Search

Your search keyword '"Haas, Brian J."' showing total 492 results
Start Over Author "Haas, Brian J."
492 results on '"Haas, Brian J."'

2. A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

Author

Creason, Allison, Haan, David, Dang, Kristen, Chiotti, Kami E, Inkman, Matthew, Lamb, Andrew, Yu, Thomas, Hu, Yin, Norman, Thea C, Buchanan, Alex, van Baren, Marijke J, Spangler, Ryan, Rollins, M Rick, Spellman, Paul T, Rozanov, Dmitri, Zhang, Jin, Maher, Christopher A, Caloian, Cristian, Watson, John D, Uhrig, Sebastian, Haas, Brian J, Jain, Miten, Akeson, Mark, Ahsen, Mehmet Eren, Participants, SMC-RNA Challenge, Zhang, Hongjiu, Wang, Yifan, Guan, Yuanfang, Nguyen, Cu, Sugai, Christopher, Jha, Alokkumar, Li, Jing Woei, Dobin, Alexander, Stolovitzky, Gustavo, Guinney, Justin, Boutros, Paul C, Stuart, Joshua M, and Ellrott, Kyle

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Cancer, Cancer Genomics, Generic health relevance, Humans, Neoplasms, Protein Isoforms, RNA, RNA-Seq, Sequence Analysis, RNA, SMC-RNA Challenge Participants, Cloud compute, DREAM Challenge, RNA fusion, RNA-seq, benchmark, crowd-sourced, evaluation, isoform quantification, Biochemistry and Cell Biology, Biochemistry and cell biology
Abstract

The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from the inference of the impacts of somatic variants to pathway analysis to biomarker development and subtype discovery. The ICGC-TCGA DREAM Somatic Mutation Calling in RNA (SMC-RNA) challenge was a crowd-sourced effort to benchmark methods for RNA isoform quantification and fusion detection from bulk cancer RNA sequencing (RNA-seq) data. It concluded in 2018 with a comparison of 77 fusion detection entries and 65 isoform quantification entries on 51 synthetic tumors and 32 cell lines with spiked-in fusion constructs. We report the entries used to build this benchmark, the leaderboard results, and the experimental features associated with the accurate prediction of RNA species. This challenge required submissions to be in the form of containerized workflows, meaning each of the entries described is easily reusable through CWL and Docker containers at https://github.com/SMC-RNA-challenge. A record of this paper's transparent peer review process is included in the supplemental information.

Published
2021

4. Next-generation characterization of the Cancer Cell Line Encyclopedia

Author

Ghandi, Mahmoud, Huang, Franklin W, Jané-Valbuena, Judit, Kryukov, Gregory V, Lo, Christopher C, McDonald, E Robert, Barretina, Jordi, Gelfand, Ellen T, Bielski, Craig M, Li, Haoxin, Hu, Kevin, Andreev-Drakhlin, Alexander Y, Kim, Jaegil, Hess, Julian M, Haas, Brian J, Aguet, François, Weir, Barbara A, Rothberg, Michael V, Paolella, Brenton R, Lawrence, Michael S, Akbani, Rehan, Lu, Yiling, Tiv, Hong L, Gokhale, Prafulla C, de Weck, Antoine, Mansour, Ali Amin, Oh, Coyin, Shih, Juliann, Hadi, Kevin, Rosen, Yanay, Bistline, Jonathan, Venkatesan, Kavitha, Reddy, Anupama, Sonkin, Dmitriy, Liu, Manway, Lehar, Joseph, Korn, Joshua M, Porter, Dale A, Jones, Michael D, Golji, Javad, Caponigro, Giordano, Taylor, Jordan E, Dunning, Caitlin M, Creech, Amanda L, Warren, Allison C, McFarland, James M, Zamanighomi, Mahdi, Kauffmann, Audrey, Stransky, Nicolas, Imielinski, Marcin, Maruvka, Yosef E, Cherniack, Andrew D, Tsherniak, Aviad, Vazquez, Francisca, Jaffe, Jacob D, Lane, Andrew A, Weinstock, David M, Johannessen, Cory M, Morrissey, Michael P, Stegmeier, Frank, Schlegel, Robert, Hahn, William C, Getz, Gad, Mills, Gordon B, Boehm, Jesse S, Golub, Todd R, Garraway, Levi A, and Sellers, William R

Subjects
Genetics, Human Genome, Lung, Cancer, Biotechnology, Lung Cancer, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Antineoplastic Agents, Biomarkers, Tumor, Cell Line, Tumor, DNA Methylation, Drug Resistance, Neoplasm, Ethnicity, Gene Editing, Histones, Humans, MicroRNAs, Molecular Targeted Therapy, Neoplasms, Protein Array Analysis, RNA Splicing, General Science & Technology
Abstract

Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR-Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines.

