Summary of talks and papers at ISCB-Asia/SCCG 2012
详细信息 查看全文
- 作者：Konstantin Tretyakov (1)
Tatyana Goldberg (2)
Victor X Jin (3)
Paul Horton (4) - 刊名：BMC Genomics
- 出版年：2013
- 出版时间：February 2013
- 年：2013
- 卷：14
- 期：2-supp
- 全文大小：1226KB
- 参考文献：1. Sch枚nbach C, Tan TW, Kelso J, Rost B, Nathan S, Ranganathan S: InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia. / BMC Genomics 2011,12(Suppl 3):S1. xternal" href="http://dx.doi.org/10.1186/1471-2164-12-S3-S1">CrossRef
2. Ranganathan S, Sch枚nbach C, Kelso J, Rost B, Nathan S, Tan TW: Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference. / BMC Bioinformatics 2011,12(Suppl 13):S1. xternal" href="http://dx.doi.org/10.1186/1471-2105-12-S13-S1">CrossRef
3. Graham-Rowe D, Goldston D, Doctorow C, Waldrop M, Lynch C, Frankel F, Reid R, Nelson S, Howe D, Rhee SY, / et al.: Big data: science in the petabyte era. / Nature 2008, 455:1鈥?0. xternal" href="http://dx.doi.org/10.1038/455001a">CrossRef
4. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A: Galaxy: a platform for interactive large-scale genome analysis. / Genome Res 2005,15(10):1451鈥?455. xternal" href="http://dx.doi.org/10.1101/gr.4086505">CrossRef
5. Goecks J, Nekrutenko A, Taylor J, Team G: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. / Genome Biol 2010,11(8):R86. xternal" href="http://dx.doi.org/10.1186/gb-2010-11-8-r86">CrossRef
6. Blankenberg D, Kuster GV, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J: Galaxy: a web-based genome analysis tool for experimentalists. / Curr Protoc Mol Biol 2010, Chapter 19:Unit 19.10.1鈥?1.
7. CBIIT-Galaxy [xy.cbiit.cuhk.edu.hk/" class="a-plus-plus">http://galaxy.cbiit.cuhk.edu.hk/]
8. Abouelhoda M, Issa SA, Ghanem M: Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support. / BMC Bioinformatics 2012, 13:77. xternal" href="http://dx.doi.org/10.1186/1471-2105-13-77">CrossRef
9. Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T: Taverna: a tool for building and running workflows of services. / Nucleic Acids Res 2006,34(Web Server):W729-W732. xternal" href="http://dx.doi.org/10.1093/nar/gkl320">CrossRef
10. EasyGenomics [https://www.easygenomics.com/]
11. Belhajjame K, Corcho O, Garijo D, Zhao J, Missier P, Newman D, Palma R, Bechhofer S, Garcia-Cuesta E, G贸mez-P茅rez J, Klyne G, Page K, Roos M, Ruiz J, Soiland-Reyes S, Verdes-Montenegro L, Roure DD, Goble C: Workflow-centric research objects: a first class citizen in the scholarly discourse. / Proceedings of the ESWC2012 Workshop on the Future of Scholarly Communication in the Semantic Web 2012.
12. Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Sui SJH, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W: Toward interoperable bioscience data. / Nat Genet 2012,44(2):121鈥?26. xternal" href="http://dx.doi.org/10.1038/ng.1054">CrossRef
13. Gymrek M, McGuire AL, Golan D, Halperin E, Erlich Y: Identifying personal genomes by surname inference. / Science 2013,339(6117):321鈥?24. xternal" href="http://dx.doi.org/10.1126/science.1229566">CrossRef
14. Tretyakov K, Laur S, Smant G, Vilo J, Prins P: Fast probabilistic file fingerprinting for big data. / BMC Genomics 2013,14(Suppl 2):S8. xternal" href="http://dx.doi.org/10.1186/1471-2164-14-S2-S8">CrossRef
15. Peng Y, Leung HCM, Yiu SM, Chin FYL: Meta-IDBA: a de Novo assembler for metagenomic data. / Bioinformatics 2011,27(13):i94鈥?01. xternal" href="http://dx.doi.org/10.1093/bioinformatics/btr216">CrossRef
16. Zhao Z, Nguyen T, Deng N, Johnson K, Zhu D: SPATA: A Seeding and Patching Algorithm for de novo Transcriptome Assembly. / Bioinformatics & Biomedicine Workshops, IEEE International Conference 2011.
17. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL: A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. / Proc Natl Acad Sci USA 1992,89(5):1827鈥?831. xternal" href="http://dx.doi.org/10.1073/pnas.89.5.1827">CrossRef
18. Frith MC, Mori R, Asai K: A mostly traditional approach improves alignment of bisulfite-converted DNA. / Nucleic Acids Res 2012,40(13):e100. xternal" href="http://dx.doi.org/10.1093/nar/gks275">CrossRef
19. Kolekar P, Kale M, Kulkarni-Kale U: Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping. / Mol Phylogenet Evol 2012,65(2):510鈥?22. xternal" href="http://dx.doi.org/10.1016/j.ympev.2012.07.003">CrossRef
20. Sun K, Chen X, Jiang P, Song X, Wang H, Sun H: iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. / BMC Genomics 2013,14(Suppl 2):S7.
21. Menor M, Baek K, Poisson G: Multiclass relevance units machine: benchmark evaluation and application to small ncRNA discovery. / BMC Genomics 2013,14(Suppl 2):S6. xternal" href="http://dx.doi.org/10.1186/1471-2164-14-S2-S6">CrossRef
22. Deng F, Cui W, Wang L: A highly accurate heuristic algorithm for the haplotype assembly problem. / BMC Genomics 2013,14(Suppl 2):S2.
23. Matsumoto H, Kiryu H: MixSIH: a mixture model for single individual haplotyping. / BMC Genomics 2013,14(Suppl 2):S5.
24. Xu F, Wang W, Wang P, Li MJ, Sham PC, Wang J: A fast and accurate SNP detection algorithm for next-generation sequencing data. / Nat Commun 2012, 3:1258. xternal" href="http://dx.doi.org/10.1038/ncomms2256">CrossRef
25. Nong G, Zhang S, Chan WH: Two Efficient Algorithms for Linear Time Suffix Array Construction. / Computers, IEEE Transactions on 2011,60(10):1471鈥?484. xternal" href="http://dx.doi.org/10.1109/TC.2010.188">CrossRef
26. Maher B: ENCODE: The human encyclopaedia. / Nature 2012,489(7414):46鈥?8. xternal" href="http://dx.doi.org/10.1038/489046a">CrossRef
27. Conner S: Scientists debunk 'junk DNA' theory to reveal vast majority of human genes perform a vital function. [http://www.independent.co.uk/news/science/scientists-debunk-junk-dna-theory-to-reveal-vast-majority-of-human-genes-perform-a-vital-function-8106777.html] / The Independent 2012.
28. McKie R: Scientists attacked over claim that 'junk DNA' is vital to life. [http://www.guardian.co.uk/science/2013/feb/24/scientists-attacked-over-junk-dna-claim] / The Observer 2013.
29. Kurosawa J, Nishiyori H, Hayashizaki Y: Deep cap analysis of gene expression. / Methods Mol Biol 2011, 687:147鈥?63. xternal" href="http://dx.doi.org/10.1007/978-1-60761-944-4_10">CrossRef
30. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z: Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. / Genome Res 2012,22(9):1798鈥?812. xternal" href="http://dx.doi.org/10.1101/gr.139105.112">CrossRef
31. Leung KS, Wong KC, Chan TM, Wong MH, Lee KH, Lau CK, Tsui SKW: Discovering protein-DNA binding sequence patterns using association rule mining. / Nucleic Acids Res 2010,38(19):6324鈥?337. xternal" href="http://dx.doi.org/10.1093/nar/gkq500">CrossRef
32. Fujiwara T, Yada T: miRNA-target prediction based on transcriptional regulation. / BMC Genomics 2013,14(Suppl 2):S3. xternal" href="http://dx.doi.org/10.1186/1471-2164-14-S2-S3">CrossRef
33. Balaga O, Friedman Y, Linial M: Toward a combinatorial nature of microRNA regulation in human cells. / Nucleic Acids Res 2012,40(19):9404鈥?416. xternal" href="http://dx.doi.org/10.1093/nar/gks759">CrossRef
34. Tsuyuzaki K, Tominaga D, Kwon Y, Miyazaki S: Two-way AIC: Detection of Differentially Expressed Genes from Large Scale Microarray Meta-Dataset. / BMC Genomics 2013,14(Suppl 2):S9.
35. Parikh AP, Wu W, Curtis RE, Xing EP: TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages. / Bioinformatics 2011,27(13):i196-i204. xternal" href="http://dx.doi.org/10.1093/bioinformatics/btr239">CrossRef
36. Davis MJ, Shin CJ, Jing N, Ragan MA: Rewiring the dynamic interactome. / Mol Biosyst 2012,8(8):2054鈥?6. xternal" href="http://dx.doi.org/10.1039/c2mb25050k">CrossRef
37. Petersen TN, Brunak S, von Heijne G, Nielsen H: SignalP 4.0: discriminating signal peptides from transmembrane regions. / Nat Methods 2011,8(10):785鈥?86. xternal" href="http://dx.doi.org/10.1038/nmeth.1701">CrossRef
38. Ashby C, Johnson D, Walker K, Kanj IA, Xia G, Huang X: New enumeration algorithm for protein structure comparison and classification. / BMC Genomics 2013,14(Suppl 2):S1. xternal" href="http://dx.doi.org/10.1186/1471-2164-14-S2-S1">CrossRef
39. Gajula MP, Vogel K, Rai A, Dietrich F, Steinhoff H: How far in-silico computing meets real experiments. A study on the structure and dynamics of spin labeled vinculin tail protein by molecular dynamics simulations and EPR spectroscopy. / BMC Genomics 2013,14(Suppl 2):S4. xternal" href="http://dx.doi.org/10.1186/1471-2164-14-S2-S4">CrossRef
40. Esquivel-Rodr铆guez J, Yang YD, Kihara D: Multi-LZerD: multiple protein docking for asymmetric complexes. / Proteins 2012,80(7):1818鈥?833.
