My Life Scienes

DUF Annotation Jamboree

2011-12-07T09:43:00.001-08:00

I am currently participating in the DUF Annotation Jamboree (December 7-9, 2011 UC San Diego).
The goal of this workshop is to annotate a possibly large number of protein families that are being referred to as having unknown functions (terms like UPF or DUF) despite (often) having a significant amount of reliable predictions, or even experimental data, about them (see also: TOPSAN AFP-DUF Annotation Jamboree page).

Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state

2011-11-05T18:00:00.000-07:00

In this interesting work, the authors successfully reprogram somatic senescent cells from very old patients into induced pluripotent stem cells (iPSCs). They also show hat many of the old-age-related changes in cells (e.g. telomere length and gene expression profiles) are reversed in such reprogrammed pluripotent cells.

Laure Lapasset et al. "Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state" Genes & Development

Mollusc Phylogeny

2011-11-01T22:06:00.000-07:00

Smith et al. "Resolving the evolutionary relationships of molluscs with phylogenomic tools" Nature

Human Brain (Development) - Genetics and Transcription

2011-11-01T22:02:00.000-07:00

Recently, three fascinating studies regarding the genetics and transcription of/in the human brain have been published:

Baillie et al. "Somatic retrotransposition alters the genetic landscape of the human brain" Nature
Kang et al. "Spatio-temporal transcriptome of the human brain" Nature
Colantuoni et al. "Temporal dynamics and genetic control of transcription in the human prefrontal cortex" Nature

Synthetic Biology Science Special Issue

2011-09-05T13:40:00.000-07:00

Special issue in Science on Synthetic Biology:
http://www.sciencemag.org/site/special/syntheticbio

Frontiers in Bioinformatics and Computational Biology

2011-09-01T17:57:00.000-07:00

I recently joined the editorial board of the new open access journal "Frontiers in Bioinformatics and Computational Biology".
See: http://www.frontiersin.org/bioinformatics_and_computational_biology

Please consider submitting your paper to this new journal! :)

BioHackathon 2011

2011-08-18T00:35:00.000-07:00

I have been invited to participate in the NBDC / DBCLS BioHackathon 2011 held in Kyoto (Japan) at the the Bioinformatics Center of Kyoto University from 21. August to 26. August, 2011. The main focus of the BioHackathon is to develop technologies for handling Linked Data in life science. We will discuss, explore and develop SPARQL endpoints, semantic web services, triple stores, ontologies, natural language processing, visualization and Open Bio* tools to utilize RDF data.

2011 Computational Phyloinformatics Course

2011-08-17T23:56:00.000-07:00

I taught the Ruby/BioRuby section ("Functional Genomics with BioRuby") of the 2011 Computational Phyloinformatics Course ("comphy2011"). This course is sponsored by NESCent, the Bioinformatics Center of Kyoto University, and NDBC. It took place in Kyoto (Japan) from 1. August to 11. August, 2011.

My section contained the following five sub-sections:

Introduction to Ruby programming
Introduction to BioRuby
Basics of Phylogenetic Inference
Multiple Sequence Alignments in BioRuby (with a focus on the MAFFT program)
Phylogenetic Trees in BioRuby

Databases for taxonomic icons

2011-05-26T09:02:00.000-07:00

Useful databases for taxonomic/species icons/images:

DBCLS/NDBC: http://biosciencedbc.jp/resource_icon/resource_icon.cgi

PhyloPic: http://phylopic.org/

Biosynthesis of Pyrrolysine − the 22nd Amino Acid

2011-04-05T15:45:00.000-07:00

The biosynthesis of pyrrolysine (O, Pyl), the twenty second amino acid found so far in some methanogenic archaea and one gram-positive bacterium (Desulfitobacterium hafniense), has been elucidated.

"How two amino acids become one" Nature News & Views
Gaston et al "The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine" Nature

Google Summer of Code 2011

2011-03-20T15:33:00.000-07:00

For this year's Google Summer of Code (GSoC) I am involved (as mentor or co-mentor) in the following proposals:

Representation of bio-objects and related information with images (BioRuby, under Open Bioinformatics Foundation umbrella)
Visualization of Protein 3D Structure Evolution (Archaeopteryx, forester, Jmol, under NESCent umbrella)
BioRuby forester (BioRuby, JRuby, forester, under NESCent umbrella)

Further BioRuby proposals (more information is here):

Primer on Cnidaria (Sea anemones, Jellyfish, Corals) and Their Significance for Research

2011-03-10T00:06:00.000-08:00

Technau and Steele "Evolutionary crossroads in developmental biology: Cnidaria" Development

Updated Classic: Hallmarks of Cancer: The Next Generation

2011-03-07T21:03:00.000-08:00

Hanahan and Weinberg "Hallmarks of Cancer: The Next Generation" Cell

Phylogenetics with BioRuby

2011-02-28T14:24:00.000-08:00

I started to write a small tutorial on phylogenetic methods using BioRuby:

http://code.google.com/p/forester/wiki/PhyloBioRuby

Suggestions and comments are welcome.

