spliced Leader, Cluster Analysis, Models, Statistical, Chromosome Mapping, Physical Chromosome Mapping, Sequence Analysis, DNA, Genomics, Evolution, Molecular, Species Specificity, Interspersed Repetitive Sequences, Conserved Sequence, Protein Structure, Tertiary, Gene Library, Multigene Family, Open Reading Frames, Genome, Introns, Exons, Plasmids, Models, Genetic, Molecular Sequence Data, Biological Evolution, Chromosomes, Artificial, Bacterial, Ribosomal, Transfer, Spliced Leader, Models, Statistical, Sequence Analysis, DNA, Evolution, Molecular, Protein Structure, Tertiary, Genetic, Developmental Biology, Biological Sciences, Medical and Health Sciences, Agricultural and Veterinary Sciences
Abstract

The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.

Published
2003

13. Calling Cards: A Customizable Platform to Longitudinally Record Protein‐DNA Interactions Over Time in Cells and Tissues

Author

Yen, Allen, primary, Mateusiak, Chase, additional, Sarafinovska, Simona, additional, Gachechiladze, Mariam A., additional, Guo, Juanru, additional, Chen, Xuhua, additional, Moudgil, Arnav, additional, Cammack, Alexander J., additional, Hoisington‐Lopez, Jessica, additional, Crosby, MariaLynn, additional, Brent, Michael R., additional, Mitra, Robi D., additional, and Dougherty, Joseph D., additional

Published
2023
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28. Segmenting Speech without a Lexicon: Evidence for a Bootstrapping Mode l of Lexical Acquisition

Author

Cartwright, Timothy A. and Brent, Michael R.

Abstract

Infants face the difficult problem of segmenting continuous speech into words without the benefit of a fully developed lexicon. Several information sources in speech—prosody, semantic correlations, phonotactics, and so on—might help infants solve this problem. Research to date has focused on determining to which of these information sources infants might be sensitive, but little work has been done to determine the usefulness of each source. The computer simulations reported here are a first attempt to measure the usefulness of distributional and phonotactic information in adult- and children directed speech. The simulations hypothesize segmentations of speech into words; the best segmentation hypothesis is selected using the Minimum Description Length paradigm. Our results indicate that while there is some useful information in both phoneme distributions and phonotactic rules, the combination of both sources is most useful. Further, this combination of information sources is more useful for segmenting childdirected speech than adult-directed speech. The implications of these results for theories of lexical acquisition are discussed.

Published
1994

29. Semantic Classifcation of verbs from their Syntactic Contexts: Automated Lexicography with Implications for Child Language Acquisition

Author

Brent, Michael R.

Abstract

Young children and natural language processing programs share an insufficient knowledge of word meanings. Children catch up by learning, using innate predisposition and observation of language use. However, no one hafi demonstrated artificial devices that robustly learn lexical semantic classifications from example sentences. This paper describes the ongoing development of such a device. A n early version discovers verbs with a non-stative sense by searching in unrestricted text for verbs in syntactic constructions forbidden to statives. Our program parses unrestricted text to the extent necessary for classification. Once the parsing is done recognizing the telltale constructions is so easy even a two-year-old child could do it. In fact, Landau and Gleitman (1985) and especially Gleitman (1989) argue that children must, can, and do use the syntactic constructions in which verbs appear to support meaning acquisition. In this paper we use our program to examine the difficulty of exploiting two particular syntactic constructions to discover the availability of non-stative senses, concluding that only very little sophistication is needed. This conclusion bolsters the general position of Gleitman (1989) that children can exploit syntactic context to aid in semantic classification of verbs.

Published
1990

31. Using Multiple Alignments to Improve Gene Prediction

Author

Gross, Samuel S., Brent, Michael R., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Miyano, Satoru, editor, Mesirov, Jill, editor, Kasif, Simon, editor, and Pevzner, Pavel A., editor

Published
2005
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33. Reexamining the Vocabulary Spurt.

