News


2017


» Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma
May 8, 2017
» GenomeScope: Fast reference-free genome profiling from short reads
April 4, 2017
» Nanopore sequencing meets epigenetics
March 31, 2017
» Proceedings of the IEEE: Bioinformatics of DNA
March 1, 2017
» Preprint on 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
Feb 24, 2017
» Personalized Phased Diploid Genomes of the EN-Tex Samples @ AGBT
Feb 15, 2017
» LRSim: a Linked Reads Simulator generating insights for better genome partitioning
Jan 26, 2017
» TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells
Jan 16, 2017
» NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads
Jan 2, 2017

2016


» Indel variant analysis of short-read sequencing data with Scalpel
Dec 8, 2016
» The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation
Nov 7, 2016
» Phased diploid genome assembly with single-molecule real-time sequencing
Oct 17, 2016
» Preprint on GenomeScope: Fast reference-free genome profiling from short reads
Sept 20, 2016
» CS 600.226 Data Structures Begins!
Sept 2, 2016
» Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read sequencing
June 26, 2016
» Assemblytics: a web analytics tool for the detection of variants from an assembly
June 17, 2016
» Preprint on Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
June 3, 2016
» Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida
May 27, 2016
» Computational biologist Michael Schatz named 21st Bloomberg Professor at Johns Hopkins
May 26, 2016
» Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
April 22, 2016
» Preprint on Third-generation sequencing and the future of genomics
April 13, 2016
» Preprint on Assemblytics: a web analytics tool for the detection of assembly-based variants
March 20, 2016
» Three presentations and two posters at Advances in Genome Biology and Technology (AGBT) 2016
Feb 12, 2016
» Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius
Feb 2, 2016
» Frontiers of Sequencing: Putting Long Reads and Graph Assemblies to Work
Jan 28, 2016
» Two presentations at Plant and Animal Genomes Conference
Jan 12, 2016

2015


» Three presentations and four posters at Genome Informatics 2015
Nov 3, 2015
» The pineapple genome and the evolution of CAM photosynthesis
Nov 2, 2015
» Teaser: Individualized benchmarking and optimization of read mapping results for NGS data
Oct 23, 2015
» Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
Oct 8, 2015
» Biological data sciences in genome research
Oct 1, 2015
» Metassembler: merging and optimizing de novo genome assemblies
Sept 24, 2015
» Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano [Press Release]
Sept 21, 2015
» Interactive analysis and assessment of single-cell copy-number variations [Press Release]
Sept 7, 2015
» Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano
Aug 31, 2015
» Big Data: Astronomical or Genomical? [Press Release]
July 7, 2015
» Rebooting the human genome in the MIT Tech Review
June 3, 2015
» Preprint on The next 20 years of genome research
June 2, 2015
» Pint-sized DNA sequencer impresses first users
May 5, 2015
» Molecular genetic diversity and characterization of conjugation genes in the fish parasite Ichthyophthirius multifiliis
March 12, 2015
» Preprint on Metassembler: Merging and optimizing de novo genome assemblies
March 10, 2015
» Two Schatzlab talks at AGBT
Feb 28, 2015
» Schatz named a 2015 Sloan Research Fellow
Feb 23, 2015
» Extending reference assembly models
Jan 28, 2015
» CSHL Scientists Sequence Yeast Genome with Oxford Nanopore MinIon
Jan 14, 2015
» Three Schatzlab talks at PAGXXIII
Jan 13, 2015
» The challenge of small-scale repeats for indel discovery
Jan 7, 2015

