2025
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From data to publication in a browser with BRC-Analytics: Evolutionary dynamics of coding overlaps in measles virus
Oct 15, 2025 | |
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Population-scale Long-read Sequencing in the All of Us Research Program
Oct 5, 2025 | |
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A complete diploid human genome benchmark for personalized genomics
Sep 22, 2025 | |
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| » |
Learning Explainable Imaging-Genetics Associations Related to a Neurological Disorder
Aug 22, 2025 | |
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| » |
Engineering compact Physalis peruviana (goldenberry) to promote its potential as a global crop
Aug 19, 2025 | |
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| » |
Improving the FAIRness and Sustainability of the NHGRI Resources Ecosystem
Aug 19, 2025 | |
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| » |
Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans
June 24, 2025 | |
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| » |
Congratulations to Mahler Revsine for being awarded an NSF GRFP fellowship
June 13, 2025 | |
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Assembling unmapped reads reveals hidden variation in South Asian genomes
May 14, 2025 | |
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| » |
Schatz featured on NPR Science Friday "Scientists Identify Genes For Tomato And Eggplant Size"
May 9, 2025 | |
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| » |
Congratulations to Arun Das for defending his PhD
April 23, 2025 | |
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| » |
Complete sequencing of ape genomes
April 9, 2025 | |
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| » |
Nature News and Views: Complete ape genomes offer a close-up view of human evolution
April 9, 2025 | |
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| » |
Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment
March 28, 2025 | |
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| » |
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
March 24, 2025 | |
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| » |
Unraveling the hidden complexity of cancer through long-read sequencing
March 22, 2025 | |
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| » |
The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project
March 17, 2025 | |
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| » |
Solanum pan-genetics reveals paralogues as contingencies in crop engineering
March 5, 2025 | |
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| » |
Nature News & Views on pan-sol paper: Genus-wide plant pangenome could inform next-generation crop design
March 5, 2025 | |
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| » |
JHU Hub Article: Scientists discover genes to grow bigger tomatoes and eggplants
March 5, 2025 | |
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Mem-based pangenome indexing for k-mer queries
March 2, 2025 | |
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k-mer approaches for biodiversity genomics
Jan 31, 2025 | |
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2024
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MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication
Dec 30, 2024 | |
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microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data
Dec 27, 2024 | |
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| » |
Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans
Dec 25, 2024 | |
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| » |
Schatz named among the most highly cited researchers in the world for 2024
Nov 19, 2024 | |
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| » |
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
Nov 6, 2024 | |
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| » |
BEATRICE: Bayesian Fine-mapping from Summary Data using Deep Variational Inference
Oct 3, 2024 | |
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High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
Oct 2, 2024 | |
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| » |
Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering
Sept 14, 2024 | |
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| » |
Differences in activity and stability drive transposable element variation in tropical and temperate maize
Sept 9, 2024 | |
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| » |
Welcome Nicole Brown to the lab!
Aug 26, 2024 | |
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| » |
ModDotPlot—rapid and interactive visualization of tandem repeats
Aug 7, 2024 | |
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| » |
Convergent evolution of plant prickles by repeated gene co-option over deep time
Aug 6, 2024 | |
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Complete sequencing of ape genomes
July 31, 2024 | |
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Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
July 1, 2024 | |
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How a small group of scientists and educators are enhancing the diversity of the genomics workforce
June 6, 2024 | |
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The complete sequence and comparative analysis of ape sex chromosomes
May 29, 2024 | |
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MEM-based pangenome indexing for k-mer queries
May 22, 2024 | |
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The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
May 21, 2024 | |
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| » |
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References
April 25, 2024 | |
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| » |
ModDotPlot - Rapid and interactive visualization of complex repeats
April 19, 2024 | |
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| » |
Guide to k-mer approaches for genomics across the tree of life
April 2, 2024 | |
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| » |
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
March 26, 2024 | |
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| » |
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
March 17, 2024 | |
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| » |
Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment
March 11, 2024 | |
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| » |
Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation
March 7, 2024 | |
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| » |
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication
Feb 23, 2024 | |
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| » |
Convergent evolution of plant prickles is driven by repeated gene co-option over deep time
Feb 22, 2024 | |
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| » |
BioDIGS at AGBT: BioDiversity and Informatics for Genomics Scholars
Feb 8, 2024 | |
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Utility of long-read sequencing for All of Us
Jan 29, 2024 | |
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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
Jan 26, 2024 | |
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2023
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| » |
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes
Dec 4, 2023 | |
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| » |
Schatz named one of the most highly cited researchers in 2023 by Clarivate
Nov 15, 2023 | |
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| » |
Schatz selected for 2023 Alumni Achievement Award at Carnegie Mellon University
Nov 10, 2023 | |
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| » |
Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats
Oct 4, 2023 | |
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| » |
The genome of the Wollemi pine, a critically endangered living fossil unchanged since the Cretaceous, reveals extensive ancient transposon activity
Aug 28, 2023 | |
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The complete sequence of a human Y chromosome
Aug 23, 2023 | |
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| » |
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 | |
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Characterization of large-scale genomic differences in the first complete human genome
July 4, 2023 | |
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| » |
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
June 30, 2023 | |
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| » |
Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy
June 23, 2023 | |
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| » |
Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet
June 21, 2023 | |
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| » |
Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids
May 30, 2023 | |
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Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
April 4, 2023 | |
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| » |
NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-Space: Reaching out to Clinicians
April 4, 2023 | |
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| » |
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
March 30, 2023 | |
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| » |
BEATRICE: Bayesian Fine-mapping from Summary Data using Deep Variational Inference
March 25, 2023 | |
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| » |
Johns Hopkins Team Using Long-Read Sequencing to Crack Genetic Code of Pancreatic Cancer
March 16, 2023 | |
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| » |
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 | |
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| » |
Putting Genetics on the Map @ JHU Engineering
Jan 28, 2023 | |
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Utility of long-read sequencing for All of Us
Jan 25, 2023 | |
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| » |
Jasmine and Iris: population-scale structural variant comparison and analysis
Jan 19, 2023 | |
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| » |
Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing
Jan 12, 2023 | |
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| » |
Method of the Year 2022: long-read sequencing
Jan 12, 2023 | |
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2022
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| » |
A refined characterization of large-scale genomic differences in the first complete human genome
Dec 19, 2022 | |
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| » |
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
Dec 15, 2022 | |
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| » |
The complete sequence of a human Y chromosome
Dec 2, 2022 | |
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| » |
Save the Date for Biological Data Science Conference at CSHl on Nov 6-9 2024
Nov 12, 2022 | |
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| » |
Sketching and sampling approaches for fast and accurate long read classification
Oct 31, 2022 | |
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| » |
PhD student Samantha Zarate wins Mark O. Robbins Prize in High-Performance Computing
Oct 24, 2022 | |
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| » |
Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome
Oct 21, 2022 | |
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| » |
Semi-automated assembly of high-quality diploid human reference genomes
Oct 19, 2022 | |
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| » |
Differences in activity and stability drive transposable element variation in tropical and temperate maize.
Oct 9, 2022 | |
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| » |
Congratulations to Schatz lab alumn Hayan Lee for starting her lab at the Fox Chase Cancer Center
Sept 12, 2022 | |
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| » |
Establishing Physalis as a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome
July 30, 2022 | |
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Diversifying the genomic data science research community
July 21, 2022 | |
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Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering
July 8, 2022 | |
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| » |
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
July 8, 2022 | |
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| » |
Schatz among 'TIME 100' most influential people in the world
May 23, 2022 | |
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| » |
Benchmarking challenging small variants with linked and long reads
April 28, 2022 | |
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| » |
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
April 22, 2022 | |
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| » |
Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome
April 21, 2022 | |
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Johns Hopkins scientists contribute to first complete sequence of human genome
March 31, 2022 | |
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Automated assembly of high-quality diploid human reference genomes
March 7, 2022 | |
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Same-Cell Co-Occurrence of RAS Hotspot and BRAF V600E Mutations in Treatment-Naive Colorectal Cancer
March 2, 2022 | |
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Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome
Feb 23, 2022 | |
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Artificial Intelligence and Cardiovascular Genetics
Feb 14, 2022 | |
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Diversifying the Genomic Data Science Research Community
Jan 24, 2022 | |
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New cloud-based platform opens genomics data to all
Jan 12, 2022 | |
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Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space
Jan 12, 2022 | |
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2021
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| » |
Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing
Nov 19, 2021 | |
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| » |
Schatz named 2021 Clarivate Highly Cited Reearcher
Nov 16, 2021 | |
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| » |
Uncovering the secrets of a model plant genome
Nov 15, 2021 | |
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The genetic and epigenetic landscape of the Arabidopsis centromeres
Nov 11, 2021 | |
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Sketching and sampling approaches for fast and accurate long read classification
