News


2024


» Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
March 26, 2024
» Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
March 17, 2024
» Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment
March 11, 2024
» Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation
March 7, 2024
» MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication
Feb 23, 2024
» Convergent evolution of plant prickles is driven by repeated gene co-option over deep time
Feb 22, 2024
» BioDIGS at AGBT: BioDiversity and Informatics for Genomics Scholars
Feb 8, 2024
» Utility of long-read sequencing for All of Us
Jan 29, 2024
» Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
Jan 26, 2024

2023


» The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes
Dec 4, 2023
» Schatz named one of the most highly cited researchers in 2023 by Clarivate
Nov 15, 2023
» Schatz selected for 2023 Alumni Achievement Award at Carnegie Mellon University
Nov 10, 2023
» Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats
Oct 4, 2023
» The genome of the Wollemi pine, a critically endangered living fossil unchanged since the Cretaceous, reveals extensive ancient transposon activity
Aug 28, 2023
» The complete sequence of a human Y chromosome
Aug 23, 2023
» Concerning the eXclusion in human genomics: The choice of sex chromosome representation in the human genome drastically affects number of identified variants
July 27, 2023
» Characterization of large-scale genomic differences in the first complete human genome
July 4, 2023
» Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
June 30, 2023
» Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy
June 23, 2023
» Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet
June 21, 2023
» Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids
May 30, 2023
» Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
April 4, 2023
» NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-Space: Reaching out to Clinicians
April 4, 2023
» The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
March 30, 2023
» BEATRICE: Bayesian Fine-mapping from Summary Data using Deep Variational Inference
March 25, 2023
» Johns Hopkins Team Using Long-Read Sequencing to Crack Genetic Code of Pancreatic Cancer
March 16, 2023
» Concerning the eXclusion in human genomics: The choice of sex chromosome representation in the human genome drastically affects number of identified variants
Feb 23, 2023
» Putting Genetics on the Map @ JHU Engineering
Jan 28, 2023
» Utility of long-read sequencing for All of Us
Jan 25, 2023
» Jasmine and Iris: population-scale structural variant comparison and analysis
Jan 19, 2023
» Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing
Jan 12, 2023
» Method of the Year 2022: long-read sequencing
Jan 12, 2023

2022


» A refined characterization of large-scale genomic differences in the first complete human genome
Dec 19, 2022
» Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
Dec 15, 2022
» The complete sequence of a human Y chromosome
Dec 2, 2022
» Save the Date for Biological Data Science Conference at CSHl on Nov 6-9 2024
Nov 12, 2022
» Sketching and sampling approaches for fast and accurate long read classification
Oct 31, 2022
» PhD student Samantha Zarate wins Mark O. Robbins Prize in High-Performance Computing
Oct 24, 2022
» Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome
Oct 21, 2022
» Semi-automated assembly of high-quality diploid human reference genomes
Oct 19, 2022
» Differences in activity and stability drive transposable element variation in tropical and temperate maize.
Oct 9, 2022
» Congratulations to Schatz lab alumn Hayan Lee for starting her lab at the Fox Chase Cancer Center
Sept 12, 2022
» Establishing Physalis as a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome
July 30, 2022
» Diversifying the genomic data science research community
July 21, 2022
» Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering
July 8, 2022
» Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
July 8, 2022
» Schatz among 'TIME 100' most influential people in the world
May 23, 2022
» Benchmarking challenging small variants with linked and long reads
April 28, 2022
» The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
April 22, 2022
» Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome
April 21, 2022
» Johns Hopkins scientists contribute to first complete sequence of human genome
March 31, 2022
» Automated assembly of high-quality diploid human reference genomes
March 7, 2022
» Same-Cell Co-Occurrence of RAS Hotspot and BRAF V600E Mutations in Treatment-Naive Colorectal Cancer
March 2, 2022
» Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome
Feb 23, 2022
» Artificial Intelligence and Cardiovascular Genetics
Feb 14, 2022
» Diversifying the Genomic Data Science Research Community
Jan 24, 2022
» New cloud-based platform opens genomics data to all
Jan 12, 2022
» Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space
Jan 12, 2022

