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CCB at JHUCenter for Computational Biology
http://ccb.jhu.edu/
Center for Computational Biology
http://ccb.jhu.edu/
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CCB at JHU | ccb.jhu.edu Reviews
https://ccb.jhu.edu
Center for Computational Biology
Operon
The method is modified from the one described in: Maria D. Ermolaeva, Owen White and Steven L. Salzberg. Prediction of Operons in Microbial Genomes. Nucleic Acids Research, 29, 1216-1221, (2001). Mihaela Pertea, Kunmi Ayanbule, Megan Smedinghoff and Steven L. Salzberg. OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Research, doi:10.1093/nar/gkn784 (2008). Last update of OperonDB: October 2015. 1700 new bacterial and archaeal genomes added! 111;perondb.
TransTermHP
Finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator. TransTermHP is described in:. Kunmi Ayanbule, and Steven Salzberg. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. A predecessor system, TransTerm, that used very different search and scoring algorithms is described in:. Last up...
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CCB Publications
http://ccb.jhu.edu/publications.shtml
Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T et al. Jun 2015) Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. 348 (6239): 1139-43. doi:10.1126/science.aaa4788. Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG et al. Apr 2015) The genomes of two key bumblebee species with primitive eusocial organization. 16: 76. doi:10.1186/s13059-015-0623-3. 12 (4): 357-60. doi:10.1038/nmeth.3317. 3: e808. doi:10.7717/peerj.808. Jan 2015) Broad CTL ...
CCB Software
http://ccb.jhu.edu/software.shtml
Next-Generation Sequence Alignment Software. Genome Assembly and Large-Scale Genome alignment. Next-generation sequence alignment software. TopHat-Fusion is an enhanced version of TopHat with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. HISAT is a new, highly efficient system for aligning RNA-seq reads. HISAT uses a new indexing scheme, hierarchical indexing, which is inherentl...
Genome Assemblers
http://ccb.jhu.edu/gage_b/genomeAssemblers/index.html
The following genome assemblers were used in GAGE-B:. ABySS v1.3.4. MIRA v3.4.0. MSRCA v1.8.3. SGA v0.9.34. SPAdes v2.3.0. Velvet v1.2.08.
Kraken
http://ccb.jhu.edu/software/kraken
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algo...18 MB...
TopHat
http://ccb.jhu.edu/software/tophat/index.shtml
A spliced read mapper for RNA-Seq. Is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie. And then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort among Daehwan Kim and Steven Salzberg in the Center for Computational Biology. At Johns Hopkins University, and Cole Trapnell in the Genome Sciences Department. Index and annotation downloads.
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Datasets – The Institute for Data Intensive Engineering and Science
http://idies.jhu.edu/datasets
The Institute for Data Intensive Engineering and Science. The Maryland Advanced Research Computing Center. Homewood High-Performance Cluster (HHPC). Coursera and Johns Hopkins. Grants & Funding Overview. IDIES Seed Funding Initiative. Research & Data. News & Events. News & Announcements. Talks & Symposia. Genomics @ JHU Seminar Series. Education & Outreach. The Data Conservancy community includes university libraries, national data centers, national research labs and information science research and educ...
Open Positions |
http://www.langmead-lab.org/open-positions
LANGMEAD LAB @ JHU. LANGMEAD LAB @ JHU. For details, contact Ben. To apply, write to Ben. With your application materials, including your CV, two letters of recommendation, and a brief statement of your postdoctoral and career goals. Johns Hopkins has a very strong, diverse community of researchers studying methods and software for genomics. We are spread across diverse departments and centers including:. Center for Computational Biology. Institute for Data Intensive Engineering and Science. July 26, 2016.
Machine Learning @ Johns Hopkins University | People
http://ml.jhu.edu/people
Filter by application area: Astrophysics. To find many more JHU faculty in each application area, follow links from the research. Page This page lists only members of the cross-cutting machine learning group. Dimensionality reduction, statistical signal processing, online learning, adversarial learning, stochastic approximation. CS 675: Statistical Machine Learning. CS 479/679: Representation Learning. Graphical models, transfer learning, structured regularization. CS 475: Machine Learning. AMS 735: Topi...
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Computational Cell Biology IMB UQ
Computational Cell Biology, Teasdale Group IMB. Protein Sequence Analysis Tools. Golgi Transmembrane Protein Prediction. Support Vector Machines For Predicting Transmembrane Domains. Protein Solvent Accessible Surface Area Predictor (ASAP). Supplementary Data For Published Papers. Supplementary data for mouse proteome analysis. Supplementary data for functional classification of the mouse secretome. Mouse Protein Subcellular Localization Databases. Type II membrane proteins.
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Center for Children's Books
Center for Children's Books. Closing the App Gap. App Authors: Closing the App Gap II. Welcome to the Center for Children’s Books! The Center for Children’s Books at the School of Information Sciences is a research center with additional interests in education and service. Our mission is to facilitate the creation and dissemination of exemplary and progressive research and scholarship related to youth-focused resources, literature, and librarianship. New to the CCB: Social Media. We have joined Twitter.
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CCB at JHU
The Center for Computational Biology. A joint research center in the McKusick-Nathans Institute of Genetic Medicine, the Department of Computer Science, and the Department of Biostatistics. March 10, 2015. Daehwan Kim, Ben Langmead and Steven Salzberg publish a study in the journal Nature Methods describing HISAT, a highly efficient software tool for .(read more). March 6, 2015. February 18, 2015. December 19, 2014. December 18, 2014. In addition to its research program, CCB provides bioinformatics exper...
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高苑電算中心
98/7/3 PM5:00關閉下列主機之服務- -成績/課務/註冊系統等所有校務系統、辦公室自動化系統、數位學院.等。 98/7/4 AM6:00 PM8:00- -電算中心主機房全部停電，影響範圍包含全校網路、無線校際漫遊、學校首頁(包含電算、教學與社團、運作於電算網頁主機下之各系所單位網頁)、教職員/學生電子郵件、成績/課務/註冊系統等所有校務系統、辦公室自動化系統、數位學院.等)，當天全校所有系所單位網頁、監視/監控系統亦無法由校外存取。 98/7/5 AM6:00 PM8:00關閉下列主機之服務- -影響範圍包含DNS、代理伺服器、教職員/學生電子郵件、成績/課務/註冊系統等所有校務系統、辦公室自動化系統、數位學院、無線校際漫遊、圖書館網頁.等，因DNS停機，故亦無法從校外瀏覽學校首頁、所有系所單位網頁。 98/7/7AM8:00 PM17:00- -上半天學生電子郵件、FTP及個人網頁停止服務，下半天會計室主機、知識檢索主機、 總務處財管系統、資傳系網站停止服務。 時間 2009.7.1 2009.7.3 (星期三 星期五). 200976 2009.7.10 (星期一 星期五). E-mai...
Center for Children's Books - Illinois
Graduate School of Library and Information Science. University of Illinois at Urbana-Champaign. World War I: What Was Once the War to End All Wars. Tales as Tall as the Trees: Arboreal Stories from Around the World. Check out more annotated bibliographies. Sorted by topic or date. Youth Lit Book Club. This summer, our Youth Lit Book Club will be based around Alaine Martaus' Fantasy YA Lit class. Please fill out this. Survey to share your preferences for the summer. Summer Youth Lit Book Club. Check out t...
