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    Resources: Protein sequence alignment display/analysis with MSAReveal.Org
    Submitted by Eric Martz; posted on Monday, September 26, 2016


    MSAReveal.Org is a new, free, open-source website for display and analysis of your protein sequences and sequence alignments:
    1. Paste in protein sequences or alignments in FASTA format.
    2. Genus and species, gene names, and UniProt IDs are extracted from the headers and tabulated. UniProt IDs are linked to UniProt.
    3. Checkboxes control coloring of amino acids/groups.
    4. Touching an amino acid reports its 3-letter abbreviation and sequence number in a tooltip. You don't have to memorize all 20 one-letter amino acid codes.
    5. The sequence listing can be horizontally scrolled, or wrapped at a specified number of amino acids.
    6. A sequence numbering offset can be specified with "start=N" in the header of each sequence. A negative number enables numbering to start at 1 for the mature protein, after a negatively numbered signal sequence.
    7. A consensus is reported with the frequencies of amino acids in each column.
    8. Statistics are tabulated including lengths (excluding gaps), percentages identity, percentages in gaps, percentages charged, percentages aromatic, net charge at neutral pH, etc. etc..
    9. Minimum, average, and maximum are given for each column in Statistics.
    10. The Statistics Table can be sorted on any column.
    11. A search mechanism finds and highlights sequence fragments/motifs regardless of gaps. It accepts multiple amino acid possibilities at a given position.
    12. Search hits are listed with links so you can jump to any hit instantly.
    13. Numerous irregularities or warnings are reported, including the ambiguous codes B, J, O, U, X, Z and illegal characters, which can be located easily with the search mechanism.
    14. A description of each alignment, added to the first header, will be displayed.
    15. A description of each sequence, added to its header, will be displayed when its taxon is touched.
    16. A Protein Data Bank ID, when added to the header (e.g. "PDB=2ace") will be tabulated and linked to display the 3D model in FirstGlance.Jmol.Org.
    17. New in September, 2016.
    A more detailed overview with snapshots:[...]rview

    Demonstration and test alignments are built in. Instructions are provided for downloading sequences from UniProt, and aligning them with free, easy, quick Jalview (using MAFFT, TCOFFEE, MUSCLE, etc.). Displays any FASTA alignments, e.g. from the ConSurf Server. MSAReveal.Org works in all popular browsers, Windows or OS X. Tested up to a total of one million amino acids, and with alignments containing hundreds of sequences.



    The challenge for Illumina, as with any other large company, is to continue to innovate while maintaining a grip on its core business. The company recently took a page from Alphabet by announcing a series of "moonshot" ventures, called Helix and Grail, which will create an App Store model for DNA informatics and bring early cancer screening tests into every doctor's office. And veteran Apple executive Phil Schiller joined Illumina's board this summer, giving the biotech company an injection of consumer marketing know-how.



    In an important breakthrough for the forensic science community, researchers have developed the first-ever biological identification method that exploits the information encoded in proteins of human hair.

    Scientists from Lawrence Livermore National Laboratory (LLNL) and a Utah startup company have developed the groundbreaking technique, providing a second science-based, statistically validated way to identify people and link individuals to evidence in addition to DNA profiling.



    According to [Ewan] Birney, the act of sharing data has been a tradition going back to the beginning of genetics. He points to innovations in the past century, such as the Protein Data Bank, the ENA Bank (formerly EMBL), and GenBank nucleotide collections, and the Human Genome Project as examples of instances where data sharing worked to positive, successful results. Birney is no stranger to the data sharing debate; he was appointed the joint Director of EMBL-EBI in 2015, and awarded the Benjamin Franklin Award for Open Access in the Life Sciences in 2005.

    Ewan's Blog:



    Numerous lines of evidence point to a genetic basis for facial morphology in humans, yet little is known about how specific genetic variants relate to the phenotypic expression of many common facial features. We conducted genome-wide association meta-analyses of 20 quantitative facial measurements derived from the 3D surface images of 3118 healthy individuals of European ancestry belonging to two US cohorts. Analyses were performed on just under one million genotyped SNPs (Illumina OmniExpress+Exome v1.2 array) imputed to the 1000 Genomes reference panel (Phase 3). We observed genome-wide significant associations (p < 5 x 10−8) for cranial base width at 14q21.1 and 20q12, intercanthal width at 1p13.3 and Xq13.2, nasal width at 20p11.22, nasal ala length at 14q11.2, and upper facial depth at 11q22.1. Several genes in the associated regions are known to play roles in craniofacial development or in syndromes affecting the face: MAFB, PAX9, MIPOL1, ALX3, HDAC8, and PAX1. We also tested genotype-phenotype associations reported in two previous genome-wide studies and found evidence of replication for nasal ala length and SNPs in CACNA2D3 and PRDM16. These results provide further evidence that common variants in regions harboring genes of known craniofacial function contribute to normal variation in human facial features. Improved understanding of the genes associated with facial morphology in healthy individuals can provide insights into the pathways and mechanisms controlling normal and abnormal facial morphogenesis.


