Article Archive

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A Terrific Post-doc Opportunity to Learn Bioinformatics

Mantis and the Counting Quotient Filter

Bioinformatics Contest - 2018

DIY Ancestry Analysis using the GPS Algorithm

Minimizer - An Introductory Tutorial

Compact Universal Set of Minimizers

Another Tutorial - This Time on Pevzner's Videos

A Tutorial with Ben Langmead's Bioinformatics Videos

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

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

KMC tools tutorial - II

A tutorial on KMC tools

Monday review - KMC3 and other seXY topics

Online Bioinformatics Contest from Stepik/Rosalind

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

Designing Molecular LEGOs in Lisp Language

Qudaich - a Smart Sequence Aligner

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

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

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

COCACOLA and BIGMAC Followed by AVOCADO !

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

Efficient Index Maintenance Under Dynamic Genome Modification

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

Is Seven Bridges Genomics Patenting All Existing Bioinformatics?

Notes from Technology Day of #AGBT16

RECKONER: Read Error Corrector Based on KMC

Combinatorial Scoring of Phylogenetic Networks

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

I have a (bioinformatics) dream

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

Integration of String and de Bruijn Graphs for Genome Assembly

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

Job Opening - Computational Biologist/Bioinformatics Scientist

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

Fast genome and metagenome distance estimation using MinHash

Latency Numbers Every Programmer Should Know

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

Centrifuge - A Low RAM Metagenomic Classifier from Salzberg Group

Sequenceserver: a modern graphical user interface for custom BLAST databases

Kaiju: Fast and sensitive taxonomic classification for metagenomics

Tardigrade Mystery Solved?

Existing Bioinformatics Workflows

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

Rushed Review by Nature Biotechnology on a Cancer Bioinformatics Paper?

The State of Software in Evolutionary Biology

BMC (Springer) Sends Shockwave through Bioinformatics Community

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

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

De bruijn Graph for Married Couples

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

A Practical Guide to de Novo Genome Assembly using Long Reads

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

Minimap - A Minimizer-based Mapping Program

"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

Why Do Scripting Languages Die?

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

My Thoughts on Dying

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

Reducing Assembly Complexity of Microbial Genomes with Single-molecule Sequencing

New Publishing Model in Mathematics

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

Origin of Eukaryotes and 'Mitonuclear Ecology'

Scripting for Biology - Online Virtual Classroom-based Module

Predictions about the Next 100 Years

Beautiful Japan

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

Honest Valuation and Ponzi Valuation

Deformed Daisies Near Fukushima - Radiation or Fasciation?

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

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

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

Metagenome Sequencing Finds Strange Biology in >15% Bacteria

A Neat Paper on FM-index

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

The Original Purpose of Peer Review

Michael Huss Provides Introduction to Three Commercial Genomic APIs

The Most Difficult Problem in Computational Biology

A Glimpse into the Techno-gaga World

Suffix Array in External Memory - Latest from Felipe Louza

Bioinformatics and Docker

Bioinformaticians, Can You Pass That Exam?

Improved genome inference in the MHC using a population reference graph

Bioinformatics at the Core Facilities

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

Free draft ebook - Pandora's Toolbox for Bioinformatics

GATK Battle and BALSA versus GATK Comparison

Compressed String Dictionary Search with Edit Distance One

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

Immunoglobulin Classification Using the Colored Antibody Graph

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

FASTAG Viewer Bandage

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

Pevzner and Compeau Are Splitting Their Bioinformatics Course into Three

Everything You Need to Know to Follow #AGBT15

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

Occasionality or Probability - What is the Right Term?

Indexing Arbitrary-length K-mers in Sequencing Reads

A Computational Method for the Rate Estimation of Evolutionary Transpositions

A Computational Method for the Rate Estimation of Evolutionary Transpositions

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

Heng Li's Mysterious New Program

An Update on Pandora's Toolbox

Fully Funded Bioinformatics PhD Position with a Very Smart Guy

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

Quality scores for 32,000 microbial genomes, no eukaryotes

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

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

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

Evolution of Genome Size - Scientific and Religious Analysis

'Best of 2014' - My Personal Opinion

Excellent Software Engineering in KMC

The Tragic Demise of BLAST

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

Challenging Times Ahead for PLOS?