Nov 5, 2021 | |
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Democratizing long-read genome assembly
Oct 20, 2021 | |
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High resolution copy number inference in cancer using short-molecule nanopore sequencing
Sept 22, 2021 | |
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Local adaptation and archaic introgression shape global diversity at human structural variant loci
Sept 16, 2021 | |
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Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
Sept 15, 2021 | |
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| » |
Random Forest Factorization Reveals Latent Structure in Single Cell RNA Sequencing Data
Sept 14, 2021 | |
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Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats
August 19, 2021 | |
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Scientists Finish the Human Genome at Last
July 23, 2021 | |
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A complete reference genome improves analysis of human genetic variation
July 13, 2021 | |
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Complete genomic and epigenetic maps of human centromeres
July 13, 2021 | |
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| » |
From telomere to telomere: the transcriptional and epigenetic state of human repeat elements
July 13, 2021 | |
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Schatz Promoted to Bloomberg Distinguished Professor of Computer Science and Biology
July 1, 2021 | |
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| » |
Pan-genomic Matching Statistics for Targeted Nanopore Sequencing
June 15, 2021 | |
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| » |
An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids
June 10, 2021 | |
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The genetic and epigenetic landscape of the Arabidopsis centromeres
May 31, 2021 | |
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| » |
Jasmine: Population-scale structural variant comparison and analysis
May 28, 2021 | |
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| » |
Epigenetic Patterns in a Complete Human Genome
May 27, 2021 | |
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| » |
The complete sequence of a human genome
May 27, 2021 | |
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| » |
A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor
April 30, 2021 | |
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| » |
The genomic basis of evolutionary differentiation among honey bees
April 28, 2021 | |
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| » |
Multi-tissue integrative analysis of personal epigenomes
April 26, 2021 | |
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| » |
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)
April 25, 2021 | |
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| » |
Natural genetic diversity in tomato flavor genes
April 23, 2021 | |
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Optimized sample selection for cost-efficient long-read population sequencing
April 2, 2021 | |
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| » |
Skyhawk: an artificial neural network-based discriminator for reviewing clinically significant genomic variants
March 31, 2021 | |
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| » |
Pan-genomic Matching Statistics for Targeted Nanopore Sequencing
March 23, 2021 | |
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| » |
Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore–Washington metropolitan area
March 22, 2021 | |
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Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy
March 20, 2021 | |
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| » |
Cell wall protein variation, break‐induced replication, and subtelomere dynamics in Candida glabrata
March 17, 2021 | |
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| » |
SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans
Feb 15, 2021 | |
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| » |
Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update
Feb 14, 2021 | |
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| » |
Sequencing your DNA with a USB dongle and open source code
Feb 3, 2021 | |
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| » |
The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure
Feb 1, 2021 | |
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Local adaptation and archaic introgression shape global diversity at human structural variant loci
Jan 27, 2021 | |
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2020
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| » |
High resolution copy number inference in cancer using short-molecule nanopore sequencing
Dec 29, 2020 | |
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Complex targeted sequencing in real time
Dec 21, 2020 | |
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| » |
Parliament2: Accurate structural variant calling at scale
Dec 21, 2020 | |
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| » |
Cold Spring Harbor Lab Develops iPhone App for Mobile Sequencing Analysis [GenomeWeb]
Dec 11, 2020 | |
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| » |
The world’s first DNA “tricorder” in your pocket
Dec 7, 2020 | |
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iGenomics: Comprehensive DNA sequence analysis on your Smartphone
Dec 7, 2020 | |
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| » |
Research team develops software that cuts time, cost from gene sequencing
Dec 4, 2020 | |
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| » |
Congratulations to Dr. T. Rhyker Ranallo-Benavidez
Dec 3, 2020 | |
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| » |
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
Nov 30, 2020 | |
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| » |
Clonal Hematopoiesis Before, During, and After Human Spaceflight
Nov 25, 2020 | |
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| » |
LongTron: Automated Analysis of Long Read Spliced Alignment Accuracy
Nov 11, 2020 | |
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| » |
Sapling: Accelerating Suffix Array Queries with Learned Data Models
Oct 27, 2020 | |
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| » |
A diploid assembly-based benchmark for variants in the major histocompatibility complex
Sept 22, 2020 | |
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| » |
Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
Sept 8, 2020 | |
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| » |
Coronavirus invaded the District and Maryland multiple times in March, genetic analysis shows
Aug 18, 2020 | |
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Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region
Aug 18, 2020 |
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Ribbon: Intuitive visualization for complex genomic variation
Aug 11, 2020 |
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| » |
SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans
Aug 8, 2020 |
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| » |
SVCollector: Optimized sample selection for cost-efficient long-read population sequencing
Aug 7, 2020 |
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| » |
The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure.