Published
2019

5. CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution

Author

Qin, Qian, primary, Popic, Victoria, additional, Yu, Houlin, additional, White, Emily, additional, Khorgade, Akanksha, additional, Shin, Asa, additional, Wienand, Kirsty, additional, Dondi, Arthur, additional, Beerenwinkel, Niko, additional, Vazquez, Francisca, additional, AlKhafaji, Aziz M., additional, and Haas, Brian J., additional

Published
2024
Full Text
View/download PDF

6. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

Author

Fields, Alexander P, Rodriguez, Edwin H, Jovanovic, Marko, Stern-Ginossar, Noam, Haas, Brian J, Mertins, Philipp, Raychowdhury, Raktima, Hacohen, Nir, Carr, Steven A, Ingolia, Nicholas T, Regev, Aviv, and Weissman, Jonathan S

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Genetics, Biological Sciences, Biotechnology, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Amino Acid Sequence, Animals, Cells, Cultured, Conserved Sequence, Dendritic Cells, Humans, Lipopolysaccharides, Mice, Open Reading Frames, Proteome, Proteomics, Regression Analysis, Ribosomes, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovered proteins violate these rules. Here we present an experimental and analytical framework, based on ribosome profiling and linear regression, for systematic identification and quantification of translation. Application of this approach to lipopolysaccharide-stimulated mouse dendritic cells and HCMV-infected human fibroblasts identifies thousands of novel CDSs, including micropeptides and variants of known proteins, that bear the hallmarks of canonical translation and exhibit translation levels and dynamics comparable to that of annotated CDSs. Remarkably, many translation events are identified in both mouse and human cells even when the peptide sequence is not conserved. Our work thus reveals an unexpected complexity to mammalian translation suited to provide both conserved regulatory or protein-based functions.

Published
2015

7. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

Author

Lamour, Kurt H., Mudge, Joann, Gobena, Daniel, Hurtado-Gonzales, Oscar P., Schmutz, Jeremy, Kuo, Alan, Miller, Neil A., Rice, Brandon J., Raffaele, Sylvain, Cano, Liliana M., Bharti, Arvind K., Donahoo, Ryan S., Finely, Sabra, Huitema, Edgar, Hulvey, Jon, Platt, Darren, Salamov, Asaf, Savidor, Alon, Sharma, Rahul, Stam, Remco, Sotrey, Dylan, Thines, Marco, Win, Joe, Haas, Brian J., Dinwiddie, Darrell L., Jenkins, Jerry, Knight, James R., Affourtit, Jason P., Han, Cliff S., Chertkov, Olga, Lindquist, Erika A., Detter, Chris, Grigoriev, Igor V., Kamoun, Sophien, and Kingsmore, Stephen F.

Abstract

The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

Published
2012

8. UCHIME improves sensitivity and speed of chimera detection

Author

Edgar, Robert C, Haas, Brian J, Clemente, Jose C, Quince, Christopher, and Knight, Rob

Subjects
Genetics, Biotechnology, Basic Behavioral and Social Science, Behavioral and Social Science, Algorithms, Artifacts, Computational Biology, Polymerase Chain Reaction, Sequence Analysis, DNA, Software, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

MotivationChimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.ResultsWe describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer.Contactrobert@drive5.comAvailabilitySource, binaries and data: http://drive5.com/uchime.Supplementary informationSupplementary data are available at Bioinformatics online.

Published
2011

10. Comparative Genomics of Trypanosomatid Parasitic Protozoa

Author

El-Sayed, Najib M., Myler, Peter J., Blandin, Gaëlle, Berriman, Matthew, Crabtree, Jonathan, Aggarwal, Gautam, Caler, Elisabet, Renauld, Hubert, Worthey, Elizabeth A., Hertz-Fowler, Christiane, Ghedin, Elodie, Peacock, Christopher, Bartholomeu, Daniella C., Haas, Brian J., Tran, Anh-Nhi, Wortman, Jennifer R., Angiuoli, Samuel, Anupama, Atashi, Badger, Jonathan, Bringaud, Frederic, Cadag, Eithon, Carlton, Jane M., Cerqueira, Gustavo C., Creasy, Todd, Delcher, Arthur L., Djikeng, Appolinaire, Embley, T. Martin, Hauser, Christopher, Ivens, Alasdair C., Kummerfeld, Sarah K., Pereira-Leal, Jose B., Nilsson, Daniel, Peterson, Jeremy, Salzberg, Steven L., Shallom, Joshua, Silva, Joana C., Sundaram, Jaideep, Westenberger, Scott, White, Owen, Melville, Sara E., Donelson, John E., Andersson, Björn, Stuart, Kenneth D., and Hall, Neil

Published
2005

12. 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

13. Annotation of the Arabidopsis Genome

Author

Wortman, Jennifer R., Haas, Brian J., Smith,, Roger K., Maiti, Rama, Ronning, Catherine M., Whitelaw, Catherine A., White, Owen R., and Town, Christopher D.

