40 results on '"Docking, T"'
Search Results
2. A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia
- Author
-
Docking, T. Roderick, Parker, Jeremy D. K., Jädersten, Martin, Duns, Gerben, Chang, Linda, Jiang, Jihong, Pilsworth, Jessica A., Swanson, Lucas A., Chan, Simon K., Chiu, Readman, Nip, Ka Ming, Mar, Samantha, Mo, Angela, Wang, Xuan, Martinez-Høyer, Sergio, Stubbins, Ryan J., Mungall, Karen L., Mungall, Andrew J., Moore, Richard A., Jones, Steven J. M., Birol, İnanç, Marra, Marco A., Hogge, Donna, and Karsan, Aly
- Published
- 2021
- Full Text
- View/download PDF
3. Loss of lenalidomide-induced megakaryocytic differentiation leads to therapy resistance in del(5q) myelodysplastic syndrome
- Author
-
Martinez-Høyer, Sergio, Deng, Yu, Parker, Jeremy, Jiang, Jihong, Mo, Angela, Docking, T. Roderick, Gharaee, Nadia, Li, Jenny, Umlandt, Patricia, Fuller, Megan, Jädersten, Martin, Kulasekararaj, Austin, Malcovati, Luca, List, Alan F., Hellström-Lindberg, Eva, Platzbecker, Uwe, and Karsan, Aly
- Published
- 2020
- Full Text
- View/download PDF
4. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
- Author
-
Bradnam, Keith R., Fass, Joseph N., Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, İnanç, Boisvert, Sébastien, Chapman, Jarrod A., Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T. Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A., Ganapathy, Ganeshkumar, Gibbs, Richard A., Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B., Ho, Isaac Y., Howard, Jason, Hunt, Martin, Jackman, Shaun D., Jaffe, David B, Jarvis, Erich, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J., Kitzman, Jacob O., Knight, James R., Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Vieira, Bruno Miguel, Naquin, Delphine, Ning, Zemin, Otto, Thomas D., Paten, Benedict, Paulo, Octávio S., Phillippy, Adam M., Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S., Ruby, J. Graham, Scalabrin, Simone, Schatz, Michael C., Schwartz, David C., Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I., Shendure, Jay, Shi, Yujian, Simpson, Jared T., Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Wang, Jun, Worley, Kim C., Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F.
- Subjects
Quantitative Biology - Genomics - Abstract
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another., Comment: Additional files available at http://korflab.ucdavis.edu/Datasets/Assemblathon/Assemblathon2/Additional_files/ Major changes 1. Accessions for the 3 read data sets have now been included 2. New file: spreadsheet containing details of all Study, Sample, Run, & Experiment identifiers 3. Made miscellaneous changes to address reviewers comments. DOIs added to GigaDB datasets
- Published
- 2013
- Full Text
- View/download PDF
5. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
- Author
-
Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F
- Abstract
Abstract Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
- Published
- 2013
6. Applications of Bayesian network models in predicting types of hematological malignancies
- Author
-
Agrahari, Rupesh, Foroushani, Amir, Docking, T. Roderick, Chang, Linda, Duns, Gerben, Hudoba, Monika, Karsan, Aly, and Zare, Habil
- Published
- 2018
- Full Text
- View/download PDF
7. Loss of FBXO11 function establishes a stem cell program in acute myeloid leukemia through dysregulation of the mitochondrial protease LONP1
- Author
-
Mo, Angela Ya-Chi, primary, Kincross, Hayle, additional, Wang, Xuan, additional, Chang, Linda Ya-Ting, additional, Duns, Gerben, additional, Kwan, Harwood, additional, Lau, Tammy, additional, Docking, T. Roderick, additional, Tran, Jessica, additional, Colborne, Shane, additional, Cheng, Se-Wing Grace, additional, Huang, Shujun, additional, Gharaee, Nadia, additional, Willie, Elijah, additional, Jiang, Jihong, additional, Parker, Jeremy, additional, Bridgers, Joshua, additional, Wood, Davis, additional, Geltink, Ramon Klein, additional, Morin, Gregg B., additional, and Karsan, Aly, additional
- Published
- 2022
- Full Text
- View/download PDF
8. A regulatory toolbox of MiniPromoters to drive selective expression in the brain
- Author
-
Portales-Casamar, Elodie, Swanson, Douglas J., Liu, Li, de Leeuw, Charles N., Banks, Kathleen G., Sui, Shannan J. Ho, Fulton, Debra L., Ali, Johar, Amirabbasi, Mahsa, Arenillas, David J., Babyak, Nazar, Black, Sonia F., Bonaguro, Russell J., Brauer, Erich, Candido, Tara R., Castellarin, Mauro, Chen, Jing, Chen, Ying, Cheng, Jason C. Y., Chopra, Vik, Docking, T. Roderick, Dreolini, Lisa, D'Souza, Cletus A., Flynn, Erin K., Glenn, Randy, Hatakka, Kristi, Hearty, Taryn G., Imanian, Behzad, Jiang, Steven, Khorasan-zadeh, Shadi, Komljenovic, Ivana, Laprise, Stéphanie, Liao, Nancy Y., Lim, Jonathan S., Lithwick, Stuart, Liu, Flora, Liu, Jun, Lu, Meifen, McConechy, Melissa, McLeod, Andrea J., Milisavljevic, Marko, Mis, Jacek, O'Connor, Katie, Palma, Betty, Palmquist, Diana L., Schmouth, Jean-François, Swanson, Magdalena I., Tam, Bonny, Ticoll, Amy, Turner, Jenna L., Varhol, Richard, Vermeulen, Jenny, Watkins, Russell F., Wilson, Gary, Wong, Bibiana K. Y., Wong, Siaw H., Wong, Tony Y. T., Yang, George S., Ypsilanti, Athena R., Jones, Steven J. M., Holt, Robert A., Goldowitz, Daniel, Wasserman, Wyeth W., and Simpson, Elizabeth M.