Aug 7, 2020 |
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| » |
Congratulations to Dr. Timothy Gilpatrick for defending his Ph.D!
Aug 6, 2020 |
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Benchmarking challenging small variants with linked and long reads
July 27, 2020 |
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Resolving the roles of structural variants
July 8, 2020 |
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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
June 17, 2020 |
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A robust benchmark for detection of germline large deletions and insertions
June 15, 2020 |
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Congratulations to Dr. Nathan Roach for defending his Ph.D!
June 12, 2020 |
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Congratulations to Dr. Charlotte Darby for defending her Ph.D!
May 26, 2020 |
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In memory of James Taylor: the birth of Galaxy
April 30, 2020 |
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Vargas: heuristic-free alignment for assessing linear and graph read aligners
April 22, 2020 |
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Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud
March 31, 2020 |
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The code breakers: From tomatoes to cancer cells in Johns Hopkins Magazine
March 25, 2020 |
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GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
March 18, 2020 |
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A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor
Feb 28, 2020 |
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De novo genome assembly of Candida glabrata reveals cell wall protein complement and structure of dispersed tandem repeat arrays
Feb 26, 2020 |
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New Algorithms Unlock Targeted Sequencing on Nanopore Platforms in GenomeWeb
Feb 12, 2020 |
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iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone
Feb 12, 2020 |
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Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
Feb 3, 2020 |
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Sapling: Accelerating Suffix Array Queries with Learned Data Models
Jan 20, 2020 |
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2019
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| » |
Vargas: heuristic-free alignment for assessing linear and graph read aligners
Dec 21, 2019 |
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Paragraph: a graph-based structural variant genotyper for short-read sequence data
Dec 20, 2019 |
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Recovering rearranged cancer chromosomes from karyotype graphs
Dec 17, 2019 |
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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 |
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SciApps: A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data
Nov 23, 2019 |
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Schatz named a 2019 Highly Cited Researcher by Clairivate Web of Science
Nov 19, 2019 |
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Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing
Nov 19, 2019 |
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RaGOO: fast and accurate reference-guided scaffolding of draft genomes
Oct 28, 2019 |
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The bracteatus pineapple genome and domestication of clonally propagated crops
Sept 30, 2019 |
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GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes
August 26, 2019 |
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Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
August 12, 2019 |
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A robust benchmark for germline structural variant detection
June 9, 2019 |
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Samovar: Single-sample mosaic single-nucleotide variant calling with linked reads
May 29, 2019 |
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Addressing confounding artifacts in reconstruction of gene co-expression networks
May 16, 2019 |
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Paragraph: A graph-based structural variant genotyper for short-read sequence data
May 10, 2019 |
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Hypo-osmotic-like stress underlies general cellular defects of aneuploidy
May 8, 2019 |
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Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato
May 6, 2019 |
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Our paper describing SAMOVAR selected for the best paper award at RECOMB-seq [preprint]
May 6, 2019 |
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First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis)
April 30, 2019 |
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A master regulator of regeneration
March 14, 2019 |
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A multi-task convolutional deep neural network for variant calling in single molecule sequencing
March 1, 2019 |
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Samovar: Single-sample mosaic SNV calling with linked reads
Feb 25, 2019 |
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Graph genomes article collection
Feb 1, 2019 |
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Where is genomics going next?