Published
2003

14. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure.

Author

Coyne, Robert S, Thiagarajan, Mathangi, Jones, Kristie M, Wortman, Jennifer R, Tallon, Luke J, Haas, Brian J, Cassidy-Hanley, Donna M, Wiley, Emily A, Smith, Joshua J, Collins, Kathleen, Lee, Suzanne R, Couvillion, Mary T, Liu, Yifan, Garg, Jyoti, Pearlman, Ronald E, Hamilton, Eileen P, Orias, Eduardo, Eisen, Jonathan A, and Methé, Barbara A

Subjects
Macronucleus, Micronucleus, Germline, Animals, Tetrahymena thermophila, Nucleic Acid Hybridization, Genes, Protozoan, Genome, Protozoan, Expressed Sequence Tags, Micronucleus, Germline, Genes, Protozoan, Genome, Genetics, Biotechnology, Human Genome, Generic Health Relevance, Bioinformatics, Biological Sciences, Medical and Health Sciences, Information and Computing Sciences
Abstract

BackgroundTetrahymena thermophila, a widely studied model for cellular and molecular biology, is a binucleated single-celled organism with a germline micronucleus (MIC) and somatic macronucleus (MAC). The recent draft MAC genome assembly revealed low sequence repetitiveness, a result of the epigenetic removal of invasive DNA elements found only in the MIC genome. Such low repetitiveness makes complete closure of the MAC genome a feasible goal, which to achieve would require standard closure methods as well as removal of minor MIC contamination of the MAC genome assembly. Highly accurate preliminary annotation of Tetrahymena's coding potential was hindered by the lack of both comparative genomic sequence information from close relatives and significant amounts of cDNA evidence, thus limiting the value of the genomic information and also leaving unanswered certain questions, such as the frequency of alternative splicing.ResultsWe addressed the problem of MIC contamination using comparative genomic hybridization with purified MIC and MAC DNA probes against a whole genome oligonucleotide microarray, allowing the identification of 763 genome scaffolds likely to contain MIC-limited DNA sequences. We also employed standard genome closure methods to essentially finish over 60% of the MAC genome. For the improvement of annotation, we have sequenced and analyzed over 60,000 verified EST reads from a variety of cellular growth and development conditions. Using this EST evidence, a combination of automated and manual reannotation efforts led to updates that affect 16% of the current protein-coding gene models. By comparing EST abundance, many genes showing apparent differential expression between these conditions were identified. Rare instances of alternative splicing and uses of the non-standard amino acid selenocysteine were also identified.ConclusionWe report here significant progress in genome closure and reannotation of Tetrahymena thermophila. Our experience to date suggests that complete closure of the MAC genome is attainable. Using the new EST evidence, automated and manual curation has resulted in substantial improvements to the over 24,000 gene models, which will be valuable to researchers studying this model organism as well as for comparative genomics purposes.

Published
2008

15. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

Author

Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, Badger, Jonathan H, Ren, Qinghu, Amedeo, Paolo, Jones, Kristie M, Tallon, Luke J, Delcher, Arthur L, Salzberg, Steven L, Silva, Joana C, Haas, Brian J, Majoros, William H, Farzad, Maryam, Carlton, Jane M, Smith, Roger K, Garg, Jyoti, Pearlman, Ronald E, Karrer, Kathleen M, Sun, Lei, Manning, Gerard, Elde, Nels C, Turkewitz, Aaron P, Asai, David J, Wilkes, David E, Wang, Yufeng, Cai, Hong, Collins, Kathleen, Stewart, B Andrew, Lee, Suzanne R, Wilamowska, Katarzyna, Weinberg, Zasha, Ruzzo, Walter L, Wloga, Dorota, Gaertig, Jacek, Frankel, Joseph, Tsao, Che-Chia, Gorovsky, Martin A, Keeling, Patrick J, Waller, Ross F, Patron, Nicola J, Cherry, J Michael, Stover, Nicholas A, Krieger, Cynthia J, del Toro, Christina, Ryder, Hilary F, Williamson, Sondra C, Barbeau, Rebecca A, Hamilton, Eileen P, and Orias, Eduardo

Abstract

The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.