    Shaffer, John R., et al. 2016. "Genome-wide association study reveals multiple loci influencing normal human facial morphology." PLoS Genet 12(8):e1006149.[...]06149



    Now, a team of Liggins Institute researchers have shown for the first time that human mitochondrial DNA leaves the mitochondria, travels into the host cell nucleus and connects to specific genes.

    "We found evidence that mitochondria DNA and nuclear DNA 'talk to each other', and these interactions aren't random," says lead researcher Dr Justin O'Sullivan, a molecular geneticist at the University of Auckland research institute.

    The findings give weight to the idea that mitochondria do much more than supply energy and regulate a cell's metabolism – the processes that keep it alive.


    Doynova, M.D., et al. 2016. "Interactions between mitochondrial and nuclear DNA in mammalian cells are non-random." Mitochondrion.[...]8.003
    Resources: Cello: Genetic circuit design automation
    Submitted by Prashanth Suravajhala; posted on Thursday, August 25, 2016



    The Cello input is a high-level logic specification written in Verilog, a hardware description language. The code is parsed to generate a truth table, and logic synthesis produces a circuit diagram with the genetically available gate types to implement the truth table. The gates in the circuit are assigned using experimentally characterized genetic gates. In assignment, a predicted circuit score guides a breadth-first search, or a Monte Carlo simulated annealing search. The assignment with the highest score is chosen, and this assignment can be physically implemented in a combinatorial number of different genetic layouts. The Eugene language is used for rule-based constrained combinatorial design of one or more final DNA sequence(s) for the designed circuit.



    Nielsen, Alec A.K., et al. 2016. "Genetic circuit design automation." Science 352(6281).[...]c7341

    February 21-23, 2017
    Porto, Portugal


    The purpose of the International Conference on Bioinformatics Models, Methods and Algorithms is to bring together researchers and practitioners interested in the application of computational systems, algorithmic concepts and information technologies to address challenging problems in Biomedical research with a particular focus on the emerging problems in Bioinformatics and computational biology. There is a tremendous need to explore how mathematical, statistical and computational models can be used to better understand biological processes and systems, while developing new methodologies and tools to analysis the massive currently-available biological data. Areas of interest to this community include systems biology, sequence analysis, biostatistics, image analysis, network and graph models, scientific data management and data mining, machine learning, pattern recognition, computational evolutionary biology, computational genomics and proteomics, and related areas.


    Regular Papers:
    Paper Submission: September 29, 2016
    Authors Notification: November 23, 2016
    Camera Ready and Registration: December 9, 2016

    Position Papers:
    Paper Submission: November 8, 2016
    Authors Notification: December 14, 2016
    Camera Ready and Registration: December 27, 2016

    Workshop Proposal: November 3, 2016

    Doctoral Consortium:
    Paper Submission: December 29, 2016
    Authors Notification: January 11, 2017
    Camera Ready and Registration: January 23, 2017

    Special Sessions:
    Special Session Proposal: November 21, 2016

    Tutorials, Demos and Panels Proposals: December 27, 2016



    A team of Japanese doctors turned to IBM's AI system, Watson for help after the treatment for an 60-year-old woman suffering from leukaemia proved unsuccessful. The AI was successfully able to find out that she actually suffered from a different, rare form of leukaemia, as the disease had gone undetected using conventional methods by the doctors.


    December 8-10, 2016
    Houston, Texas, USA

    You are invited to submit papers with unpublished original work describing recent advances on all aspects of bioinformatics, systems biology, intelligent computing, and biomedical informatics.


    Deadline for paper submission: August 15, 2016 (extended)
    Notification to authors of papers: September 15, 2016
    Notification to authors of highlight paper: October 1, 2016
    Deadline for abstract submission: September 24, 2016
    Notification to authors of abstracts: October 1, 2016
    Conference early registration: October 1, 2016
    Conference early registration deadline: October 31, 2016
    ICIBM conference: December 8-10, 2016


    Prospective authors are invited to submit unpublished work to ICIBM 2016. All papers and abstracts will be submitted through EasyChair Conference System. Detailed information is available through:[...]20160

    All submitted papers will be peer-reviewed. The accepted papers of registered authors will be published in special issues of several journals, including BMC Systems Biology, BMC Genomics, BMC Bioinformatics, BMC Biomedical Informatics and Decision Making, and International Journal of Computational Biology and Drug Design. Authors need to prepare manuscripts in the format of the corresponding journal that they prefer.


    Up to 20 travel awards are available to students/postdocs; awards will be granted through an NSF grant. A certificate will be given to each awardee during conference.
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