Systems biology and bioinformatics
4.8K views | +0 today
Follow
Systems biology and bioinformatics
Your new post is loading...
Your new post is loading...
Scooped by Dmitry Alexeev
Scoop.it!

Current Issue

Current Issue | Systems biology and bioinformatics | Scoop.it
Issue 1.1 now available Click on above link or on the image below to download pdf of full issue (8.76MB). The only graphics heavy part of C+T is the cover and though there are some coloured design ...
Dmitry Alexeev's insight:

suddenly came across a new journal - the cover is beautiful - let's go deeper into the text

more...
No comment yet.
Rescooped by Dmitry Alexeev from Global Brain
Scoop.it!

Ontological Engineering

Ontological Engineering | Systems biology and bioinformatics | Scoop.it
Barry Smith, “the ontology king”, has made freely available his Fall 2013 Ontological Engineering class. There is no better resource than here.

Via Spaceweaver
Dmitry Alexeev's insight:

if one is to go deeper into ontology - there is a resource

we believe it will be the basis of data integration in biomed

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

Accelerated discovery via a whole-cell model : Nature Methods : Nature Publishing Group

Accelerated discovery via a whole-cell model : Nature Methods : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Discrepancies between model prediction and experimental measurements enable molecular-level discovery with a whole-cell model of Mycoplasma genitalium.
Dmitry Alexeev's insight:

provides the most extesive so far model on flux balance of essentiality and comparison to experimental gene disruption model  

more...
No comment yet.
Rescooped by Dmitry Alexeev from Amazing Science
Scoop.it!

J Craig Venter wants to digitize DNA and transmit the signal to teleport organisms

J Craig Venter wants to digitize DNA and transmit the signal to teleport organisms | Systems biology and bioinformatics | Scoop.it

Craig Venter states:

 

"As the industrial age is drawing to a close, I think that we're witnessing the dawn of the era of biological design. DNA, as digitized information, is accumulating in computer databases. Thanks to genetic engineering, and now the field of synthetic biology, we can manipulate DNA to an unprecedented extent, just as we can edit software in a computer. We can also transmit it as an electromagnetic wave at or near the speed of light and, via a "biological teleporter", use it to recreate proteins, viruses and living cells at another location, changing forever how we view life."

 

"At this point in time we are limited to making protein molecules, viruses, phages and single microbial cells, but the field will move to more complex living systems. I am confident that we will be able to convert digitised information into living cells that will become complex multicellular organisms or functioning tissues."

 

"We could send sequence information to a digital-biological converter on Mars in as little as 4.3 minutes, that's at the closest approach of the red planet, to provide colonists with personalised drugs. Or, if Nasa's Mars Curiosity rover were equipped with a DNA-sequencing device, it could transmit the digital code of a Martian microbe back to Earth, where we could recreate the organism in the laboratory. We can rebuild the Martians in a P4 spacesuit lab -- that is, a maximum-containment lab -- instead of risking them crash-landing on the surface. I am assuming that Martian life is, like life on Earth, based on DNA. I think that because we know that Earth and Mars have continually exchanged material, in the order of 100kg a year, making it likely that Earth microbes have travelled to and populated Martian oceans long ago and that Martian microbes have survived to thrive on Earth. Simple calculations indicate that there is as much biology and biomass in the subsurface of our Earth as in the entire visible world on the planet's surface. The same could be true for Mars."

 

"If the life-digitalizing technology works, then we will have a new means of exploring the universe and the Earth-sized exoplanets and super Earths. To get a sequencer to them soon is out of the question with present-day rocket technology -- the planets orbiting the red dwarf Gliese 581 are "only" about 22 light-years away -- but it would take only 22 years to get the beamed data back. And that if advanced DNA-based life does exist in that system, perhaps it has already been broadcasting sequence information."

 

"Creating life at the speed of light is part of a new industrial revolution. Manufacturing will shift from centralised factories to a distributed, domestic manufacturing future, thanks to the rise of 3D printer technology. Since my own genome was sequenced, my software has been broadcast into space in the form of electromagnetic waves, carrying my genetic information far beyond Earth. Whether there is any creature out there capable of making sense of the instructions in my genome, well, that's another question."


Via Dr. Stefan Gruenwald
Dmitry Alexeev's insight:

J Craig Venter has already been teleported))

I love him for his style of reporting simple deeds as awesome technologies) 

 

more...
Nalina Nagarajan's curator insight, November 9, 2013 4:24 PM

Star trekkies for real!

Scooped by Dmitry Alexeev
Scoop.it!