Author

Ganger, Jennifer and Brent, Michael R.

Abstract

The authors asked whether there is evidence to support the existence of the vocabulary spurt, an increase in the rate of word learning that is thought to occur during the 2nd year of life. Using longitudinal data from 38 children, they modeled the rate of word learning with two functions, one with an inflection point (logistic), which would indicate a spurt, and one without an inflection point (quadratic). Comparing the fits of these two functions using likelihood ratios, they found that just 5 children had a better logistic fit, which indicated that these children underwent a spurt. The implications for theories of cognitive and language development are considered.

Published
2004

34. Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Author

The modeENCODE Consortium, Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V., Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L., Landolin, Jane M., Bristow, Christopher A., Ma, Lijia, Lin, Michael F., Washietl, Stefan, Arshinoff, Bradley I., Ay, Ferhat, Meyer, Patrick E., Robine, Nicolas, Washington, Nicole L., Di Stefano, Luisa, Berezikov, Eugene, Brown, Christopher D., Candeias, Rogerio, Carlson, Joseph W., Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y., Will, Sebastian, Alekseyenko, Artyom A., Artieri, Carlo, Booth, Benjamin W., Brooks, Angela N., Dai, Qi, Davis, Carrie A., Duff, Michael O., Feng, Xin, Gorchakov, Andrey A., Gu, Tingting, Henikoff, Jorja G., Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K., Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K., Riddle, Nicole C., Sakai, Akiko, Samsonova, Anastasia, Sandler, Jeremy E., Schwartz, Yuri B., Sher, Noa, Spokony, Rebecca, Sturgill, David, van Baren, Marijke, Wan, Kenneth H., Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E., Brent, Michael R., Cherbas, Lucy, Elgin, Sarah C. R., Gingeras, Thomas R., Grossman, Robert, Hoskins, Roger A., Kaufman, Thomas C., Kent, William, Kuroda, Mitzi I., Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W., Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R., Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J., Celniker, Susan E., Henikoff, Steven, Karpen, Gary H., Lai, Eric C., MacAlpine, David M., Stein, Lincoln D., White, Kevin P., and Kellis, Manolis

Published
2010

36. The Role of Exposure to Isolated Words in Early Vocabulary Development.

Author

Brent, Michael R. and Siskind, Jeffrey M.

Abstract

Examined role of isolated words in early vocabulary development. Found that isolated words are a reliable feature of speech to infants; that they include a variety of word types; and that a substantial fraction of words infants produce are words that mothers speak in isolation. Frequency of hearing words in isolation better predicts learning than total frequency of exposure. (Author/KB)

Published
2001

39. Distributional Regularity and Phonotactic Constraints Are Useful for Segmentation.

Author

Brent, Michael R. and Cartwright, Timothy A.

Abstract

Explains distributional regularity (DR), an intuition that sound sequences occurring frequently and in multiple contexts are candidates for the lexicon. Describes study that proposed hypotheses about children's segmenting sounds using DR functions, exploiting phonotactic constraints on pronunciation, and learning word-boundary clusters. Details results of a computational simulation showing that DR functions and phonotactic constraints can significantly improve segmentation. (BC)

Published
1996

40. Advances in the Computational Study of Language Acquisition.

Author

Brent, Michael R.

Abstract

This paper locates computational and behavioral studies of children's language learning in a theoretical framework; reviews four articles in this journal issue on learning word meanings and sounds and on setting grammatical parameters; highlights "autonomous bootstrapping" strategies that children use to represent uncertain linguistic knowledge; and suggests directions for future research. (BC)

