BOL: Related items

SYSTEMS BIOLOGY APPROACH TO MODEL INFLAMMATION IN HUMAN (2).pptx

ROSHNI — Thu, 17 Oct 2013 00:54:13 -0500

Reference Sequence Resource!

LEGE — Wed, 15 Sep 2021 21:15:22 -0500

The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse (mm9/mm10) genomes for historical comparability. Drosophia melanogaster experiments are mapped to either dm3 or dm6 and Caenorhabdilis elegans experiments are mapped to ce10 or ce11. T

Address of the bookmark: https://www.encodeproject.org/data-standards/reference-sequences/

The Atlas of Nine Billion Possibilities

Jitendra Narayan — Wed, 09 Sep 2026 02:07:58 -0500

Imagine a book that holds all the instructions for building a human, made up of billions of letters. What if you changed just one letter? Maybe nothing would happen. Or that tiny change could affect how a gene works, quietly shaping a cell’s biology or even helping cause disease.

Scientists face a big challenge with the human genome. They can read its letters, but understanding their roles is much harder. Only about 2 percent of the genome codes for proteins. The rest acts like a huge control panel, deciding when and where genes turn on. With about 9 billion possible single-letter changes, testing them all in a lab just isn’t possible.

So, Google DeepMind asked a new question: what if we could predict what those changes might do?

This question led to the AlphaGenome Atlas (https://deepmind.google.com/science/alphagenome/atlas?), a detailed map of nearly every possible single-letter change in the human genome. Instead of checking each change one by one, researchers can use the Atlas to spot the ones most likely to matter. The AlphaGenome Variant Impact (AVI) score works like a trail marker, pointing scientists toward the changes worth a closer look.

This is where the Atlas gets especially useful. Much of the genome lies outside the protein-coding regions, where DNA acts as a switch or controller for genes. AlphaGenome lets researchers explore these areas and see how small changes could affect gene activity.

An atlas isn't the destination; it's a guide.

The AlphaGenome Atlas doesn’t replace experiments or solve every mystery. Instead, it helps scientists decide where to begin. From billions of possibilities, it turns the vast genetic landscape into something researchers can start to explore.

There are nine billion possibilities, a vast map, and maybe among them therWith nine billion possibilities and a huge map to explore, there may be clues hidden here to some of medicine’s toughest mysteries.

More at https://storage.googleapis.com/deepmind-media/DeepMind.com/Blog/alphagenome-atlas-a-predictive-map-of-every-possible-dna-letter-change-in-the-human-genome/alphagenome-atlas.pdf

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

Rahul Agarwal — Thu, 21 Dec 2017 17:01:44 -0600

TRRUST contains 8,444 and 6,552 TF-target regulatory relationships of 800 human TFs and 828 mouse TFs, respectively. They have been derived from 11,237 pubmed articles, which describe small-scale experimental studies of transcriptional regulations. To efficiently search for regulatory relationships from over 20 million pubmed articles, we used sentence-based text mining approach.

TRRUST database also provides information of mode of regulation (activation or repression). Currently 8,972 (59.8%) regulatory relationships are known for mode of regulation.

Search at : http://www.grnpedia.org/trrust/Network_search_form.php

Address of the bookmark: http://www.grnpedia.org/trrust/

5700 year-old human genome !

Jit — Thu, 19 Dec 2019 11:22:18 -0600

A Landmark in genomics, scientists have done something that hasn't been done ever.

Scientists have reconstructed the genome of an ancient human who lived nearly 5,700 years ago in Southern Denmark from the birch pitch- an ancient tar-like substance.

By sequencing the sample, researchers not only discovered the ancient human DNA but also microbial DNA reflecting the oral microbiome of the person who chewed the pitch, along with plant and animal DNA that could be the recent meal she might have consumed.