41. Esquivel-Rodr铆guez J, Kihara D: Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors. / J Phys Chem B 2012,116(23):6854鈥?861. xternal" href="http://dx.doi.org/10.1021/jp212612t">CrossRef
42. Yuan Y, Failmezger H, Rueda OM, Ali HR, Gr盲f S, Chin SF, Schwarz RF, Curtis C, Dunning MJ, Bard-well H, Johnson N, Doyle S, Turashvili G, Provenzano E, Aparicio S, Caldas C, Markowetz F: Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling. / Sci Transl Med 2012,4(157):157ra143. xternal" href="http://dx.doi.org/10.1126/scitranslmed.3004330">CrossRef
43. Beckman RA, Schemmann GS, Yeang CH: Impact of genetic dynamics and single-cell heterogeneity on development of nonstandard personalized medicine strategies for cancer. / Proc Natl Acad Sci USA 2012,109(36):14586鈥?4591. xternal" href="http://dx.doi.org/10.1073/pnas.1203559109">CrossRef
44. Zhang S, Liu CC, Li W, Shen H, Laird PW, Zhou XJ: Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. / Nucleic Acids Res 2012,40(19):9379鈥?391. xternal" href="http://dx.doi.org/10.1093/nar/gks725">CrossRef
45. Ding D, Lou X, Hua D, Yu W, Li L, Wang J, Gao F, Zhao N, Ren G, Li L, Lin B: Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing-based approach. / PLoS Genet 2012,8(12):e1003065. xternal" href="http://dx.doi.org/10.1371/journal.pgen.1003065">CrossRef
46. Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NST, Abeysinghe S, Krawczak M, Cooper DN: Human Gene Mutation Database (HGMD): 2003 update. / Hum Mutat 2003,21(6):577鈥?81. xternal" href="http://dx.doi.org/10.1002/humu.10212">CrossRef
47. HKU Lab Software Downloads [http://paed.hku.hk/uploadarea/yangwl/html/software.html]
48. Jiang P, Chan KCA, Liao GJW, Zheng YWL, Leung TY, Chiu RWK, Lo YMD, Sun H: FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma. / Bioinformatics 2012,28(22):2883鈥?890. xternal" href="http://dx.doi.org/10.1093/bioinformatics/bts549">CrossRef
49. Pungpapong V: Empirical Bayes Variable Selection for High-Dimensional Regression. / PhD thesis. Purdue University; 2012.
50. Pungpapong V, Muir WM, Li X, Zhang D, Zhang M: A fast and efficient approach for genomic selection with high-density markers. / G3 (Bethesda) 2012,2(10):1179鈥?184. xternal" href="http://dx.doi.org/10.1534/g3.112.003822">CrossRef
51. Meuwissen TH, Hayes BJ, Goddard ME: Prediction of total genetic value using genome-wide dense marker maps. / Genetics 2001,157(4):1819鈥?829. - 作者单位：Konstantin Tretyakov (1)
Tatyana Goldberg (2)
Victor X Jin (3)
Paul Horton (4)
1. Institute of Computer Science, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia
2. Faculty of Informatics, Department for Bioinformatics and Computational Biology, Technical University Munich, Boltzmannstrasse 3, Garching, 85748, Germany
3. Department of Biomedical Informatics, The Ohio State University, 460 W 12th Ave., 212 BRT, Columbus, OH, 43210, USA
4. Computational Biology Research Center, AIST, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
文摘
The second ISCB-Asia conference of the International Society for Computational Biology took place December 17-19, 2012, in Shenzhen, China. The conference was co-hosted by BGI as the first Shenzhen Conference on Computational Genomics (SCCG). 45 talks were presented at ISCB-Asia/SCCG 2012. The topics covered included software tools, reproducible computing, next-generation sequencing data analysis, transcription and mRNA regulation, protein structure and function, cancer genomics and personalized medicine. Nine of the proceedings track talks are included as full papers in this supplement. In this report we first give a short overview of the conference by listing some statistics and visualizing the talk abstracts as word clouds. Then we group the talks by topic and briefly summarize each one, providing references to related publications whenever possible. Finally, we close with a few comments on the success of this conference.