Article Archive

Welcome to the archive! There are 1640 posts waiting for you…

Time to Shrink the National Institute of Health (NIH)?

Is Google Tweaking Search Results to Block Our Posts Critical of NIH Director?

Gullible's Troubles

Another Tutorial - This Time on Pevzner's Videos

A Tutorial with Ben Langmead's Bioinformatics Videos

Genome assembly algorithms through jigsaw puzzles - III

Tuesday Review - SAVE your day for CRISPR, Nature Fake News and Other Stories

Genome assembly algorithms through jigsaw puzzles - II

Monday review - Myers' dBG Paper, Pacbio's Multiplexing and Bioinformaticians' Foray into Escapism

KMC tools tutorial - II

A tutorial on KMC tools

Genome assembly algorithms through jigsaw puzzles

Monday review - KMC3 and other seXY topics

Online Bioinformatics Contest from Stepik/Rosalind

Roche Dumps Pacbio

Business analysis - Oxford Nanopore

GRASS for Rapid Reannotation of RNAseq Data

Using Multidimensional Bloom filters to Search RNAseq Libraries - (i)

Postdoctoral Scholar Position in Comparative Plant Genomics and Bioinformatics

Zipper plot for visualizing transcriptional activity of genomic regions

SuperTranscript - a reference for analysis and visualization of the transcriptome

Designing Molecular LEGOs in Lisp Language

Upgrade to the blog

Lior Pachter's Zika Paper

Ongoing Pacbio bioinformatics meeting (#SMRTBFX)

Qudaich - a Smart Sequence Aligner

Suicide Epidemic: Since NIH-funded Clowns Do Not Want to Discuss It, We Will

Population Genetics of Ancient Jewish Population in India

Was Google Really Censoring Elhaik's Khazar Research in 2013?

Transistors, Translation and tRNAs

Organoids and the Coming Medical Revolution - (ii)

Transfer RNAs and Neurodegenerative Disorders

Organoids and the Coming Medical Revolution - (i)

The Wall Will be Built and Mexico Will Pay for It

Job Opening - Postdoctoral Scholar: Forest Genomics Database and Software Developer

Jewish Genetics - Forward Magazine Makes Elhaik's Work Go Viral

Epigenetics Debacle - Do You Feel Sad for Sid Mukherjee?

A Graph Extension of the Positional Burrows-Wheeler Transform and its Applications

Geopolitics - Several New Developments Will Define the World in the Coming Decades

Freedom of Speech

Peak Sequencing and 'Moore's Law' Deception

After Docker

The Lab That Invented Nanopore Sequencing

Someone Asked Francis Collins about the Retraction Boom. Here is What he Did not Say.

Comments on Our New Paper - "Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P"

Experts Puzzled about Massive Increase in Suicide among Americans. Here is What our Non-expert Thinks

Illumina's 'Surprise' Announcement is not Surprising

Sequencing Technology Comparison Chart - 2016

UC Berkeley Needs at Least 18% Layoffs Soon to Survive

COCACOLA and BIGMAC Followed by AVOCADO !

Single-Molecule Protein Identification by Sub-Nanopore Sensors

Sequencing That Stimulates The Sensors (Fascinating Ted Talk by David Eccles)

metaSPAdes: a new versatile de novo metagenomics assembler

FPGA - GateKeeper: Enabling Fast Pre-Alignment in DNA Short Read Mapping with a New Streaming Accelerator Architecture

Efficient Index Maintenance Under Dynamic Genome Modification

Accurate selfcorrection of errors in long reads using de Bruijn graphs

When Venter Goes IPO

Nanopore - Two New Basecallers Released

Mosquito Genome is Shown as the Front Page Image in NY Times

Higher Education Is Morally & Financially Bankrupt

Quasi-essential genes supporting yet undiscovered functions for life?

Formin Is Associated with Left-Right Asymmetry in the Pond Snail and the Frog

Retweets and Social Media Impressions Do Not Mean Truth

New Paper by Elhaik Shows that Ashkenazi Jews Came from Northeastern Turkey

Assemblytics: a web analytics tool for the detection of assembly-based variants

Is "Huge" Business Downturn Coming in the Sequencing Industry?

Clinton Emails Reveal Google Played Active Role in Trying to Overthrow Syrian Government

Minimap and Miniasm Paper is out

Nate Silver has Peaked, and that’s a Good Thing

Jonathan Pevsner's Popular Bioinformatics Textbook Released in Third Edition

PLoS One Publishes Creationist Paper from Four Chinese Authors

Addiction Valley

UC Berkeley Plans to Dissolve Chemistry Department

The Lifecycle of Bureaucracy and Coming Implosion of UC Berkeley

Trimming of sequence reads alters RNA-Seq gene expression estimates

Growing Human Brain on a Petri Dish

CRISPR-directed mitotic recombination enables genetic mapping without crosses

Illumina Sues Britain's 'Most Highly Valued Company' at US International Trade Commission

'Sci-hub is Breaking Laws' - Argues Chemistry Blogger, Who Himself is Breaking Laws !

Patents vs GPL, Who Wins? A Case Study

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

Boiler: Lossy compression of RNA-seq alignments using coverage vectors

War of Standards - XML vs JSON

Is this the Future of Cloud-connected Hospitals Delivering 'Precision Medicine'?

Major Security Hole Discovered in Popular Library glibc

Is Seven Bridges Genomics Patenting All Existing Bioinformatics?

Peter Visscher Predicts Future, Makes a Fool of Himself

Is NCBI Getting Sold to Private Companies?

Our #AGBT16 Forecast - Oxford Nanopore Will Go Out of Business by 2017

The Virus Spreading in Europe

The Most Important Part of Flatley's #AGBT16 Talk

Notes from Technology Day of #AGBT16

Live Streaming of Pacbio Session at #AGBT16

Future of Science is Being Decided in Aleppo, Syria

UC Berkeley is Running out of Money. Here is What They Plan to Do

RECKONER: Read Error Corrector Based on KMC

Combinatorial Scoring of Phylogenetic Networks

Zika Oxitech Connection Can be Explained without Resorting to 'Conspiracies'

They lost half of the DATA !

Two Potentially Important Developments on Nanopore

ENCODE Scholar Resigns from UChicago after Sex Scandal

MetaFlow: Metagenomic profiling based on whole-genome coverage analysis with min-cost flows

I have a (bioinformatics) dream

Genomic Analysis with Spark - A Few Examples

A survey of best practices for RNA-seq data analysis

Please Sign up for our Membership Section

Apache Spark

USA's Second John Brown Moment Arrives

Pacbio Assembly - Miniasm Works Best (Chaisson)

Changing Face of the Publishing World

Rubbish DNA: The functionless fraction of the human genome

rHAT: fast alignment of noisy long reads with regional hashing.

Kary Mullis - Celebrating the Scientific Experiment

Integration of String and de Bruijn Graphs for Genome Assembly

CRISPR Fight and the Corrosive Role of Bayh-Dole Act in Damaging Basic Science

The Heroes of CRISPR - Lander

A New Metagenome Search Program from the LMAT Group

RapMap - Today's Must Read Paper

pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data

An opinionated guide to the proper care and feeding of your transcriptome

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data

Integration of String and de Bruijn Graphs for Genome Assembly

Protip - Don't Shout at Your Computer

Job Opening - Computational Biologist/Bioinformatics Scientist

Safe and Complete Contig Assembly via Omnitigs

Inside story of a great bioinformatics MOOC (an interview with Ben Langmead)

An opinionated guide to the proper care and feeding of your transcriptome

Merry Christmas

"Years since I Left Academia Have Been the Happiest of my Life" - Fred Ross

Fast genome and metagenome distance estimation using MinHash

Latency Numbers Every Programmer Should Know

tximport: import and summarize transcript-level estimates for gene-level analysis

A bloated FM-index reducing the number of cache misses during the search

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

"If You Learn from MOOC, You Are an Evil Person" - Science

Humor - Dilbert Joins ENCODE 'Precision Medicine' Project

Centrifuge - A Low RAM Metagenomic Classifier from Salzberg Group

Chimeric Pacbio Reads and Tardigrade Controversy

HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads

Sequenceserver: a modern graphical user interface for custom BLAST databases

Kaiju: Fast and sensitive taxonomic classification for metagenomics

Cost of Human-sized Genome Sequencing with PacBio Sequel

Two Excellent Reviews on Metagenomics

Timecourse analysis with Sleuth

Tardigrade Mystery Solved?

Existing Bioinformatics Workflows

Environmental Destruction, 'Green Energy' Scams and Nature-like Technologies

Bringing Arbitrary Compute to Authoritative Data

“Into the Sciences” – Frederick J. Ross

Turkey and Thanksgiving

Peak Sequencing Consequence? - BGI Delays Launch of ‘Nation-scale’ Sequencer

Matthew Cunningham-Cook: How the TPP Will Create a Medical Privacy Hellscape

Friday Humor

Rushed Review by Nature Biotechnology on a Cancer Bioinformatics Paper?

Discovering Russia and Russians through the Eyes of an Ex-US Military Analyst

A Different Vision from 'Singularity'

The State of Software in Evolutionary Biology

Does Gangolf Jobb's Treefinder Program Have Any "Value"?

Solute Carrier Proteins and Their Therapeutic Implication

Please Try New and Polished HaploMerger2 for Assembly of Heterozygous Genomes

New Blog Post from Gene Myers on "Intrinsic Quality Values" of Pacbio Sequences

Springer Ups Ante in its Anti-Russia Battle by Retracting Treefinder Paper

Refugee Crisis - a Vivid Description of What is Currently Going on in Europe

First Human Bioinformatician Criticizes Bad Science of NIH-funded Bigshots, Disappears

Condensed Matter Physicist Leo Kadanoff Passes Away

BMC (Springer) Sends Shockwave through Bioinformatics Community

JGI Researchers on The Economics of New PacBio Instrument

Discuss Mathematical Oncology Preprints at "Warburg's Lens" Blog

Researchers Dig into US Mortality Data, Discover Disturbing Trends

Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies

LXC/LXD -(iii) [Sorry, No LXC]

After Metagenomics: Drug Discovery from Microbial Genomes

A Report on our Two Online Bioinformatics Classes so Far

"Happy Halloween" - Says Illumina Stock

Wobble Modification and Human Diseases (3 old links)

De bruijn Graph for Married Couples

BGI Launched Its Desktop Sequencer BGISEQ-500 in China

Agmatidine in Archael tRNA

A Request to Cold Spring Harbor Lab Regarding 'Genome' Conferences

Using LXC and LXD for Bioinformatics - (ii)

The March of Pseudoalignment - Two Papers

Talks and Posters at the Genome Informatics Conference

Several Flaws in Ewan Birney's Description of Publicly Funded Science

Properties of HflX, an Enigmatic Protein from Escherichia coli▿

Using LXC and LXD for bioinformatics

"Russian Government is Beheading Scientists in Red Square" - Nature Reports

Are Geneticists Qualified to Talk about GMOs?

PLoS Biology in Hot Water Over GMO Scandal

New Paper from Nanopore (ONT) Consortium Submitted in F1000

A Practical Guide to de Novo Genome Assembly using Long Reads

TPP Intellectual Property Chapter is “A Disaster for Global Health”

Genome scaffolding with PE-contaminated mate-pair libraries

'Cut Down NIH Funding by Half' - Argues Ex-employee in Science Journal

Accurate, fast, and model-aware transcript expression quantification with Salmon

Is Illumina at a Strategic Inflection Point?

NHGRI's Epigenetics Investments Starting to Pay Off

Interview with Gangolf Jobb, the Author of Treefinder

Discovery that Neutrinos Have Mass Gets Nobel Prize in Physics

'Scripting for Biology' Module - for Students living in Asia

Only the French Speaking World Cares about Nobel Prize

Nobel Prize for Diseases of Poor People

Farmer-managed Natural Regeneration (FMNR) in Sahel

Oxford Nanopore Keeps Falling Behind

Lior Pachter Snubbed for Asking Relevant Questions on a Paper

Who Wins - Long Noisy Reads or Short Clean Reads ?