- Published
- 2010
9. DYNLL1 mis-splicing is associated with replicative genome instability in SF3B1 mutant cells
- Author
-
Tam, Annie S., primary, Tsai, Shuhe, additional, Chang, Emily Yun-Chia, additional, Mathew, Veena, additional, Shanks, Alynn, additional, Docking, T. Roderick, additional, Kumar, Arun, additional, Bernard, Delphine G., additional, Karsan, Aly, additional, and Stirling, Peter C., additional
- Published
- 2021
- Full Text
- View/download PDF
10. Assessing Limit of Detection in Clinical Sequencing
- Author
-
Starks, Elizabeth R., primary, Swanson, Lucas, additional, Docking, T. Roderick, additional, Bosdet, Ian, additional, Munro, Sarah, additional, Moore, Richard A., additional, and Karsan, Aly, additional
- Published
- 2021
- Full Text
- View/download PDF
11. Retrotransposon Sequence Variation in Four Asexual Plant Species
- Author
-
Docking, T. Roderick, Saadé, Fabienne E., Elliott, Miranda C., and Schoen, Daniel J.
- Published
- 2006
- Full Text
- View/download PDF
12. Altered microRNA expression links IL6 and TNF-induced inflammaging with myeloid malignancy in humans and mice
- Author
-
Grants, Jennifer M., primary, Wegrzyn, Joanna, primary, Hui, Tony, primary, O’Neill, Kieran, primary, Shadbolt, Marion, primary, Knapp, David J. H. F., primary, Parker, Jeremy, primary, Deng, Yu, primary, Gopal, Aparna, primary, Docking, T. Roderick, primary, Fuller, Megan, primary, Li, Jenny, primary, Boldin, Mark, primary, Eaves, Connie J., primary, Hirst, Martin, primary, and Karsan, Aly, primary
- Published
- 2020
- Full Text
- View/download PDF
13. Sample Tracking Using Unique Sequence Controls
- Author
-
Moore, Richard A., primary, Zeng, Thomas, additional, Docking, T. Roderick, additional, Bosdet, Ian, additional, Butterfield, Yaron S., additional, Munro, Sarah, additional, Li, Irene, additional, Swanson, Lucas, additional, Starks, Elizabeth R., additional, Tse, Kane, additional, Mungall, Andrew J., additional, Holt, Robert A., additional, and Karsan, Aly, additional
- Published
- 2020
- Full Text
- View/download PDF
14. Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera
- Author
-
Hesse-Orce, Uljana, DiGuistini, Scott, Keeling, Christopher I, Wang, Ye, Li, Maria, Henderson, Hannah, Docking, T Roderick, Liao, Nancy Y, Robertson, Gordon, Holt, Robert A, Jones, Steven JM, Bohlmann, Jörg, and Breuil, Colette
- Published
- 2010
- Full Text
- View/download PDF
15. Fixation Effects on Variant Calling in a Clinical Resequencing Panel
- Author
-
Parker, Jeremy D.K., primary, Yap, Shyong Quin, additional, Starks, Elizabeth, additional, Slind, Jillian, additional, Swanson, Lucas, additional, Docking, T. Roderick, additional, Fuller, Megan, additional, Zhou, Chen, additional, Walker, Blair, additional, Filipenko, Douglas, additional, Xiong, Wei, additional, Karimuddin, Ahmer A., additional, Phang, P. Terry, additional, Raval, Manoj, additional, Brown, Carl J., additional, and Karsan, Aly, additional
- Published
- 2019
- Full Text
- View/download PDF
16. Genomic testing in myeloid malignancy
- Author
-
Docking, T. Roderick, primary and Karsan, Aly, additional
- Published
- 2019
- Full Text
- View/download PDF
17. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees
- Author
-
de Graaf Dirk C, Jones Steven JM, Taylor Greg A, Jackman Shaun D, Docking T Roderick, Chan Simon K, Liao Nancy Y, Birol Inanc, Cornman R Scott, Chan Queenie WT, Evans Jay D, and Foster Leonard J
- Subjects
Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background As scientists continue to pursue various 'omics-based research, there is a need for high quality data for the most fundamental 'omics of all: genomics. The bacterium Paenibacillus larvae is the causative agent of the honey bee disease American foulbrood. If untreated, it can lead to the demise of an entire hive; the highly social nature of bees also leads to easy disease spread, between both individuals and colonies. Biologists have studied this organism since the early 1900s, and a century later, the molecular mechanism of infection remains elusive. Transcriptomics and proteomics, because of their ability to analyze multiple genes and proteins in a high-throughput manner, may be very helpful to its study. However, the power of these methodologies is severely limited without a complete genome; we undertake to address that deficiency here. Results We used the Illumina GAIIx platform and conventional Sanger sequencing to generate a 182-fold sequence coverage of the P. larvae genome, and assembled the data using ABySS into a total of 388 contigs spanning 4.5 Mbp. Comparative genomics analysis against fully-sequenced soil bacteria P. JDR2 and P. vortex showed that regions of poor conservation may contain putative virulence factors. We used GLIMMER to predict 3568 gene models, and named them based on homology revealed by BLAST searches; proteases, hemolytic factors, toxins, and antibiotic resistance enzymes were identified in this way. Finally, mass spectrometry was used to provide experimental evidence that at least 35% of the genes are expressed at the protein level. Conclusions This update on the genome of P. larvae and annotation represents an immense advancement from what we had previously known about this species. We provide here a reliable resource that can be used to elucidate the mechanism of infection, and by extension, more effective methods to control and cure this widespread honey bee disease.
