https://function.princeton.edu/

• 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

Feel free to add more useful article links below by commenting on this page. Your comments are welcome.

Ref https://www.lncrnablog.com/lncpipe-a-nextflow-based-pipeline-for-identification-and-analysis-of-long-non-coding-rnas-from-rna-seq-data/

Address of the bookmark: https://github.com/likelet/LncPipe

Effective July 10, 2023, NCBI’s Assembly and Genome record pages now redirect to new NCBI Datasets pages. As previously announced, these updates are part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.   

The following pages have been updated:

• The NCBI Assembly record pages now redirect to the new NCBI Datasets Genome record pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST.  
• The NCBI Genome record pages now redirect to the NCBI Datasets Taxonomy record pages that provide a taxonomy-focused portal to genes, genomes, and additional NCBI resources.   

During this transition, you will have the option to return to the legacy Genome and Assembly record pages. We will remove the legacy pages in early 2024.  

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

Ever since a monk called Mendel started breeding pea plants we've been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix. Then, in 2001, scientists wrote down the entire 3-billion letter code contained in the average human genome. Now they're trying to interpret that code; to work out how it's used to make different types of cells and different people. The ENCODE project, as it's called, is the latest chapter in the story of you. To read the ENCODE research papers and more, visit http://www.nature.com/ENCODE

View full lesson: http://ed.ted.com/lessons/james-watson-on-how-he-discovered-dna Nobel laureate James Watson opens TED2005 with the frank and funny story of how he and his research partner, Francis Crick, discovered the structure of DNA. Talk by James Watson.

The vital metaphase stage of cell division, when the sister chromatids migrated to the centre and lined up in a row, and pulled apart using attached microtubules in such a way that half the DNA ends up in each daughter cell. However, before the mitotic spindle‐mediated movement gets start and pulled DNA apart, the chromosomes are free to undergo recombination which involves the exchange of genetic material either between multiple chromosomes or between different regions of the same chromosome.

During recombination, the precise breakage of each strand, exchange between the strands, and sealing of the resulting recombined molecules happens. The “chromosomal breakpoints” refers to these places where they break. Mostly, this process occurs with a high degree of accuracy at high frequency in both eukaryotic and prokaryotic cells. But occasionally this “break and sealing/ break and reattach” process goes wrong and the reattachment happens in the wrong place which usually create disaster (with few exceptions).These chromosome disaster or abnormalities involve the gain, loss or rearrangement of visible amounts of genetic material during cell division. These abnormalities are of two type, the first one is numerical abnormalities  where severe disorders are caused by the loss or gain of whole chromosomes, which affect the copy number of hundreds or even thousands of genes. The second are structural abnormalities which can be unbalanced or balanced. The former are similar to numerical abnormalities in that genetic material is either gained or lost. The natural defects in chromosome segregation are linked to cancer and several genetic diseases (http://en.wikipedia.org/wiki/List_of_genetic_disorders). Therefore, the enzymes involved in regulating cell division are still the attractive drug targets for many diseases.

Apart from certain chromosome abnormalities, these “crossing over” of segments of maternal and paternal chromosomes to form hybrid chromosomes have some evolutionary importance and considered as a driver of genetic variation. Moreover, the chromosome breakage in evolution is considered to be non-random in nature(http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020014). In addition the study of breakpoint regions and non-breakpoint (stable) regions of chromosomes indicates both the regions evolved in distinctly different ways ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/). These breakage may lead to genetic diseases or participate to chromosomal rearranmgnets and contributed in development of new species.

I will try to explain the genome hotspots/Evolutionary Breakpoint Regions(EBRs)/fragile regions/weak fragments/  in my next blog.

Software for recombination detection:

RAT http://cbr.jic.ac.uk/dicks/software/RAT/

Breakpointer https://github.com/ruping/Breakpointer

DRP http://web.cbio.uct.ac.za/~darren/rdp.html

RB-finder http://www.ncbi.nlm.nih.gov/pubmed/18707535

LDhat2.0 http://ldhat.sourceforge.net/LDhat2.0/instructions.shtml

Reference:

http://www.nature.com/scitable/topicpage/genetic-recombination-514#

Image: Wikipedia , sciencelearn.org.nz

Recommended Articles:

http://www.friendshipcircle.org/blog/2012/05/22/13-chromosomal-disorders-youve-never-heard-of/

http://web.udl.es/usuaris/e4650869/docencia/segoncicle/genclin98/recursos_classe_%28pdf%29/revisionsPDF/chromosyndromes.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775595/table/T2/

http://learn.genetics.utah.edu/content/disorders/chromosomal/

http://www.ncert.nic.in/html/learning_basket/biology/cc&cd.pdf

EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0918-z

Address of the bookmark: https://github.com/apeltzer/EAGER-GUI