MOOCs Are Actually Books

Approaching Single-Cell Sequencing by Understanding NGS Library Complexity and Bias

PacBio Mini?

Minimap - A Minimizer-based Mapping Program

Was July 20 a Turning Point for Stock Markets?

Casey Dunn Reviews 'The Evolution of Animal Genomes'

"Basically, Avoid Comments" (Good Coding Practice 101)

XcodeGhost Will Say Boo in this Halloween

Is Docker for Suckers?

An Electronics Enthusiast Takes Apart Ahmed Mohamed's Clock Story

SPAdes Assembler Team is Looking for Help to Improve Assembler

Why Do Scripting Languages Die?

Today's Exercise - 'Save us from Malicious Hackers'

My Thoughts on Dying

The evolution of animal genomes - Review by Casey Dunn

Should Life Scientists Understand the Implementations of Software Packages They Use?

Reducing Assembly Complexity of Microbial Genomes with Single-molecule Sequencing

Pacbio Bioinformatics Workshop - Slides from All Presentations

New Publishing Model in Mathematics

Eric H. Davidson (1937 - 2015)

The Two-domain Tree of Life is linked to a New Root for the Archaea

Origin of Eukaryotes and 'Mitonuclear Ecology'

"There is a Black Hole in the Middle of Evolutionary Biology"

Scripting for Biology - Online Virtual Classroom-based Module

Predictions about the Next 100 Years

Beautiful Japan

Slides from Gene Myers

Nick Lane's "The Vital Question: Energy, Evolution, and the Origins of Complex Life"

Gene Myers at the Pacbio Bioinformatics Workshop - Follow #SMRTBFX in Twitter

How Much of Evolution is Influenced by Extinction?

High-throughput Pairing of T Cell Receptor Alpha and Beta Sequences

Achilles Heel of 'Big Data' Science

Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds

RapMap - Rob Patro's Reimplements Kallisto's Pseudoalignment Code

Honest Valuation and Ponzi Valuation

Deformed Daisies Near Fukushima - Radiation or Fasciation?

Oxford Nanopore Blows Up Lab, Raises $150M

Evolutionary Biologists to Follow - Sally Leys and Casey Dunn

International Maths Olympiad - 2015

An Email Interview with Evolutionary Developmental Biologists Isabelle Peter and Eric Davidson

A conserved role for Notch signaling in priming the cellular response to Shh through ciliary localisation of the key Shh transducer Smo

Will I Use Kallisto? Definitely, Most Likely and Never

Twitter Justice versus Due Process - Tim Hunt's Case

Publishing Madness - Book Review Costs A Whole Lot More than the Book

Steven Salzberg Publishes Reanalysis of UCSF's Defective Lancet Paper in F1000

QuorUM: An Error Corrector for Illumina Reads

Veli Mäkinen's Book - Genome-Scale Algorithm Design

Tools or Algorithms, What is More Important in Bioinformatics? - The Answer Will Shock You

Optimal Seed Solver: Optimizing Seed Selection in Read Mapping

BGT: Efficient and Flexible Genotype Query Across Many Samples

A Polynomial Delay Algorithm for the Enumeration of Bubbles with Directed Graph

UCSC's David Haussler Wins Award through Deceptive Claims, Gene Myers Loses

TransRate: Reference Free Quality Assessment of de-novo Transcriptome Assemblies

There Will be no Grexit and Here Are the Consequences

NASA Predicts Dope Will be Legalized in Entire USA by 2025 :)

Metagenome Sequencing Finds Strange Biology in >15% Bacteria

How Much Should a Poor Scientist Pay to Access Old Research Papers?

Getting the Most Out of RNA-seq Data Analysis

Diploid Human Genome Assembly using Pacbio Technology

Scientists Are Seeking Refund from OPERA-LG Authors :)

After Nanopore Sequencing Comes Quantum Pore Sequencing

Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees

Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees

Central Planner Ron Germain Reinvents Round Wheel

Oxford Nanopore Fans are Asking Three Questions Today

Homolog.us Introduces Video Interview Series with Respected Scientists

A Neat Paper on FM-index

Why Are Some Genomes Extremely Large?

The Chastity of Amoebae: Re-evaluating Evidence for Sex in Amoeboid Organisms

Nature Promotes Cancer Cell Line Factory Proposed by Broadsters Boehm and Golub

Intelligence of Slime Mold

The Evolution of the Cilium and the Eukaryotic Cell (Twelve Fundamental Problems for Bioinformatics)

Where Does the Genetic Code Come From? (Twelve Fundamental Problems for Bioinformatics)

To Maintain Integrity of Science, Kellis and Birney Should be Investigated

GraphMap for Fast and Sensitive Mapping of Long Noisy Reads

Thymic Involution - an Evolutionary Mystery

Heng Li and Coauthors Publish New SAM/BAM Format For de novo Assemblies

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

Optimizing error correction of RNAseq reads

OPERA-LG: Efficient and Exact Scaffolding of Large, Repeat-rich Eukaryotic Genomes with Performance Guarantees

The Original Purpose of Peer Review

Peak Sequencing? BGI Unveils 'Nation-scale' Sequencer

Michael Huss Provides Introduction to Three Commercial Genomic APIs

The Most Difficult Problem in Computational Biology

Structural and functional features of central nervous system lymphatic vessels

Proper Role of Bioinformatics in Biology

A Glimpse into the Techno-gaga World

RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation

Breakdown of Trust

Practical Olefin Hydroamination with Nitroarenes

On The Origin of Phyla - Interview with Valentine

How Do Fish Hear?

Evolving gene regulatory networks into cellular networks guiding adaptive behavior: an outline how single cells could have evolved into a centralized neurosensory system

YOAVGILAD Consortium on Results Published by ENCODE and GTEx

Twitter Conversations (or Lack Thereof) between ENCODE/GTEx and Yoav Gilad in One Video

REVIEW: Organogenesis in a dish: Modeling development and disease using organoid technologies

Pachter's Kallisto Comes with Unconventional License

On The Evolution of Noggin Gene

Notch Signaling - Where Did it Come from? (four papers)

Suffix Array in External Memory - Latest from Felipe Louza

Lightweight Algorithms for RNAseq Expression Analysis - Sailfish, Kallisto and Salmon

Genetic Diversity and Evolutionary Dynamics of Ebola Virus in Sierra Leone

Bioinformatics and Docker

Using Humans as a Model Organism - Sydney Brenner

Pachter Blogs on Sailfish vs Kallisto

Evaluation of tools for differential gene expression analysis by RNA-seq on a 48 biological replicate experiment

Seventy Years Since the End of WWII

Top Ten Genomes - (x) The Human Genome

Top Ten Genomes - (viii) Trichomonas vaginalis

Top Ten Genomes - (vii) Bladderwort

Top Ten Genomes - (ix) Pacific oyster

Understanding the Algorithm behind Pbdagcon and POA for Multiple Sequence Alignment

Top Ten Genomes – (vi) Oxytricha trifallax for MIC and MAC in Ciliates

Top Ten Genomes - (v) Ich

Origins of major archaeal clades correspond to gene acquisitions from bacteria

Top Ten Genomes - (iv) Methanococcus jannaschii

Kallisto from Pachterlab for RNAseq Quantification

Bioinformaticians, Can You Pass That Exam?

Top Ten Genomes - (iii) Paris japonica

Top Ten Genomes – (ii) Dynamically Changing Genomes

Top Ten Genomes - (i) Lamprey

Why Weight? Modelling Sample and Observational Level Variability Improves Power in RNA-seq Analyses

A Must Read Book, If You Like to Understand Genomes

SplAdder: Identification, quantification and testing of alternative splicing events from RNA-Seq data

Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees

Improved genome inference in the MHC using a population reference graph

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

On the readability of overlap digraphs

Metassembler: Merging and optimizing de novo genome assemblies

FermiKit: assembly-based variant calling for Illumina resequencing data

Bioinformatics at the Core Facilities

BamHash: a checksum program for verifying the integrity of sequence data

ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching

Free draft ebook - Pandora's Toolbox for Bioinformatics

Eukaryogenesis, How Special Really?

Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference

A Mouse Geneticist’s Practical Guide to CRISPR Applications

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

GATK Battle and BALSA versus GATK Comparison

Using de Bruijn Graphs for Short-read Assembly - (ii)

Using de Bruijn Graphs for Short-read Assembly - (i)

Today's thought-provoking paper - Evolution evolves: physiology returns to centre stage

GATK Battle - 2015 Edition

Someone Please Take Titus Brown for a Drink

POA and Nanopolish

How Much Will the Americans Suffer, If NIH Shuts Down?

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols

Is the Bioinformatics Journal Unfairly Overcharging Researchers?

Guangzhou Researcher Debunks 'Duon' Discovery of Stamatoyannopoulos

LINKS - Long Interval Nucleotide K-mer Scaffolder

Homolog.us Reports from Asia - 'Will Hong Kong be the Bioinformatics Capital of the World?'

Compressed String Dictionary Search with Edit Distance One

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

After SPAdes and Rosalind, Russians Fail Again

The Hidden Biology of Sponges and Ctenophores

Supergenes and Complex Phenotypes

RNA-guided gene drives can efficiently and reversibly bias inheritance in wild yeast

T4 phages against Escherichia coli diarrhea: Potential and problems

Report from Asia - Will Asia 'Unfollow' NIH's Failed Research Model?

Report from Asia - Multidrug Resistance and Phage Therapy

Quality-Controlled Small-Scale Production of a Well- Defined Bacteriophage Cocktail for Use in Human Clinical Trials

Phage Therapy - Reviews

Origins and evolution of viruses of eukaryotes: The ultimate modularity

Immunoglobulin Classification Using the Colored Antibody Graph

Experimental Phage Therapy on Multiple Drug Resistant Pseudomonas aeruginosa Infection in Mice

Experimental phage therapy of burn wound infection: difficult first steps

Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems.

MEDUSA: a Multi-draft Based Scaffolder

Homolog.us Reports from Asia – 'Calcutta - a New Beginning?'

Data Science MOOC from John Hopkins (starring Steven Salzberg)

A perceptual hash function to store and retrieve large scale DNA sequences

Ultrafast SNP Analysis using the Burrows-Wheeler Transform of Short-read Data

The Current Status of the Introductory Book on Genome Assembly

rnaQUAST: Quality Assessment Tool for Transcriptome Assemblies

Homolog.us Reports from Asia - 'Bangkok - a Wild Ride'

FASTAG Viewer Bandage

Stalin's Forgotten Cure

Phage Therapy

Evolution of Liver and Kidney

Outrageous Prediction 2015 - USA Will Start to See Exodus of Russian Scientists

'Coding' in Genetics is not the Same as 'Coding' in Computing

Nanopore Assembly Improves with HMM Polishing of Signal Level Data

Junk DNA Debate - T. Ryan Gregory versus Francis Collins

Perfect Genome Assembly - BGI's Solution

Evolution of Adaptive Immune System - Two Papers we are Reading Today

Perspectives on rare diseases - from a patient and a researcher

Pacbio Talks at #AGBT - What to Expect

Highlights of Gene Myers' Talk at #AGBT15

Adaptive Immunity - Connecting Evolutionary Dots from Bacteria to Mammals

Pevzner and Compeau Are Splitting Their Bioinformatics Course into Three

Everything You Need to Know to Follow #AGBT15

The Conspiracy of Epigenome?

E. coli Genome Assembled using Nanopore Data Only

StringTie - A New Alignment + Assembly Based Method for RNAseq

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

Occasionality or Probability - What is the Right Term?