Published
2006

16. Supplementary Data from Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival

Author

Gillani, Riaz, primary, Seong, Bo Kyung A., primary, Crowdis, Jett, primary, Conway, Jake R., primary, Dharia, Neekesh V., primary, Alimohamed, Saif, primary, Haas, Brian J., primary, Han, Kyuho, primary, Park, Jihye, primary, Dietlein, Felix, primary, He, Meng Xiao, primary, Imamovic, Alma, primary, Ma, Clement, primary, Bassik, Michael C., primary, Boehm, Jesse S., primary, Vazquez, Francisca, primary, Gusev, Alexander, primary, Liu, David, primary, Janeway, Katherine A., primary, McFarland, James M., primary, Stegmaier, Kimberly, primary, and Van Allen, Eliezer M., primary

Published
2023
Full Text
View/download PDF

17. Data from Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival

Author

Gillani, Riaz, primary, Seong, Bo Kyung A., primary, Crowdis, Jett, primary, Conway, Jake R., primary, Dharia, Neekesh V., primary, Alimohamed, Saif, primary, Haas, Brian J., primary, Han, Kyuho, primary, Park, Jihye, primary, Dietlein, Felix, primary, He, Meng Xiao, primary, Imamovic, Alma, primary, Ma, Clement, primary, Bassik, Michael C., primary, Boehm, Jesse S., primary, Vazquez, Francisca, primary, Gusev, Alexander, primary, Liu, David, primary, Janeway, Katherine A., primary, McFarland, James M., primary, Stegmaier, Kimberly, primary, and Van Allen, Eliezer M., primary

Published
2023
Full Text
View/download PDF

19. Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector

Author

Haas, Brian J

Subjects
FusionInspector transcriptomics rna-seq STAR-Fusion CTAT
Abstract

Supplementary Code and Data for manuscript: Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector by Brian J. Haas, Alexander Dobin, Mahmoud Ghandi, Anne Van Arsdale, Timothy Tickle, James T. Robinson, Riaz Gillani, Simon Kasif,and Aviv Regev &nbsp

Published
2023
Full Text
View/download PDF

23. Erratum: The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation

Author

Wallrapp, Antonia, Riesenfeld, Samantha J., Burkett, Patrick R., Abdulnour, Raja-Elie E., Nyman, Jackson, Dionne, Danielle, Hofree, Matan, Cuoco, Michael S., Rodman, Christopher, Farouq, Daneyal, Haas, Brian J., Tickle, Timothy L., Trombetta, John J., Baral, Pankaj, Klose, Christoph S. N., Mahlakõiv, Tanel, Artis, David, Rozenblatt-Rosen, Orit, Chiu, Isaac M., Levy, Bruce D., Kowalczyk, Monika S., Regev, Aviv, and Kuchroo, Vijay K.

Published
2017
Full Text
View/download PDF

24. The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation

Author

Wallrapp, Antonia, Riesenfeld, Samantha J., Burkett, Patrick R., Abdulnour, Raja-Elie E., Nyman, Jackson, Dionne, Danielle, Hofree, Matan, Cuoco, Michael S., Rodman, Christopher, Farouq, Daneyal, Haas, Brian J., Tickle, Timothy L., Trombetta, John J., Baral, Pankaj, Klose, Christoph S. N., Mahlakõiv, Tanel, Artis, David, Rozenblatt-Rosen, Orit, Chiu, Isaac M., Levy, Bruce D., Kowalczyk, Monika S., Regev, Aviv, and Kuchroo, Vijay K.

Published
2017
Full Text
View/download PDF

25. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

Author

Grad, Yonatan H., Lipsitch, Marc, Feldgarden, Michael, Arachchi, Harindra M., Cerqueira, Gustavo C., FitzGerald, Michael, Godfrey, Paul, Haas, Brian J., Murphy, Cheryl I., Russ, Carsten, Sykes, Sean, Walker, Bruce J., Wortman, Jennifer R., Young, Sarah, Zeng, Qiandong, Abouelleil, Amr, Bochicchio, James, Chauvin, Sara, DeSmet, Timothy, Gujja, Sharvari, McCowan, Caryn, Montmayeur, Anna, Steelman, Scott, Frimodt-Møller, Jakob, Petersen, Andreas M., Struve, Carsten, Krogfelt, Karen A., Bingen, Edouard, Weill, François-Xavier, Lander, Eric S., Nusbaum, Chad, Birren, Bruce W., Hung, Deborah T., and Hanage, William P.