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

2011-01-17T14:20:00.000-08:00

Our paper, Zmasek and Godzik (2011) "Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires" has been published in Genome Biology (http://genomebiology.com/2011/12/1/R4/).

By reconstructing the domain repertoires ("domainomes") of putative ancestral eukaryotes, we show (that):

while protein domain gains and losses are common throughout eukaryote evolution, losses oftentimes outweigh gains and lead to significant differences in genome functional profiles
only at the base of the animal and the vertebrate sub-trees do domain gains significantly and consistently outnumber domain losses
a general trend of losses in metabolic capabilities and gain in regulatory complexity during the rise of animals
metabolic functions lost during animal evolution are likely being replaced by the metabolic capabilities of symbiotic organisms such as gut microbes

Top 10 Composers

2011-01-16T10:37:00.000-08:00

Anthony Tommasini explores what makes a classical composer great, maybe even the best, in this video series.

Related: the greatest composers.

ISMB/ECCB 2011

2011-01-12T13:08:00.000-08:00

ISMB/ECCB 2011

Special Interest Group Meetings: 15 July – 16 July
Conference: 17 July – 19 July

Workshop Track: 11 February
Highlights Track: 4 March
Posters Track: 18 March
Technology Track: 29 April
Late Breaking Research Track: opens17 January

DARK Apoptosome

2011-01-12T12:58:00.000-08:00

Shujun Yuan et al "Structure of the Drosophila Apoptosome at 6.9 A Resolution" Structure
Chu-Chiao Wu and Shawn B Bratton "DARK Apoptosome Secrets Come to Light" Structure (summary)

Origin and Evolution of Deuterostome microRNAs

2011-01-11T12:10:00.000-08:00

Florent Campo-Paysaa et al "microRNA complements in deuterostomes: origin and evolution of microRNAs" Evolution & Development

3D Reconstruction of Brain Wiring Networks in Drosophila

2011-01-11T12:07:00.000-08:00

Ann-Shyn Chiang et al "Three-Dimensional Reconstruction of Brain-wide Wiring Networks in Drosophila at Single-Cell Resolution" Current Biology

Functional Proteins Designed From Scratch

2011-01-07T15:53:00.000-08:00

Mark Isalan et al "De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth" PLoS ONE

Chromothripsis - 'Punctuated Equilibrium' Evolutionary Model for Cancer Development

2011-01-06T13:48:00.000-08:00

Philip J Stephens et al "Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development" Cell

Bioluminescence - and Efficient Light Diffusion and Transmission - in a Marine Snail

2011-01-03T12:09:00.000-08:00

Dimitri D Deheyn and Nerida G Wilson "Bioluminescent signals spatially amplified by wavelength-specific diffusion through the shell of a marine snail" Proceedings of the Royal Socienty B

Six3-otx Head Patterning System Universal to Bilaterian Animals?

2010-12-30T17:12:00.000-08:00

Patrick RH Steinmetz et al "Six3 demarcates the anterior-most developing brain region in bilaterian animals" EvoDevo

Fungal Evo-Devo

2010-12-30T16:16:00.000-08:00

Gregory Jedd "Fungal evo–devo: organelles and multicellular complexity" Trends in Cell Biology

Strawberry and Cacao (genomes)

2010-12-29T12:33:00.000-08:00

Vladimir Shulaev et al "The genome of woodland strawberry (Fragaria vesca)" Nature Genetics
Xavier Argout et al "The genome of Theobroma cacao" Nature Genetics

SMBE 2011 Annual Meeting will be held in Kyoto

2010-12-21T13:16:00.000-08:00

SMBE 2011 Annual Meeting, Kyoto University, July 26-30, 2011

BOSC 2010 Proceedings articles have been published

2010-12-21T13:13:00.000-08:00

Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010

The first BioRuby world wide IRC conference

2010-12-19T08:33:00.000-08:00

The topic is: "Current and future BioRuby development"
Sunday, Dec. 19, 2010, at 23pm JST (Japanese Standard Time), which is 15pm CET (Central European Time) and 9am EST (New York) and 6am PST (California time).
#bioruby irc.freenode.org
Archives (monthly): http://bioruby.org/irc/

Some notes:

http://bioruby.open-bio.org/wiki/BioRuby_IRC_conference
G-language: http://www.g-language.org/wiki/documents
Deploying, Monitoring and Troubleshooting Rails on the JVM with JRuby: http://vimeo.com/14435288
BioRuby issues: https://github.com/bioruby/bioruby/issues
Bioruby wishlist: http://bioruby.open-bio.org/wiki/Plugins#Candidate_Whish_List
Nadoka: http://www.atdot.net/nadoka/

Next BioRuby IRC conferences: 11pm JST, 3pm CET, 6am PST every Thursday.

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

2010-12-19T07:35:00.001-08:00

Accepted for publication in Genome Biology.