Chromosome-scale Shotgun Assembly using an in vitro Method for Long-range Linkage

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

The Future of Work and Asynchronous Teams

A Sequel to Heng Li’s Mysterious New Program

Minia 2.0.1 is Released

Indexing Arbitrary-length K-mers in Sequencing Reads

2014 - the Hottest Year on Record

Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing

An Update on the Introductory Book on Genome Assembly

A Computational Method for the Rate Estimation of Evolutionary Transpositions

A Computational Method for the Rate Estimation of Evolutionary Transpositions

The Most Interesting Genome in the World

Scrm: efficiently simulating long sequences using the approximated coalescent with recombination

Francis Collins is Out Again with 'New' Ideas on How to Waste Other People's Money

An Evolutionary Classification of Genomics Researchers

Greeks Are Free and They Are Running Away to Russia

A New and Efficient Method to Help Base-calling from Nanopore Electrical Signals

Vitamin A and Lung Regeneration

PLoS Will Not Require Bank Statements to Let Researchers Publish

Parallel de Bruijn Graph Construction and Traversal for de novo Genome Assembly

Isn't Serious discussion Needed before Throwing Money into Million Genome Sequencing Projects?

The Evolution of Lungs

Do Read Errors Matter for Genome Assembly?

Only three driver gene mutations are required for the development of lung and colorectal cancers

LoRDEC: Accurate and Efficient Long Read Error Correction

MICA: A fast short-read aligner that takes Full Advantage of Intel Many Integrated Core Architecture (MIC)

Horror !! NIH is Now Funding Loving Kindness Meditation of Positivity Lady through Multi-year Grant

Francis Collins Admits NIH Under Him Has Been Failing

Obama Plans to Cure Polio, Diabetes and [name any disease] through Personalized Medicine

Arduino Punched Card Reader

The Genome Institute and Its Role - Ken Weiss

Poor People Need to Provide Bank Statements to Publish in PLoS

Let's Discuss - Is it Time to Shut Down NHGRI?

Heng Li's Mysterious New Program

Ex-student of George Church Invents Genome Assembly from Short Reads !!

An Update on Pandora's Toolbox

A Good Day to Value Freedom of Speech

UK Plans to Piss Away a Lot of Money on Genomics Misadventure

Fully Funded Bioinformatics PhD Position with a Very Smart Guy

Oxford Nanopore Sequences are Very Noisy - Michael Schatz

Most lncRNAs are Junk and lncRNA Papers are Hype

Forecasts Made Ten Years Back

Dear 'Bright and Insatiably Curious' 23andMe Customer, Did you Get 'Grubered' by George Church?

Introducing 'Pandora's Toolbox' and 'Pandora's Modules'

Happy New Year and a New Direction

Quality scores for 32,000 microbial genomes, no eukaryotes

Promoter architecture dictates cell-to-cell variability in gene expression

Evaluation of de novo transcriptome assemblies from RNA-Seq data

A review of the physonect siphonophore genera Halistemma (Family Agalmatidae) and Stephanomia (Family Stephanomiidae)

Today's Rainbow Chasing Paper by ENCODE Leader-in-Exile Ewan Birney

Highly-efficient Cas9-mediated transcriptional programming

Compression of High Throughput Sequencing Data with Probabilistic de Bruijn Graph

A perceptual hash function to store and retrieve large scale DNA sequences

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

Evolution of Genome Size - Scientific and Religious Analysis

'Best of 2014' - My Personal Opinion

Taiwanese Nanotech Paper Heading for Retraction, Professor/Student Punished

Dear BGI, Please Stop 'Revealing' Any More 'Insights' :)

Alternative Splicing - the New Snake Oil to Explain 'Human Complexity'

HISAT: Hierarchical Indexing for Spliced Alignment of Transcripts

Excellent Software Engineering in KMC

The Tragic Demise of BLAST

Chordate Evolution and the Three-phylum System

A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus

New Nanopore Paper by Phil Ashton

Searching and Indexing Genomic Databases via Kernelization

Gene Myers Needs Postdoc, Gets Endorsed by Legendary Evolutionary Biologist Ewan Birney

Data Structures in Bioinformatics Workshop

Genome alignment with graph data structures: a comparison

The Entire World of Bit Twiddling Hacks

An Incredibly Tragic Event at UK's Imperial Colllege

If You are Using Gene Myers' Daligner

Dan Graur elected as AAAS Fellow, Birney/Gerstein Quietly Drop Out of ENCODE

Challenging Times Ahead for PLOS?

Downloading Basespace Files using Command Line

Sdsl-lite and Cosmo - Useful Github Repositories

Misassembly Detection using Paired-End Sequence Reads and Optical Mapping Data

'Compare and swap' vs Software Transactional Memory

An Opinionated Bioinformatics Manual that Also Teaches You How to Do Experiments

An Easy-to-follow Introductory Book on NGS Assembly Algorithms

Human Genetics and Clinical Aspects of Neurodevelopmental Disorders

Evolution, not Hadoop, is the Biggest Missing Block in Bioinformatics

RNA-seq Data Analysis Course Materials

Prediction is very Difficult, Especially if it's about the Future

Finally Some Honest Reporting of GWAS for a Change

Reference-free detection of isolated SNPs

Reddit AMA by Weiss and Buchanan - Please Spread the News

Variable-Order de Bruijn Graphs

Nature Promotes GWAS Madness to Study 'Mental Health'

An Evolutionary Perspective on the Kinome of Malaria Parasites

HBP1, a novel protein from lamprey can repress proliferation of cancer cells (TUM7P.926)

Rothberg’s New Gadget (ii) - Is this the 'Secret Sauce'?

Review paper - Data compression for sequencing data

#Biodata14 Conference - Twitter Summary and Links

A Number of Genetic Tools Developed to Study Choanoflagellates

Bizarro Details Coming out on 'Nanopore Sequencing by Divine Intervention' Story

Technical Details of Rothberg's New Machine - (i)

Imaging - The New Frontier?

Study Bioinformatics Algorithms from Youtube Videos

Steven McKnight Identifies the Riff-raffs

Quick Update on Pacbio and DALIGNER - Jared Simpson's GFA Module

Origins and Evolution of the Formin Multigene Family That Is Involved in the Formation of Actin Filaments

Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution

On the Origin of Cilia

Myosin domain evolution and the primary divergence of eukaryotes

Early evolution without a tree of life

A new fusion hypothesis for the origin of Eukarya: better than previous ones, but probably also wrong

Vaccinating with the genome: a Sisyphean task?

The GWAS Era is Over - Declares Jay Shendure

On the Origin of Cells and Viruses: Primordial Virus World Scenario

Generating genetically modified mice using CRISPR/Cas-mediated genome engineering

CRISPR/cas9 Success Stories in Plasmodium

Biological Complexity

A Few Other Useful Resources

The Most Challenging Problem in Bioinformatics

Eugene Myers on the Future Direction of Bioinformatics

Two Papers from Koonin on Genome Architecture

Evolution before Genes - Two Review Papers

Koonin: The Origin and Early Evolution of Eukaryotes in the Light of Phylogenomics

Why are Bacteria Different from Eukaryotes?

Why are Bacteria Different from Eukaryotes? - (ii)

The Histology of a Siphonophore - Nanomia bijuga

Personalized Cancer Screening Will Lead to Many False Diagnosis of Blood Cancer

Tragedy of the Day - New 'Revealing' Human Transcriptome Paper at Biorxiv

Cuckoo Filter to Replace Bloom Filter?

Chimeras and Fusion Transcripts in RNAseq Assembly

RNAseq: Does it Really Matter How You Analyze the Data?

Renowned Human Geneticist Michael Hammer Shamed, Joe Pickrell Continues to Support Bad Science

FPGA-accelerated Bioinformatics at #ASHG - Dragen Aligner from Edico Genome

Nanopore Updates from David Eccles

SUPPA: a super-fast pipeline for alternative splicing analysis from RNA-Seq

ASHG/GA4GH Special - A Recap of Interesting NGS Algorithms of the Year

Alternative meiotic chromatid segregation in the holocentric plant Luzula elegans

Crossroads (iii) - a New Direction for Bioinformatics with Twelve Fundamental Problems

Very Efficient Hybrid Assembler for PacBio Data

Latest from Steven McKnight on Harvard/Broadster Citation Culture

New Book: RNA-seq Data Analysis: A Practical Approach

Nanopore - Truth and Nothing but the Truth

MUSiCC for Metagenomes and Lior Pachter's Code for Transcriptomes

MEGAHIT: An Ultra-fast Single-node Solution for Large and Complex Metagenomics Assembly via Succinct de Bruijn Graph

High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing

How Much of Complex Diseases are Controlled by the Genome? (Ken Weiss)

Genome Informatics 2014 Conference (#gi2014)

Lane-by-lane Sequencing Using Illumina's Genome Analyzer II

Antarctic Sea Ice Reaches Highest Levels Since Record Began

T. Ryan Gregory Starts 'Evolution Consulting Service' after Reading Gibbon Paper in Nature

T. Ryan Gregory Starts 'Evolution Consulting Service' after Reading Gibbon Paper in Nature

E. coli Nanopore Data Release and #baltiandbioinformatics Nanopore Conference

Cross-post: The prestige of “Jewish Genome” papers

Tutorial on David Tse's Work on DNA/RNA Assembly Presented at ISIT 2014

Long Term Direction of Nanopore Sequencing - Three Ways from Here

Nick Loman and Clive Brown's Nanopore Presentation - Live Feed

WABIstan Report

Open Science Fail - Oxford Nanopore Kicks Out Alex Mikheyev from its MAP Program

New Paper and Raw Data: "A first look at the Oxford Nanopore MinION Sequencer"

Merging of Multi-String BWTs with Applications

Nick Loman Presents Nanopore Data, #NotsoNickLoman Mocks Him

Crossroads (ii) - Is It Too Late to Acknowledge that Systems Biology and GWAS Failed?

Broke UK Government Taxing Soldiers' Medal for Bravery to Fund #100KGP GWAS Madness

A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria

Our New PNAS Paper Debunks the Genomics of Positivity

Gene expression study shows those enjoying subtle humor are healthier than those who do not

Benchmarking of Red-colored Bridges

An Algorithmic Comparison of BLASR/BWA-MEM, DALIGN and MHAP

Biology Student Faces 8 Years in Jail for Posting Scientist's Thesis on Scribd

New Bioinformatics Blog to Keep an Eye on - James Knight

BWT Construction Parallelized in 'Parabwt'

After HGAP And SPAdes Comes New PacBio Assembler - MHAP

Who Has Legal Control Over Your 'Big' Data?

Shadow Enhancers Enable Hunchback Bifunctionality in the Drosophila Embryo

Influence of RNA Extraction Methods and Library Selection Schemes on RNA-seq Data

Nicholas Wade's Other Controversial Book

Bioinformatics at a Crossroad Again - Which Way Next?

PNAS Publishes the Equation of Happiness

Informatics Humor: Hitler Learns about NP-hard Problems

Barbara Ehrenreich: How Positive Thinking Undermines America

Evolution of my Little Pet Dinosaur

Error-correction of Noisy Short Read Library using Clean Short-read Library

A Review of “Bioinformatics Algorithms – An Active Learning Approach” by Compeau and Pevzner

Stunning Siphonophore

On the Mythology of Natural Selection

Adam Smith and Theory of Evolution

In DALIGN Paper, Gene Myers Delivers a Major Blow to His Biggest Competitor

Genome Assembly - Discussion on Standardization of How to Represent Assembled 'Genome'

How Does the Unix Diff Algorithm Work?

Insane Decision of the Day - Broad Institute Gets $650M to Cure Insanity !!

Using Mathematical Induction to Design Algorithms

'Epigenetics' Explained, in the Context of Descendants of Holocaust and Slavery Victims

Minia's New Home - GATB (Genome Assembly & Analysis Tool Box)

Benchmark Analysis of RNA-Seq is an Excellent Confirmation of 'Short Read' Noise

The New K-mer Counter and a Genome Assembly - (ii)

The New K-mer Counter and a Genome Assembly - (i)

Minimizer Revolution Continues with KMC-2 K-mer Counter

After SAM and BAM Comes ADAM !