Downloading Basespace Files using Command Line

Sdsl-lite and Cosmo - Useful Github Repositories

'Compare and swap' vs Software Transactional Memory

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

Human Genetics and Clinical Aspects of Neurodevelopmental Disorders

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

Reference-free detection of isolated SNPs

Reddit AMA by Weiss and Buchanan - Please Spread the News

An Evolutionary Perspective on the Kinome of Malaria Parasites

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

Review paper - Data compression for sequencing data

#Biodata14 Conference - Twitter Summary and Links

A Number of Genetic Tools Developed to Study Choanoflagellates

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

Imaging - The New Frontier?

Study Bioinformatics Algorithms from Youtube Videos

Steven McKnight Identifies the Riff-raffs

Vaccinating with the genome: a Sisyphean task?

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

Cuckoo Filter to Replace Bloom Filter?

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

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

Latest from Steven McKnight on Harvard/Broadster Citation Culture

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

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

Antarctic Sea Ice Reaches Highest Levels Since Record Began

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

WABIstan Report

Merging of Multi-String BWTs with Applications

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'

Who Has Legal Control Over Your 'Big' Data?

Shadow Enhancers Enable Hunchback Bifunctionality in the Drosophila Embryo

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

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

Stunning Siphonophore

On the Mythology of Natural Selection

How Does the Unix Diff Algorithm Work?

Using Mathematical Induction to Design Algorithms

Minimizer Revolution Continues with KMC-2 K-mer Counter

After SAM and BAM Comes ADAM !

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

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

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

Latest from Tony-Cox - BEETL-fastq

Error Correction and Assembly Complexity of Single Molecule Sequencing Reads

University of California is Being Sold to Businesses

The Cellular Automaton Interpretation of Quantum Mechanics

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

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)

Computer Science Bubble and STEM Shortage Myth

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

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

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

Links to a Bunch of Useless Papers

Plactic Monoid, Schubert Polynomial and Combinatorics of Words

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

General Description and First Puzzle Emailed to All Who Asked

Dangerous Central Planners Coming to 'Rescue' US Biomedical Research

We Have Six Interesting Bioinformatics Puzzles, Any Takers?

scTurtle Algorithm for Kmer Counting

Kmer Counting - a 2014 Recap

2014 - The Year of Minimizers in Bioinformatics

Mutation and Cancer - A View from Retirement

Feynman: Mathematicians versus Physicists

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?

On FPGA Acceleration of Bioinformatics Programs - Latency

Seeking Readers' Feedback on Subscription and Redesign

On FPGA Acceleration of Bioinformatics Programs

NWDB Conference - Slides from Eric Haag and Update

BWA-MEM Gets Very Slow in Highly Repetitive Regions

Sea Anemone is Genetically Half Animal, Half Plant

Trichoplax adhaerens at the Root of Multicellular Animal Tree

A Good Paper on Hox-TALE Puzzle

Reporting on the Northwest Developmental Biology Conference - (2)

Animal Ancestors - Sponges or Comb Jellies?

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

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

Seattle Sequencing Meetup with Bina Technologies

Kraken - Very Good Application of Jellyfish and Minimizer

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"

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

RECOMB 2014 Talks

AGBT Slides from W. McCombie and V. Schneider

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

GPU-Accelerated BWT Construction for Large Collection of Short Reads

Dancing Links Algorithm and Less Known Data Structures

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

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)

Announcing the Results of 'Best of 2013'