Quinolone-resistant Escherichia coli from the faecal microbiota of healthy volunteers after ciprofloxacin exposure are highly adapted to a commensal lifestyle

Quinolone-resistant Escherichia coli from the faecal microbiota of healthy volunteers after ciprofloxacin exposure are highly adapted to a commensal lifestyle | Systems biology and bioinformatics | Scoop.it
more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

The ISME Journal - Abstract of article: Metagenomic mining for microbiologists

Microbial ecologists can now start digging into the accumulating mountains of metagenomic data to uncover the occurrence of functional genes and their correlations to microbial community members. Limitations and biases in DNA extraction and sequencing technologies impact sequence distributions, and therefore, have to be considered. However, when comparing metagenomes from widely differing environments, these fluctuations have a relatively minor role in microbial community discrimination. As a consequence, any functional gene or species distribution pattern can be compared among metagenomes originating from various environments and projects. In particular, global comparisons would help to define ecosystem specificities, such as involvement and response to climate change (for example, carbon and nitrogen cycle), human health risks (eg, presence of pathogen species, toxin genes and viruses) and biodegradation capacities. 

 

Dmitry Alexeev's insight:

getting ready to our first soil metagenome article

more...
No comment yet.
Rescooped by Dmitry Alexeev from Microbes Inside
Scoop.it!

Bacterial colonization factors control specificity and stability of the gut microbiota : Nature : Nature Publishing Group

Bacterial colonization factors control specificity and stability of the gut microbiota : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Mammals harbour a complex gut microbiome, comprising bacteria that confer immunological, metabolic and neurological benefits.

Via Clara Belzer
Dmitry Alexeev's insight:

polysaccharide utilization loci found resposible for success of colonization


more...
No comment yet.
Rescooped by Dmitry Alexeev from Innovation and Science breakthroughs
Scoop.it!

Human Microbiome May Be Seeded Before Birth

Human Microbiome May Be Seeded Before Birth | Systems biology and bioinformatics | Scoop.it
Scientists are studying whether mothers pass microbes to their fetuses during gestation, research that could help fight some pregnancy complications.

Via Pedro Barbosa
Dmitry Alexeev's insight:

a comprehensive assay on unsterile fetus paradigm shift

more...
No comment yet.
Rescooped by Dmitry Alexeev from Bioinformatics Training
Scoop.it!

New Study: Blood Test May Help Diagnose Early-Stage Lung Cancer

New Study: Blood Test May Help Diagnose Early-Stage Lung Cancer | Systems biology and bioinformatics | Scoop.it
Oct. 16, 2013

When it comes to determining whether lung nodules are malignant or benign, a patient typically faces surgery and a biopsy. It's an invasive and costly response, and, in 80 percent of cases, unnecessary.

Via Pedro Fernandes
Dmitry Alexeev's insight:
We will be able to distinguish normal from diseased individuals.In most cases, we’ll be able to diagnose the disease very early.We will be able to follow the progression of disease.We will be able to follow the response to the therapy and how effective it is.We can take the disease such as lung cancer and stratify it into its different subgroups, which will be 
more...
Pedro Fernandes's curator insight, October 17, 2013 3:31 AM

"A Blood-Based Proteomic Classifier for the Molecular Characterization of Pulmonary Nodules."

Scooped by Dmitry Alexeev
Scoop.it!

Electrostatics of DNA compaction in viruses, bacteria and eukaryotes: functional insights and evolutionary perspective - Soft Matter (RSC Publishing)

Electrostatics of DNA compaction in viruses, bacteria and eukaryotes: functional insights and evolutionary perspective - Soft Matter (RSC Publishing) | Systems biology and bioinformatics | Scoop.it
The molecular support of genetic information, DNA, has to be packaged and organized inside the tiny volume of nuclei, cells, or virus capsids, in an ordered and dynamical way.
Dmitry Alexeev's insight:

one should not forget that dna is a sharged wire apart from information storage

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

Scientific Data Has Become So Complex, We Have to Invent New Math to Deal ... - Wired

Scientific Data Has Become So Complex, We Have to Invent New Math to Deal ... - Wired | Systems biology and bioinformatics | Scoop.it
Scientific Data Has Become So Complex, We Have to Invent New Math to Deal ...
Wired
The Two Flavors of a 'One Web' Approach: Responsive vs. Adaptive ...
Dmitry Alexeev's insight:

think of it all the time

 

more...
No comment yet.
Rescooped by Dmitry Alexeev from Amazing Science
Scoop.it!