'Transcriptome Assembly is Hard', but Not Any More with Richard Smith's Transrate

Science after Government Money Disappears

Kmers Rock - Improved Genome Inference in the MHC using a Population Reference Graph

Google's 'Censorship Engine' Makes Guardian Articles Disappear

Latest Hardware Trends - ARM Servers and FPGA-integrated Intel Xeon Chip

Europeans Scientists Threaten to Boycott Europe's ENCODE Project

bíogo: a simple high-performance bioinformatics toolkit for the Go language

Bayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling

Our Bootstrapped Genome Paper Is Published

Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNA-seq Data

Whiskey Tango Foxtrot - Arianna Huffington Embraces PNAS-published Junk Science of Positivity !!!

UC Berkeley, Lior Pachter's University, Offers MOOC Course on 'Science' of Positivity

SSPACE, the Popular Free-standing Scaffolder, Goes Pacbio

RNAseq - RSEM Group Fights Back

Latest from Tony-Cox - BEETL-fastq

A Textbook-free 'Introduction to Biological Anthropology'

SPAdes Group's Long-awaited Repeat Resolver Paper is Published

'For Your Pacbios Only' - Gene Myers' June 1 Dazzler Update

Error Correction and Assembly Complexity of Single Molecule Sequencing Reads

Another PacBio Development - Adam Phillippy's New MHAP Module

University of California is Being Sold to Businesses

The Cellular Automaton Interpretation of Quantum Mechanics

Single-cell RNA-seq Reveals Dynamic Paracrine Control of Cellular Variation

Nanopore Better Than PacBio or Worse? That is the Question

How Google Manipulates Its Search Results

Fast construction of FM-index for long sequence reads

An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function

A Novel Machine Learning Method for Orthology Assignment of Whole de novo Assembled Transcriptomes

Why no Nobel Prize for Biologists (and Mathematicians) ?

Non-random DNA fragmentation in next-generation sequencing

Computer Program Fools 33% Judges, Will Write Nature Papers Next

A Tale of Two Papers

SFAF Meeting at Los Alamos (#SFAF2014)

A single female-specific piRNA is the primary determiner of sex in the silkworm

Minimizer Success - Disk-based Genome Sequencing Data Compression

Lighter: fast and memory-efficient error correction without counting

Computer Science Bubble and STEM Shortage Myth

What Approach Do Researchers Take to Avoid 'Short Read' Noise?

Sponge Jelly Genome is Studied to Find Evolutionary Origins of Neural Systems

What is the State of the Art for Bacterial Genome Assembly from Illumina Reads?

Scottification of Burrows Wheeler Transform

Fast BWT in Small Space by Blockwise Suffix Sorting (Juha Kärkkäinen - 2007)

Not Only Bioinformatics Programs Crash Due to Insufficient RAM

New Breakthrough in High-Tc Superconductivity?

Helix IO - Ultrafast Metagenome Sequence Classifier

Did CIA's Fake Polio Vaccination Drive Result in Global Resurgence of an Eradicated Disease?

Topics Being Covered Elsewhere in our Blog

Snyder/Lander Publicity Photo Reminds us of Dirac and Feynman, except...

In Support of Closed-access Publishing?

Course: Logical Reasoning in Human Genetics, Aug 18 - 22, Helsinki

BARCODE: Fast Lossless Compression via Cascading Bloom Filters

Posters and Slides from #BoG14

At #BoG14, Posters Are Far More Interesting than Talks

RNAseq: Estimating Transcript Expression using Min-cost Flow Method

Links to a Bunch of Useless Papers

Can Algebraic Geometry Contribute to Condensed Matter Physics?

Plactic Monoid, Schubert Polynomial and Combinatorics of Words

ENCODE Conflict of Interest - Personalis, Genapsys, Illumina?

The Slow Death of Purposeless Research

Efficient de novo Assembly of Highly Heterozygous Genomes from Whole-genome Shotgun Short Reads

America's Class Hierarchy and the Rise of 'Mobile Creatives'

Algorithms for Constructing of Phylogenetic Network (Reticulate Evolution)

New Method from Elhaik Can Find Your Ancestral Village or Island of Origin

A Few Thoughts on Reviving Biomedical Research in a Deflationary Era

What Will Replace GATK in the BALSA Age?

Measuring Reproducibility in Computer Systems Research

Github Book on "Introduction To Applied Bioinformatics"

ENCODE Backers Want US to Retract Commentary, Should We?

BALSA: Integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

A Very Good Discussion on 'Missing Heritability Problem'

Mapping to a Graph-style Reference Genome - Arxiv Paper

How to Enhance Career by Publishing in Open-access Journal

General Description and First Puzzle Emailed to All Who Asked

Debunking ENCODE's Latest Propaganda Piece Para by Para

Goodbye RSEM, Sailfish Paper Published

Dangerous Central Planners Coming to 'Rescue' US Biomedical Research

Transcriptome in Vivo Analysis (TIVA) of Spatially Defined Single Cells in Live Tissue

I Often Repeat Repeat Myself, I Often Repeat Repeat

Who Deserves the ENCODE Nobel Prize? Ans. Ron Davis

We Have Six Interesting Bioinformatics Puzzles, Any Takers?

Journal Impact (Visibility) Factor

How Dan Graur's History of DNA Ended

Hijacking Other Websites Using CVE-2014-0160 - Code and Demo

scTurtle Algorithm for Kmer Counting

Is It Time to Get the ENCODE Paper Retracted?

Splitting Our Blog into Different Subsections

For Today's Comic Relief

Major Shakeup Coming for Biotech Companies?

Kmer Counting - a 2014 Recap

BWA-MEM vs BLASR for PacBio - Need Help with Benchmarking

SplitMEM: Graphical Pan-genome Analysis with Suffix Skips

On Algorithmic Complexity of Biomolecular Sequence Assembly Problem

2014 - The Year of Minimizers in Bioinformatics

Mutation and Cancer - A View from Retirement

Feynman: Mathematicians versus Physicists

PacBio P4-C2, P5-C3, etc. - What Do They Mean?

How Noisy Are Those Variant Calls from Short Reads Really?

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation and Alignment

What Is Really the Salary of a Bioinformatician/Computational Biologist?

Peanut Genome Released

On FPGA Acceleration of Bioinformatics Programs - Latency

BESST Scaffolder

Three Amazing Applications of CRISPR/cas9

Seeking Readers' Feedback on Subscription and Redesign

On FPGA Acceleration of Bioinformatics Programs

NWDB Conference - Slides from Eric Haag and Update

Incredibly Powerful Speech from Brenner, but Ewan Birney Disagrees

BWA-MEM Gets Very Slow in Highly Repetitive Regions

Flexible Isoform-level Differential Expression Analysis with Ballgown

Alarming - Is Nature using Legalese to Dupe Scientists?

Highly Efficient Transformation of Diatom

Type I, II and III CRISPR/cas Systems

Targeted Genome Editing in Drosophila and Zebrafish using CRISPR/cas9

Sea Anemone is Genetically Half Animal, Half Plant

A Plant Genome Assembly Question

Trichoplax adhaerens at the Root of Multicellular Animal Tree

Molecular Mechanisms of CRISPR‑mediated Microbial Immunity - Review Paper

Going Through the Code of SOAPdenovo-trans

CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes

A Good Paper on Hox-TALE Puzzle

Reporting on the Northwest Developmental Biology Conference - (2)

JGI Looking Beyond Sequencing to Become 'Cutting Edge' Press Release Generating Facility

Saving Bacteria from Diseases and the Cas9-CRISPR Revolution

Pacbio - Jason Chin's AGBT Presentation on Diploid Assembly

Animal Ancestors - Sponges or Comb Jellies?

Why is Gene Myers Dancing? Answer - Long Reads !!

Reporting on the Northwest Developmental Biology Conference - (1)

Arxiv and BioRxiv Fans - Please Help

An Update on Our Nanopore Petition for Lex Nederbragt's Group

Ethan Perlstein Goes Indy - What Gives?

Columbia U. Kicks Out 'Star' Profs for not Getting Enough NIH Grants to Cover 80% Salary

Genome-based Personalized Medicine - a Letter

Oxford Nanopore Slides Say 50KB Read Length Easily Obtained

PLoS Requires PIs to Cut and Deposit a Finger during Each Submission

Seattle Sequencing Meetup with Bina Technologies

A Question on MaSuRCA Assembler

Kraken - Very Good Application of Jellyfish and Minimizer

Feynman on Science vs Advertising (for New Generation of ENCODE-inspired 'Scientists')

Keith Robison's Perfect Scaffolder Delivered, What Next?

Two Good Pictures to Show Evolution

Simple Design for a Scalable Graph Database System – on Just a PC

"Darwin Never Proved Natural Selection is the Driving Force of Evolution — Because It Isn't"

Sydney Brenner's "Lawsuit against Editors and Publishers of Nascence"

Scott Edmunds: Having a Finger on the Pulse of Data Citation

Titus Brown's Transcriptome Talk at UC-Davis

RECOMB 2014 Talks

dipSpades Beats Haplomerger Hands Down in Diploid Assembly

An Opinionated History of Genome Assembly Algorithms - (ii)

An Opinionated History of Genome Assembly Algorithms - (i)

No Genomic Evidence of Khazar Origin for the Ashkenazi Jews?

AGBT Slides from W. McCombie and V. Schneider

Science Launches New PLOS One-like Journal 'Science Advances'

'Network Nonsense' at Lior Pachter's Blog Escalates

The 'Horror' that Awaits You, if You Quit Bioinformatics (or Academia)

Finding Causative Mutation Candidates in Rare Disease Studies using NextGENe’s Variant Comparison Tool

Scientists Predict Longer, Harsher Winter

A Petition to Request Early Access to Minion Nanopore for Lex Nederbragt's Group

Revisiting Fred's Viral "A Farewell to Bioinformatics" One Year Later

Nanopore Talk by David Jaffe - Various Links

Dazzler Assembler for PacBio Reads - Gene Myers

The 'Right Way' and the 'Wrong Way' to Criticize Science

Hybrid Assembly - (ii): The Error Models of PacBio Reads

De Novo Hybrid Assembly of PacBio and Illumina Reads - (i)

PacBio - Human Genome Assembly, Cod Slides and a Number of Useful Data Sets

(Satire) Nanopore Sequencing Crosses Two Major Hurdles

What is the Cost of Scaling Up Genome Assembly Massively?

BWA-MEM Poster by Heng Li

Alignment-free Comparison of Next-gen Sequences using Compression-based Distance Measures

New Bioinformatics Business Model - Make Software Free, Charge for Manual

Small Science and Big Science

GPU-Accelerated BWT Construction for Large Collection of Short Reads

Vindicated by Victory over Nature, Eisen Brothers Pick a New Enemy - BGI

A New Nanoscale Sequencing Company Comes into Fray and Releases Data !!

Dancing Links Algorithm and Less Known Data Structures

Sunday Funnies and Not-so-funnies

The Astonishing Story of Nick Brown, Who Debunked the Mathematics of Happiness

Dan Graur's Latest Bombshell and Implications for Jewish Genetics

BlindCall: Ultra-fast Base-calling Algorithm Using Blind Deconvolution

The Story of Adam and Eve Revisited

Quilt Plot: A New Visualization Tool

GPL License is Dying in the World Outside Bioinformatics (aka Real World)

Good C++ Development Practices in Sailfish Code

De Novo Assembly of Human Genome with Only 1.5 GB RAM

Unicorn Genome Published

Announcing the Results of 'Best of 2013'

What is the True Computing Cost of RNAseq Analysis? - Titus Brown's Slides

TRAPID: Online Tool for Annotation/Analysis of RNAseq Assembly

Evomics Conference and a Paper by Carl Woese

Why are 'Cool Kids' at Github Moving to GO Language?