Jan 22, 2019 |
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Rapid Nanopore Sequencing of 100 Tomato Genomes Enables Structural Variant Analysis
Jan 16, 2019 |
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Fast and accurate reference-guided scaffolding of draft genomes
Jan 13, 2018 |
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Highly-accurate long-read sequencing improves variant detection and assembly of a human genome
Jan 13, 2018 |
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Schatz recognized as a Highly Cited Research for 2018 by Clarivate Analytics
Jan 1, 2019 |
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2018
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| » |
Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish
Dec 6, 2018 |
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Parrot Genomes and the Evolution of Heightened Longevity and Cognition
Dec 6, 2018 |
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Applying Rapid Whole Genome Sequencing to Predict Phenotypic Antimicrobial Susceptibility Testing Results Among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates
Oct 29, 2018 |
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Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.
Oct 10, 2018 |
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Our breast cancer analysis on the cover of Genome Research
Aug 1, 2018 |
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Conservation genomics of the declining North American bumblebee Bombus terricola reveals inbreeding and selection on immune genes.
July 24, 2018 |
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Tallying a cancer’s vast array of genetic changes
July 11, 2018 |
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Massive genome havoc in breast cancer is revealed
July 11, 2018 |
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KBase: The United States Department of Energy Systems Biology Knowledgebase
July 6, 2018 |
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Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
July 1, 2018 |
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Schatz lab receives JHU Discovery Award to study Mendelian diseases with long read sequencing
June 6, 2018 |
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SVCollector: Optimized sample selection for validating and long-read resequencing of structural variants
June 8, 2018 |
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Precise detection of de novo single nucleotide variants in human genomes
May 7, 2018 |
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New Tools Highlight Long-Read Sequencing Platforms' Ability to Call Structural Variants @ GenomeWeb
May 1, 2018 |
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Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants
May 1, 2018 |
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Accurate detection of complex structural variations using single-molecule sequencing
April 30, 2018 |
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Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
April 29, 2018 |
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Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae
April 13, 2018 |
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New HEART Seminar Course Explores Algorithms and Computational Complexity Theory
April 6, 2018 |
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Piercing the dark matter: bioinformatics of long- range sequencing and mapping
March 29, 2018 |
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New method can more precisely determine when a cell has ‘cashed’ RNA ‘checks’ written by active genes
Feb 26, 2018 |
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Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution
January 17, 2018 |
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Reference-quality diploid genomes without de novo assembly @ PAG
January 16, 2018 |
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Technology Improvements Help Elucidate Previously Indecipherable Structural Variants in GenomeWeb
January 16, 2018 |
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Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library
January 12, 2018 |
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2017
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LRSim: A Linked-Reads Simulator generating insights for better genome partitioning
November 9, 2017 |
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Addressing confounding artifacts in reconstruction of gene co-expression networks
October 13, 2017 |
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Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
August 10, 2017 |
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Accurate detection of complex structural variations using single molecule sequencing
July 28, 2017 |
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Hybrid assembly with long and short reads improves discovery of gene family expansions
July 19, 2017 |
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Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution
June 28, 2017 |
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Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library
June 21, 2017 |
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16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
June 15, 2017 |
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In pursuit of perfect genome sequencing
May 22, 2017 |
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Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma
May 8, 2017 |
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GenomeScope: Fast reference-free genome profiling from short reads
April 4, 2017 |
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Nanopore sequencing meets epigenetics
March 31, 2017 |
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Proceedings of the IEEE: Bioinformatics of DNA
March 1, 2017 |
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Preprint on 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
Feb 24, 2017 |
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Personalized Phased Diploid Genomes of the EN-Tex Samples @ AGBT
Feb 15, 2017 |
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Applied Comparative Genomics Course Begins
Jan 31, 2017 |
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LRSim: a Linked Reads Simulator generating insights for better genome partitioning
Jan 26, 2017 |
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TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells
Jan 16, 2017 |
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NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads
Jan 2, 2017 |
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2016
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Indel variant analysis of short-read sequencing data with Scalpel
Dec 8, 2016 |
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The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation
Nov 7, 2016 |
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Phased diploid genome assembly with single-molecule real-time sequencing
Oct 17, 2016 |
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Preprint on GenomeScope: Fast reference-free genome profiling from short reads
Sept 20, 2016 |
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CS 600.226 Data Structures Begins!