- Published
- 2011
- Full Text
- View/download PDF
18. Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera
- Author
-
Robertson Gordon, Liao Nancy Y, Docking T Roderick, Henderson Hannah, Li Maria, Wang Ye, Keeling Christopher I, DiGuistini Scott, Hesse-Orce Uljana, Holt Robert A, Jones Steven JM, Bohlmann Jörg, and Breuil Colette
- Subjects
Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Grosmannia clavigera is a bark beetle-vectored fungal pathogen of pines that causes wood discoloration and may kill trees by disrupting nutrient and water transport. Trees respond to attacks from beetles and associated fungi by releasing terpenoid and phenolic defense compounds. It is unclear which genes are important for G. clavigera's ability to overcome antifungal pine terpenoids and phenolics. Results We constructed seven cDNA libraries from eight G. clavigera isolates grown under various culture conditions, and Sanger sequenced the 5' and 3' ends of 25,000 cDNA clones, resulting in 44,288 high quality ESTs. The assembled dataset of unique transcripts (unigenes) consists of 6,265 contigs and 2,459 singletons that mapped to 6,467 locations on the G. clavigera reference genome, representing ~70% of the predicted G. clavigera genes. Although only 54% of the unigenes matched characterized proteins at the NCBI database, this dataset extensively covers major metabolic pathways, cellular processes, and genes necessary for response to environmental stimuli and genetic information processing. Furthermore, we identified genes expressed in spores prior to germination, and genes involved in response to treatment with lodgepole pine phloem extract (LPPE). Conclusions We provide a comprehensively annotated EST dataset for G. clavigera that represents a rich resource for gene characterization in this and other ophiostomatoid fungi. Genes expressed in response to LPPE treatment are indicative of fungal oxidative stress response. We identified two clusters of potentially functionally related genes responsive to LPPE treatment. Furthermore, we report a simple method for identifying contig misassemblies in de novo assembled EST collections caused by gene overlap on the genome.
- Published
- 2010
- Full Text
- View/download PDF
19. Meis2 as a critical player in MN1-induced leukemia
- Author
-
Lai, C K, primary, Norddahl, G L, additional, Maetzig, T, additional, Rosten, P, additional, Lohr, T, additional, Sanchez Milde, L, additional, von Krosigk, N, additional, Docking, T R, additional, Heuser, M, additional, Karsan, A, additional, and Humphries, R K, additional
- Published
- 2017
- Full Text
- View/download PDF
20. Draft Genome Of The Mountain Pine Beetle, Dendroctonus Ponderosae Hopkins, A Major Forest Pest
- Author
-
Keeling, Christopher, Yuen, Macaire, Liao, Nancy, Roderick Docking, T., Chan, Simon, Taylor, Greg, Palmquist, Diana, Jackman, Shaun, Nguyen, Anh, Li, Maria, Henderson, Hannah, Janes, Jasmine, Zhao, Yongjun, Pandoh, Pawan, Moore, Richard, Sperling, Felix, W Huber, Dezene, Birol, Inanc, Jones, Steven, and Bohlmann, Joerg
- Subjects
fungi ,food and beverages - Abstract
Background The mountain pine beetle, Dendroctonus ponderosae Hopkins, is the most serious insect pest of western North American pine forests. A recent outbreak destroyed more than 15 million hectares of pine forests, with major environmental effects on forest health, and economic effects on the forest industry. The outbreak has in part been driven by climate change, and will contribute to increased carbon emissions through decaying forests. Results We developed a genome sequence resource for the mountain pine beetle to better understand the unique aspects of this insect's biology. A draft de novo genome sequence was assembled from paired-end, short-read sequences from an individual field-collected male pupa, and scaffolded using mate-paired, short-read genomic sequences from pooled field-collected pupae, paired-end short-insert whole-transcriptome shotgun sequencing reads of mRNA from adult beetle tissues, and paired-end Sanger EST sequences from various life stages. We describe the cytochrome P450, glutathione S-transferase, and plant cell wall-degrading enzyme gene families important to the survival of the mountain pine beetle in its harsh and nutrient-poor host environment, and examine genome-wide single-nucleotide polymorphism variation. A horizontally transferred bacterial sucrose-6-phosphate hydrolase was evident in the genome, and its tissue-specific transcription suggests a functional role for this beetle. Conclusions Despite Coleoptera being the largest insect order with over 400,000 described species, including many agricultural and forest pest species, this is only the second genome sequence reported in Coleoptera, and will provide an important resource for the Curculionoidea and other insects.