Bounds from a Card Trick

Bioinformatics One-liners

Wait-free and Lock-free Queues

Lessons for Creating Good Open Source Software

No Clear Link Between Passive Smoking and Lung Cancer

BWT Construction and K-mer Counting

Global Warming, Scripted Media and the Havoc Caused by Comment Section

SPAdes 3.0 Released with PacBio Hybrid Assembly Module

BGI Applies for Genome Assembly Patent, Claims Priority/Benefits from Chinese Patent Application

Seven Major Trend Changes of 2013 - (vii) Larger Society

Cross-post: Is trimming beneficial for RNA-Seq??

Seven Major Trend Changes of 2013 - (iv) Publishing and Social Media

Seven Major Trend Changes of 2013 - (vi) Business World

Seven Major Trend Changes of 2013 - (iii) Genomics

Seven Major Trend Changes of 2013 - (ii) Bioinformatics

Seven Major Trend Changes of 2013 - (v) Era of Contention Begins

Seven Major Trend Changes of 2013 - (i) Sequencing Technology

The Most Important Talk of the Year

#UCDAssemble Workshop - Friday Update

#UCDAssemble Workshop Covering Genome Assembly

Cancer: Story of a Real Patient

Finally a Good Idea from Francis Collins

Antifragile - N. N. Taleb's Talk

Collaborative Effort to Learn About Oxford Nanopore's Data Ends with Chase by Lawyers

A Free Market Approach to Improving Human Health

Life of Soay Sheep and Relevance to Human Society

Homolog.us Blog Congratulates ENCODE's Stamatoyannopoulos for Rediscovering Enhancers

Compressed Spaced Suffix Arrays

A Series of Good Ideas

The Rise and Fall of Human Genetics and the Common Variant - Common Disease Hypothesis

TIGRA: A Targeted Iterative Graph Routing Assembler for Breakpoint Assembly

From a Shot Against Cell/Nature/Science to Generational Warfare

Nicolas Bourbaki and M. Lothaire - Two Prolific Mathematicians

Nick Brown on Disrupting Science of Happiness Lady

kSNP v2 - Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes

If You Like Your Bioinformatics Code, You Can Keep it :)

Burrows-Wheeler Transform (BWT) is de Bruijn Graph is BWT

Evolution versus 'Intelligent Design' - a Beautiful Case Study on Fire Ants

'Baffling' New Hominim Found in Sima de los Huesos, Spain

Where Will Next Generation of Scientists (NGS) Come From?

The Tragedy of Centrally Funded Research

Genome Assembly - An Exchange between Two Experts

Big Data - Where Increasing Sample Size Adds More Errors

Top Bioinformatics Contributions of 2013

PLOS One Paper - "Comparing Memory-Efficient Genome Assemblers on Stand-Alone and Cloud Infrastructures"

Science Nobel Laureates Mock E-conmen on Stage of Award Ceremony

Who Should Go Away - FDA or 23andMe?

Denisovans, Extremely Ancient Africans - the Role Cheap Sequencing Plays in Rewriting Human History

SSP Transcriptome Assembler from Tehran, TIGER, PEGASAS Genome Assemblers

Science Reporting: a New Trend Emerges

Oh No !! Indians Are Suing Retraction Watch to Get Articles on Anil Potti Removed

CSHL Keynote Talk - Lior Pachter

WTF? Illumina Wants to Patent All Online Bioinformatics Programs !!

New Kind of Science

Coming Soon - Genomics of Unicorns

How Basic Math Limits Scientific Discoveries

10th Anniversary of Berlin Declaration on Open Access

A Bioinformatician is a Technician, no More

What Problems are Being Solved by the Top NGS Bioinformaticians Today?

How We Came to Know Dan Graur

TPP: One More Attempt to End Internet Freedom after Failed SOPA/PIPA

What if Angelina Jolie Were Simply Wrong

Sun is the Weakest in 200 Years

PacBio Posts Slides from User Group Meeting

Pacbio Assembly and Phasing

Using State Machines to Improve Read Error Rates in Ion Torrent Data

Friday Humor - Genome Scientists Compared to Twitter Leaders

Dude Gets Nobel Prize, Writes Blog Post Defending His Field as Science !!!

If Agatha Christie Were Around, She Could Easily Write a Novel on Nature Retraction

PacBio Data on Drosophila Release from Bergman Lab

Today's News - BEETL v0.8 Release and RNA Comparison Papers

Rules for Copying/Reposting our Blog Posts (CC BY-NC)

Is the 'Readers' Comment' Button at HUGO Journal for Show Only?

A Tale of Two 'Peer Reviewed' Papers

The Unraveling of 'We Do not Trust Chinese' Business Model

Trinity, Oases, SOAPdenovo-trans - Many Helpful Tips from Richard Smith

List of Many Bioinformaticians with Twitter Account

A Video Dedicated to #ENCODE, #GWAS and Other Government-funded 'Big Science' Projects

A Few Useful Terms

Genome Informatics Meeting at CSHL #GI2013

A Cuban Blog on Bioinformatics and Proteomics

Kalman Filter - a Way to Reconstruct Signal from Noisy Data (as in Nanopore)

Fractals and Scale-free Networks

Is BWA-MEM as Good as BLASR for Aligning PacBio Reads? – Part 2

Weekend Humor

Khash by Attractive Chaos

Heng Li Releases Ropebwt2

Everything You Want to Know about Oxford Nanopore

Some Oxford Nanopore Raw Data

New Announcements from Ion Torrent and Oxford Nanopore

Pevzner's Bioinformatics Course at Coursera Delayed by Two Weeks

Are Graph Databases Ready for Bioinformatics?

Is BWA-MEM as Good as BLASR for Aligning PacBio Reads? - Part 1

AfterParty - a Promising Post Processing Tool for Transcriptome Data

PacBio Achieves 500Mb/SMRT Cell Throughput in Newly Released Human Data

NCBI Runs out of Money and Starts a New Service

Two More #ENCODE Heretics Came Out

Human Transcriptome is Extremely Complex and Snyderome is the Most Complex of All

Changing Dynamics of the Sequencing World

US Science Funding - Proposal for a Better Alternative (Part II)

US Science Funding - Proposal for a Better Alternative

A Few Good Posts on Transcriptome Assembly and Analysis

What Kind of Jobs Are 'Reserved' for Bioinformaticians?

Our Chemistry Blog Covers Stapled Peptides

Using Stapled Peptides to Target 'Undruggable' Proteins

Physics Nobel Prize - Big Slap for Big Science?

New Paper Debunks Junk Science of Jewish Origin by Behar and Ostrer

The GenoChip: A New Tool for Genetic Anthropology

Book 'Probably Approximately Correct' Follows ENCODE-style Marketing

New Announcement from the Rosalind Team

Global Warming Update: Here is Halloween and Boo !!!

Cool Blog: Gas Station Without Pumps

Survival Tips During Federal Government Shutdown

A Silver Lining in Mozilla's Plan to Review 'Scientific Code'

RNAseq Annotation Issues - A Good Post by Stuart Brown

Gnubio - Mixture of Hardware and Cool Informatics?

Magic Touch of Roche, New Convey Server, 'Deep Understanding' of Variants and Other News of the Day

Human Tragedy, Unsustainability and Alternative to a Failing System

End of Short-Read Era? – (Part II)

End of Short-Read Era? - (Part I)

The Jewish Genome Challenge

No WWIII !! We are Back

Seeing the Future: What Will Our Electronic Devices be Like in 2053?

Personalized Genomics from Pacbio, if You Want to be Reborn as Bacteria

Good, Bad and Ugly

Efficient Online k-mer Counting using a Probabilistic Data Structure

Sequence Your Narcissome with 23 and Me

Altera, Micron Demo Hybrid Memory Cube Interoperability

What Do Government-funded #GWAS Scientists Spend Most Time on?

(As We Predicted Six Months Back), BGI Plans IPO

Functions, Variants, Traits and Diseases - Three Interesting Commentaries (#GWAS)

Compressed Full-Text Indexes for Highly Repetitive Collections (Jouni Sirén)

Arxiv Paper: Biological Averaging in RNA-Seq

Metagenomics - the Ticket is Expensive, but is the Train Going Anywhere?

A Challenge to Mike Eisen - Please Help Researchers Get Ostrer's Data

"Genome Patent Fights Erupts"

New Species of "Walking" Shark Found in Indonesia

SPAdes Assembler, Python in Bio, US Effect, Return of Lysenko and Other Stories of the Day

Cause of Heart Disease in Salmon Solved with Next-gen Sequencing, but....

Flux Simulator for RNA-seq Simulation

DEseq and Sailfish Papers for RNAseq

Teaching Bioinformatics on Raspberry Pi

SOAPdenovo2 on Github, Now 'Searching Soul' on Assemblers

New Paper on Comparing Genome Assemblies

Real and Unreal Disasters

Julian Assange Presents on Metagenome Assembly

'Zombies' of the Ocean

Going Through the Lyndom Word Paper

Big Brother App from Apple and Others Data Privacy Concerns

Are You Feeling Lucky?

Today's Dinosaur Stories

Skyrocketing Cost of Publication

Modularizing SOAPdenovo2 Code into Four Components

Chinese Hamster Genome Sequenced from Sorted Chromosomes

"Why We Didn't Use a Bloom Filter"

Open-source Legal Site Groklaw is Shutting Down on Privacy Concerns

Jumping Read Assembler - Before it is News

Enlightenment, Technology and the Rise of Democracy

Ted Talk by Ben Goldacre on Manipulation of Clinical Trials

New AJHG Paper: 'Born Again' Dinosaurs Question Effectiveness of #GWAS

How Novel Ideas Trickle Down from Computer Science to Biology

A Rabbi, a Priest, and a Minister Walk Into a Bar - part II

All About Federal Funding for Research

How Real Are Those 600,000 Spliced Genes in Your Transcriptome Data?

New CNV Algorithm in NextGENe v2.3.4

A Few Quotes from Benjamin Franklin

Performing Burrows Wheeler Transform on Trees

OMICS Publishing Group - An Indian Open Access Scam?

Oh So Scary !! Sequestration Starts a Dark Age for Science :)

A Constant-Space Comparison-Based Algorithm for Computing the Burrows–Wheeler Transform

BGI's K-mer Analysis Paper

Assessing De Novo Transcriptome Assembly Metrics for Consistency and Utility

Study History and Read Papers Written by 'Dinosaurs' (#GWAS)

Scott Edmunds Covers ISMB

Schrodinger's Lost Notebook from 1925

"Hydrogen Atom" to Learn Inner Workings of Genome Assembly Programs

Getting PhD for Master's Thesis

Weekend Videos - Enjoy !

Sites Closing........

Cerulean: A Hybrid Assembly using High Throughput Short and Long Reads

Bioinformatics at its Best

Happiness, Anger, Selfishness, Monogamy - All Explained by Science Today

Can a Proposal Lack 'Intellectual Merit', but Fly on its 'Broader Impact'?

Today's Update - BWT Patent, LSC Improvements and Nabsys

SOAPdenovo2 Demystified, BWA Mystified

Is Social Behavior Hardware or Software Coded?

Prehistoric Agreement Reached on HeLa Cells

Lyndon Word and Lyndon Factorization

Generalizing the Burrows-Wheeler Transform

Some People Want to Race Cars. Others Need a Vehicle to Get Their Groceries

Single Author Bioinformatics Paper - 'I' or 'We'?

Mapping Algorithms - How They all Arrived

Sending Programmer to Jail for Sharing Open-source Code?

Detecting Superbubbles in Assembly Graphs

Tragedy of the Day: PNAS Got Duped by Positivity Lady !!

Large Jump in PacBio Stock Price

HMMER and Viterbi Algorithm

Trials and Tribulations with PacBio Data

Sibelia, a dBG-based Tool to Find Synteny in Multiple Closely Related Microbes

Scholarly Publication - Using Arxiv to Maximize Substance

Russia - Best Assembler, Best French Actor and now Freest Country !!