Published
2012

26. Comparative Functional Genomics of the Fission Yeasts

Author

Rhind, Nicholas, Chen, Zehua, Yassour, Moran, Thompson, Dawn A., Haas, Brian J., Habib, Naomi, Wapinski, Ilan, Roy, Sushmita, Lin, Michael F., Heiman, David I., Young, Sarah K., Furuya, Kanji, Guo, Yabin, Pidoux, Alison, Chen, Huei Mei, Robbertse, Barbara, Goldberg, Jonathan M., Aoki, Keita, Bayne, Elizabeth H., Berlin, Aaron M., Desjardins, Christopher A., Dobbs, Edward, Dukaj, Livio, Fan, Lin, FitzGerald, Michael G., French, Courtney, Gujja, Sharvari, Hansen, Klavs, Keifenheim, Dan, Levin, Joshua Z., Mosher, Rebecca A., Müller, Carolin A., Pfiffner, Jenna, Priest, Margaret, Russ, Carsten, Smialowska, Agata, Swoboda, Peter, Sykes, Sean M., Vaughn, Matthew, Vengrova, Sonya, Yoder, Ryan, Zeng, Qiandong, Allshire, Robin, Baulcombe, David, Birren, Bruce W., Brown, William, Ekwall, Karl, Kellis, Manolis, Leatherwood, Janet, Levin, Henry, Margalit, Hanah, Martienssen, Rob, Nieduszynski, Conrad A., Spatafora, Joseph W., Friedman, Nir, Dalgaard, Jacob Z., Baumann, Peter, Niki, Hironori, Regev, Aviv, and Nusbaum, Chad

Published
2011
Full Text
View/download PDF

27. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

Author

Kirkness, Ewen F., Haas, Brian J., Sun, Weilin, Braig, Henk R., Perotti, M. Alejandra, Clark, John M., Lee, Si Hyeock, Robertson, Hugh M., Kennedy, Ryan C., Elhaik, Eran, Gerlach, Daniel, Kriventseva, Evgenia V., Elsik, Christine G., Graur, Dan, Hill, Catherine A., Veenstra, Jan A., Walenz, Brian, Tubío, José Manuel C., Ribeiro, José M. C., Rozas, Julio, Johnston, J. Spencer, Reese, Justin T., Popadic, Aleksandar, Tojo, Marta, Raoult, Didier, Reed, David L., Tomoyasu, Yoshinori, Krause, Emily, Mittapalli, Omprakash, Margam, Venu M., Li, Hong-Mei, Meyer, Jason M., Johnson, Reed M., Romero-Severson, Jeanne, VanZee, Janice Pagel, Alvarez-Ponce, David, Vieira, Filipe G., Aguadé, Montserrat, Guirao-Rico, Sara, Anzola, Juan M., Yoon, Kyong S., Strycharz, Joseph P., Unger, Maria F., Christley, Scott, Lobo, Neil F., Seufferheld, Manfredo J., Wang, NaiKuan, Dasch, Gregory A., Struchiner, Claudio J., Madey, Greg, Hannick, Linda I., Bidwell, Shelby, Joardar, Vinita, Caler, Elisabet, Shao, Renfu, Barker, Stephen C., Cameron, Stephen, Bruggner, Robert V., Regier, Allison, Johnson, Justin, Viswanathan, Lakshmi, Utterback, Terry R., Sutton, Granger G., Lawson, Daniel, Waterhouse, Robert M., Venter, J. Craig, Strausberg, Robert L., Berenbaum, May R., Collins, Frank H., Zdobnov, Evgeny M., and Pittendrigh, Barry R.

Published
2010

29. Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis

Author

Carlton, Jane M., Hirt, Robert P., Silva, Joana C., Delcher, Arthur L., Schatz, Michael, Zhao, Qi, Wortman, Jennifer R., Bidwell, Shelby L., Alsmark, U. Cecilia M., Besteiro, Sébastien, Sicheritz-Ponten, Thomas, Noel, Christophe J., Dacks, Joel B., Foster, Peter G., Simillion, Cedric, Van de Peer, Yves, Miranda-Saavedra, Diego, Barton, Geoffrey J., Westrop, Gareth D., Müller, Sylke, Dessi, Daniele, Fiori, Pier Luigi, Ren, Qinghu, Paulsen, Ian, Zhang, Hanbang, Bastida-Corcuera, Felix D., Simoes-Barbosa, Augusto, Brown, Mark T., Hayes, Richard D., Mukherjee, Mandira, Okumura, Cheryl Y., Schneider, Rachel, Smith, Alias J., Vanacova, Stepanka, Villalvazo, Maria, Haas, Brian J., Pertea, Mihaela, Feldblyum, Tamara V., Utterback, Terry R., Shu, Chung-Li, Osoegawa, Kazutoyo, de Jong, Pieter J., Hrdy, Ivan, Horvathova, Lenka, Zubacova, Zuzana, Dolezal, Pavel, Malik, Shehre-Banoo, Logsdon, John M., Henze, Katrin, Gupta, Arti, Wang, Ching C., Dunne, Rebecca L., Upcroft, Jacqueline A., Upcroft, Peter, White, Owen, Salzberg, Steven L., Tang, Petrus, Chiu, Cheng-Hsun, Lee, Ying-Shiung, Embley, T. Martin, Coombs, Graham H., Mottram, Jeremy C., Tachezy, Jan, Fraser-Liggett, Claire M., and Johnson, Patricia J.

