Address of the bookmark: https://bioinformatik.de/en/bioinformatics-in-germany/research/research-groups.html

More at https://rgcb.res.in/jobs.php

Address of the bookmark: https://github.com/quinlan-lab/applied-computational-genomics

The fellowship will be for a period of 3 years, or for a period of 4 years, with 25 % compulsory work (e.g. teaching responsibilities at the department) contingent on the qualifications of the candidate and the teaching needs of the department.

Starting date no later than October 1, 2021.

More at https://www.jobbnorge.no/en/available-jobs/job/199984/phd-research-fellow-in-genomics-and-bioinformatics

Like other indel callers, Scalpel works by performing de novo assembly of regions of interest, so that misalignment to the reference genome cannot obscure the presence of an insertion or deletion. Scalpel's innovation is to repeatedly check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats are eliminated. This ensures that the final assembly of the exon is highly accurate while minimizing compute time.

The Cold Spring Harbor team's validation of Scalpel, published over the weekend in Nature Methods, compares Scalpel's performance on a live whole exome against HaplotypeCaller and SOAPindel. The donor is an individual with serious neurological disorders, which may be linked to a high incidence of indels. One thousand indels from this individual's exome, called by one or more of the informatics pipelines, were selected for focused resequencing. This resequencing revealed a 77% true positive rate for Scalpel calls, dramatically better than the rates for either of the competing tools; Scalpel performed especially well with indels longer than five base pairs, a traditional weak point for indel callers.

Finally, the authors demonstrate Scalpel's use on a large set of genetic data from nearly 600 families who donated samples to the Simons Simplex Collection, a project of the Simons Foundation Autism Research Initiative. Scalpel found a very high enrichment for indels in children affected by autism, compared with their unaffected siblings, a pattern that persisted even after excluding common variants.

More at sandbox.bio

Address of the bookmark: http://sandbox.bio

• In a GitHub or GitLab repository
• Free to use
• Written in markdown or similar

NOTE: This list of courses is selected only based on the above criteria.
There are no checks on quality.

https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

Address of the bookmark: https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

1. NCBI (National Center for Biotechnology Information):

   • NCBI provides various databases related to genetic information, including 16S rRNA sequences.
   • You can access the 16S ribosomal RNA sequences from NCBI's Nucleotide database (https://www.ncbi.nlm.nih.gov/nucleotide/).
   • Perform a search using keywords like "16S rRNA" or specific bacterial names to find relevant sequences.
   • You can download sequences individually or in batches using the provided tools.

2. GreenGenes:

   • GreenGenes is a widely used 16S rRNA gene sequence database.
   • You can access it at http://greengenes.secondgenome.com/.
   • GreenGenes provides precompiled databases for various purposes, including classification, alignment, and phylogenetic analysis.

3. SILVA:

   • SILVA (https://www.arb-silva.de/) is another comprehensive database for ribosomal RNA (rRNA) sequences.
   • It covers not only 16S rRNA but also other ribosomal RNA sequences.
   • SILVA provides precompiled databases for various purposes, including taxonomic classification and alignment.

4. Ribosomal Database Project (RDP):

   • RDP (http://rdp.cme.msu.edu/) is a curated database that offers 16S rRNA sequences.
   • It provides tools for sequence analysis and classification.
   • You can download sequences and taxonomy information from their website.

5. QIIME (Quantitative Insights Into Microbial Ecology):

   • QIIME (https://qiime2.org/) is a widely used bioinformatics platform for microbiome analysis.
   • It provides tools for analyzing microbial communities, including processing 16S rRNA sequences.
   • QIIME often includes its own preprocessed 16S rRNA databases that can be used for analysis within the platform.

Before downloading any database, make sure to read the terms of use and citation requirements, as some databases may have specific usage policies. Additionally, consider the compatibility of the database with your analysis pipeline and software tools.