- Published
- 2013
21. Barnacle: Detecting and Characterizing Tandem Duplications and Fusions in Transcriptome Assemblies
- Author
-
Swanson, Lucas, Robertson, Gordon, Mungall, Karen, Butterfield, Yaron, Chiu, Readman, Corbett, Richard, Docking, T., Hogge, Donna, Jackman, Shaun, Moore, Richard, Mungall, Andrew, Nip, Ka, Parker, Jeremy, Qian, Jenny, Raymond, Anthony, Sung, Sandy, Tam, Angela, Thiessen, Nina, Varhol, Richard, Yorukoglu, Deniz, Zhao, YongJun, Hoodless, Pamela, Sahinalp, S., Karsan, Aly, and Birol, Inanc
- Abstract
Background Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers. Results We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data, and supports prioritizing them for review and validation by reporting the relative coverage of co-occurring chimeric and wild-type transcripts. We demonstrate applications in large-scale disease studies, by identifying PTDs in MLL, ITDs in FLT3, and reciprocal fusions between PML and RARA, in two deeply sequenced acute myeloid leukemia (AML) RNA-seq datasets. Conclusions Our analyses of real and simulated data sets show that, with appropriate filter settings, Barnacle makes highly specific predictions for three types of chimeric transcripts that are important in a range of cancers: PTDs, ITDs, and fusions. High specificity makes manual review and validation efficient, which is necessary in large-scale disease studies. Characterizing an extended range of chimera types will help generate insights into progression, treatment, and outcomes for complex diseases.
- Published
- 2013
22. KLEAT: CLEAVAGE SITE ANALYSIS OF TRANSCRIPTOMES
- Author
-
BIROL, INANÇ, primary, RAYMOND, ANTHONY, additional, CHIU, READMAN, additional, NIP, KA MING, additional, JACKMAN, SHAUN D, additional, KREITZMAN, MAAYAN, additional, DOCKING, T RODERICK, additional, ENNIS, CATHERINE A, additional, ROBERTSON, A GORDON, additional, and KARSAN, ALY, additional
- Published
- 2014
- Full Text
- View/download PDF
23. Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species
- Author
-
Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. -C, Corbeil, J., Fabbro, C. D., Docking, T. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., Ganapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. -W, Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., MacCallum, I., MacManes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. -M, Yuan, J., Zhang, G., Zhang, H., Zhou, S., Korf, I. F., Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. -C, Corbeil, J., Fabbro, C. D., Docking, T. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., Ganapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. -W, Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., MacCallum, I., MacManes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. -M, Yuan, J., Zhang, G., Zhang, H., Zhou, S., and Korf, I. F.
- Abstract
Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another., QC 20170307
- Published
- 2013
- Full Text
- View/download PDF
24. Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies
- Author
-
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Yorukoglu, Deniz, Swanson, Lucas, Robertson, Gordon, Mungall, Karen L., Butterfield, Yaron S., Chiu, Readman, Corbett, Richard D., Docking, T. R., Hogge, Donna, Jackman, Shaun D., Moore, Richard A., Mungall, Andrew J., Nip, Ka Ming, Parker, Jeremy D. K., Qian, Jenny Q., Raymond, Anthony, Sung, Sandy, Tam, Angela, Thiessen, Nina, Varhol, Richard, Wang, Sherry, Zhao, YongJun, Hoodless, Pamela A., Sahinalp, S. C., Karsan, Aly, Birol, Inanc, Qian, Jenny, Sahinalp, S., Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Yorukoglu, Deniz, Swanson, Lucas, Robertson, Gordon, Mungall, Karen L., Butterfield, Yaron S., Chiu, Readman, Corbett, Richard D., Docking, T. R., Hogge, Donna, Jackman, Shaun D., Moore, Richard A., Mungall, Andrew J., Nip, Ka Ming, Parker, Jeremy D. K., Qian, Jenny Q., Raymond, Anthony, Sung, Sandy, Tam, Angela, Thiessen, Nina, Varhol, Richard, Wang, Sherry, Zhao, YongJun, Hoodless, Pamela A., Sahinalp, S. C., Karsan, Aly, Birol, Inanc, Qian, Jenny, and Sahinalp, S.
- Abstract
Background: Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers. Results: We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data, and supports prioritizing them for review and validation by reporting the relative coverage of co-occurring chimeric and wild-type transcripts. We demonstrate applications in large-scale disease studies, by identifying PTDs in MLL, ITDs in FLT3, and reciprocal fusions between PML and RARA, in two deeply sequenced acute myeloid leukemia (AML) RNA-seq datasets. Conclusions: Our analyses of real and simulated data sets show that, with appropriate filter settings, Barnacle makes highly specific predictions for three types of chimeric transcripts that are important in a range of cancers: PTDs, ITDs, and fusions. High specificity makes manual review and validation efficient, which is necessary in large-scale disease studies. Characterizing an extended range of chimera types will help generate insights into progression, treatment, and outcomes for complex diseases., Simon Fraser University. Bioinformatics for Combating Infectious Disease Project, Simon Fraser University (Graduate Fellowship), Pacific Century Institute (Graduate Scholarship), Genome Canada (Firm), Canadian Institutes of Health Research, Genome British Columbia (Firm) (Grant #121AML), Provincial Health Services Authority (British Columbia, Canada), BC Cancer Foundation
- Published
- 2013
25. Barnacle: Detecting and characterizing tandem duplications and fusions in transcriptome assemblies
- Author
-
Swanson, L., Robertson, G., Mungall, K., Butterfield, Y., Chiu, R., Corbett, R., Docking, T., Hogge, D., Jackman, S., Moore, R., Mungall, A., Nip, K., Parker, J., Qian, J., Raymond, A., Sung, S., Tam, A., Thiessen, N., Varhol, Richard, Wang, S., Yorukoglu, D., Zhao, Y., Hoodless, P., Sahinalp, S., Karsan, A., Birol, I., Swanson, L., Robertson, G., Mungall, K., Butterfield, Y., Chiu, R., Corbett, R., Docking, T., Hogge, D., Jackman, S., Moore, R., Mungall, A., Nip, K., Parker, J., Qian, J., Raymond, A., Sung, S., Tam, A., Thiessen, N., Varhol, Richard, Wang, S., Yorukoglu, D., Zhao, Y., Hoodless, P., Sahinalp, S., Karsan, A., and Birol, I.