Gene activity and transcript patterns visualized for the first time in thousands of single cells

Gene activity and transcript patterns visualized for the first time in thousands of single cells | Systems biology and bioinformatics | Scoop.it
Biologists of the University of Zurich have developed a method to visualize the activity of genes in single cells. The method is so efficient that, for the first time, a thousand genes can be studied in parallel in ten thousand single human cells.

 

Applications lie in fields of basic research and medical diagnostics. The new method shows that the activity of genes, and the spatial organization of the resulting transcript molecules, strongly vary between single cells. Whenever cells activate a gene, they produce gene specific transcript molecules, which make the function of the gene available to the cell. The measurement of gene activity is a routine activity in medical diagnostics, especially in cancer medicine. Today's technologies determine the activity of genes by measuring the amount of transcript molecules. However, these technologies can neither measure the amount of transcript molecules of one thousand genes in ten thousand single cells, nor the spatial organization of transcript molecules within a single cell. The fully automated procedure, developed by biologists of the University of Zurich under the supervision of Prof. Lucas Pelkmans, allows, for the first time, a parallel measurement of the amount and spatial organization of single transcript molecules in ten thousands single cells. The results, which were recently published in the scientific journal Nature Methods, provide completely novel insights into the variability of gene activity of single cells.

 

The method developed by Pelkmans' PhD students Nico Battich and Thomas Stoeger is based upon the combination of robots, an automated fluorescence microscope and a supercomputer. "When genes become active, specific transcript molecules are produced. We can stain them with the help of a robot", explains Stoeger. Subsequently, fluorescence microscope images of brightly glowing transcript molecules are generated. Those images were analyzed with the supercomputer Brutus, of the ETH Zurich. With this method, one thousand human genes can be studied in ten thousand single cells. According to Pelkmans, the advantages of this method are the high number of single cells and the possibility to study, for the first time, the spatial organization of the transcript molecules of many genes.

The analysis of the new data shows that individual cells distinguish themselves in the activity of their genes. While the scientists had been suspecting a high variability in the amount of transcript molecules, they were surprised to discover a strong variability in the spatial organization of transcript molecules within single cells and between multiple single cells. The transcript molecules adapted distinctive patterns.

 

The importance of these new insights was summarized by Pelkmans: "Our method will be of importance to basic research and the understanding of cancer tumors because it allows us to map the activity of genes within single tumor cells.


Via Dr. Stefan Gruenwald
Dmitry Alexeev's insight:

i would expect to find more tricky distributions of the gene expression pattern among cells - but... however it looks that the high throughputness is being reaching via automatization and robotization either then novell principles

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

Understanding the interactions between bacteria in the human gut through metabolic modeling : Scientific Reports : Nature Publishing Group

Understanding the interactions between bacteria in the human gut through metabolic modeling : Scientific Reports : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
The human gut microbiome plays an influential role in maintaining human health, and it is a potential target for prevention and treatment of disease.
Dmitry Alexeev's insight:

little bit on metabolomic modelling from gurus. Surprising is the journal chosen for that

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

Modified nucleotides m2G966/m5C967 of Escherichia coli 16S rRNA are required for attenuation of tryptophan operon : Scientific Reports : Nature Publishing Group

Modified nucleotides m2G966/m5C967 of Escherichia coli 16S rRNA are required for attenuation of tryptophan operon : Scientific Reports : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Ribosomes contain a number of modifications in rRNA, the function of which is unclear.
Dmitry Alexeev's insight:

one more article published with our presence this year)

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

POGO-DB—a database of pairwise-comparisons of genomes and conserved orthologous genes

POGO-DB—a database of pairwise-comparisons of genomes and conserved orthologous genes | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

fastest way to compare genbank submitted bacterial genomes

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

Accelerated growth in the absence of DNA replication origins : Nature : Nature Publishing Group

Accelerated growth in the absence of DNA replication origins : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
DNA replication initiates at defined sites called origins, which serve as binding sites for initiator proteins that recruit the replicative machinery.
Dmitry Alexeev's insight:

never seen it before - you can guess the origins via normalization of readcounts in scyn and synced cells - and further you can get the insights 

more...
No comment yet.
Rescooped by Dmitry Alexeev from Microbes Inside
Scoop.it!

Metabolic niche of a prominent sulfate-reducing human gut bacterium

Metabolic niche of a prominent sulfate-reducing human gut bacterium | Systems biology and bioinformatics | Scoop.it

Via Clara Belzer
Dmitry Alexeev's insight:

lets double check the data accunulated)

more...
Clara Belzer's curator insight, October 30, 2013 5:50 AM

Desulfovibrio piger, the most frequent SRB presentin the microbiota

Scooped by Dmitry Alexeev
Scoop.it!