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

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

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

A Free Market Approach to Improving Human Health

Life of Soay Sheep and Relevance to Human Society

Compressed Spaced Suffix Arrays

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

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

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

Big Data - Where Increasing Sample Size Adds More Errors

Top Bioinformatics Contributions of 2013

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

Science Reporting: a New Trend Emerges

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

New Kind of Science

Coming Soon - Genomics of Unicorns

A Bioinformatician is a Technician, no More

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

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

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

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

List of Many Bioinformaticians with Twitter Account

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

A Cuban Blog on Bioinformatics and Proteomics

Khash by Attractive Chaos

Heng Li Releases Ropebwt2

New Announcements from Ion Torrent and Oxford Nanopore

Pevzner's Bioinformatics Course at Coursera Delayed by Two Weeks

Are Graph Databases Ready for Bioinformatics?

What Kind of Jobs Are 'Reserved' for Bioinformaticians?

Book 'Probably Approximately Correct' Follows ENCODE-style Marketing

New Announcement from the Rosalind Team

Survival Tips During Federal Government Shutdown

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

The Jewish Genome Challenge

No WWIII !! We are Back

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

Good, Bad and Ugly

Efficient Online k-mer Counting using a Probabilistic Data Structure

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

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

New Species of "Walking" Shark Found in Indonesia

Teaching Bioinformatics on Raspberry Pi

Real and Unreal Disasters

Julian Assange Presents on Metagenome Assembly

Going Through the Lyndom Word Paper

Big Brother App from Apple and Others Data Privacy Concerns

"Why We Didn't Use a Bloom Filter"

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

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

How Novel Ideas Trickle Down from Computer Science to Biology

A Few Quotes from Benjamin Franklin

Performing Burrows Wheeler Transform on Trees

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

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

Scott Edmunds Covers ISMB

Schrodinger's Lost Notebook from 1925

Getting PhD for Master's Thesis

Weekend Videos - Enjoy !

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

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

Mapping Algorithms - How They all Arrived

HMMER and Viterbi Algorithm

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

Scholarly Publication - Using Arxiv to Maximize Substance

Strategies for Perfect Hash and Minimal Perfect Hash

Exploring Genome Characteristics and Sequence Quality Without a Reference

AMBA and Wishbone Protocols

Short Read Alignment with Populations of Genomes

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?

Overconfidence Leads to Success

Genomic evidence for ameiotic evolution Adineta vaga

CUBELP: Cranfield University Bioinformatics Learning Platform

Rayan Chikhi's KmerGenie Slides from HitSeq 2013

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

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

Bias in Animal Studies and Nature versus PLOS Tit for Tat

Random DNA Sequence Mimics #ENCODE !!

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

Parallelization Horror Story: How Not to Run String Graph Assembler

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

#Usegalaxy Lights up Northern Skies

On MaSuRCA Paper and Algorithm

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

Minimal Genome

For Bioinformatics Humor, Follow Twitter Hashtag #altbioinf

Six Tutorials in Various Stages of Completeness

Digging into BWA-mem Code

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

Alignment Papers We are Trying to Make Sense of

Many Good Slides at MSU NGS Analysis Workshop

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

Entropy of Never Born Protein Sequences

Another Bioinformatics Job Posted

Biostar, Biological Communities and Biological Databases

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

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

Characterizing and Measuring Bias in Sequence Data

Mapping God Found 'Scientifically Dishonest' by Anonymous Peer Reviewers

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

Various NGS Platforms in Animation

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

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

External Memory Generalized Suffix and LCP Arrays Construction

Ways to Find Homologous Genes

Steven Salzberg at #bog13: Assembling 22Gb Conifer Genome

Fastest Way to Reverse Complement a Sequence

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

Why Computer Science Professors Dislike Hash Functions

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

MrBayes tgMC3: A Tight GPU Implementation of MrBayes

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

Are Researchers Accumulating Oceans of Data for no Clear Purpose?

A Comparison of Two Turtle Papers

Hardware-based Hash Functions

DISCOVAR - Broad Institute will Release a New Assembler

Coelacanth Genome Meeting - Live Coverage

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

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

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

Still Working on the Second Set of Tutorials

Compressed Gk Arrays for K-mer Counting

Do Good Scientists Need to be Expert Mathematicians?