2014


» Whole genome assemblies of 3 divergent strains of rice used to discover their novel genes
Dec 3, 2014
» Lecture Notes from the Advanced Sequencing Course
Nov 22, 2014
» SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips
Nov 14, 2014
» The contribution of de novo coding mutations to autism spectrum disorder
Oct 29, 2014
» Reducing INDEL calling errors in whole-genome and exome sequencing data
Oct 27, 2014
» Schatz promoted to assoicate professor of quantitative biology
Sept 30, 2014
» New algorithm detects DNA insertions and deletions
Sept 10, 2014
» Accurate de novo and transmitted indel detection in exome-capture data using microassembly [Press Release]
Aug 17, 2014
» Lecture notes from our undergraduate research program in bioinformatics
Aug 14, 2014
» 101 questions with a bioinformatician @ ACGT
Aug 7, 2014
» CSHL quantitative biologist Michael Schatz wins prestigious NSF Early CAREER Award
July 30, 2014
» High-coverage sequencing and annotated assemblies of the budgerigar genome
July 8, 2014
» Preprint on Error correction and assembly complexity of single molecule sequencing reads.
June 18, 2014
» Preprint on Reducing INDEL errors in whole-genome and exome sequencing.
June 18, 2014
» Schatz receives prestiguous NSF CAREER award to develop Algorithms for single molecule sequencing analysis
June 7, 2014
» Accepted Preprint on the Algorithmic Complexity of the Biomolecular Sequence Assembly Problem
April 7, 2014
» Preprint on SplitMEM: Graphical pan-genome analysis with suffix skips
April 6, 2014
» Preprint on New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica
March 31, 2014
» Genome Sequencing and Assembly @ Genome Access Course
March 31, 2014
» The next 10 years of quantitative biology @ Keystone Symposia on Big Data in Biology
March 25, 2014
» Genome Assembly and Disease Analytics @ Brown
Feb 19, 2014
» A near perfect assembly of a eukaryotic genome @ AGBT
Feb 14, 2014
» Is the $1000 genome for real?
Jan 15, 2014
» De novo assembly of complex genomes using single molecule sequencing at PAG
Jan 14, 2014

2013


» Preprint on Accurate detection of de novo and transmitted INDELs within exome-capture data
Dec 13, 2013
» Genome Assembly with iPlant [Video]
Dec 4, 2013
» CSHL Advanced Sequencing Course
Nov 20, 2013
» Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis
Oct 23, 2013
» Our Bodies, Our Data [@Wired]
Oct 8, 2013
» Transcriptome Assembly, No Reference Required!
Oct 8, 2013
» Beyond the Genome Informatics Challenge
Oct 3, 2013
» WSBS QB Bootcamp
Sept 3-5, 2013
» CSHL Undergraduate Research Program in Bioinformatics
June 4 - Aug 9, 2013
» Results from Assemblathon 2 competition published in GigaScience
July 22, 2013
» The advantages of SMRT sequencing
July 3, 2013
» The DNA60IFX Contest [blog]
June 28, 2013
» The DNA Data Deluge in IEEE Spectrum
June 27, 2013
» Hybrid de novo assembly of eukaryotic genomes
June 18, 2013
» Genomics puzzles and prizes
May 29, 2013
» Genome of the sacred lotus published in Genome Biology
May 10, 2013
» HMP Webinar on Microbiome Asembly [slides]
May 2, 2013
» Sixty years of genome biology
April 25, 2013
» DNA60 Bioinformatics Challenge Begins
April 22, 2013
» Genome Access: Sequencing and Assembly
April 21, 2013
» De novo assembly of complex genomes @ UVA
April 10, 2013
» Companies 'going long' generate sequencing buzz at Marco Island
April 5, 2013
» Selling your most personal item: You
March 27, 2013
» Cloud-scale Sequence Analysis @ NY Genome Center/AWS Meetup
Mar 18, 2013
» Aluminum tolerance in maize is associated with higher MATE1 gene copy number
March 12, 2013
» Assembling Crop Genomes with Single Molecule Sequencing
Feb 22, 2013
» Wired magazine on big data challenges in genomics
Feb 20, 2013
» Gene sequencing leaves the laboratory
Feb 19, 2013
» Searching for GATTACA: Notes on the BWT
Feb 6, 2013
» Schatz comments on using Knome for genomics in the NY Times
Feb 2, 2013
» Computer Science and Genetics at Cold Spring Harbor High School
Jan 8, 2013