NCBI 16s RNA database location ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz

• What is Bioinformatics - An introduction article by Mark Gerstein at Yale University.
• The powerful world of bioinformatics
• Bioinformatics: Key to 21st Century Biology
• The commercialization of bioinformatics by Phillip B.C. Jones
• A Curriculum for Bioinformatics: The Time is Ripe This article proproses requirements for a standard bioinformatics curriculum. By Russ Altman.
• Human Genome Research A description of the Human Genome Project.
• Retooling for Bioinformatics An article from The Scientist
• A Programming Course in Bioinformatics A discussion of the task of teaching an introductory bioinformatics course. By Russ Altman and John Koza.
• Sequence analysis Keith Robison's guide to the exciting world of biosequence comparison! Useful background information on a variety of computational biology algorithms.
• Bioinformatics, Supercomputing, and Complex Genome Analysis ,DOE/NIH Human Genome News , 4(5) January 1993.
• Medical Informatics Training at Stanford University School of MedicineAn article from 1995 by Edward Shortliffe describing our medical informatics training program, the nature of the curriculum, the backgrounds of our students, and the career paths of our graduates.
• Elementary Sequence Analysis - Database Searching by B. Golding Jan 1996. Fasta, blast, blitz, blaze, flash, blocks. 
• Bioinformatics in Support of Molecular Medicine A description of bioinformatics and its connection to clinical informatics. By Russ Altman.
• Biology as a Business Venture and the Rise of Bioinformatics , 1996.
• Preface to Molecular Bioinformatics- Sequence Analysis , 1997.
• Bioinformatics & Cheminformatics in the Drug Discovery Cycle , 1997.
• Bioinformatics in a post-genomics age Sept 1997
• Bioinformatics takes charge , Trends in Biotech. , Vol. 16 No. 3 (170), pp. 104-107, March 1998.
• "A Curriculum For Bioinformatics: The Time Is Ripe" An editorial from the journal BIOINFORMATICS-Bioinformatics, Vol 14, Issue 7, pages 549-550 (August 1998)
• Bioinformatics, pharma and farmers , Trends in Biotech. , Vol. 17 No. 3 (182) , pp. 85-88. March 1999.
• Bioinformatics/Computational Biology Programs (May 1999)
• Biocomputing For Everone an introduction to biocomputing for the layperson published by the VSNS biocomputing division.
• Biocomputing For Schools Another VSNS publication - this time aimed at highschool students, but fun to read for everyone.  Includes articles on the application of bioinformatics to BSE research, and a ``Do-It-Yourself'' detailed example of a WWW search.
• Understanding the human genome By D. L. Brutlag, in Scientific American: Introduction to Molecular Medicine , P. In Leder, D. A. Clayton, E. Rubenstein, Eds., (New York: Scientific American , 1994), pp. 153-168.
• Viva bioinformatics, but who survives? , 1999.
• Bioinformatics: Playing The Numbers Game June 1999
• Mining the Genome Sept 1999
• Commercialization of biological information and the rise of bioinformatics - Part I , Nov/Dec 1999, 20/21, pp. 40-47.
• Commercialization of biological information and the rise of bioinformatics - Part II , Jan 2000, pp. 51-56.
• Turbo-charging bioinformation for drug discovery , Feb 2000, pp. 38-49.
• Bioinformatics: low supply, high demand June 2000
• The Next Wave of the Genomics Business July 2000
• The Bioinformatics Gold Rush July 2000
• Bioinformatics . Next Wave feature on careers in bioinformatics.September 2000
• A prerequisite for working in thie field: love of computers article from The Scientist (Nov 2000)
• Sep/Oct 2000 issue of the MIT Technology Review
• How to become a bioinformatics expert , including a listing ofEuropean opportunities to study bioinformatics. Compiled by theVirtual School of Natural Sciences BioComputing Division.
