Bioinformatics Education - Bioinformatics Algorithms (Part 1) by Pavel Pevzner, Phillip E. C. Compeau, Nikolay Vyahhi, Son Pham

 At 2013-12-19 11:56:03 PM  |   570

This class provides an automated homework testing environment called Stepic, which is inspired by our Rosalind project aimed at learning bioinformatics through programming. You can find the first two weeks of material on Stepic and on our class homepage in the form of video lectures. Note: you must sync your Coursera account with Stepic in order to receive credit for your assignments. To do so, please see the Important Course Details page. Read more

Human Genetics - Genomic Medicine 2015 - From 20 - 23 July 2015, HoChiMinh City, Vietnam

 At 2015-02-26 08:38:05 PM  |   456

Genomic Medicine 2015! 20 - 23 July 2015, HoChiMinh City Genomic Medicine Conference is devoted to the latest advances in the use of omics data in medical practice. Read more

EpiGenetics - STAR: an integrated solution to management and visualization of sequencing data

 At 2013-11-11 04:05:43 PM  |   441

STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. Read more

Genome Assembly - SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

 At 2013-09-26 12:31:09 AM  |   438

Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly. Read more

Genome Assembly - C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison

 At 2013-11-25 09:58:11 AM  |   419

We present Comparative Sibelia software (C-Sibelia) for the comparison of two bacterial genomes in the form of complete sequences or draft assemblies. C-Sibelia is able to compare genomes in the presence of rearrangements and duplications. C-Sibelia takes as input two FASTA files (the assembly and reference files; if the reference genome is not available, it can be substituted by another draft assembly) and produces: (1) a VCF file containing all identified single nucleotide variations (SNVs) and indels; (2) annotation of these variants by SnpEff; (3) an XMFA1 file containing alignment information. The web-based version also produces a circular diagram visualizing the rearrangement of synteny blocks in two genomes. Read more

EpiGenetics - Cancer epigenomics: DNA methylomes and histone-modification maps

 At 2014-02-25 08:05:13 PM  |   365

An altered pattern of epigenetic modifications is central to many common human diseases, including cancer. Many studies have explored the mosaic patterns of DNA methylation and histone modification in cancer cells on a gene-by-gene basis; among their results has been the seminal finding of transcriptional silencing of tumour-suppressor genes by CpG-island-promoter hypermethylation. Read more

Comparative Genomics - THetA: Inferring intra-tumor heterogeneity from high- throughput DNA sequencing data

 At 2013-09-26 12:27:11 AM  |   342

THetA (Tumor Heterogeneity Analysis), an algorithm that infers the most likely collection of genomes and their proportions in a sample, for the case where copy number aberrations distinguish subpopulations. Read more

Neuroscience - Palmitoylation of δ-catenin by DHHC5 mediates activity-induced synapse plasticity

 At 2014-02-25 07:58:12 PM  |   323

Synaptic cadherin adhesion complexes are known to be key regulators of synapse plasticity. However, the molecular mechanisms that coordinate activity-induced modifications in cadherin localization and adhesion and the subsequent changes in synapse morphology and efficacy remain unknown. We demonstrate that the intracellular cadherin binding protein δ-catenin is transiently palmitoylated by DHHC5 after enhanced synaptic activity and that palmitoylation increases δ-catenin–cadherin interactions at synapses.  Read more

Bioinformatics Education - Epigenetic Control of Gene Expression

 At 2014-03-18 02:01:05 AM  |   325

Each mammalian cell has the same genes, yet performs distinct functions. This is achieved by epigenetic control of gene expression; the switching on and switching off of genes. This course will cover the principles of epigenetic control of gene expression, how epigenetic control contributes to cellular differentiation and development, and how it goes wrong in disease. Read more

Genome Assembly - De novo genome assembly: what every biologist should know

 At 2014-02-27 07:24:38 AM  |   304

Asked how mature the field of genome assembly is, Ian Korf at the University of California, Davis, compares it to a teenager with great capabilities. “It's got bold assertions about what it can do, but at the same time it's making embarrassing mistakes,” he says. Perhaps the biggest barrier to maturity is that there are few ways to distinguish true insight from foolish gaffe. When a species' genome is newly assembled, no one knows what's real, what's missing, and what's experimental artifact. Read more

Genome Assembly - IDBA-UD: A single cell assembler.