Published
2007
Full Text
View/download PDF

31. A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

Author

Zhang, Hongjiu, Wang, Yifan, Guan, Yuanfang, Nguyen, Cu, Sugai, Christopher, Jha, Alokkumar, Li, Jing Woei, Dobin, Alexander, Creason, Allison, Haan, David, Dang, Kristen, Chiotti, Kami E., Inkman, Matthew, Lamb, Andrew, Yu, Thomas, Hu, Yin, Norman, Thea C., Buchanan, Alex, van Baren, Marijke J., Spangler, Ryan, Rollins, M. Rick, Spellman, Paul T., Rozanov, Dmitri, Zhang, Jin, Maher, Christopher A., Caloian, Cristian, Watson, John D., Uhrig, Sebastian, Haas, Brian J., Jain, Miten, Akeson, Mark, Ahsen, Mehmet Eren, Stolovitzky, Gustavo, Guinney, Justin, Boutros, Paul C., Stuart, Joshua M., and Ellrott, Kyle

Published
2021
Full Text
View/download PDF

32. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Author

Haas, Brian J, Papanicolaou, Alexie, Yassour, Moran, Grabherr, Manfred, Blood, Philip D, Bowden, Joshua, Couger, Matthew Brian, Eccles, David, Li, Bo, Lieber, Matthias, MacManes, Matthew D, Ott, Michael, Orvis, Joshua, Pochet, Nathalie, Strozzi, Francesco, Weeks, Nathan, Westerman, Rick, William, Thomas, Dewey, Colin N, Henschel, Robert, LeDuc, Richard D, Friedman, Nir, and Regev, Aviv

Published
2013
Full Text
View/download PDF

34. Abstract 96: Gene fusions create partner and collateral dependencies that are essential to cancer cell survival

Author

Gillani, Riaz, primary, Seong, Bo Kyung A., additional, Crowdis, Jett, additional, Conway, Jake R., additional, Dharia, Neekesh V., additional, Alimohamed, Saif, additional, Haas, Brian J., additional, Han, Kyuho, additional, Park, Jihye, additional, Liu, David, additional, Dietlein, Felix, additional, He, Meng Xiao, additional, Imamovic, Alma, additional, Ma, Clement, additional, Bassik, Michael C., additional, Boehm, Jesse S., additional, Vazquez, Francisca, additional, Gusev, Alexander, additional, Janeway, Katherine A., additional, McFarland, James M., additional, Stegmaier, Kimberly, additional, and Van Allen, Eliezer M., additional

Published
2021
Full Text
View/download PDF

35. Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival

Author

Gillani, Riaz, primary, Seong, Bo Kyung A., additional, Crowdis, Jett, additional, Conway, Jake R., additional, Dharia, Neekesh V., additional, Alimohamed, Saif, additional, Haas, Brian J., additional, Han, Kyuho, additional, Park, Jihye, additional, Dietlein, Felix, additional, He, Meng Xiao, additional, Imamovic, Alma, additional, Ma, Clement, additional, Bassik, Michael C., additional, Boehm, Jesse S., additional, Vazquez, Francisca, additional, Gusev, Alexander, additional, Liu, David, additional, Janeway, Katherine A., additional, McFarland, James M., additional, Stegmaier, Kimberly, additional, and Van Allen, Eliezer M., additional

Published
2021
Full Text
View/download PDF

36. Full-length transcriptome assembly from RNA-Seq data without a reference genome

Author

Grabherr, Manfred G, Haas, Brian J, Yassour, Moran, Levin, Joshua Z, Thompson, Dawn A, Amit, Ido, Adiconis, Xian, Fan, Lin, Raychowdhury, Raktima, Zeng, Qiandong, Chen, Zehua, Mauceli, Evan, Hacohen, Nir, Gnirke, Andreas, Rhind, Nicholas, di Palma, Federica, Birren, Bruce W, Nusbaum, Chad, Lindblad-Toh, Kerstin, Friedman, Nir, and Regev, Aviv

Published
2011
Full Text
View/download PDF

39. Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants (1[w])

Author

Xiao, Yong-Li, Smith, Shannon R., Ishmael, Nadeeza, Redman, Julia C., Kumar, Nihkil, Monaghan, Erin L., Ayele, Mulu, Haas, Brian J., Wu, Hank C., and Town, Christopher D.