• Protein Sequence Alignment and Database Scanning Geoff Barton's review.
• Pattern matching and motifs 
• Knowledge-based Analysis of Microarray Gene Expression Data Using Support Vector Machines
• VHG Virtural HyperGlossary. Defines terms used in different subfields, currently Glycoscience, Protein Structure.
• LASSAP a LArge Scale Sequence compArison Package
• Bioinformatics in pre- and post-genomics eras , Trends in Biotech. ,Vol. 18 , pp. 133-135, April 2000.
• Confluence of Western and Traditional Medicines and Future Prospectes - Part I , Mar/Apr 2000, pp. 34-37.
• Confluence of Western and Traditional Medicines and Future Prospectes - Part II , May/Jun 2000, pp. 66-74.
• Computers + Biology = Bioinformatics April 2001
• Bioinformatics U., Genome Technology, September, 2001 An article from Genome Technology written by Nat Goodman about bioinformatics curricula.
• Training in a Hybrid Discipline, Nature, October 25, 2001 An article from Nature written by Potter Wickare and Paul Smaglik on bioinformatics training programmes in North America.
• Bioinformatics Knowledge Vital to Careers - Competition from mathematicians and computer scientists compels biologists to become computational article from The Scientist (Sept 2002)
• The babel of bioinformatics By Teresa Attwood, Science , 5491: 471 (2000).
• The quiet revolution: Biodiversity informatics and the internet By Frank A. Bisby, Science , 289: 2309 (2000).
• Are you ready for the revolution? By Declan Butler, Nature , 409: 758-760 (2001).
• Beyond the genome: Biotech's next holy grail By Ellen Licking, Business Week , April 10, 2000.
• The genome explained By Ellen Licking, Business Week , June 12, 2000.
• Why bioinformatics is hot career By Stacey Wells, San Francisco Chronicle , March 4, 2001.
• Proteomics: Beyond the genome Edited by Patricia O'Connell, Business Week Online, June 7, 2001.
• A true believer dismisses indifference to bioinformatics By Terence Chea, Washington Post , March 14, 2002.
• Genome map on a grain of rice By Kristen Philipkoski, Wired News , March 29, 2002.
• Informatics moves to the head of the class By Beth Schachter, Bio-IT World , June 12, 2002.
• The proteomics odyssey By Malorye Branca, Bio-IT World , Aug. 13, 2002.
• Dell goes nuts for clusters By Michael Kanellos, CNET News.com , Sept. 2, 2002.
• IBM teams with TurboGenomics By Salvatore Salamone, Bio-IT World , Sept. 5, 2002.
• The new, new pharmacogenomics By Malorye Branca, Bio-IT World , Sept. 9, 2002.
• RLX introduces a biocluster in a box By Salvatore Salamone, Bio-IT World , Sept. 17, 2002.
• CombinatorX gets $40 million to look for drug synergies By Salvatore Salamone, Bio-IT World , Sept. 24, 2002.
• Calculating with DNA By Salvatore Salamone, Bio-IT World , October 2002.
• Hitachi Soft develops low-cost human genome DNA chip By Kuriko Miyake, ITworld.com , Oct. 8, 2002.
• IBM chooses Linux for 'Blue Gene' supercomputer By Lisa Gill,NewsFactor Network , Oct. 24, 2002.
• The international 'HapMap' project cbsnews.com , Oct. 29, 2002.
• US stem cell policy deters investors By Steve Mitchell, UPI , Nov. 2, 2002.
• Biochip sprouts DNA strands By Kimberly Patch, Technology Research News , Nov. 13, 2002
• Genomics consolidation � no pain, no gain By Malorye Branca, Bio-IT World , Dec. 10, 2002.
• Data stored in multiplying bacteria By Natasha McDowell,NewScientist.com , Jan. 3, 2003.
• Cowabunga! Scientists to start Bovine Genome Project Science Daily , March 5, 2003.
• Computational Analysis of Complexity in Gene Expression Arrays
• Building your own Bioinformatics Supercomputer for Cheap Using Grid Technology
• Career Advice for Computational Biology By Amjad-Ali Khoja at U. Texas.
• Proceedings of the National Academy of Sciences
• A Practical Guide to protein sequence and structure analysis at UCL

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