Sept 2, 2016 |
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Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read sequencing
June 26, 2016 |
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Assemblytics: a web analytics tool for the detection of variants from an assembly
June 17, 2016 |
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Preprint on Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
June 3, 2016 |
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Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida
May 27, 2016 |
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Computational biologist Michael Schatz named 21st Bloomberg Professor at Johns Hopkins
May 26, 2016 |
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Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
April 22, 2016 |
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Preprint on Third-generation sequencing and the future of genomics
April 13, 2016 |
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Preprint on Assemblytics: a web analytics tool for the detection of assembly-based variants
March 20, 2016 |
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Three presentations and two posters at Advances in Genome Biology and Technology (AGBT) 2016
Feb 12, 2016 |
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Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius
Feb 2, 2016 |
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Frontiers of Sequencing: Putting Long Reads and Graph Assemblies to Work
Jan 28, 2016 |
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Two presentations at Plant and Animal Genomes Conference
Jan 12, 2016 |
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2015
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Three presentations and four posters at Genome Informatics 2015
Nov 3, 2015 |
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The pineapple genome and the evolution of CAM photosynthesis
Nov 2, 2015 |
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Teaser: Individualized benchmarking and optimization of read mapping results for NGS data
Oct 23, 2015 |
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Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
Oct 8, 2015 |
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Biological data sciences in genome research
Oct 1, 2015 |
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Metassembler: merging and optimizing de novo genome assemblies
Sept 24, 2015 |
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Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano [Press Release]
Sept 21, 2015 |
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Interactive analysis and assessment of single-cell copy-number variations [Press Release]
Sept 7, 2015 |
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Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano
Aug 31, 2015 |
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Big Data: Astronomical or Genomical? [Press Release]
July 7, 2015 |
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Rebooting the human genome in the MIT Tech Review
June 3, 2015 |
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Preprint on The next 20 years of genome research
June 2, 2015 |
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Pint-sized DNA sequencer impresses first users
May 5, 2015 |
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Molecular genetic diversity and characterization of conjugation genes in the fish parasite Ichthyophthirius multifiliis
March 12, 2015 |
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Preprint on Metassembler: Merging and optimizing de novo genome assemblies
March 10, 2015 |
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Two Schatzlab talks at AGBT
Feb 28, 2015 |
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Schatz named a 2015 Sloan Research Fellow
Feb 23, 2015 |
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Extending reference assembly models
Jan 28, 2015 |
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CSHL Scientists Sequence Yeast Genome with Oxford Nanopore MinIon
Jan 14, 2015 |
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Three Schatzlab talks at PAGXXIII
Jan 13, 2015 |
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The challenge of small-scale repeats for indel discovery
Jan 7, 2015 |
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2014
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Whole genome assemblies of 3 divergent strains of rice used to discover their novel genes
Dec 3, 2014 |
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Lecture Notes from the Advanced Sequencing Course
Nov 22, 2014 |
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SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips
Nov 14, 2014 |
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The contribution of de novo coding mutations to autism spectrum disorder
Oct 29, 2014 |
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Reducing INDEL calling errors in whole-genome and exome sequencing data
Oct 27, 2014 |
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Schatz promoted to assoicate professor of quantitative biology
Sept 30, 2014 |
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New algorithm detects DNA insertions and deletions
Sept 10, 2014 |
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Accurate de novo and transmitted indel detection in exome-capture data using microassembly [Press Release]
Aug 17, 2014 |
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Lecture notes from our undergraduate research program in bioinformatics
Aug 14, 2014 |
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101 questions with a bioinformatician @ ACGT
Aug 7, 2014 |
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CSHL quantitative biologist Michael Schatz wins prestigious NSF Early CAREER Award
July 30, 2014 |
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High-coverage sequencing and annotated assemblies of the budgerigar genome
July 8, 2014 |
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Preprint on Error correction and assembly complexity of single molecule sequencing reads.
June 18, 2014 |
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Preprint on Reducing INDEL errors in whole-genome and exome sequencing.
June 18, 2014 |
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Schatz receives prestiguous NSF CAREER award to develop Algorithms for single molecule sequencing analysis
June 7, 2014 |
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Accepted Preprint on the Algorithmic Complexity of the Biomolecular Sequence Assembly Problem
April 7, 2014 |
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Preprint on SplitMEM: Graphical pan-genome analysis with suffix skips
April 6, 2014 |
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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 |
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Genome Sequencing and Assembly @ Genome Access Course
March 31, 2014 |
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The next 10 years of quantitative biology @ Keystone Symposia on Big Data in Biology
March 25, 2014 |
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Genome Assembly and Disease Analytics @ Brown
Feb 19, 2014 |
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A near perfect assembly of a eukaryotic genome @ AGBT
Feb 14, 2014 |
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Is the $1000 genome for real?