- Abstract
Background: Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers.Results: We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data, and supports prioritizing them for review and validation by reporting the relative coverage of co-occurring chimeric and wild-type transcripts. We demonstrate applications in large-scale disease studies, by identifying PTDs in MLL, ITDs in FLT3, and reciprocal fusions between PML and RARA, in two deeply sequenced acute myeloid leukemia (AML) RNA-seq datasets.Conclusions: Our analyses of real and simulated data sets show that, with appropriate filter settings, Barnacle makes highly specific predictions for three types of chimeric transcripts that are important in a range of cancers: PTDs, ITDs, and fusions. High specificity makes manual review and validation efficient, which is necessary in large-scale disease studies. Characterizing an extended range of chimera types will help generate insights into progression, treatment, and outcomes for complex diseases. © 2013 Swanson et al.; licensee BioMed Central Ltd.
- Published
- 2013
26. A Clinically Validated Diagnostic Second-Generation Sequencing Assay for Detection of Hereditary BRCA1 and BRCA2 Mutations
- Author
-
Bosdet, Ian E., primary, Docking, T. Roderick, additional, Butterfield, Yaron S., additional, Mungall, Andrew J., additional, Zeng, Thomas, additional, Coope, Robin J., additional, Yorida, Erika, additional, Chow, Katie, additional, Bala, Miruna, additional, Young, Sean S., additional, Hirst, Martin, additional, Birol, Inanc, additional, Moore, Richard A., additional, Jones, Steven J., additional, Marra, Marco A., additional, Holt, Rob, additional, and Karsan, Aly, additional
- Published
- 2013
- Full Text
- View/download PDF
27. A regulatory toolbox of MiniPromoters to drive selective expression in the brain
- Author
-
Portales-Casamar, E., Swanson, D., Liu, L., De Leeuw, C., Banks, K., Ho Sui, S., Fulton, D., Ali, J., Amirabbasi, M., Arenillas, D., Babyak, N., Black, S., Bonaguro, R., Brauer, E., Candido, T., Castellarin, M., Chen, J., Chen, Y., Cheng, J., Chopra, V., Docking, T., Dreolini, L., D'Souza, C., Flynn, E., Glenn, R., Hatakka, K., Hearty, T., Imanian, B., Jiang, S., Khorasan-zadeh, S., Komljenovic, I., Laprise, S., Liao, N., Lim, J., Lithwick, S., Liu, F., Liu, J., Lu, M., McConechy, M., McLeod, A., Milisavljevic, M., Mis, J., O'Connor, K., Palma, B., Palmquist, D., Schmouth, J., Swanson, M., Tam, B., Ticoll, A., Turner, J., Varhol, Richard, Vermeulen, J., Watkins, R., Wilson, G., Wong, B., Wong, S., Wong, T., Yang, G., Ypsilanti, A., Jones, S., Holt, R., Goldowitz, D., Wasserman, W., Simpson, E., Portales-Casamar, E., Swanson, D., Liu, L., De Leeuw, C., Banks, K., Ho Sui, S., Fulton, D., Ali, J., Amirabbasi, M., Arenillas, D., Babyak, N., Black, S., Bonaguro, R., Brauer, E., Candido, T., Castellarin, M., Chen, J., Chen, Y., Cheng, J., Chopra, V., Docking, T., Dreolini, L., D'Souza, C., Flynn, E., Glenn, R., Hatakka, K., Hearty, T., Imanian, B., Jiang, S., Khorasan-zadeh, S., Komljenovic, I., Laprise, S., Liao, N., Lim, J., Lithwick, S., Liu, F., Liu, J., Lu, M., McConechy, M., McLeod, A., Milisavljevic, M., Mis, J., O'Connor, K., Palma, B., Palmquist, D., Schmouth, J., Swanson, M., Tam, B., Ticoll, A., Turner, J., Varhol, Richard, Vermeulen, J., Watkins, R., Wilson, G., Wong, B., Wong, S., Wong, T., Yang, G., Ypsilanti, A., Jones, S., Holt, R., Goldowitz, D., Wasserman, W., and Simpson, E.
- Abstract
The Pleiades Promoter Project integrates genomewide bioinformatics with large-scale knockin mouse production and histological examination of expression patterns to develop MiniPromoters and related tools designed to study and treat the brain by directed gene expression. Genes with brain expression patterns of interest are subjected to bioinformatic analysis to delineate candidate regulatory regions, which are then incorporated into a panel of compact human MiniPromoters to drive expression to brain regions and cell types of interest. Using single-copy, homologous-recombination "knockins" in embryonic stem cells, each MiniPromoter reporter is integrated immediately 5' of the Hprt locus in the mouse genome. MiniPromoter expression profiles are characterized in differentiation assays of the transgenic cells or inmouse brains following transgenic mouse production. Histological examination of adult brains, eyes, and spinal cords for reporter gene activity is coupled to costaining with cell-type - specific markers to define expression. The publicly available Pleiades MiniPromoter Project is a key resource to facilitate research on brain development and therapies.