Published
1996

41. Evolution of genes and genomes on the Drosophila phylogeny

Author

Clark, Andrew G., Eisen, Michael B., Smith, Douglas R., Bergman, Casey M., Oliver, Brian, Markow, Therese A., Kaufman, Thomas C., Kellis, Manolis, Gelbart, William, Iyer, Venky N., Pollard, Daniel A., Sackton, Timothy B., Larracuente, Amanda M., Singh, Nadia D., Abad, Jose P., Abt, Dawn N., Adryan, Boris, Aguade, Montserrat, Akashi, Hiroshi, Anderson, Wyatt W., Aquadro, Charles F., Ardell, David H., Arguello, Roman, Artieri, Carlo G., Barbash, Daniel A., Barker, Daniel, Barsanti, Paolo, Batterham, Phil, Batzoglou, Serafim, Begun, Dave, Bhutkar, Arjun, Blanco, Enrico, Bosak, Stephanie A., Bradley, Robert K., Brand, Adrianne D., Brent, Michael R., Brooks, Angela N., Brown, Randall H., Butlin, Roger K., Caggese, Corrado, Calvi, Brian R., Bernardo de Carvalho, A., Caspi, Anat, Castrezana, Sergio, Celniker, Susan E., Chang, Jean L., Chapple, Charles, Chatterji, Sourav, Chinwalla, Asif, Civetta, Alberto, Clifton, Sandra W., Comeron, Josep M., Costello, James C., Coyne, Jerry A., Daub, Jennifer, David, Robert G., Delcher, Arthur L., Delehaunty, Kim, Do, Chuong B., Ebling, Heather, Edwards, Kevin, Eickbush, Thomas, Evans, Jay D., Filipski, Alan, Findeiß, Sven, Freyhult, Eva, Fulton, Lucinda, Fulton, Robert, Garcia, Ana C. L., Gardiner, Anastasia, Garfield, David A., Garvin, Barry E., Gibson, Greg, Gilbert, Don, Gnerre, Sante, Godfrey, Jennifer, Good, Robert, Gotea, Valer, Gravely, Brenton, Greenberg, Anthony J., Griffiths-Jones, Sam, Gross, Samuel, Guigo, Roderic, Gustafson, Erik A., Haerty, Wilfried, Hahn, Matthew W., Halligan, Daniel L., Halpern, Aaron L., Halter, Gillian M., Han, Mira V., Heger, Andreas, Hillier, LaDeana, Hinrichs, Angie S., Holmes, Ian, Hoskins, Roger A., Hubisz, Melissa J., Hultmark, Dan, Huntley, Melanie A., Jaffe, David B., Jagadeeshan, Santosh, Jeck, William R., Johnson, Justin, Jones, Corbin D., Jordan, William C., Karpen, Gary H., Kataoka, Eiko, Keightley, Peter D., Kheradpour, Pouya, Kirkness, Ewen F., Koerich, Leonardo B., Kristiansen, Karsten, Kudrna, Dave, Kulathinal, Rob J., Kumar, Sudhir, Kwok, Roberta, Lander, Eric, Langley, Charles H., Lapoint, Richard, Lazzaro, Brian P., Lee, So-Jeong, Levesque, Lisa, Li, Ruiqiang, Lin, Chiao-Feng, Lin, Michael F., Lindblad-Toh, Kerstin, Llopart, Ana, Long, Manyuan, Low, Lloyd, Lozovsky, Elena, Lu, Jian, Luo, Meizhong, Machado, Carlos A., Makalowski, Wojciech, Marzo, Mar, Matsuda, Muneo, Matzkin, Luciano, McAllister, Bryant, McBride, Carolyn S., McKernan, Brendan, McKernan, Kevin, Mendez-Lago, Maria, Minx, Patrick, Mollenhauer, Michael U., Montooth, Kristi, Mount, Stephen M., Mu, Xu, Myers, Eugene, Negre, Barbara, Newfeld, Stuart, Nielsen, Rasmus, Noor, Mohamed A. F., O'Grady, Patrick, Pachter, Lior, Papaceit, Montserrat, Parisi, Matthew J., Parisi, Michael, Parts, Leopold, Pedersen, Jakob S., Pesole, Graziano, Phillippy, Adam M., Ponting, Chris P., Pop, Mihai, Porcelli, Damiano, Powell, Jeffrey R., Prohaska, Sonja, Pruitt, Kim, Puig, Marta, Quesneville, Hadi, Ravi Ram, Kristipati, Rand, David, Rasmussen, Matthew D., Reed, Laura K., Reenan, Robert, Reily, Amy, Remington, Karin A., Rieger, Tania T., Ritchie, Michael G., Robin, Charles, Rogers, Yu-Hui, Rohde, Claudia, Rozas, Julio, Rubenfield, Marc J., Ruiz, Alfredo, Russo, Susan, Salzberg, Steven L., Sanchez-Gracia, Alejandro, Saranga, David J., Sato, Hajime, Schaeffer, Stephen W., Schatz, Michael C., Schlenke, Todd, Schwartz, Russell, Segarra, Carmen, Singh, Rama S., Sirot, Laura, Sirota, Marina, Sisneros, Nicholas B., Smith, Chris D., Smith, Temple F., Spieth, John, Stage, Deborah E., Stark, Alexander, Stephan, Wolfgang, Strausberg, Robert L., Strempel, Sebastian, Sturgill, David, Sutton, Granger, Sutton, Granger G., Tao, Wei, Teichmann, Sarah, Tobari, Yoshiko N., Tomimura, Yoshihiko, Tsolas, Jason M., Valente, Vera L. S., Venter, Eli, Craig Venter, J., Vicario, Saverio, Vieira, Filipe G., Vilella, Albert J., Villasante, Alfredo, Walenz, Brian, Wang, Jun, Wasserman, Marvin, Watts, Thomas, Wilson, Derek, Wilson, Richard K., Wing, Rod A., Wolfner, Mariana F., Wong, Alex, Ka-Shu Wong, Gane, Wu, Chung-I, Wu, Gabriel, Yamamoto, Daisuke, Yang, Hsiao-Pei, Yang, Shiaw-Pyng, Yorke, James A., Yoshida, Kiyohito, Zdobnov, Evgeny, Zhang, Peili, Zhang, Yu, Zimin, Aleksey V., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Christophe Acer, St, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Erii Husby, M, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Grabherr, Manfred, Kleber, Michael, Mauceli, Evan, and MacCallum, Iain

