Son Pham Simon Cockell Yury Ivanov       

       Guillaume Nicolas Ярослав Баранов Jarle Pahr       

       Vincent Chiang Ksenia Krasheninnikova Илья Минкин       

 

C-Sibelia will help you in the next step: Comparing assemblies to a reference genome.

 

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Educational resources for students.

We select the best resources for students to start exploring bioinformatics.

 

 

 

  • Comparative analysis of RNA sequencing methods for degraded or low-input samples

     At 2014-03-09 08:36:46 AM  |   25

    RNA-seq is an effective method for studying the transcriptome, but it can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations or cadavers. Recent studies have proposed several methods for RNA-seq of low-quality and/or low-quantity samples, but the relative merits of these methods have not been systematically analyzed.  Read more
  • Highly Multiplexed Subcellular RNA Sequencing in Situ

     At 2014-02-27 11:37:08 PM  |   76

    Scientists can now take snapshots of where and how thousands of genes are expressed in intact tissue samples, ranging from a slice of a human brain to the embryo of a fly. Read more
  • Focus on pain

     At 2014-03-05 07:27:23 PM  |   2

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

     At 2014-02-25 07:58:12 PM  |   2

    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
  • Imagined gait modulates neuronal network dynamics in the human pedunculopontine nucleus

     At 2014-02-24 04:33:06 PM  |   5

    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
  • A neural mechanism underlying failure of optimal choice with multiple alternatives

     At 2014-02-24 04:30:39 PM  |   3

    Despite widespread interest in neural mechanisms of decision-making, most investigations focus on decisions between just two options. Here we adapt a biophysically plausible model of decision-making to predict how a key decision variable, the value difference signal—encoding how much better one choice is than another—changes with the value of a third, but unavailable, alternative.  Read more
  • Use of whole-genome sequencing to diagnose a cryptic fusion oncogene.

     At 2014-03-28 02:38:21 AM  |   20

    Whole-genome sequencing is becoming increasingly available for research purposes, but it has not yet been routinely used for clinical diagnosis. Read more
  • The genomic complexity of primary human prostate cancer

     At 2014-02-26 09:14:25 PM  |   2

    Prostate cancer is the second most common cause of male cancer deaths in the United States. However, the full range of prostate cancer genomic alterations is incompletely characterized. Here we present the complete sequence of seven primary human prostate cancers and their paired normal counterparts. Several tumours contained complex chains of balanced (that is, ‘copy-neutral’) rearrangements that occurred within or adjacent to known cancer genes. Rearrangement breakpoints were enriched near open chromatin, androgen receptor and ERG DNA binding sites in the setting of the ETS gene fusion TMPRSS2–ERG, but inversely correlated with these regions in tumours lacking ETS fusions.  Read more
  • Initial genome sequencing and analysis of multiple myeloma

     At 2014-02-25 08:01:24 PM  |   2

    Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs. Several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set. Read more
  • CREBBP mutations in relapsed acute lymphoblastic leukaemia

     At 2014-02-22 01:19:11 AM  |   4

    Relapsed acute lymphoblastic leukaemia (ALL) is a leading cause of death due to disease in young people, but the biological determinants of treatment failure remain poorly understood. Recent genome-wide profiling of structural DNA alterations in ALL have identified multiple submicroscopic somatic mutations targeting key cellular pathways, and have demonstrated substantial evolution in genetic alterations from diagnosis to relapse. However, DNA sequence mutations in ALL have not been analysed in detail. To identify novel mutations in relapsed ALL, we resequenced 300 genes in matched diagnosis and relapse samples from 23 patients with ALL.  Read more
  • An environmental bacterial taxon with a large and distinct metabolic repertoire

     At 2014-03-06 11:04:16 AM  |   3

    Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such ‘talented’ producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Read more
  • Biogenesis and functions of bacterial S-layers

     At 2014-03-01 08:20:03 PM  |   3

    The outer surface of many archaea and bacteria is coated with a proteinaceous surface layer (known as an S-layer), which is formed by the self-assembly of monomeric proteins into a regularly spaced, two-dimensional array. Bacteria possess dedicated pathways for the secretion and anchoring of the S-layer to the cell wall, and some Gram-positive species have large S-layer-associated gene families. Read more
  • Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column

     At 2014-02-22 01:35:00 AM  |   21

    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
  • Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions

     At 2013-11-26 11:55:14 AM  |   121

    The potential of bacterial whole-genome sequencing (WGS) to complement existing diagnostic infrastructures in clinical microbiology has been shown in proof-of-principle examples and extensively discussed. However, less attention has been drawn to bioinformatic challenges that are associated with the clinical adoption of WGS-based molecular diagnostics. This Perspective article discusses questions that are related to standard operating procedures, computational resource management, and data storage and integration in the context of recent developments in the sequencing and bioinformatics service markets.  Read more
  • Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses

     At 2014-03-18 02:05:18 AM  |   7

    The Miscellaneous Crenarchaeota group (MCG) Archaea is one of the predominant archaeal groups in anoxic environments and may have significant roles in the global biogeochemical cycles. However, no isolate of MCG has been cultivated or characterized to date. In this study, we investigated the genetic organization, ecophysiological properties and evolutionary relationships of MCG archaea with other archaeal members using metagenome information and the result of gene expression experiments. Read more
  • Brain initiatives galore, smiles aplenty

     At 2014-02-15 11:52:43 AM  |   22

    The brain is hot. Despite dismay about the recent 16-day US government shutdown, the impact of automatic budget cuts–the sequester–taking effect in light of federal budget disagreements in Washington, and the general economic malaise, there is palpable excitement. New large-scale initiatives are getting underway around the world to develop technologies to empower neuroscientists. Read more
  • Genome hacker uncovers largest-ever family tree

     At 2013-10-29 10:05:07 AM  |   101

    Using data pulled from online genealogy sites, a renowned ‘genome hacker’ has constructed what is likely the biggest family trees ever assembled. The researcher and his team now plan to use the data — including a single uber-pedigree comprising 13 million individuals, which stretches back to the 15th century — to analyse the inheritance of complex genetic traits, such as longevity and facial features.  Read more
  • Adjusting for technical noise in single-cell RNA-seq experiments

     At 2013-09-29 08:55:07 PM  |   214

    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
  • Single cell transcriptomes

     At 2013-09-26 12:15:09 AM  |   100

    Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells Read more
  • De novo genome assembly: what every biologist should know

     At 2014-02-27 07:24:38 AM  |   2

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

     At 2013-11-25 09:58:11 AM  |   210

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

     At 2013-09-26 12:31:09 AM  |   136

    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
  • IDBA-UD: A single cell assembler.

     At 2013-09-26 12:30:58 AM  |   250

    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
  • Initial sequencing and comparative analysis of the mouse genome

     At 2014-03-16 02:40:49 AM  |   2

    The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome.  Read more
  • Microarray-based Comparative Genomic Hybridization (aCGH)

     At 2014-02-25 08:09:11 PM  |   2

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

     At 2013-09-28 04:26:06 AM  |   96

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

     At 2013-09-26 12:27:11 AM  |   215

    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
  • Epigenetic Control of Gene Expression

     At 2014-03-18 02:01:05 AM  |   9

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

     At 2013-12-19 11:56:03 PM  |   232

    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
  • Bioinformatics course on Coursera is starting today

     At 2013-09-30 09:07:36 AM  |   176

    Watch the first video about DNA replication today on coursera http://coursera.org/course/bioinformatics  Read more
  • Bionformatics course on Coursera

     At 2013-09-26 12:07:12 AM  |   190

    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