BMC Genomics | Abstract | DNA repair in Mycoplasma gallisepticum

DNA repair is essential for the maintenance of genome stability in all living beings. Genome size as well as the repertoire and abundance of DNA repair components may vary among prokaryotic species.
Dmitry Alexeev's insight:

wow we got published again) 

more...
No comment yet.
Rescooped by Dmitry Alexeev from Papers
Scoop.it!

For Preventing Disease, Data Are the New Drugs

For Preventing Disease, Data Are the New Drugs | Systems biology and bioinformatics | Scoop.it

One of the world’s most advanced data mining projects applies this same kind of analysis to cancer. Ilya Shmulevich, a lead genomicist who directs a Genome Data Analysis Center at the National Institutes of Health’s The Cancer Genome Atlas, says the project was born out of a shared frustration among cancer researchers at being forced, by a dearth of data, to study cancer one defective gene at a time, even while suspecting that the disease is actually the result of many genomic malfunctions, all happening at once.

 

http://nautil.us/issue/6/secret-codes/for-preventing-disease-data-are-the-new-drugs


Via Complexity Digest
Dmitry Alexeev's insight:

dataawareness is a new skill for scientists

 

more...
No comment yet.
Rescooped by Dmitry Alexeev from Bioinformatics Training
Scoop.it!

IBM Research: WatsonPaths

IBM Research: WatsonPaths | Systems biology and bioinformatics | Scoop.it
Learn about a new cognitive computing project that enables more natural interaction between physicians, data and electronic medical records.

Via Pedro Fernandes
Dmitry Alexeev's insight:

we are on the way of new variants for data representation - to make an interface between us computer and data

more...
Pedro Fernandes's curator insight, October 17, 2013 3:20 AM

A step in the right direction!

 

Rescooped by Dmitry Alexeev from CBiB - Bordeaux Bioinformatics Center
Scoop.it!

BMC Bioinformatics | Abstract | Finishing bacterial genome assemblies with Mix

BMC Bioinformatics | Abstract | Finishing bacterial genome assemblies with Mix | Systems biology and bioinformatics | Scoop.it

Via CBiB
Dmitry Alexeev's insight:

one more to the genomic moneybox of assembley algorithms

 

more...
No comment yet.
Rescooped by Dmitry Alexeev from Amazing Science
Scoop.it!

First time ever: Researchers rewrite an entire bacterial genome and add a healthy twist

First time ever: Researchers rewrite an entire bacterial genome and add a healthy twist | Systems biology and bioinformatics | Scoop.it

Scientists from Yale and Harvard have recoded the entire genome of an organism and improved a bacterium’s ability to resist viruses, a dramatic demonstration of the potential of rewriting an organism’s genetic code.

“This is the first time the genetic code has been fundamentally changed,” said Farren Isaacs, assistant professor of molecular, cellular, and developmental biology at Yale and co-senior author of the research published Oct. 18 in the journal Science. “Creating an organism with a new genetic code has allowed us to expand the scope of biological function in a number of powerful ways.”

 

The creation of a genomically recoded organism raises the possibility that researchers might be able to retool nature and create potent new forms of proteins to accomplish a myriad purposes — from combating disease to generating new classes of materials.

 

The research — headed by Isaacs and co-author George Church of Harvard Medical School — is a product of years of studies in the emerging field of synthetic biology, which seeks to re-design natural biological systems for useful purposes.

 

In this case, the researchers changed fundamental rules of biology.

Proteins, which are encoded by DNA’s instructional manual and are made up of 20 amino acids, carry out many important functional roles in the cell. Amino acids are encoded by the full set of 64 triplet combinations of the four nucleic acids that comprise the backbone of DNA. These triplets (sets of three nucleotides) are called codons and are the genetic alphabet of life.

 

Isaacs, Jesse Rinehart of Yale, and the Harvard researchers explored whether they could expand upon nature’s handywork by substituting different codons or letters throughout the genome and then reintroducing entirely new letters to create amino acids not found in nature. This work marks the first time that the genetic code has been completely changed across an organism’s genome.

 

In the new study, the researchers working with E. coli swapped a codon and eliminated its natural stop sign that terminates protein production. The new genome enabled the bacteria to resist viral infection by limiting production of natural proteins used by viruses to infect cells. Isaacs — working with Marc Lajoie of Harvard, Alexis Rovner of Yale, and colleagues — then converted the “stop” codon into one that encodes new amino acids and inserted it into the genome in a plug-and-play fashion. 