2012


» Genome sequencing's big fix in the CSHL Harbor Transcript
Dec 15, 2012
» CSHL Quantitative Biology Bioinformatics Slides.
Dec 4, 2012
» Computational thinking in the era of big data biology
Nov 29, 2012
» Human Genetics and Plant Genomics: The long and the short of it.
Nov 22, 2012
» SBU Graduate Genetics slides.
Nov 6, 2012
» Assembling crop genomes with 2nd and 3rd gen sequencing.
Oct 8, 2012
» Answering the demands of digital genomics.
Oct 4, 2012
» F1000 review on the Interdependence of cell growth and gene expression: origins and consequences.
Sept 26, 2012
» Genotyping in the Cloud with Crossbow
Sept 6, 2012
» WSBS Quantitative Biology Bootcamp 2012
August 30, 2012
» Lectures posted from CSHL undergraduate research program
July 27, 2012
» The rise of a digital immune system
July 12, 2012
» Hybrid error correction and de novo assembly of single-molecule sequencing reads
July 1, 2012
» Schatz joins the editorial board at Genome Biology
June 29, 2012
» Genomic Dark Matter: The reliability of short read mapping illustrated by the Genome Mappability Score
June 6, 2012
» Current challenges in de novo plant genome sequencing and assembly
April 27, 2012
» De novo gene disruptions in children on the autistic spectrum [Watch]
April 25, 2012
» Classic paper on precise biophysical modeling of transcriptional regulation
April 3, 2012
» De novo genome assembly: what every biologist should know
March 27, 2012
» Meeting report from AGBT
March 27, 2012
» DNA in the Cloud at Big Think
Feb 18, 2012
» Improving de novo genome assembler with Metassembler at AGBT
Feb 17, 2012
» Feature-by-Feature: Evaluating De Novo Sequence Assembly
Feb 14, 2012
» F1000 review of Cortex
Feb 12, 2012
» The DNA Storage Saga
Jan 24, 2012
» De novo assembly of complex genomes using 3rd generation sequencing (GenomeWeb report)
Jan 15, 2012

2011


» Lippman, Schatz lab collaboration uncovers a molecular "maturation clock" that modulates branching architecture in tomato plants
Dec 27, 2011
» Visualizing and assessing the quality of genome assemblies
Dec 24, 2011
» Applications of micro-, mega- and meta- assembly
Dec 12, 2011
» Slides from 2011 Quantitative Biology class posted
Dec 12, 2011
» Genome Research paper on GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Dec 6, 2011
» Schatz, McCombie interviewed by NY Times on the DNA Data Deluge
Dec 1, 2011
» PNAS paper on the sea squirt microbiome and the cancer-fighting agents in creates
Nov 28, 2011
» Giuseppe Narzisi joins the lab
Oct 28, 2011
» Meeting report from Beyond the Genome
Oct 24, 2011
» Frontiers in genomics: computational genomics
Oct 4-5, 2011
» Beyond the Genome: Keynote, Demo, and Panel
Sept 20, 2011
» Assemblathon 1 paper published in Genome Research
Sept 16, 2011
» Schatz quoted in Reuters on the future of funding of genomic research
Sept 12, 2011
» SMRT-Assembly Approaches: De Novo Assembly with 3rd Generation Sequencing
Sept 7, 2011
» Got Hadoop? Commentary in Genome Technology
Sept 1, 2011
» New paper on the comparative genomics of the deadly plant pathogen Xanthomonas
July 26, 2011
» Schatz and Ware awarded $5M DOE grant to assemble knowledgebase to aid biofuels and environmental efforts
July 15, 2011
» Lecture from undergraduate research program on bioinformatics posted
July 6, 2011
» Schatz quoted in article on future of GPUs for genomics
July 1, 2011
» New Paper Published on Genome Indexing with MapReduce
June 19, 2011
» Slides posted from joint ECMLS/3DAPAS Keynote and MapReduce'11
June 8, 2011
» Schatz appointed as associate member of the Laufer Center for Quantitative Biology at SBU
May 25, 2011
» Schatz awarded 2011 CSHL Winship Herr Award for Excellence in Teaching
May 1, 2011
» Proceedings from Data-Intensive Analysis Conference Available Online
April 18, 2011
» Computational Postdoc position posted
April 12, 2011
» Will Computers Crash Genomics?
Feb. 11 2011

2010


» Schatz credited for putting Hadoop "on-the-map" in bioinformatics
Dec. 21, 2010
» Call for papers announced for MapReduce 2011
Dec. 21, 2010
» Report on the Beyond the Genome Conference
Dec. 9, 2010
» Schatz selected as a Young Investigator of the Year
Dec. 1, 2010
» Quake error correction method published in Genome Biology
Nov. 29, 2010
» Efficient Large-Scale Graph Analysis with Hadoop & Part 2
Nov. 18, 2010
» Lecture notes from 2010 CSHL QB & Bioinformatics course
Oct. 29, 2010
» Genome Assembly of the honey bee pest Varroa destructor
Oct. 25, 2010
» Research Highlight on Hydra published on F1000.
Sept. 16, 2010
» Turkey genome assembled from NGS reads published in PLoS Biology.
Sept. 7, 2010
» Research Highlight on Galaxy published in Genome Biology.
Aug 25, 2010
» Commentary on Cloud Computing published in Nature Biotechnology.
July 1, 2010.