2021


» Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing
Nov 19, 2021
» Schatz named 2021 Clarivate Highly Cited Reearcher
Nov 16, 2021
» Uncovering the secrets of a model plant genome
Nov 15, 2021
» The genetic and epigenetic landscape of the Arabidopsis centromeres
Nov 11, 2021
» Sketching and sampling approaches for fast and accurate long read classification
Nov 5, 2021
» Democratizing long-read genome assembly
Oct 20, 2021
» High resolution copy number inference in cancer using short-molecule nanopore sequencing
Sept 22, 2021
» Local adaptation and archaic introgression shape global diversity at human structural variant loci
Sept 16, 2021
» Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
Sept 15, 2021
» Random Forest Factorization Reveals Latent Structure in Single Cell RNA Sequencing Data
Sept 14, 2021
» Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats
August 19, 2021
» Scientists Finish the Human Genome at Last
July 23, 2021
» A complete reference genome improves analysis of human genetic variation
July 13, 2021
» Complete genomic and epigenetic maps of human centromeres
July 13, 2021
» From telomere to telomere: the transcriptional and epigenetic state of human repeat elements
July 13, 2021
» Schatz Promoted to Bloomberg Distinguished Professor of Computer Science and Biology
July 1, 2021
» Pan-genomic Matching Statistics for Targeted Nanopore Sequencing
June 15, 2021
» An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids
June 10, 2021
» The genetic and epigenetic landscape of the Arabidopsis centromeres
May 31, 2021
» Jasmine: Population-scale structural variant comparison and analysis
May 28, 2021
» Epigenetic Patterns in a Complete Human Genome
May 27, 2021
» The complete sequence of a human genome
May 27, 2021
» A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor
April 30, 2021
» The genomic basis of evolutionary differentiation among honey bees
April 28, 2021
» Multi-tissue integrative analysis of personal epigenomes
April 26, 2021
» Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)
April 25, 2021
» Natural genetic diversity in tomato flavor genes
April 23, 2021
» Optimized sample selection for cost-efficient long-read population sequencing
April 2, 2021
» Skyhawk: an artificial neural network-based discriminator for reviewing clinically significant genomic variants
March 31, 2021
» Pan-genomic Matching Statistics for Targeted Nanopore Sequencing
March 23, 2021
» Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore–Washington metropolitan area
March 22, 2021
» Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy
March 20, 2021
» Cell wall protein variation, break‐induced replication, and subtelomere dynamics in Candida glabrata
March 17, 2021
» SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans
Feb 15, 2021
» Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update
Feb 14, 2021
» Sequencing your DNA with a USB dongle and open source code
Feb 3, 2021
» The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure
Feb 1, 2021
» Local adaptation and archaic introgression shape global diversity at human structural variant loci
Jan 27, 2021

2020


» High resolution copy number inference in cancer using short-molecule nanopore sequencing
Dec 29, 2020
» Complex targeted sequencing in real time
Dec 21, 2020
» Parliament2: Accurate structural variant calling at scale
Dec 21, 2020
» Cold Spring Harbor Lab Develops iPhone App for Mobile Sequencing Analysis [GenomeWeb]
Dec 11, 2020
» The world’s first DNA “tricorder” in your pocket
Dec 7, 2020
» iGenomics: Comprehensive DNA sequence analysis on your Smartphone
Dec 7, 2020
» Research team develops software that cuts time, cost from gene sequencing
Dec 4, 2020
» Congratulations to Dr. T. Rhyker Ranallo-Benavidez
Dec 3, 2020
» Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
Nov 30, 2020
» Clonal Hematopoiesis Before, During, and After Human Spaceflight
Nov 25, 2020
» LongTron: Automated Analysis of Long Read Spliced Alignment Accuracy
Nov 11, 2020
» Sapling: Accelerating Suffix Array Queries with Learned Data Models
Oct 27, 2020
» A diploid assembly-based benchmark for variants in the major histocompatibility complex
Sept 22, 2020
» Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
Sept 8, 2020
» Coronavirus invaded the District and Maryland multiple times in March, genetic analysis shows
Aug 18, 2020
» Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region
Aug 18, 2020
» Ribbon: Intuitive visualization for complex genomic variation
Aug 11, 2020
» SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans
Aug 8, 2020
» SVCollector: Optimized sample selection for cost-efficient long-read population sequencing
Aug 7, 2020
» The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure.
Aug 7, 2020
» Congratulations to Dr. Timothy Gilpatrick for defending his Ph.D!
Aug 6, 2020
» Benchmarking challenging small variants with linked and long reads
July 27, 2020
» Resolving the roles of structural variants
July 8, 2020
» Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
June 17, 2020
» A robust benchmark for detection of germline large deletions and insertions
June 15, 2020
» Congratulations to Dr. Nathan Roach for defending his Ph.D!
June 12, 2020
» Congratulations to Dr. Charlotte Darby for defending her Ph.D!
May 26, 2020
» In memory of James Taylor: the birth of Galaxy
April 30, 2020
» Vargas: heuristic-free alignment for assessing linear and graph read aligners
April 22, 2020
» Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud
March 31, 2020
» The code breakers: From tomatoes to cancer cells in Johns Hopkins Magazine
March 25, 2020
» GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
March 18, 2020
» A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor
Feb 28, 2020
» De novo genome assembly of Candida glabrata reveals cell wall protein complement and structure of dispersed tandem repeat arrays
Feb 26, 2020
» New Algorithms Unlock Targeted Sequencing on Nanopore Platforms in GenomeWeb
Feb 12, 2020
» iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone
Feb 12, 2020
» Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
Feb 3, 2020
» Sapling: Accelerating Suffix Array Queries with Learned Data Models
Jan 20, 2020