- Published
- 2010
28. Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies
- Author
-
Swanson, Lucas, primary, Robertson, Gordon, additional, Mungall, Karen L, additional, Butterfield, Yaron S, additional, Chiu, Readman, additional, Corbett, Richard D, additional, Docking, T Roderick, additional, Hogge, Donna, additional, Jackman, Shaun D, additional, Moore, Richard A, additional, Mungall, Andrew J, additional, Nip, Ka Ming, additional, Parker, Jeremy DK, additional, Qian, Jenny Qing, additional, Raymond, Anthony, additional, Sung, Sandy, additional, Tam, Angela, additional, Thiessen, Nina, additional, Varhol, Richard, additional, Wang, Sherry, additional, Yorukoglu, Deniz, additional, Zhao, YongJun, additional, Hoodless, Pamela A, additional, Sahinalp, S Cenk, additional, Karsan, Aly, additional, and Birol, Inanc, additional
- Published
- 2013
- Full Text
- View/download PDF
29. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest
- Author
-
Keeling, Christopher I, primary, Yuen, Macaire MS, additional, Liao, Nancy Y, additional, Roderick Docking, T, additional, Chan, Simon K, additional, Taylor, Greg A, additional, Palmquist, Diana L, additional, Jackman, Shaun D, additional, Nguyen, Anh, additional, Li, Maria, additional, Henderson, Hannah, additional, Janes, Jasmine K, additional, Zhao, Yongjun, additional, Pandoh, Pawan, additional, Moore, Richard, additional, Sperling, Felix AH, additional, W Huber, Dezene P, additional, Birol, Inanc, additional, Jones, Steven JM, additional, and Bohlmann, Joerg, additional
- Published
- 2013
- Full Text
- View/download PDF
30. KLEAT: CLEAVAGE SITE ANALYSIS OF TRANSCRIPTOMES.
- Author
-
BIROL, INANÇ, RAYMOND, ANTHONY, CHIU, READMAN, KA MING NIP, JACKMAN, SHAUN D., KREITZMAN, MAAYAN, DOCKING, T. RODERICK, ENNIS, CATHERINE A., ROBERTSON, A. GORDON, and KARSAN, ALY
- Subjects
GENETIC transcription ,SCISSION (Chemistry) ,BIOINFORMATICS ,POLYADENYLIC acid ,RNA sequencing - Published
- 2014
31. Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests
- Author
-
Keeling, Christopher I., primary, Henderson, Hannah, additional, Li, Maria, additional, Yuen, Mack, additional, Clark, Erin L., additional, Fraser, Jordie D., additional, Huber, Dezene P.W., additional, Liao, Nancy Y., additional, Roderick Docking, T., additional, Birol, Inanc, additional, Chan, Simon K., additional, Taylor, Greg A., additional, Palmquist, Diana, additional, Jones, Steven J.M., additional, and Bohlmann, Joerg, additional
- Published
- 2012
- Full Text
- View/download PDF
32. Assemblathon 1: A competitive assessment of de novo short read assembly methods
- Author
-
Earl, Dent, primary, Bradnam, Keith, additional, St. John, John, additional, Darling, Aaron, additional, Lin, Dawei, additional, Fass, Joseph, additional, Yu, Hung On Ken, additional, Buffalo, Vince, additional, Zerbino, Daniel R., additional, Diekhans, Mark, additional, Nguyen, Ngan, additional, Ariyaratne, Pramila Nuwantha, additional, Sung, Wing-Kin, additional, Ning, Zemin, additional, Haimel, Matthias, additional, Simpson, Jared T., additional, Fonseca, Nuno A., additional, Birol, İnanç, additional, Docking, T. Roderick, additional, Ho, Isaac Y., additional, Rokhsar, Daniel S., additional, Chikhi, Rayan, additional, Lavenier, Dominique, additional, Chapuis, Guillaume, additional, Naquin, Delphine, additional, Maillet, Nicolas, additional, Schatz, Michael C., additional, Kelley, David R., additional, Phillippy, Adam M., additional, Koren, Sergey, additional, Yang, Shiaw-Pyng, additional, Wu, Wei, additional, Chou, Wen-Chi, additional, Srivastava, Anuj, additional, Shaw, Timothy I., additional, Ruby, J. Graham, additional, Skewes-Cox, Peter, additional, Betegon, Miguel, additional, Dimon, Michelle T., additional, Solovyev, Victor, additional, Seledtsov, Igor, additional, Kosarev, Petr, additional, Vorobyev, Denis, additional, Ramirez-Gonzalez, Ricardo, additional, Leggett, Richard, additional, MacLean, Dan, additional, Xia, Fangfang, additional, Luo, Ruibang, additional, Li, Zhenyu, additional, Xie, Yinlong, additional, Liu, Binghang, additional, Gnerre, Sante, additional, MacCallum, Iain, additional, Przybylski, Dariusz, additional, Ribeiro, Filipe J., additional, Yin, Shuangye, additional, Sharpe, Ted, additional, Hall, Giles, additional, Kersey, Paul J., additional, Durbin, Richard, additional, Jackman, Shaun D., additional, Chapman, Jarrod A., additional, Huang, Xiaoqiu, additional, DeRisi, Joseph L., additional, Caccamo, Mario, additional, Li, Yingrui, additional, Jaffe, David B., additional, Green, Richard E., additional, Haussler, David, additional, Korf, Ian, additional, and Paten, Benedict, additional
- Published
- 2011
- Full Text
- View/download PDF
33. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees
- Author
-
Chan, Queenie WT, primary, Cornman, R Scott, additional, Birol, Inanc, additional, Liao, Nancy Y, additional, Chan, Simon K, additional, Docking, T Roderick, additional, Jackman, Shaun D, additional, Taylor, Greg A, additional, Jones, Steven JM, additional, de Graaf, Dirk C, additional, Evans, Jay D, additional, and Foster, Leonard J, additional
- Published
- 2011
- Full Text
- View/download PDF
34. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
- Author
-
DiGuistini, Scott, primary, Liao, Nancy Y, additional, Platt, Darren, additional, Robertson, Gordon, additional, Seidel, Michael, additional, Chan, Simon K, additional, Docking, T Roderick, additional, Birol, Inanc, additional, Holt, Robert A, additional, Hirst, Martin, additional, Mardis, Elaine, additional, Marra, Marco A, additional, Hamelin, Richard C, additional, Bohlmann, Jörg, additional, Breuil, Colette, additional, and Jones, Steven JM, additional
- Published
- 2009
- Full Text
- View/download PDF
35. A Clinically Validated Diagnostic Second-Generation Sequencing Assay for Detection of Hereditary BRCA1and BRCA2Mutations
- Author
-
Bosdet, Ian E., Docking, T. Roderick, Butterfield, Yaron S., Mungall, Andrew J., Zeng, Thomas, Coope, Robin J., Yorida, Erika, Chow, Katie, Bala, Miruna, Young, Sean S., Hirst, Martin, Birol, Inanc, Moore, Richard A., Jones, Steven J., Marra, Marco A., Holt, Rob, and Karsan, Aly