Perverse Incentive: Why Universities Love Constructing New Buildings

Oxford Nanopore Announcement 'Again'

A Snapshot of How PacBio Reads Look Like

Strategies for Perfect Hash and Minimal Perfect Hash

Reducing Assembly Complexity of Microbial Genomes with Single-molecule Sequencing

Journal that Sells by Hype Tells Scientists not to Hype their Work

Hilarious Turn in Fight against Global Warming, Thanks to Hard-working Chinese

Exploring Genome Characteristics and Sequence Quality Without a Reference

Another Reason GPL is a Bad License

Battle over #GWAS: Ken Weiss Edition

Dr. John Stamatoyannopoulos Receives UW Alumni Early Achievement Award (2013)

Exo-Klenow Fragment for A-tailing and T-tailing

AMBA and Wishbone Protocols

Short Read Alignment with Populations of Genomes

Cancer, Stroke and Diabetes in USA - Environment versus Genetics

Laser Show Plans to Send Jonathan Rothberg's Genome to Space Aliens

Blogger Power: Bloggers Expose Japanese Data Tampering in Clinical Trial

Helpful Discussion on KA and SA-IS Algorithm and Possible Improvement

#genereg Conference - A Good Hashtag to Follow

If Your University Shuts Down, Are you Still Tenured?

Low-cost FPGA Implementation of Smith-Waterman

Failure to Fund #GWAS Leads to Increase in Cancer in a Chinese Village

Genome Wide Association Studies (#GWAS) - Are They Replicable?

Tenure-track is 'Seven Year Post-doc', but What Exactly is Tenure Today?

Memory Bandwidth and Recursive Variable Expansion - PhD Thesis of Zubair Nawaz

Pacbio: Why We Stopped Using PacBioToCA and Lived Happily Thereafter

Molecular Dynamics on FPGA at Boston University (Martin Herbordt)

To Do (PhD in Bioinformatics) or Not To Do? - Six Months Later

Overconfidence Leads to Success

Genomic evidence for ameiotic evolution Adineta vaga

CUBELP: Cranfield University Bioinformatics Learning Platform

Two Important Papers Published - Assemblathon and First Genome using Moleculo

Rayan Chikhi's KmerGenie Slides from HitSeq 2013

How to Kill Software Patents - a DIY Guide with an Example that Worked

Biology of Vampires

Method for Identification and Sequencing of Proteins

Bioinformatics Patents on Burrows Wheeler Transform

Bioinformatics Open Source Conference (#BOSC2013) at Berlin

RACER: Rapid and Accurate Correction of Errors in Reads

Large-scale Mouse Deletion Study Published

Inserting XIST ncRNA on Human Chromosome 21

Henry Bourne's Five Axioms for Mediocracy and Disaster

Bias in Animal Studies and Nature versus PLOS Tit for Tat

Why Don't Transcription Factors Get Lost in Huge DNA Maze?

From de Bruijn Graph to Minimal Promoter

Random DNA Sequence Mimics #ENCODE !!

True Cost of Publishing in Various Journals

Portable Peer Review - BMC, PLoS and EMBO Form Peer Review Consortium

Open Access: Can Humans Survive on Planet Earth?

"Nothing is so Alien to the Human Mind as the Idea of Randomness"

Assemblathon, GAGE and Four Dimension of Evaluating Genome Assembly Programs

Three Hacks to Get More Data from Your Illumina Sequencer

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

Science and Religion - the Battle over the 'Time' Axis

Parallelization Horror Story: How Not to Run String Graph Assembler

Our Readers Moved from Google Reader to.....

Myriad Genetics and University of Utah Sue Competitors for Breast Cancer Tests

Metagenomics of Buried Lake in Antarctica - Paper Differs from Earlier Press Release

#Usegalaxy Lights up Northern Skies

On MaSuRCA Paper and Algorithm

Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs

Cleverness of the Ray Assembler

PacBio Experiences at Norwegian Sequencing Center

Minimal Genome

PacBio: Debunking the Error Myth

More on Succint de Bruijn Graph

Genome Sequence of an Ancient Horse

For Bioinformatics Humor, Follow Twitter Hashtag #altbioinf

Very Helpful Preprocessing Module for Those Interested in Assembling Genomes

What is Faster - CPU, GPU or FPGA? Our Investigation of Leading Alignment Algorithms - (i)

What is Faster - CPU, GPU or FPGA? Our Investigation of Leading Alignment Algorithms - (ii)

Six Tutorials in Various Stages of Completeness

Opinion: ‘Big science’, big hype, big mistake

MS-thesis: FPGA-based Genome Assembler

Mathematical Olympiad in China Problems and Solutions

Ion Torrent, Diffraction Limit and SOLiD Technology

Comparison of Sequencing Instruments (Wish they Included PacBio)

Richard Durbin at International Maths Olympiad

Digging into BWA-mem Code

The Potential of Preprints to Accelerate Scholarly Communication - A Bibliometric Analysis Based on Selected Journals

Philip Ashton: Assembly Optimisation – Impact of Error Correction and a New Assembler, SPAdes

Global Warming Research: Where is Dan Graur, When We Need Him?

Alignment Papers We are Trying to Make Sense of

"PacBio Instruments - Are They Still Around?"

Google and Bing Usage by Bioinformaticians

Forget Gene Patents. Co-founder of 23andMe Patents Personalized Genomics

Many Good Slides at MSU NGS Analysis Workshop

A Number of Informative Comments from Heng Li on BWA-MEM Aligner

Let's Lend Ruibang a Helping Hand to Fix SOAPdenovo2

Entropy of Never Born Protein Sequences

Physicist Ken Wilson Passes Away

Government is the Mother of All Invention

Counting Animals

Whitepaper: Accelerated BLAST Performance with Tera-BLAST™: a comparison of FPGA versus GPU and CPU BLAST implementations

Another Bioinformatics Job Posted

Web Software Section is Open

DORA Pledge - YASI from Government-funded Scientists

Biostar, Biological Communities and Biological Databases

Metagenome Biologist Titus Brown Offers New Course on Internet Realities

RNA-seq Data on Prostate Cancer Publicly Available from BGI

Why Homolog.us Avoids Google Analytics, OpenID and Other 'Cool' Silicon Valley Products

SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

PLOS One Wins 16-1 against Nature, Science, GigaScience or BioMed Central

Notes on PacBio-based Assembly of Plasmodium 3D7

Jared Simpson's 2011 Talk at JGI on Memory Efficient Assembly

Designing a Traffic Signal Light - II

De novo Assembly is not at all Black Art

Blogs Are Dangerous - says Geoffrey North of Current Biology

A Rabbi, a Priest, and a Minister Walk Into a Bar

Shocking Finding that a Genome by Itself Provides Little Insight

Academic Bioinformaticians Uncomfortable with Illumina's Publication of Variant Caller

#Bog13: Simultaneous Assembly of Thousands of Human Genomes - Erik Garrison from Marthlab

Bi-directional BWT and 2BWT Alignment Algorithm

Slides from Deanna Church at #SFAF13

Tin-Lap Lee's Slides from his #BioIT13 talk: Next-Gen Sequencing Analysis by GigaGalaxy

SOAPdenovo-Trans Paper Shows the Complexity of Transcriptome Assembly

CoRAL: Predicting Non-coding RNAs from Small RNA-sequencing Data

Characterizing and Measuring Bias in Sequence Data

Mapping God Found 'Scientifically Dishonest' by Anonymous Peer Reviewers

GAM-NGS and REAPR Papers are Published

Designing a Traffic Signal Light

BWA-MEM - Heng Li's Answer to Bowtie2

Cells as Living Calculators

GPU and FPGA-accelerated Bioinformatics Algorithms

ISMB - Accepted Talks

Human Embryonic Stem Cells Derived by Somatic Cell Nuclear Transfer

After Nanopore and Stem Cell, Major Breakthrough Reported on Cold Fusion

Various NGS Platforms in Animation

Big Data and Buzzword-driven Science

Private Competitions and Crowdfunding Sources to Fund Bioinformatics Research

HAL: a Hierarchical Format for Storing and Analyzing Multiple Genome Alignments

Long-term Criminal Fraud at Indian Drug-maker Ranbaxy

Cancer Genomics and Parable of Streetlight Effect

Unknown Mathematician Solves a Major Problem in Number Theory

Citing BioStar and SeqAnswers Papers Does not Make Sense

Lightweight LCP Construction for Next-Generation Sequencing Datasets

Bioinformatics Job at Dupont Pioneer and New Jobs Section

At #baltibio - Torsten Seemann's Bioinformatics Programs and TGAC

SPAdes and MaSuRCA Assemblers Performed Best in GAGE-B Evaluation

Philip Ball on How Scientists Stopped Being Curious

Legs of Snakes and Religion of Biologists

Nanopore Sequencing by Divine Intervention?

Introduction to Chaos and Nonlinear Dynamics for Biologists, Perl Code Included

Severe Biodiversity Loss Expected by Year 2080

How about a Chaotic Genome Assembler?

External Memory Generalized Suffix and LCP Arrays Construction

Ways to Find Homologous Genes

Titus Brown's Commentary on the Cost of Open Science

Should Genome Assembly Improve with More and More Reads?

Google Censorship: Scariest Thing for Academic Freedom

#bog13 Posters on Pine and Coelacanth

A Few Useful Links on Khazar History for Population Biologists

Study on Return of US College Education is Less Alarming than Reality

Carnivorous Bladderwort Plant Genome Shows Some Designers are More Intelligent than Others

Steven Salzberg at #bog13: Assembling 22Gb Conifer Genome

Fastest Way to Reverse Complement a Sequence

Why Do Respected University Professors Teach on Coursera?

What Blogging on Bioinformatics Tells us about the World

Population Genetics Study on Khazar Origin of Jews is Back in Spotlight

What Fraction of Genome is Really Functional? (Our lncRNA story)

NGS Assembly Programs - What Hash Functions Do They Use?

Biology of Genomes Conference 2013

Why Computer Science Professors Dislike Hash Functions

How Sponges will Take over the World

HGAP Assembler Paper for PacBio Reads is [....]

Good Riddance - "Death of the Genome Paper"

The Future of Computers - Multicore and the Memory Wall

What Will Scientific Publishing Be Like Ten Years from Now?

MrBayes tgMC3: A Tight GPU Implementation of MrBayes

Why Are Sequencing Costs Falling in Italy and Europe?

Is 'Systems Biology' a Paradigm Shift?

Philip Ashton: Assessment of Assembly

Why Blogging is Bad For Science

Israeli Paper on Efficient Pre-processing of PE Reads is Now Published

Are Researchers Accumulating Oceans of Data for no Clear Purpose?

Turtle - the Luckiest Animal of the Month

Surprise of the Day - Zebrafish Genome 'Published'

New Grad Student Bloggers, Homolog.us Blog Will Feature Your Posts

Epigenetics in Stem Cells - Is It a Significant Paradigm Shift in Biology?

A Comparison of Two Turtle Papers

Titus Brown's Advice to Young Graduate Students - Blog

High Speed PCIe Communications Package Between Host Computer and FPGA

Hardware-based Hash Functions

TopHat2: Accurate Alignment of Transcriptomes in the Presence of Insertions, Deletions and Gene Fusions

DISCOVAR - Broad Institute will Release a New Assembler

China vs USA and Other Social Posts

Today's Highlights - "Is @DanGraur the Only Real Scientist Left on #DNA60?"