The DNA sample is comparable in quality to well-preserved teeth and skull bones. The DNA suggests that the chewer was a female, most likely with dark skin, dark brown hair and blue eyes.

https://www.nature.com/articles/s41467-019-13549-9

Artistic reconstruction. (Tom Björklund)

More at https://gizmodo.com/scientists-reconstruct-lola-after-finding-her-dna-in-1840481633

Claus-Peter Stelzer Lab

Mon, 15 Mar 2021 15:24:41 -0500

Interested in various topics at the intersection of ecology and evolution. In my research I use rotifers as model organisms for experimental studies at the individual and population level. Rotifers are ideally suited for this, because populations of thousands can be kept in small containers in the lab, while single individuals can still be handled conveniently.

More at https://www.uibk.ac.at/limno/personnel/stelzer/index.html.en#research

04- Informatics Approach to Cancer - Interview with Dr. Joel Saltz

Mon, 07 Oct 2013 14:35:43 -0500

For additional information visit http://www.cancerquest.org/joel-saltz-interview. Dr. Joel Saltz is a Professor in the Departments of Pathology, Biostatistics and Bioinformatics, and Mathematics and Computer Science at Emory University. Dr. Saltz's research on bioinformatics spans several disciplines. One project involves applying computer analysis to medical imaging to yield better results for patients. As an example, a computer program may able to help doctors detect small cancers in a CT scan or mammogram. In this interview segment, Dr. Saltz discusses the informatics approach to cancer. To learn more about cancer and watch additional interviews, please visit the CancerQuest website at http://www.cancerquest.org.

Oldest Hominin DNA Sequenced

Surajeet — Fri, 27 Dec 2013 19:58:31 -0600

Matthias Meyer and his team from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have developed new techniques for retrieving and sequencing highly degraded ancient DNA. They then joined forces with Juan-Luis Arsuaga and applied the new techniques to a cave bear from the Sima de los Huesos site. After this success, the researchers sampled two grams of bone powder from a hominin thigh bone from the cave. They extracted its DNA and sequenced the genome of the mitochondria or mtDNA, a small part of the genome that is passed down along the maternal line and occurs in many copies per cell. The researchers then compared this ancient mitochondrial DNA with Neandertals, Denisovans, present-day humans, and apes.

From the missing mutations in the old DNA sequences the researchers calculated that the Sima hominin lived about 400,000 years ago. They also found that it shared a common ancestor with the Denisovans, an extinct archaic group from Asia related to the Neandertals, about 700,000 years ago. "The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neandertal mtDNAs is unexpected since its skeletal remains carry Neandertal-derived features," says Matthias Meyer. Considering their age and Neandertal-like features, the Sima hominins were likely related to the population ancestral to both Neandertals and Denisovans. Another possibility is that gene flow from yet another group of hominins brought the Denisova-like mtDNA into the Sima hominins or their ancestors.

Reference

http://www.sciencedaily.com/releases/2013/12/131204132018.htm

Landry Lab

Thu, 17 Jul 2014 14:33:57 -0500

EVOLUTIONARY AND INTEGRATIVE CELL BIOLOGY

Our research is at the crossroad between cell biology, ecological genomics, systems biology, molecular evolution and population genetics. We study the architecture and evolution of protein and signalling networks.

More at http://landrylab.ibis.ulaval.ca/

Yannick Wurm Lab

Thu, 07 Aug 2014 18:02:37 -0500

Evolutionary genomics of social insects. Extensive theoretical work has explained how and why complex societies evolve. However, only little is known about the genes and molecular mechanisms responsible for social phenotypes. We have been identifying genes and mechanisms involved in the evolution of insect societies using modern genomics tools (Illumina, RNAseq, RADseq...). For example we recently:

1. sequenced and analyzed the genome of the invasive red fire ant Solenopsis invicta (PNAS 2011)

2. discovered that a fundamental social trait in this species (how many queens are accepted in the colony) is determined by variants of a social chromosome (Nature 2013).

3. described the gene expression changes that occur in a virgin queen when she is given the opportunity of replacing her mother (Mol Ecol 2010).

Homepage: http://yannick.poulet.org/