Jan 15, 2014 |
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De novo assembly of complex genomes using single molecule sequencing at PAG
Jan 14, 2014 |
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2013
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Preprint on Accurate detection of de novo and transmitted INDELs within exome-capture data
Dec 13, 2013 |
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Genome Assembly with iPlant [Video]
Dec 4, 2013 |
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CSHL Advanced Sequencing Course
Nov 20, 2013 |
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Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis
Oct 23, 2013 |
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Our Bodies, Our Data [@Wired]
Oct 8, 2013 |
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Transcriptome Assembly, No Reference Required!
Oct 8, 2013 |
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Beyond the Genome Informatics Challenge
Oct 3, 2013 |
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WSBS QB Bootcamp
Sept 3-5, 2013 |
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CSHL Undergraduate Research Program in Bioinformatics
June 4 - Aug 9, 2013 |
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Results from Assemblathon 2 competition published in GigaScience
July 22, 2013 |
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The advantages of SMRT sequencing
July 3, 2013 |
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The DNA60IFX Contest [blog]
June 28, 2013 |
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The DNA Data Deluge in IEEE Spectrum
June 27, 2013 |
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Hybrid de novo assembly of eukaryotic genomes
June 18, 2013 |
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Genomics puzzles and prizes
May 29, 2013 |
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Genome of the sacred lotus published in Genome Biology
May 10, 2013 |
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HMP Webinar on Microbiome Asembly [slides]
May 2, 2013 |
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Sixty years of genome biology
April 25, 2013 |
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DNA60 Bioinformatics Challenge Begins
April 22, 2013 |
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Genome Access: Sequencing and Assembly
April 21, 2013 |
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De novo assembly of complex genomes @ UVA
April 10, 2013 |
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Companies 'going long' generate sequencing buzz at Marco Island
April 5, 2013 |
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Selling your most personal item: You
March 27, 2013 |
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Cloud-scale Sequence Analysis @ NY Genome Center/AWS Meetup
Mar 18, 2013 |
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Aluminum tolerance in maize is associated with higher MATE1 gene copy number
March 12, 2013 |
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Assembling Crop Genomes with Single Molecule Sequencing
Feb 22, 2013 |
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Wired magazine on big data challenges in genomics
Feb 20, 2013 |
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Gene sequencing leaves the laboratory
Feb 19, 2013 |
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Searching for GATTACA: Notes on the BWT
Feb 6, 2013 |
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Schatz comments on using Knome for genomics in the NY Times
Feb 2, 2013 |
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Computer Science and Genetics at Cold Spring Harbor High School
Jan 8, 2013 |
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2012
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Genome sequencing's big fix in the CSHL Harbor Transcript
Dec 15, 2012 |
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CSHL Quantitative Biology Bioinformatics Slides.
Dec 4, 2012 |
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Computational thinking in the era of big data biology
Nov 29, 2012 |
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Human Genetics and Plant Genomics: The long and the short of it.
Nov 22, 2012 |
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SBU Graduate Genetics slides.
Nov 6, 2012 |
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Assembling crop genomes with 2nd and 3rd gen sequencing.
Oct 8, 2012 |
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Answering the demands of digital genomics.
Oct 4, 2012 |
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F1000 review on the Interdependence of cell growth and gene expression: origins and consequences.