DNA discoverer Crick's Nobel, Letter Fetch Millions at Auction

Coelacanth Genome Meeting - Live Coverage

Today's Highlights - "The Other Side of Academic Freedom"

Today's Highlights - "A Guide for the Lonely Bioinformatician"

Reinhart and Rogoff-Gate Reaction Shows Failure of 'Data Science'

Informed and Automated k-Mer Size Selection for Genome Assembly

Google Hangout Meeting on Coelacanth Genome Paper (and 'Controversy')

BGI’s Youth Culture

Today's Highlights - “I Think I’ve Just Thought Up Something Important”

Still Working on the Second Set of Tutorials

Earth Day Special - Responding to Reader's Comment On Global Warming

Genome of Western Painted Turtle

Genome of a 'Living Fossil'

Fred's Rant on Data Science Degrees

Compressed Gk Arrays for K-mer Counting

Scientists Show that Global Warming is Destroying Antarctica

VAT Tax on Sequencing - Biomickwatson Connects Only Half of the Dots

The Eroding Premium on Truth and Trust

Optimal DNA Shotgun Sequencing: Noisy Reads are as Good as Noiseless Reads

Genome Size Estimation and Polymorphism from K-mer Distribution

Final Words on De Novo Assembly of Complex Genomes

Wiki and Tutorial Sections

Do Good Scientists Need to be Expert Mathematicians?

New York Times Propaganda Article Discredits Open Access

Homolog.us Blog Calls for Sean Eddy be Fired for the Sake of Good Science

Step by Step Guide on Genome Assembly with blasr and python

In Large-scale Biology, Who Has Ownership of the Data?

Genome Assembly from Random Sequence

Biological Publishing Landscape Changes with Arrival of PeerJ

Pulling HeLa from Public Domain Sets a Bad Scientific Precedent

Joe Pickrell 'Publishes' Henrietta Lacks’s Genome from Public Data

Rarefaction Curve - Question for Readers

Physics of Dominoes

Overlap-Layout-Consensus versus de Bruijn Graph Assemblers

Next Set of Tutorials - Hardware and Software Concepts

Bootstrapped Genome Project (iv) - More on Triplicate Experiments

The Mother of All Demos

Restored Comments

De Bruijn Graph Tutorials are Here

Is Biostar Really Dying?

Mystery Uptick Added to Paper Published in Science

Dan Graur's Granddaughter Expressed Her Opinion on ENCODE Paper

Beyond the PDF2 - Slides from Scott Edmunds BGI @GigaScience

A comparison of Methods for Differential Expression Analysis of RNA-seq Data

Commercial Value of Efficient Metagenomics Pipeline

Skip Lists and Other Efficient Data Structures

Protests about HeLa Sequencing, Research Crowdsourcing and Other News of the Day

A Day to Remember

Methods to study Event/Isoform Expression and Alternative Splicing from RNA-Seq

Bootstrapped Genome Project (iii) – on Mindless Triplicate Experiments

Vista Genome Browser from Inna Dubchak's Group

First Issue of Nature

Mutation Identification By Comparing Whole Genome NGS Data Using k-mers

Ivar Giaever on Religion of Global Warming

Bootstrapped Genome Project (ii) - Planning Stage

Sequester Genome Browser Project - An Update

Personalized Medicine and BRCA Case Study

Is New Life Form Found Under Antarctic Ice?

Dark Side of Arxiv.org?

Lamprey Genome Paper is not Lucky Either

Did Josephson Lose His Mind or Was He Ahead of His Time?

Ancient Genome Duplication

Tutorial Section Coming

Sequester Special - A Bootstrapped Genome Project (i)

International Appeal for the Protection of Academic Independence

Sequester Special - Announcing a New Genome Browser Project

Do You Feel Lucky Any More?

Please Save the Unsolicited R01s - Salzberg

Theodosius Dobzhansky

Sixth Sense in Vertebrates

Contrast Our Top Bioinformatics Contributions of 2012 with 'Breakthrough Prize'

QUAST: Quality Assessment Tool for Genome Assemblies

Lamprey Genome Shows When Humans Evolved Jaws, Matching Arms, Legs and More (?)

Junk DNA and Creationist Lies

Humanizing Einstein

Four Rules of Thumb, if You Have More Data than You Can Handle

Conference Budget - the Next Big Cut

Why Waste 3 Billion Dollars on Human Brain Activity Map Alchemy Project?

Role of 'Professionalism' in Science

NabSys Unveiled (Omics! Omics! Blog)

Is the Era of Short Reads and de Bruijn Assembly Over?

Are 'They' Scientists or Bad Technicians?

Titus Brown's Thoughts on the Assemblathon 2 paper

Slides from AGBT Conference

Biomickwatson's Ridiculous Criticism of ENCODE Critics

Ads in Disqus Commenting System

Was ENCODE's Claim of 80% of Human Genome Being Functional all Hype?

Construction of Suffix Array in External Memory - Follow Up

The Mapping God Speaketh

Rosalind Will Get Even More Marvelous

How We Successfully Fought Wordpress Spam Comments :)

Global Warming and Other Superstitions

Genome Reassembly with High-throughput Sequencing Data

Internet Posting Removal Act

Possibly the Best Book on Personal Genomics and Personalized Medicine

Happy New Year

A day to Think, to Pause, to Ponder - Jonathan Eisen

SCARPA: Scaffolding Algorithm from Hapsembler Group

"Researchers Opt to Limit Uses of Open-access Publications"

Hapsembler - An Assembler for Highly Polymorphic Genomes

BGI - It is the Wild West of Genomics

To Do (PhD in Bioinformatics) or Not To Do? That is the Question

Shaking Up Science?

Gut Metagenome in Children during Cholera and Recovery

DSK: K-mer Counting with Very Low Memory Usage

SOAPdenovo2 Demystified - A Rough Guideline of Functionality

PacBioToCA for Error-correcting Pacbio Reads

LSC, an Alternative to PacBioToCA for Error-correction of PacBio Reads

Vaccination, Antibiotics and Genomic Medicine

More SOAPdenovo2 Commentaries Will Come in February

Mathematical Notes on SAMtools Algorithms

RECOMB'seq 2013 Accepted Papers

On Constructing Suffix Arrays and LCP Arrays in External Memory

Most Cited Bioinformatics Articles (Why none before 2011)?

Index to Entire Set of Fred's 'Rants'

Huge Rise in Bioinformatics Jobs, Who is Losing?

SOAPdenovo2 Demystified – part (b) [multi-thread implementations]

'A Farewell to Bioinformatics'

Assembling Large, Complex Environmental Metagenomes

Are We Incentivizing Hype in Science? A Case Study

Working to Increase Diversity of PLOS Biology Academic Editors and Advisory Board Members?

Why Do We Blog? (2013 Version)

Notes on Assemblathon Paper

CEGMA - a pipeline to accurately annotate core genes in eukaryotic genomes

Assemblathon 2 Paper is Available at Arxiv !!

New Study Sheds Light on the Origin of the European Jewish Population

A survey of tools for variant analysis of next-generation genome sequencing data

Lightweight BWT Construction for Very Large String Collections

Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets

Good Sources for gcc Inline Assembly Language Coding and Multi-threading

Isolation and Characterization of RNA-Containing Exosomes

Personal Genomics - the Ultimate Privacy Killer?

Leveraged Buyouts are Back !!

A Quick Update on What We are up to

piRNA Databases

lncRNA Databases

Our Non-bioinformatics Commentaries are Going Away

Homolog.us Welcomes #PAGXXI Attendees With a Blog Guide

Expect Some Really Amazing Metagenome Data from Russia

Working Through the Code of Cortex Variant Assembler

Openness and Online Reputation Recognized in Grant Reviews!

High-throughput Microbial Population Genomics using the Cortex Variation Assembler

Three Helpful Guides for Those Working on Genome Assembly

Top Bioinformatics Contributions of 2012

Structure-based whole genome realignment reveals many novel non-coding RNAs

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study

A Quantitative Comparison of DNA Sequence Assembly Programs

Open Peer-review Model for Publishing Scientific Results

mMass - Open Source Tool for Analyzing Mass Spec Data

Burrow Wheeler Transform - Matlab Code, Animation

antiSMASH: Rapid Identification, Annotation and Analysis of Secondary Metabolite Biosynthesis Gene Clusters

Transcriptomic Research around the Globe

SOAPdenovo2 Demystified - part (a)

SOAPdenovo2 Demystified - part 1

Optimal Assembly for High Throughput Shotgun Sequencing

X-Rank Algorithm for Analyzing LC-MS/MS Peaks

Genomes Published in 2012

January is Our 'Learn How SOAPdenovo2 Works' Month

Happy New Year 2013 !!

'Top Five Bioinformatics Innovations of 2012' Contest

Our First Look at SOAPdenovo2 Source Code

Should SOAPdenovo2 Source Code be Made Public?

Ray Meta: Scalable de Novo Metagenome Assembly and Profiling

More Details on Velvet Roadmaps File Based on Reader's Question

FASTG - A New Format for Representing Sequences

Merry Christmas - Homolog.us Readers

Google Trends - Bioinformatics

How to Deal with Massive Sequence Libraries (Slides: CTB)

Twelve Developments on 12/12/12

The World of Mapping Programs

Recipes for Assembling Genomes from GAGE

Exploring Single-sample SNP and indel Calling with Whole-Genome Assembly

Challenges in Assembling Fish Genomes

Various Developments in Bioinformatics (12/5/2012)

Ray Cloud Browser for Viewing de Bruijn Graphs

Illumina Creates Phony Concerns to Derail BGI Acquisition of US Company

When to Leave the 'Academia' (University Cartel)?

Do Illumina and Pacific Bio Fit Together?

Ranking of Bioinformatics Journals, Who is at #6?

Various Developments - 11/30/2012

Various Developments - 11/28/2012

If You Want to Take Your Bioinformatics Analysis to the Cloud

CHREC Slides from Supercomputing Conference

Various Developments - 11/26/2012

A Question on de Bruijn Graphs of Transcriptomes (RNA-seq)

Linear Probing and Power of Two Choices

Happy Thanksgiving !!

Various Developments in the Bioinformatics World

Two Thoughtful Comments

Sanger Dropping Broad's GATK after License Change

Notes from Supercomputing Conference (SC12)

Genome Research Journal Changes its Preprint Policy

Bringing New Computing Hardware Architecture to 'Life'

CHANCE - A Comprehensive and Easy-to-use Software for ChIP-seq QC

Bioinformatics Gangnam Style

Congratulations to Rayan Chikhi for Finishing Rosalind near Top

Ph. D. Thesis: Computational Metagenomics: Network, Classification and Assembly

HGAp - Very Accurate de novo Genome Assembly from PacBio Data

A Simulator for Pacbio Reads

Food for Thought - Really

Very Funny - Hitler on IonTorrent Proton

Thought-provoking Article on Systems Biology from Sydney Brenner

The Beachcomber's Dilemma and Diginorm Manual

STAR: Really Kick-ass RNA-seq Aligner

On Teaching/Learning Bioinformatics Online - Socraticqs, Rosalind

Next Generation Shotgun Sequencing and the Challenges of de novo Genome Assembly

Humor at Professor Brown's Expense :)

Scafetta’s Solar-lunar Cycle Forecast -vs- Global Temperature

What They Never Teach You in Programming Classes

SNP Map of Human Population of 'Entire World' Published

Best Algorithm for Bit Reversal

Patterns of Three

Do We Need to Reinterpret all Published Gene Expression Studies?

More on GPL Licensing of Bioinformatics Programs

Many RNA-seq Presentations/Posters at ASHG Conference, San Francisco

Rectangular Graph Algorithm

PACB: This Does not Look Right

Taking the 'Eulearian Path'

Simple Examples to Learn Bioinformatics Programming

Notes on Jay Shendure's Seattle Meetup Presentation

The Chinese Mailman, Who Does not Like to Walk

Quip paper, CRAM paper and CRAM Tools

Several Good Posts on Compressing NGS Libraries

IPython Notebook and de Bruijn Graph

Thoughts on Blogging and Haldane’s Sieve(s) – part II

Thoughts on Blogging and Haldane's Sieve(s) - part I

Software Licenses in Bioinformatics Programs and Their Legal Implications

Going Through the SPAdes Code (Rectangular Graph)

Cuckoo Hashing vs Bloom Filter

SiBELia/SyntenyFinder - A de Bruijn Graph-based Tool for Finding Syntenies

SEQuel - A Software Tool for Improving Assembled Genome

de Bruijn Graphs Simplified

Jay Shendure's Presentation at Seattle Sequencing Meetup

De Bruijn Graph of a Palindromic Sequence

Question from a Reader on Studying Bioinformatics

Why Core Facility Model Adopted by US Universities is a Bad Model

From Multiple Kmers to Multi-kmer de Bruijn Graph

Cars are Powerful, but Driving is Hard to Learn; Ride A Mule to Work Today

Why Efficiency Matters in Big Data Biology

Are Ultra-low RAM Assemblers Useful for those with Kick-ass Servers?