 At 2013-09-26 12:30:58 AM  |   285

IDBA-UD: an algorithm that is based on the de Bruijn graph approach for assembling reads from single-cell sequencing or metagenomic sequencing technologies with uneven sequencing depths.  Read more

Single Cell Genomics - Adjusting for technical noise in single-cell RNA-seq experiments

 At 2013-09-29 08:55:07 PM  |   285

Punchline: use spike-ins for every cell in your single-cell experiments to adjust for relative RNA levels per cell. Single-cell RNA-seq can yield valuable insights about the variability within a population of seemingly homogeneous cells. We developed a quantitative statistical method to distinguish true biological variability from the high levels of technical noise in single-cell experiments. Our approach quantifies the statistical significance of observed cell-to-cell variability in expression strength on a gene-by-gene basis. We validate our approach using two independent data sets from Arabidopsis thaliana and Mus musculus. Read more

Genome Assembly - From Indexing Data Structures to de Bruijn Graphs

 At 2014-10-31 03:03:42 PM  |   290

New technologies have tremendously increased sequencing throughput compared to traditional techniques, thereby complicating DNA assembly. Read more

Neuroscience - Focus on pain

 At 2014-03-05 07:27:23 PM  |   275

Pain can be defined simply as the subjective experience of harm in a part of one's body. In reality, however, there are multiple forms of pain, which involve a variety of distinct biological processes. Exposure to extreme heat, cold or pressure can be noxious, triggering nociceptive pain. Inflammatory pain, involving the release of cytokines and the infiltration of immune cells, also occurs subsequent to injury, but can be triggered independently by bacterial infections. Although pain has an important physiological role in preserving the integrity of the body, pathological pain also exists. Nerve damage, in surgery patients for instance, sometimes leads to chronic pain conditions that can last years or even decades. Read more

Bioinformatics Education - Bionformatics course on Coursera

 At 2013-09-26 12:07:12 AM  |   247

This course will cover some of the common algorithms underlying the following fundamental topics in bioinformatics: assembling genomes, comparing DNA and protein sequences, finding regulatory motifs, analyzing genome rearrangements, identifying proteins, and many other topics. Read more

Cancer Genomics - Mutational landscape and significance across 12 major cancer types

 At 2013-10-28 12:14:10 AM  |   247

This paper presents data and analytical results for point mutations and small insertions/deletions from 3,281 tumours across 12 tumour types as part of the TCGA Pan-Cancer effort. Read more

Comparative Genomics - Microarray-based Comparative Genomic Hybridization (aCGH)

 At 2014-02-25 08:09:11 PM  |   228

Many human genetic disorders result from unbalanced chromosomal abnormalities, in which there is net gain or loss of genetic material. Traditionally, cytologists have detected such abnormalities by generating a karyotype of a person's chromosomes and analyzing the banding patterns therein. Indeed, since its development in the 1970s, cytogenetic analysis of banding patterns has been the primary tool for the clinical assessment of patients with a variety of congenital anomalies. Under ideal conditions, aberrations as small as approximately 5 megabases (Mb) can be detected with banding analysis; such chromosome rearrangements are termed "microscopic." Read more

Comparative Genomics - The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA.

 At 2013-09-28 04:26:06 AM  |   229

The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages.  Read more

Microbial Genomics - Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column

 At 2014-02-22 01:35:00 AM  |   235

Microbial gene expression in the environment has recently been assessed via pyrosequencing of total RNA extracted directly from natural microbial assemblages. Several such 'metatranscriptomic' studies have reported that many complementary DNA sequences shared no significant homology with known peptide sequences, and so might represent transcripts from uncharacterized proteins.  Read more

Neuroscience - Imagined gait modulates neuronal network dynamics in the human pedunculopontine nucleus

 At 2014-02-24 04:33:06 PM  |   211

The pedunculopontine nucleus (PPN) is a part of the mesencephalic locomotor region and is thought to be important for the initiation and maintenance of gait. Lesions of the PPN induce gait deficits, and the PPN has therefore emerged as a target for deep brain stimulation for the control of gait and postural disability.  Read more