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

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

Rarefaction Curve - Question for Readers

Next Set of Tutorials - Hardware and Software Concepts

The Mother of All Demos

Is Biostar Really Dying?

Mystery Uptick Added to Paper Published in Science

Beyond the PDF2 - Slides from Scott Edmunds BGI @GigaScience

Commercial Value of Efficient Metagenomics Pipeline

Skip Lists and Other Efficient Data Structures

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

Bootstrapped Genome Project (ii) - Planning Stage

Sequester Genome Browser Project - An Update

Ancient Genome Duplication

Tutorial Section Coming

Sequester Special - A Bootstrapped Genome Project (i)

Sequester Special - Announcing a New Genome Browser Project

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

QUAST: Quality Assessment Tool for Genome Assemblies

Junk DNA and Creationist Lies

Humanizing Einstein

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

Role of 'Professionalism' in Science

Construction of Suffix Array in External Memory - Follow Up

The Mapping God Speaketh

Rosalind Will Get Even More Marvelous

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

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)?

Huge Rise in Bioinformatics Jobs, Who is Losing?

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

piRNA Databases

lncRNA Databases

Homolog.us Welcomes #PAGXXI Attendees With a Blog Guide

Top Bioinformatics Contributions of 2012

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

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

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

'Top Five Bioinformatics Innovations of 2012' Contest

FASTG - A New Format for Representing Sequences

Google Trends - Bioinformatics

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

Twelve Developments on 12/12/12

The World of Mapping Programs

Various Developments in Bioinformatics (12/5/2012)

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

Linear Probing and Power of Two Choices

Various Developments in the Bioinformatics World

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

Congratulations to Rayan Chikhi for Finishing Rosalind near Top

The Beachcomber's Dilemma and Diginorm Manual

On Teaching/Learning Bioinformatics Online - Socraticqs, Rosalind

What They Never Teach You in Programming Classes

Best Algorithm for Bit Reversal

Patterns of Three

More on GPL Licensing of Bioinformatics Programs

Simple Examples to Learn Bioinformatics Programming

Notes on Jay Shendure's Seattle Meetup Presentation

Quip paper, CRAM paper and CRAM Tools

Several Good Posts on Compressing NGS Libraries

Software Licenses in Bioinformatics Programs and Their Legal Implications

Cuckoo Hashing vs Bloom Filter

Question from a Reader on Studying Bioinformatics

Why Efficiency Matters in Big Data Biology

Ultrafast Clustering Algorithms for Metagenomic Sequence Analysis

Software Carpentry - Very Good Place to Learn Scientific Programming

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

Bye bye Python; Enter Haskell

Rosalind Project at Algorithmic Biology Laboratory, St. Petersburg

Informative Slides on the Scale of Data Problem in New Biology

Streaming Lossy Compression of Biological Sequence Data using Probabilistic Data Structures

Presenting an Interesting Exchange. Any Thoughts?

Probabilistic Data Structures - an Excellent Introduction

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

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

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

Where are Innovative NGS Algorithms Coming from?

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

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

Browsers for Viewing NGS Data

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

A Review of Bioinformatics Blogs

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

The World of Biological Databases

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

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

What is in the News?

The Best Way to Understand Algorithms

Burrows Wheeler Transform in Animation

Digital Normalization from C. Titus Brown

Using Bloom Filter - A Simple Introduction for Bioinformaticians

Efficient Methods for Counting K-mers

Bowtie Alignment with and without Quality Score

For Those Running Core Facilities (part 2)

For those Running Core Facilities

Paircomp on Steroid (using Bowtie)

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

Suffix Arrays

R / Bioconductor (limma)

Do not Go for a Swim after Having an Ice Cream

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

Finding us in homolog.us

Must-have Tools for a Bioinformatician

Comparison of data analysis packages

Highlights - 7/30/2011

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

Web Statistics