Subject
26 entries
Genomics
Bookmarks
ARK Big Ideas 2022
ARK Invest's 2022 annual Big Ideas report lays out their investment thesis across five disruptive technology platforms: genomics, robotics, energy storage, artificial intelligence, and blockchain. It's both a market forecast and a statement of where ARK believes exponential cost curves will reshape entire industries over the next decade.
Big Data: The Power of Petabytes (Genomics Edition)
Nature's supplement on big data in genomics, covering the arrival of the $1,000 genome and what it means for medicine — the data storage, analysis, and clinical interpretation challenges of a world where genome sequencing is routine. A milestone in the convergence of biology and data infrastructure.
Topological Data Analysis from Ayasdi
Tweet from DataBeat 2013 noting Ayasdi's topological data analysis platform for sequential/genomic data. TDA was an emerging approach to finding structure in high-dimensional data without requiring dimensionality reduction assumptions.
Ex-Yahoo CEO Backs Genomics Big Data Startup Bina
FierceBiotechIT covering Bina Technologies, a genomics big data startup backed by ex-Yahoo CEO Scott Thompson, building hardware-accelerated pipelines for processing whole-genome sequencing data. A 2013 marker of when genomics data volumes began requiring big data infrastructure at clinical scale.
Creating a Bioinformatics Nation
Nature commentary on the challenge of building bioinformatics capacity nationally — the growing gap between genomic data production and the computational skills needed to analyze it. Published in 2002, it presaged the data science talent shortage that would affect all data-intensive fields.
New Chip Delivers DNA Results Within an Hour
A 2013 report on a microfluidic chip that could return DNA diagnostic results in under an hour — compressing a process that took days in a lab. A snapshot of point-of-care genomics before it became a commercial reality.
Finally a Nanopore Sequencer That Works
CoreGenomics blog covering Oxford Nanopore's MinION — the first nanopore sequencer that actually worked reliably in practice. A 2013 milestone post documenting the moment nanopore sequencing moved from theoretical promise to real instrument.
Doctors Use Big Data to Improve Cancer Treatments
Mashable on how doctors were using big data to improve cancer treatment outcomes in 2013 — early coverage of precision oncology using genomic data and clinical records. A snapshot of the medical establishment's first serious engagement with large-scale data-driven treatment.
Biological Computer: Stanford's Genetic Transistors Turn Cells into Computers
Stanford researchers created genetic transistors that turn living cells into biological computers — RNA-based logic gates that implement Boolean operations inside E. coli. A 2013 milestone in synthetic biology demonstrating programmable cellular computation.
BioInformatics: A Data Deluge with Hadoop to the Rescue
Datanami on using Apache Hadoop for bioinformatics data pipelines — how genomic sequencing data had outpaced traditional computational biology infrastructure and why Hadoop's distributed file system and MapReduce were being adopted to handle the deluge.
A List of Bioinformatics Courses
MSU's C. Titus Brown maintained this list of bioinformatics courses as a community resource during the period when academic bioinformatics was just starting to formalize. A map of where to learn computational biology before MOOCs dominated.
Statistics for Genomics: Introduction to RNA-seq
A YouTube lecture series on statistical methods for RNA-seq analysis — covering the mathematical foundations behind differential expression analysis, normalization, and count modeling. A bioinformatics education resource from the early RNA-seq era.
GenomeBrowse: Free Tool for Visualizing DNA-seq and RNA-seq BAM Files
GenomeBrowse from Golden Helix — a free desktop genome browser for visualizing DNA-seq and RNA-seq BAM files. A 2013 alternative to IGV for exploring aligned sequencing data.
BamH1.com: Bleeding Edge Bio/Tech News for Nerds
BamH1.com — a 'bleeding edge bio/tech news for nerds' aggregator site. The name is a molecular biology pun: BamHI is a restriction enzyme from Bacillus amyloliquefaciens, used ubiquitously in cloning. A niche but well-positioned site for the biohacker/biotech audience.
The Role of Mutations in Epigenetic Regulators in Myeloid Malignancies
Nature Reviews Cancer 2012 paper on the role of epigenetic regulator mutations in myeloid malignancies (AML, MDS, MPN) — summarizing how mutations in DNMT3A, TET2, IDH1/2, EZH2, and others alter the cancer epigenome. A key reference from the early next-generation sequencing era of cancer genomics.
CanvasXpress: Scientific Data Visualization
CanvasXpress — a JavaScript library for scientific and genomics data visualization, specifically designed for bioinformatics use cases like expression heatmaps, scatter plots with gene annotations, and interactive exploration of multi-dimensional biological data.
Using Your 23andMe Data: How Inbred Are You?
Razib Khan's guide to analyzing your 23andMe raw data for runs of homozygosity — a proxy for inbreeding coefficient. Part of the early era when direct-to-consumer genomics made population genetics analyses available to anyone.
If You Read Only One Book About the Future of Biology, This Should Be It
io9's recommendation of George Church and Ed Regis's 'Regenesis' as the essential book on the future of biology — saved with 'in for one' indicating intent to read. Church's vision of reading and writing genomes to re-engineer life itself.
Analyzing Human Genomes with Hadoop
Cloudera's 2009 blog post (bookmarked in 2012) showing how MapReduce and Hadoop can process human genome sequences at scale — an early example of big data infrastructure being applied to life sciences problems that were previously computationally intractable.
Coming Soon: Apps That Use Your DNA
ReadWrite's 2012 preview of consumer apps built on top of personal genomic data — when 23andMe and others were opening APIs for third-party developers to build health and ancestry tools. An early look at a platform shift that never quite scaled as expected.
Atlas of Gene Expression in the Human Brain (Nature, 2012)
A 2012 Nature paper presenting a comprehensive atlas of gene expression across the human brain — mapping which genes are active in which brain regions across two donor brains. Foundational dataset for understanding the molecular basis of brain organization and neurological disease.
DNA Blueprint for Fetus Built Using Samples From Parents
NYT coverage of a 2012 breakthrough: reconstructing a fetal genome from samples of parents' blood and the father's saliva, without invasive amniocentesis. A preview of prenatal genomics that raised immediate ethical questions about what to do with the information.
DIYHarappaWorld: Population Genetics for Personal Genomes
DIYHarappaWorld let people run the Harappa Ancestry Project's South Asian population genetics analysis on their own genetic data. An early example of citizen science genomics — taking academic ADMIXTURE tools and making them accessible to personal genome hobbyists.
Value of Genomics and Personalized Medicine Is Wrongly Downplayed
UCSF researchers pushing back against a widely-reported study claiming DNA's power to predict illness is limited — arguing that the value of genomics for personalized medicine is being systematically underestimated. A 2012 snapshot of a debate that's still ongoing.
Accurate Identification of RNA Editing Sites from High-Throughput Sequencing Data
A Genomes Unzipped guest post on the bioinformatics challenge of accurately identifying RNA editing sites from high-throughput sequencing data — a technically demanding problem because RNA-DNA differences look similar to sequencing artifacts. Written at the height of the RNA editing research wave.
Why We Haven't Cured Cancer: Personalized Medicine vs. Evolution
Science-Based Medicine's argument for why personalized medicine is harder than it looks: tumors are genetically heterogeneous mosaics that evolve under treatment pressure, so targeting a single mutation is like targeting one soldier in an army that reproduces faster than you can shoot. The evolutionary biology of cancer makes resistance nearly inevitable.