Succinct de Bruijn Graphs from Tetsuo Shibuya's Group

What are the Puzzle Pieces in a Rectangle Graph?

De novo Genome Assembly: What Every Biologist Should Know

Ultrafast Clustering Algorithms for Metagenomic Sequence Analysis

Software Carpentry - Very Good Place to Learn Scientific Programming

Tweet or Perish?

Our Response to "Best Practices for Scientific Computing" Paper

If You Need Break From Science, Here is US Presidential Debate - Homolog.us Edition :)

Book Chapter - Genome Reconstruction: A Puzzle with a Billion Pieces

Trinity Run Completed. Is This Typical?

Perfect Hash Algorithm of Meraculous Assembler

Big Collection of (bio)Informative Slides from C. Titus Brown

Minia Assembler and French Revolution

Heads Up for Readers - SPAdes vs Ray Benchmarking is Done

Bye bye Python; Enter Haskell

An Experience with New Trinity

#ngsban - How to Implement

Energy - the Hidden Cost of NGS Analysis

COPE (for Joining PE Reads) and Arapan-S (for Small Genomes)

Weekend Humor

BGI Model

Excellent Slides from Fisherman Lex on Combining PacBio and Short Reads

A Comment from Developer of Ray Assembler

Pacific Oyster Genome Published

Kind of Comments We Receive Every Day

Basic Local Alignment with Successive Refinement (BLASR) for PacBio

Rosalind Project at Algorithmic Biology Laboratory, St. Petersburg

Informative Slides on the Scale of Data Problem in New Biology

What is Life?

Obituary of Nimblegen

Starting to Understand the SPAdes Papers

A Real-life Example of Our Forecast for 21st Century

Creating Confusion

In Turf Battle for Computational Biology, CTB Fires a Shot

SOAPdenovo2 Binary is on SourceForge

What Does BTW Stand for?

How World Solved its First BigData Problem

From de Bruijn Graphs to Rectangle Graphs for Genome Assembly

Telescoper: de novo Assembly of Highly Repetitive Regions

Streaming Lossy Compression of Biological Sequence Data using Probabilistic Data Structures

How Will arxiv.org Work for a Large Consortium Project?

ENCODE paper and Ewan Birney's Interview

CB on ENCODE Embargo

We See the Light - Source Code Should be Published

Thoughts on 'Anecdotal Science' by CTB

On 'Research Code' by Deepak Singh

Korean Theft of Creative Ideas from World's Greatest Thinker(s)

How Do Haplotype Differences Appear to de Bruijn Assemblers ?

Presenting an Interesting Exchange. Any Thoughts?

HapCompass: An Elegant Use of Graphs for Haplotype Assembly/Phasing

Probabilistic Data Structures - an Excellent Introduction

Parallel de novo Assembly of Large Genomes from High-Throughput Short Reads

Sequencing War and NextEra Kit

A Great Review of Various Sequencing Instruments/Technologies

Compression of Next-generation Sequencing Reads Aided by Highly Efficient de novo Assembly

Bioinformatics and Computational Biology - same? Si, Si, Si.

Few Simple Trinity Tips

Cargo Cult Science

Study Shows Men are Better than Women in Bioinformatics (p<0.05)

Rage Against the Impact Factor

Where are Innovative NGS Algorithms Coming from?

Nextgen Humor

Genome Assembly - MERmaid and Meraculous

Severe Abnormalities Found in Fukushima Butterflies

Blog 'Kevin's GATTACC World' Brings Humor into Bioinformatics

Olympic Training Camps are no Fun

Top N Reasons NOT to do a Ph.D. in Bioinformatics/Computational Biology

Homolog.us Continues Its Interview of ex-Olympian

Browsers for Viewing NGS Data

Thesis Slides from Rayan Chikhi

Solving the Other PacBio Puzzle (non-bioinformatics)

Building an NGS Reference List (SNP/variant calling category)

Homolog.us Blog Covers Olympiad

Algorithmic Differences between Oases and Trinity

Bad News: Cheap Cure for Type 1 Diabetes Found

Oases Transcriptome Assembler

Building an NGS Reference List (de novo assembly category)

Question for Readers - Do You like Homolog.us Blog to Cover the Olympics?

Nature Journal Recognizes arXiv.org (or its own Wile E. Coyote Moment)

Mixing Illumina and PacBio Data for Genome Finishing

A Math Puzzle

Traits of a Good Scientist

An Elegant Use of NG Sequencing - Finding T-cell Diversity

When is your birthday? (on hashing, sparsehash and murmurhash)

Using SOAPdenovo2 with SOLiD Sequences

NASA Changes Biology Textbooks - Again

An Efficient Preprocessing Module for Joining Paired end Reads before Assembly

On Global Warming

A Review of Bioinformatics Blogs

Quip, Minia, SlimGene and Titus Brown's paper on Scaling Metagenome

How do JGI Data Release Policy and Bleeding Edge Bioinformatics Fit Together?

Analysis of NGS miRNA Data – a Paired-ended Library

Standard Steps for RNAseq Experiment

Sequencing miRNAs with NGS Technology

Analysis of NGS miRNA Library - an Example

Improved the Search Routine in Our Website

All About miRNAs

Question for the Readers - What is the Convention for Submission of Raw Reads these Days?

More on the World of Biological Databases

Two RNAseq Papers - Worm and Sea urchin

HaploMerger: A Software Tool for Assembling Highly Polymorphic Genomes

Testing SOAPdenovo2 Prerelease – V (map and scaff)

Physicists are Looking for Large Hadron Collider's Replacement

More is Different !!

HDF5 Data Format for PacBio Sequences

Testing SOAPdenovo2 Prerelease - IV (building contigs)

Testing SOAPdenovo2 Prelease Version - III

Testing SOAPdenovo2 Pre-release Version - II (pregraph_sparse)

Quarterly Growth of Array Express

The World of Biological Databases

On Discovery of 'God Particle'

How to Download Abstracts of All Biology-related Papers for Text-mining

Few Quick Comments Regarding the Website

Animals Do not Eat their Own Offsprings

Back on Track, Malware Cleaned

Testing SOAPdenovo2 Pre-release Version

What is Wrong with N50? How can we make it better?

What is Wrong with N50? How can we make it better? - part II

SOAPdenovo2 and Other News from BGI

An Update on Using Pacific Bio Sequences for Genome Assembly

What is Causing European Banking Crisis?

Gossamer - 'Succinct' data structure for efficient storage of de Bruijn graphs

In our Trends Section

In our Trends Section - II

An Intuitive Explanation for Running Velvet with Varying K-mer Sizes

What is in the News?

Digital and Analog Transcriptomics

Which Next-gen Technologies are Popular?

NOSQL Databases for Bioinformatics

Humor - Announcement of a New Sequencing Technology

Excellent Introductory Tutorials for Velvet, ABySS, Bowtie, BWA and Newbler

An Explanation of Velvet Parameter exp_cov

Animations for Sequencing Technologies from the Web

The Genome Assembly Process and How Pac Bio can Help

Pacific Bio Sequences

The Best Way to Understand Algorithms

FPGA-based Hardware Accelerators for NGS Analysis

Full Cycle of Science in Protestant World

Is 1000 Genome Project an Example of Modern Day Alchemy?

Burrows Wheeler Transform in Animation

Digital Normalization from C. Titus Brown

Using Bloom Filter - A Simple Introduction for Bioinformaticians

Can Trinity be Used for Genome Assembly?

Part 3 - GC Distribution of Genomes (Casual)

Efficient Methods for Counting K-mers

Part 2 - When a City is Carpet bombed, Only the Strongest Structures Survive

Oddball - Part 1: General Format of Our Presentation

I Want to Try a Publishing Experiment

Explosion of Transcriptome Data on Drosophila

Under the Surface

Does Citation-index Count in the Era of Google?

March 2012 Update on GEO Trends (Countries)

SRA Trends - March 9, 2012

Untangling Genomes from Metagenomes (Attn. SOLiD users)

Hadoop at JGI (NERSC)?

Bowtie Alignment with and without Quality Score

A Strategy for Running Trinity on Very Large NGS Library or Reducing Number of Genes

For Those Running Core Facilities (part 2)

For those Running Core Facilities

Illumina Paired End Libraries - Inward and Outwardly Directed Reads

Paircomp on Steroid (using Bowtie)

String Graph of a Genome

String Graph Assembler

Happy New Year

Paircomp - Comparing Two Genomes to Find Conserved cis-regulatory Segments

Custom Array Experiment - Complete Pipeline

Velvet Optimizer and MetaVelvet

Format of Velvet Output File 'Roadmaps'

....and Econ Lesson of the Day

Suffix Arrays

R / Bioconductor (limma)

If You are New Here

Do not Go for a Swim after Having an Ice Cream

The Report of our Death was an Exaggeration

Sharing a K-mer Story

K-mer Distribution of a Transcriptome

Few Small Updates with the Website

Two Simple Rules

HOTAIR - a cancer lincRNA

Data Compression Algorithms

Burrows Wheeler transform, Suffix Arrays and FM Index

Finding us in homolog.us III (Search Algorithm and Indexing)

Finding us in homolog.us - part II

Output of Oases Transcriptome Assembler

Explaining Output of Trinity Component - Inchworm

Finding us in homolog.us

Partitioning Libraries to Fit Small RAM Size

Updating a de Bruijn Assembler Code for Color Space Data in Six Easy Steps

K-mer Sizes for Genome Assembly

Watching a de Bruijn Assembler in Action (Contrail)

Maximizing Utility of Available RAMs in K-mer World

Wordpress Comment Section is Open

Must-have Tools for a Bioinformatician

Trinity and Contrail for Color Space

Do de Bruijn Assemblers Work in Color Space?

Contrail - A de Bruijn Genome Assembler that uses Hadoop

Hadoop Example - FAQ

Away from this World

Using Hadoop for Transcriptomics - An Example to Get Started

GEO and SRA - Quarterly Growth in Transcriptomic Research

De Novo Transcriptome Assemblers – Oases, Trinity, etc. – IV

Where are the global hotbeds of transcriptomic research?

De Novo Transcriptome Assemblers – Oases, Trinity, etc. – III

De Novo Transcriptome Assemblers – Oases, Trinity, etc. - II

Transcriptomic Research around the Globe

We are on Twitter

Using Mate Pair Information in de Bruijn Graphs

A Bird's Eye View of NCBI GEO Database - II

De Novo Transcriptome Assemblers - Oases, Trinity, etc.

A Drawback of de Bruijn Graph Approach

Why no comments section?

Large Computer, Distributed Cluster or Amazon Cloud?

De Bruijn Graphs for Alternative Splicing and Repetitive Regions

Using Hadoop for Transcriptomics

A Road Map for our Journey through the Transcriptomic Maze

Comparison of data analysis packages

Using R for Transcriptome Analysis - I

A Bird's Eye View of NCBI GEO Database

How do sequencing errors affect de Bruijn graphs?

De Bruijn Graphs - III

Highlights - 7/30/2011

De Bruijn graphs - II

De Bruijn graphs - I

Highlights - 7/25/2011

Algorithms for Next-gen Sequence Analysis

A beginner's guide to bioinformatics - part II

A beginner's guide to bioinformatics - part I

The Mathematics of Color Space Sequencing



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