Abstract

Author(s): Drosophila 12 Genomes Consortium; Project Leaders; Andrew G. Clark (corresponding author) [1]; Michael B. Eisen (corresponding author) [2, 3]; Douglas R. Smith (corresponding author) [4]; Casey M. Bergman (corresponding [...]

Published
2007
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44. The DNA sequence of human chromosome 7

Author

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

Abstract

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

Published
2003
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46. Initial sequencing and comparative analysis of the mouse genome

Author

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

Abstract

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

Published
2002
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47. The developmental transcriptome of Drosophila melanogaster

Author

Graveley, Brenton R., Brooks, Angela N., Carlson, Joseph W., Duff, Michael O., Landolin, Jane M., Yang, Li, Artieri, Carlo G., van Baren, Marijke J., Boley, Nathan, Booth, Benjamin W., Brown, James B., Cherbas, Lucy, Davis, Carrie A., Dobin, Alex, Li, Renhua, Lin, Wei, Malone, John H., Mattiuzzo, Nicolas R., Miller, David, Sturgill, David, Tuch, Brian B., Zaleski, Chris, Zhang, Dayu, Blanchette, Marco, Dudoit, Sandrine, Eads, Brian, Green, Richard E., Hammonds, Ann, Jiang, Lichun, Kapranov, Phil, Langton, Laura, Perrimon, Norbert, Sandler, Jeremy E., Wan, Kenneth H., Willingham, Aarron, Zhang, Yu, Zou, Yi, Andrews, Justen, Bickel, Peter J., Brenner, Steven E., Brent, Michael R., Cherbas, Peter, Gingeras, Thomas R., Hoskins, Roger A., Kaufman, Thomas C., Oliver, Brian, and Celniker, Susan E.

Published
2011
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