- Abstract
Individuals who inherit mutations in BRCA1or BRCA2are predisposed to breast and ovarian cancers. However, identifying mutations in these large genes by conventional dideoxy sequencing in a clinical testing laboratory is both time consuming and costly, and similar challenges exist for other large genes, or sets of genes, with relevance in the clinical setting. Second-generation sequencing technologies have the potential to improve the efficiency and throughput of clinical diagnostic sequencing, once clinically validated methods become available. We have developed a method for detection of variants based on automated small-amplicon PCR followed by sample pooling and sequencing with a second-generation instrument. To demonstrate the suitability of this method for clinical diagnostic sequencing, we analyzed the coding exons and the intron–exon boundaries of BRCA1and BRCA2in 91 hereditary breast cancer patient samples. Our method generated high-quality sequence coverage across all targeted regions, with median coverage greater than 4000-fold for each sample in pools of 24. Sensitive and specific automated variant detection, without false-positive or false-negative results, was accomplished with a standard software pipeline using bwafor sequence alignment and samtoolsfor variant detection. We experimentally derived a minimum threshold of 100-fold sequence depth for confident variant detection. The results demonstrate that this method is suitable for sensitive, automatable, high-throughput sequence variant detection in the clinical laboratory.
- Published
- 2013
- Full Text
- View/download PDF
36. Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera
- Author
-
Hesse-Orce, Uljana, DiGuistini, Scott, Keeling, Christopher I, Wang, Ye, Li, Maria, Henderson, Hannah, Docking, T R, Liao, Nancy Y, Robertson, Gordon, Holt, Robert A, Jones, Steven J, Bohlmann, Jörg, and Breuil, Colette
- Subjects
food and beverages ,15. Life on land - Abstract
Background: Grosmannia clavigera is a bark beetle-vectored fungal pathogen of pines that causes wood discoloration and may kill trees by disrupting nutrient and water transport. Trees respond to attacks from beetles and associated fungi by releasing terpenoid and phenolic defense compounds. It is unclear which genes are important for G. clavigera's ability to overcome antifungal pine terpenoids and phenolics. Results We constructed seven cDNA libraries from eight G. clavigera isolates grown under various culture conditions, and Sanger sequenced the 5' and 3' ends of 25,000 cDNA clones, resulting in 44,288 high quality ESTs. The assembled dataset of unique transcripts (unigenes) consists of 6,265 contigs and 2,459 singletons that mapped to 6,467 locations on the G. clavigera reference genome, representing ~70% of the predicted G. clavigera genes. Although only 54% of the unigenes matched characterized proteins at the NCBI database, this dataset extensively covers major metabolic pathways, cellular processes, and genes necessary for response to environmental stimuli and genetic information processing. Furthermore, we identified genes expressed in spores prior to germination, and genes involved in response to treatment with lodgepole pine phloem extract (LPPE). Conclusions We provide a comprehensively annotated EST dataset for G. clavigera that represents a rich resource for gene characterization in this and other ophiostomatoid fungi. Genes expressed in response to LPPE treatment are indicative of fungal oxidative stress response. We identified two clusters of potentially functionally related genes responsive to LPPE treatment. Furthermore, we report a simple method for identifying contig misassemblies in de novo assembled EST collections caused by gene overlap on the genome.
37. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees
- Author
-
Chan, Queenie W, Cornman, R S, Birol, Inanc, Liao, Nancy Y, Chan, Simon K, Docking, T R, Jackman, Shaun D, Taylor, Greg A, Jones, Steven J, De Graaf, Dirk C, Evans, Jay D, and Foster, Leonard J
- Subjects
2. Zero hunger - Abstract
Background: As scientists continue to pursue various 'omics-based research, there is a need for high quality data for the most fundamental 'omics of all: genomics. The bacterium Paenibacillus larvae is the causative agent of the honey bee disease American foulbrood. If untreated, it can lead to the demise of an entire hive; the highly social nature of bees also leads to easy disease spread, between both individuals and colonies. Biologists have studied this organism since the early 1900s, and a century later, the molecular mechanism of infection remains elusive. Transcriptomics and proteomics, because of their ability to analyze multiple genes and proteins in a high-throughput manner, may be very helpful to its study. However, the power of these methodologies is severely limited without a complete genome; we undertake to address that deficiency here. Results: We used the Illumina GAIIx platform and conventional Sanger sequencing to generate a 182-fold sequence coverage of the P. larvae genome, and assembled the data using ABySS into a total of 388 contigs spanning 4.5 Mbp. Comparative genomics analysis against fully-sequenced soil bacteria P. JDR2 and P. vortex showed that regions of poor conservation may contain putative virulence factors. We used GLIMMER to predict 3568 gene models, and named them based on homology revealed by BLAST searches; proteases, hemolytic factors, toxins, and antibiotic resistance enzymes were identified in this way. Finally, mass spectrometry was used to provide experimental evidence that at least 35% of the genes are expressed at the protein level. Conclusions: This update on the genome of P. larvae and annotation represents an immense advancement from what we had previously known about this species. We provide here a reliable resource that can be used to elucidate the mechanism of infection, and by extension, more effective methods to control and cure this widespread honey bee disease.
38. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest
- Author
-
Keeling, Christopher I, Yuen, Macaire M, Liao, Nancy Y, Roderick Docking, T, Chan, Simon K, Taylor, Greg A, Palmquist, Diana L, Jackman, Shaun D, Nguyen, Anh, Li, Maria, Henderson, Hannah, Janes, Jasmine K, Zhao, Yongjun, Pandoh, Pawan, Moore, Richard, Sperling, Felix A, W Huber, Dezene P, Birol, Inanc, Jones, Steven J, and Bohlmann, Joerg
- Subjects
13. Climate action ,fungi ,food and beverages ,15. Life on land - Abstract
Background: The mountain pine beetle, Dendroctonus ponderosae Hopkins, is the most serious insect pest of western North American pine forests. A recent outbreak destroyed more than 15 million hectares of pine forests, with major environmental effects on forest health, and economic effects on the forest industry. The outbreak has in part been driven by climate change, and will contribute to increased carbon emissions through decaying forests. Results We developed a genome sequence resource for the mountain pine beetle to better understand the unique aspects of this insect's biology. A draft de novo genome sequence was assembled from paired-end, short-read sequences from an individual field-collected male pupa, and scaffolded using mate-paired, short-read genomic sequences from pooled field-collected pupae, paired-end short-insert whole-transcriptome shotgun sequencing reads of mRNA from adult beetle tissues, and paired-end Sanger EST sequences from various life stages. We describe the cytochrome P450, glutathione S-transferase, and plant cell wall-degrading enzyme gene families important to the survival of the mountain pine beetle in its harsh and nutrient-poor host environment, and examine genome-wide single-nucleotide polymorphism variation. A horizontally transferred bacterial sucrose-6-phosphate hydrolase was evident in the genome, and its tissue-specific transcription suggests a functional role for this beetle. Conclusions Despite Coleoptera being the largest insect order with over 400,000 described species, including many agricultural and forest pest species, this is only the second genome sequence reported in Coleoptera, and will provide an important resource for the Curculionoidea and other insects.
39. Assemblathon 1: A competitive assessment of de novo short read assembly methods.
- Author
-
Earl, Dent, Bradnam, Keith, John, John St., Darling, Aaron, Dawei Lin, Fass, Joseph, Hung On Ken Yu, Buffalo, Vince, Zerbino, Daniel R., Diekhans, Mark, Ngan Nguyen, Ariyaratne, Pramila Nuwantha, Wing-Kin Sung, Zemin Ning, Haimel, Matthias, Simpson, Jared T., Fonseca, Nuno A., Birol, İnanç, Docking, T. Roderick, and Ho, Isaac Y.
- Subjects
- *
GENOMICS , *MOLECULAR genetics , *GENOMES , *HAPLOTYPES , *GENETIC research - Abstract
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/. [ABSTRACT FROM AUTHOR]
- Published
- 2013
40. Kleat: cleavage site analysis of transcriptomes.
- Author
-
Birol I, Raymond A, Chiu R, Nip KM, Jackman SD, Kreitzman M, Docking TR, Ennis CA, Robertson AG, and Karsan A
- Subjects
- 3' Untranslated Regions, Binding Sites, Cell Line, Computational Biology, Gene Library, Humans, ROC Curve, Sequence Alignment statistics & numerical data, Sequence Analysis, RNA statistics & numerical data, Transcriptome
- Abstract
In eukaryotic cells, alternative cleavage of 3' untranslated regions (UTRs) can affect transcript stability, transport and translation. For polyadenylated (poly(A)) transcripts, cleavage sites can be characterized with short-read sequencing using specialized library construction methods. However, for large-scale cohort studies as well as for clinical sequencing applications, it is desirable to characterize such events using RNA-seq data, as the latter are already widely applied to identify other relevant information, such as mutations, alternative splicing and chimeric transcripts. Here we describe KLEAT, an analysis tool that uses de novo assembly of RNA-seq data to characterize cleavage sites on 3' UTRs. We demonstrate the performance of KLEAT on three cell line RNA-seq libraries constructed and sequenced by the ENCODE project, and assembled using Trans-ABySS. Validating the KLEAT predictions with matched ENCODE RNA-seq and RNA-PET libraries, we show that the tool has over 90% positive predictive value when there are at least three RNA-seq reads supporting a poly(A) tail and requiring at least three RNA-PET reads mapping within 100 nucleotides as validation. We also compare the performance of KLEAT with other popular RNA-seq analysis pipelines that reconstruct 3' UTR ends, and show that it performs favourably, based on an ROC-like curve.
- Published
- 2015
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.