Sept 26, 2012 |
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Genotyping in the Cloud with Crossbow
Sept 6, 2012 |
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WSBS Quantitative Biology Bootcamp 2012
August 30, 2012 |
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Lectures posted from CSHL undergraduate research program
July 27, 2012 |
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The rise of a digital immune system
July 12, 2012 |
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Hybrid error correction and de novo assembly of single-molecule sequencing reads
July 1, 2012 |
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Schatz joins the editorial board at Genome Biology
June 29, 2012 |
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Genomic Dark Matter: The reliability of short read mapping illustrated by the Genome Mappability Score
June 6, 2012 |
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Current challenges in de novo plant genome sequencing and assembly
April 27, 2012 |
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De novo gene disruptions in children on the autistic spectrum [Watch]
April 25, 2012 |
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Classic paper on precise biophysical modeling of transcriptional regulation
April 3, 2012 |
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De novo genome assembly: what every biologist should know
March 27, 2012 |
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Meeting report from AGBT
March 27, 2012 |
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DNA in the Cloud at Big Think
Feb 18, 2012 |
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Improving de novo genome assembler with Metassembler at AGBT
Feb 17, 2012 |
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Feature-by-Feature: Evaluating De Novo Sequence Assembly
Feb 14, 2012 |
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F1000 review of Cortex
Feb 12, 2012 |
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The DNA Storage Saga
Jan 24, 2012 |
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De novo assembly of complex genomes using 3rd generation sequencing (GenomeWeb report)
Jan 15, 2012 |
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2011
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| » |
Lippman, Schatz lab collaboration uncovers a molecular "maturation clock" that modulates branching architecture in tomato plants
Dec 27, 2011 |
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Visualizing and assessing the quality of genome assemblies
Dec 24, 2011 |
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Applications of micro-, mega- and meta- assembly
Dec 12, 2011 |
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Slides from 2011 Quantitative Biology class posted
Dec 12, 2011 |
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Genome Research paper on GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Dec 6, 2011 |
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Schatz, McCombie interviewed by NY Times on the DNA Data Deluge
Dec 1, 2011 |
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PNAS paper on the sea squirt microbiome and the cancer-fighting agents in creates
Nov 28, 2011 |
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Giuseppe Narzisi joins the lab
Oct 28, 2011 |
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Meeting report from Beyond the Genome
Oct 24, 2011 |
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Frontiers in genomics: computational genomics
Oct 4-5, 2011 |
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Beyond the Genome: Keynote, Demo, and Panel
Sept 20, 2011 |
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Assemblathon 1 paper published in Genome Research
Sept 16, 2011 |
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Schatz quoted in Reuters on the future of funding of genomic research
Sept 12, 2011 |
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SMRT-Assembly Approaches: De Novo Assembly with 3rd Generation Sequencing
Sept 7, 2011 |
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Got Hadoop? Commentary in Genome Technology
Sept 1, 2011 |
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New paper on the comparative genomics of the deadly plant pathogen Xanthomonas
July 26, 2011 |
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Schatz and Ware awarded $5M DOE grant to assemble knowledgebase to aid biofuels and environmental efforts
July 15, 2011 |
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Lecture from undergraduate research program on bioinformatics posted
July 6, 2011 |
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Schatz quoted in article on future of GPUs for genomics
July 1, 2011 |
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New Paper Published on Genome Indexing with MapReduce
June 19, 2011 |
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Slides posted from joint ECMLS/3DAPAS Keynote and MapReduce'11
June 8, 2011 |
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| » |
Schatz appointed as associate member of the Laufer Center for Quantitative Biology at SBU
May 25, 2011 |
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Schatz awarded 2011 CSHL Winship Herr Award for Excellence in Teaching
May 1, 2011 |
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Proceedings from Data-Intensive Analysis Conference Available Online
April 18, 2011 |
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Computational Postdoc position posted
April 12, 2011 |
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Will Computers Crash Genomics?
Feb. 11 2011 |
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2010
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| » |
Schatz credited for putting Hadoop "on-the-map" in bioinformatics
Dec. 21, 2010 |
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Call for papers announced for MapReduce 2011
Dec. 21, 2010 |
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Report on the Beyond the Genome Conference
Dec. 9, 2010 |
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Schatz selected as a Young Investigator of the Year
Dec. 1, 2010 |
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Quake error correction method published in Genome Biology
Nov. 29, 2010 |
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Efficient Large-Scale Graph Analysis with Hadoop & Part 2
Nov. 18, 2010 |
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Lecture notes from 2010 CSHL QB & Bioinformatics course
Oct. 29, 2010 |
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Genome Assembly of the honey bee pest Varroa destructor
Oct. 25, 2010 |
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Research Highlight on Hydra published on F1000.
Sept. 16, 2010 |
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Turkey genome assembled from NGS reads published in PLoS Biology.
Sept. 7, 2010 |
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Research Highlight on Galaxy published in Genome Biology.
Aug 25, 2010 |
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Commentary on Cloud Computing published in Nature Biotechnology.
July 1, 2010. |
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