Subjects
Arabidopsis -- Research, Arabidopsis -- Physiological aspects, Chromosomes -- Research, DNA -- Research, Genomes -- Research, Genetic transcription -- Research, Biological sciences, Science and technology
Published
2005

40. Comparative genomics of trypanosomatid parasitic protozoa

Author

Sayed, Najib M. El-, Myler, Peter J., Blandin, Gaelle, Berriman, Matthew, Crabtree, Jonathan, Aggarwal, Gautam, Caler, Elisabet, Renauld, Hubert, Worthey, Elizabeth A., Hertz-Fowler, Christiane, Ghedin, Elodie, Peacock, Christopher, Bartholomeu, Daniella C., Haas, Brian J., Tran, Anh-Nhi, Wortman, Jennifer R., Alsmark, U. Cecilia M., Angiuoli, Samuel, Anupama, Atashi, Badger, Jonathan, Bringaud, Frederic, Cadag, Eithon, Carlton, Jane M., Cerqueira, Gustavo C., Creasy, Todd, Delcher, Arthur L., Djikeng, Appolinaire, Embley, T. Martin, Hauser, Christopher, Ivens, Alasdair C., Kummerfeld, Sarah K., Pereira-Leal, Jose B., Nilsson, Daniel, Peterson, Jeremy, Salzberg, Steven L., Shallom, Joshua, Silva, Joana C., Sundaram, Jaideep, Westenberger, Scott, White, Owen, Melville, Sara E., Donelson, John E., Andersson, Bjorn, Stuart, Kenneth D., and Hall, Neil

Subjects
Leishmaniasis -- Genetic aspects, Trypanosoma cruzi -- Genetic aspects, Trypanosoma brucei -- Genetic aspects, Science and technology, Genetic aspects
Abstract

A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that--along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions--have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont., The protozoan pamogens Leishmania major, Trypanosoma cruzi, and Trypanosoma brucei (family Trypanosomatidae, order Kinetoplastida) collectively cause disease and death in millions of humans and countless infections in other mammals, primarily [...]

Published
2005

43. A framework for human microbiome research

Author

Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
Full Text
View/download PDF

44. Structure, function and diversity of the healthy human microbiome

Author

Huttenhower, Curtis, Gevers, Dirk, Knight, Rob, Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Creasy, Heather H., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Giglio, Michelle G., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien, Brooks, Paul J., Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S. G., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm Michael, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry J., Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haake, Susan Kinder, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, King, Nicholas B., Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavromatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Pop, Mihai, Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Christopher S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, YuanQing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Methé, Barbara A., Nelson, Karen E., Petrosino, Joseph F., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
Full Text
View/download PDF

45. Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes

Author

Gevaert, Olivier, primary, Nabian, Mohsen, additional, Bakr, Shaimaa, additional, Everaert, Celine, additional, Shinde, Jayendra, additional, Manukyan, Artur, additional, Liefeld, Ted, additional, Tabor, Thorin, additional, Xu, Jishu, additional, Lupberger, Joachim, additional, Haas, Brian J., additional, Baumert, Thomas F., additional, Hernaez, Mikel, additional, Reich, Michael, additional, Quintana, Francisco J., additional, Uhlmann, Erik J., additional, Krichevsky, Anna M., additional, Mesirov, Jill P., additional, Carey, Vincent, additional, and Pochet, Nathalie, additional

Published
2020
Full Text
View/download PDF

46. Cover Image: Volume 22, Issue 4

Author

Leigh, Nicholas D., primary, Sessa, Sofia, additional, Dragalzew, Aline C., additional, Payzin‐Dogru, Duygu, additional, Sousa, Josane F., additional, Aggouras, Anthony N., additional, Johnson, Kimberly, additional, Dunlap, Garrett S., additional, Haas, Brian J., additional, Levin, Michael, additional, Schneider, Igor, additional, and Whited, Jessica L., additional

Published
2020
Full Text
View/download PDF

47. von Willebrand factor D and EGF domains is an evolutionarily conserved and required feature of blastemas capable of multitissue appendage regeneration

Author

Leigh, Nicholas D., primary, Sessa, Sofia, additional, Dragalzew, Aline C., additional, Payzin‐Dogru, Duygu, additional, Sousa, Josane F., additional, Aggouras, Anthony N., additional, Johnson, Kimberly, additional, Dunlap, Garrett S., additional, Haas, Brian J., additional, Levin, Michael, additional, Schneider, Igor, additional, and Whited, Jessica L., additional

Published
2020
Full Text
View/download PDF

48. Purification and characterization of Thermotoga maritima endonuclease IV, a thermostable apurinic/apyrimidinic endonuclease and 3'-repair diesterase

Author

Haas, Brian J., Sandigursky, Margarita, Tainer, John A., Franklin, William A., and Cunningham, Richard P.