 

The work now sets the stage to convert the recoded bacterium into a living foundry, capable of biomanufacturing new classes of  “exotic” proteins and polymers. These new molecules could lay the foundation for a new generation of materials, nanostructures, therapeutics, and drug delivery vehicles, Isaacs said.

 

“Since the genetic code is universal, it raises the prospect of recoding genomes of other organisms,” Isaacs said. “This has tremendous implications in the biotechnology industry and could open entirely new avenues of research and applications.”


Via Dr. Stefan Gruenwald
Dmitry Alexeev's insight:

thats a new generation biological tool although there has been already attempts to encode non-standard amino acids - but never before on a full genome scale - intrestingle how soon wilkl this be available as a conventional instrument? this is a novel scientific tool - which will among others help us to study life

more...
odysseas spyroglou's curator insight, October 19, 2013 8:46 AM

The brave new world starts here. I hope we'll find our way to a less dystopian future.

Leire Tapia's curator insight, October 21, 2013 4:08 PM

He elegido esta noticia porque la relaciono con la libertad de investigación. Es un derecho vinculado al ser humano y es un derecho exigible. Es también importante comunicar los resultados y no caer en el peligro de la censura. No hay que esconder lo que la ciencia descubre pero si es importante establecer límites relacionados con la protección de la salud y con la dignidad humana.

Scooped by Dmitry Alexeev
Scoop.it!

PLOS Genetics: Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution

PLOS Genetics: Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution | Systems biology and bioinformatics | Scoop.it
PLOS Genetics is an open-access
Dmitry Alexeev's insight:

smrt on mycoplasma - i wonder how i missed it

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

Dmitry Alexeev's insight:

Counter part to TCGA - looks more in depth thinking and more results

more...
No comment yet.
Rescooped by Dmitry Alexeev from Amazing Science
Scoop.it!

Gene activity and transcript patterns visualized for the first time in thousands of single cells

Gene activity and transcript patterns visualized for the first time in thousands of single cells | Systems biology and bioinformatics | Scoop.it
Biologists of the University of Zurich have developed a method to visualize the activity of genes in single cells. The method is so efficient that, for the first time, a thousand genes can be studied in parallel in ten thousand single human cells.

 

Applications lie in fields of basic research and medical diagnostics. The new method shows that the activity of genes, and the spatial organization of the resulting transcript molecules, strongly vary between single cells. Whenever cells activate a gene, they produce gene specific transcript molecules, which make the function of the gene available to the cell. The measurement of gene activity is a routine activity in medical diagnostics, especially in cancer medicine. Today's technologies determine the activity of genes by measuring the amount of transcript molecules. However, these technologies can neither measure the amount of transcript molecules of one thousand genes in ten thousand single cells, nor the spatial organization of transcript molecules within a single cell. The fully automated procedure, developed by biologists of the University of Zurich under the supervision of Prof. Lucas Pelkmans, allows, for the first time, a parallel measurement of the amount and spatial organization of single transcript molecules in ten thousands single cells. The results, which were recently published in the scientific journal Nature Methods, provide completely novel insights into the variability of gene activity of single cells.

 

The method developed by Pelkmans' PhD students Nico Battich and Thomas Stoeger is based upon the combination of robots, an automated fluorescence microscope and a supercomputer. "When genes become active, specific transcript molecules are produced. We can stain them with the help of a robot", explains Stoeger. Subsequently, fluorescence microscope images of brightly glowing transcript molecules are generated. Those images were analyzed with the supercomputer Brutus, of the ETH Zurich. With this method, one thousand human genes can be studied in ten thousand single cells. According to Pelkmans, the advantages of this method are the high number of single cells and the possibility to study, for the first time, the spatial organization of the transcript molecules of many genes.

The analysis of the new data shows that individual cells distinguish themselves in the activity of their genes. While the scientists had been suspecting a high variability in the amount of transcript molecules, they were surprised to discover a strong variability in the spatial organization of transcript molecules within single cells and between multiple single cells. The transcript molecules adapted distinctive patterns.

 

The importance of these new insights was summarized by Pelkmans: "Our method will be of importance to basic research and the understanding of cancer tumors because it allows us to map the activity of genes within single tumor cells.


Via Dr. Stefan Gruenwald
more...
Dmitry Alexeev's curator insight, October 8, 2013 2:45 AM

i would expect to find more tricky distributions of the gene expression pattern among cells - but... however it looks that the high throughputness is being reaching via automatization and robotization either then novell principles