2019


» Vargas: heuristic-free alignment for assessing linear and graph read aligners
Dec 21, 2019
» Paragraph: a graph-based structural variant genotyper for short-read sequence data
Dec 20, 2019
» Recovering rearranged cancer chromosomes from karyotype graphs
Dec 17, 2019
» Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop
Nov 29, 2019
» SciApps: A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data
Nov 23, 2019
» Schatz named a 2019 Highly Cited Researcher by Clairivate Web of Science
Nov 19, 2019
» Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing
Nov 19, 2019
» RaGOO: fast and accurate reference-guided scaffolding of draft genomes
Oct 28, 2019
» The bracteatus pineapple genome and domestication of clonally propagated crops
Sept 30, 2019
» GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes
August 26, 2019
» Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
August 12, 2019
» A robust benchmark for germline structural variant detection
June 9, 2019
» Samovar: Single-sample mosaic single-nucleotide variant calling with linked reads
May 29, 2019
» Addressing confounding artifacts in reconstruction of gene co-expression networks
May 16, 2019
» Paragraph: A graph-based structural variant genotyper for short-read sequence data
May 10, 2019
» Hypo-osmotic-like stress underlies general cellular defects of aneuploidy
May 8, 2019
» Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato
May 6, 2019
» Our paper describing SAMOVAR selected for the best paper award at RECOMB-seq [preprint]
May 6, 2019
» First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis)
April 30, 2019
» A master regulator of regeneration
March 14, 2019
» A multi-task convolutional deep neural network for variant calling in single molecule sequencing
March 1, 2019
» Samovar: Single-sample mosaic SNV calling with linked reads
Feb 25, 2019
» Graph genomes article collection
Feb 1, 2019
» Where is genomics going next?
Jan 22, 2019
» Rapid Nanopore Sequencing of 100 Tomato Genomes Enables Structural Variant Analysis
Jan 16, 2019
» Fast and accurate reference-guided scaffolding of draft genomes
Jan 13, 2018
» Highly-accurate long-read sequencing improves variant detection and assembly of a human genome
Jan 13, 2018
» Schatz recognized as a Highly Cited Research for 2018 by Clarivate Analytics
Jan 1, 2019

2018


» Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish
Dec 6, 2018
» Parrot Genomes and the Evolution of Heightened Longevity and Cognition
Dec 6, 2018
» Applying Rapid Whole Genome Sequencing to Predict Phenotypic Antimicrobial Susceptibility Testing Results Among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates
Oct 29, 2018
» Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.
Oct 10, 2018
» Our breast cancer analysis on the cover of Genome Research
Aug 1, 2018
» Conservation genomics of the declining North American bumblebee Bombus terricola reveals inbreeding and selection on immune genes.
July 24, 2018
» Tallying a cancer’s vast array of genetic changes
July 11, 2018
» Massive genome havoc in breast cancer is revealed
July 11, 2018
» KBase: The United States Department of Energy Systems Biology Knowledgebase
July 6, 2018
» Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
July 1, 2018
» Schatz lab receives JHU Discovery Award to study Mendelian diseases with long read sequencing
June 6, 2018
» SVCollector: Optimized sample selection for validating and long-read resequencing of structural variants
June 8, 2018
» Precise detection of de novo single nucleotide variants in human genomes
May 7, 2018
» New Tools Highlight Long-Read Sequencing Platforms' Ability to Call Structural Variants @ GenomeWeb
May 1, 2018
» Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants
May 1, 2018
» Accurate detection of complex structural variations using single-molecule sequencing
April 30, 2018
» Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
April 29, 2018
» Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae
April 13, 2018
» New HEART Seminar Course Explores Algorithms and Computational Complexity Theory
April 6, 2018
» Piercing the dark matter: bioinformatics of long- range sequencing and mapping
March 29, 2018
» New method can more precisely determine when a cell has ‘cashed’ RNA ‘checks’ written by active genes
Feb 26, 2018
» Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution
January 17, 2018
» Reference-quality diploid genomes without de novo assembly @ PAG
January 16, 2018
» Technology Improvements Help Elucidate Previously Indecipherable Structural Variants in GenomeWeb
January 16, 2018
» Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library
January 12, 2018

2017


» LRSim: A Linked-Reads Simulator generating insights for better genome partitioning
November 9, 2017
» Addressing confounding artifacts in reconstruction of gene co-expression networks
October 13, 2017
» Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
August 10, 2017
» Accurate detection of complex structural variations using single molecule sequencing
July 28, 2017
» Hybrid assembly with long and short reads improves discovery of gene family expansions
July 19, 2017
» Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution
June 28, 2017
» Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library
June 21, 2017
» 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
June 15, 2017
» In pursuit of perfect genome sequencing
May 22, 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
» Applied Comparative Genomics Course Begins
Jan 31, 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.