Subjects
Bacteria, Thermophilic -- Genetic aspects, Microbial enzymes -- Research, DNA repair -- Research, Biological sciences
Abstract

A study of the cloned Thermotoga maritima endonuclease IV gene reveals that its expressed protein display enzymatic activities similar to those of the apurinic/apyrimidinic endonuclease. The protein is also found to have repair activities similar to those of 3'-phosphates, 3'-phosphoglycolates and 3'-trans-4-hydroxy-2-pentenal-5-phosphates. Moreover, the structure of the T. maritima endonuclease IV is more stable than the Escherichia coli endonuclease IV.

Published
1999

49. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

Author

Haas, Brian J., Kamoun, Sophien, Zody, Michael C., Jiang, Rays H. Y., Handsaker, Robert E., Cano, Liliana M., Grabherr, Manfred, Kodira, Chinnappa D., Raffaele, Sylvain, Torto-Alalibo, Trudy, Bozkurt, Tolga O., Ah-Fong, Audrey M. V., Alvarado, Lucia, Anderson, Vicky L., Armstrong, Miles R., Avrova, Anna, Baxter, Laura, Beynon, Jim, Boevink, Petra C., Bollmann, Stephanie R., Bos, Jorunn I. B., Bulone, Vincent, Cai, Guohong, Cakir, Cahid, Carrington, James C., Chawner, Megan, Conti, Lucio, Costanzo, Stefano, Ewan, Richard, Fahlgren, Noah, Fischbach, Michael A., Fugelstad, Johanna, Gilroy, Eleanor M., Gnerre, Sante, Green, Pamela J., Grenville-Briggs, Laura J., Griffith, John, Grünwald, Niklaus J., Horn, Karolyn, Horner, Neil R., Hu, Chia-Hui, Huitema, Edgar, Jeong, Dong-Hoon, Jones, Alexandra M. E., Jones, Jonathan D. G., Jones, Richard W., Karlsson, Elinor K., Kunjeti, Sridhara G., Lamour, Kurt, Liu, Zhenyu, Ma, LiJun, MacLean, Daniel, Chibucos, Marcus C., McDonald, Hayes, McWalters, Jessica, Meijer, Harold J. G., Morgan, William, Morris, Paul F., Munro, Carol A., O’Neill, Keith, Ospina-Giraldo, Manuel, Pinzón, Andrés, Pritchard, Leighton, Ramsahoye, Bernard, Ren, Qinghu, Restrepo, Silvia, Roy, Sourav, Sadanandom, Ari, Savidor, Alon, Schornack, Sebastian, Schwartz, David C., Schumann, Ulrike D., Schwessinger, Ben, Seyer, Lauren, Sharpe, Ted, Silvar, Cristina, Song, Jing, Studholme, David J., Sykes, Sean, Thines, Marco, van de Vondervoort, Peter J. I., Phuntumart, Vipaporn, Wawra, Stephan, Weide, Rob, Win, Joe, Young, Carolyn, Zhou, Shiguo, Fry, William, Meyers, Blake C., van West, Pieter, Ristaino, Jean, Govers, Francine, Birch, Paul R. J., Whisson, Stephen C., Judelson, Howard S., and Nusbaum, Chad

Published
2009
Full Text
View/download PDF

50. The genome of the blood fluke Schistosoma mansoni

Author

Berriman, Matthew, Haas, Brian J., LoVerde, Philip T., Wilson, Alan R., Dillon, Gary P., Cerqueira, Gustavo C., Mashiyama, Susan T., Al-Lazikani, Bissan, Andrade, Luiza F., Ashton, Peter D., Aslett, Martin A., Bartholomeu, Daniella C., Blandin, Gaelle, Caffrey, Conor R., Coghlan, Avril, Coulson, Richard, Day, Tim A., Delcher, Art, DeMarco, Ricardo, Djikeng, Appolinaire, Eyre, Tina, Gamble, John A., Ghedin, Elodie, Gu, Yong, Hertz-Fowler, Christiane, Hirai, Hirohisha, Hirai, Yuriko, Houston, Robin, Ivens, Alasdair, Johnston, David A., Lacerda, Daniela, Macedo, Camila D., McVeigh, Paul, Ning, Zemin, Oliveira, Guilherme, Overington, John P., Parkhill, Julian, Pertea, Mihaela, Pierce, Raymond J., Protasio, Anna V., Quail, Michael A., Rajandream, Marie-Adèle, Rogers, Jane, Sajid, Mohammed, Salzberg, Steven L., Stanke, Mario, Tivey, Adrian R., White, Owen, Williams, David L., Wortman, Jennifer, Wu, Wenjie, Zamanian, Mostafa, Zerlotini, Adhemar, Fraser-Liggett, Claire M., Barrell, Barclay G., and El-Sayed, Najib M.

Published
2009
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results