Search Results for: genome

We are a bioinformatics team within the Center for Biomedical Informatics and Information Technology’s (CBIIT’s) Cancer Informatics Branch (CIB)—soon to be referred to as the Informatics and Data Science (IDS) Program. Headed Read More...

The Advanced Biomedical Computational Sciences (ABCS) group provides technology development, scientific consultation, collaboration and training, research, software development, and high-performance computing support. ABCS encompasses specialized groups focusing on machine learning applied to the interpretation of 2 Read More...

The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Read More...

The CCR Collaborative Bioinformatics Resource (CCBR) is a centrally funded resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals. The group has Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More. New Resources on CREx NIMH Human Brain Collection Core (HBCC) The HBCC obtains human brain tissue, hair, and blood Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx Program Manager The CREx Team is happy to announce Deepika Velampati as the new CREx Program Read More...

CCR Office of Science and Technology Resources (OSTR) The Center for Cancer Research (CCR) Office of Science and Technology Resources (OSTR) explores and evaluates the latest technologic advancements and then makes them available to all Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. If you haven’t Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Research Festival The NIH Research Festival highlights the groundbreaking science and the vibrant NIH community driving our Read More...

Proteomic Data Common (PDC) represents the NCI’s largest public repository of proteogenomic comprehensive tumor datasets, essentially a Proteogenomic Cancer Atlas. It was developed to advance our understanding of how proteins help shape the risk, Read More...

Radiation Oncology Branch is part of CCR. Bioinformatics core is a collaborative resource to support ROB branch and provide service to ROB investigators from NCI and other Institutes access to new technologies, bioinformatics, statistical analysis Read More...

The NCI Cloud Resources are components of the NCI Cancer Research Data Commons (CRDC) that bring data and computational power together to enable cancer research and discovery. These cloud-based platforms eliminate the need for researchers Read More...

The OSTR offers cutting-edge technology platforms to the CCR scientific community through centralized facilities. The videos accessed through this page are designed to introduce the various scientific methodologies OSTR makes available through the cores on Read More...

What is Visium FFPE v2 with CytAssist? Visium FFPE v2 is sequencing-based spatial profiling technology developed by 10x Genomics. This assay can take mouse or human tissue sections on normal glass slides as input and Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Spotlight The NIH Lab Managers Working Group have developed a new NIH-wide database of cold Read More...

2024 Date: Tuesday, October 15, 2024 Time and Location: 11 am EST, ZOOM (INVITATION BY LMIG LIST SERVER) Speaker: Dr. Diego Presman (U Buenos Aires) Title: “Insights on Glucocorticoid Receptor Activity Through Live Cell Imaging” Summary: Eucaryotic transcription factors ( Read More...

10/05/2021 - This course walks through using and applying two popular, freely available genome browsers and how they can help bioinformatics analysis: the University of California Santa Cruz (UCSC) Genome Browser and the Integrative Genomics Viewer ( Read More...

09/16/2021 - In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. While these drafts and the updates that followed effectively covered Read More...

04/27/2021 - Register Session Description This course walks through using and applying two popular, freely available genome browsers and how they can help bioinformatics analysis: the University of California Santa Cruz (UCSC) Genome Browser and the Read More...

11/04/2020 - This course walks through using and applying two popular, freely available genome browsers and how they can help bioinformatics analysis: the University of California Santa Cruz (UCSC) Genome Browser and the Integrative Genomics Viewer ( Read More...

09/08/2020 - This course walks through using and applying two popular, freely available genome browsers and how they can help bioinformatics analysis: the University of California Santa Cruz (UCSC) Genome Browser and the Integrative Genomics Viewer ( Read More...

06/17/2020 - This course walks through using and applying two popular, freely available genome browsers and how they can help bioinformatics analysis: the University of California Santa Cruz (UCSC) Genome Browser and the Integrative Genomics Viewer ( Read More...

Why do we need a reference genome? {{Sdet}} Solution{{Esum}} The reference genome serves as a "known" that guides us in constructing the genome of the unknown from sequencing data. {{Edet}} What file Read More...

Here, we are going to align the Golden Snidget sequencing files to it's genome. Recall that we are working with RNA sequencing data. Given HISAT2 and Bowtie2 as the options for aligners, which is Read More...

To proceed with converting the bedgraph files to bigWig, we need to first create an index of our genome using SAMTOOLS. samtools faidx refs/22.fa Listing the contents of our refs directory, we now see Read More...

05/24/2021 - Dr. Adam Phillippy, a Senior Investigator at NHGRI will give an extremely interesting talk on Monday, 5/24 at 11 am via WebEx at https://nih.webex.com/nih/j.php?MTID=m237a8e77868c23cc4 Read More...

06/08/2020 - Extensive investigations have revealed intra-genomic variation in somatic mutation rates influenced by the sequence composition, structure, and local chromatin features of the genome. I will review the literature on mechanisms underlying the intra-genome mutational Read More...

06/01/2020 - After nearly two decades of improvements, the current human reference genome is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to end, and hundreds of Read More...

03/10/2020 - This course walks through using and applying two popular, freely available genome browsers and how they can help bioinformatics analysis: the University of California Santa Cruz (UCSC) Genome Browser and the Integrative Genomics Viewer ( Read More...

03/10/2020 - This course walks through using and applying two popular, freely available genome browsers and how they can help bioinformatics analysis: the University of California Santa Cruz (UCSC) Genome Browser and the Integrative Genomics Viewer ( Read More...

09/25/2012 - As the scientific world has moved from the pre-genomic to the post-genomic era the need for tools that enable the visualization, integration and interrogation of genomic-scale data has never been greater. This talk will Read More...

09/12/2024 - Telomere to telomere (T2T) genome assemblies represent a paradigm shift in comparative genomics, offering insights into chromosome structure, evolution, and function at the highest resolution. Dr. O'Neill's lab has made recent Read More...

02/28/2024 - In this seminar, you'll learn about the somatic variant caller named Lancet. This accurate, open-source tool leverages local assembly and joint analysis of tumor-normal, paired, high-throughput sequence data. New York Genome Center& Read More...

01/22/2024 - Dear Colleagues,    Optical Genome Maps (OGM) provide scaffolding information for large DNA molecules. In this talk, we describe the use of this technology for detecting structural variants and chaining them Read More...

11/29/2023 - In this seminar, you'll learn about the somatic variant caller named Lancet. This accurate, open-source tool leverages local assembly and joint analysis of tumor-normal, paired, high-throughput sequence data. New York Genome Center& Read More...

Let's start our exploration of sequencing read alignment by discussing the reference genome for human chromosome 22. For this, change into our ~/biostar_class/hbr_uhr/refs folder. In Lesson 9, we discussed why we need Read More...

Let's start our exploration of sequencing read alignment by discussing the reference genome for human chromosome 22. For this, change into our ~/biostar_class/hbr_uhr/refs folder. In Lesson 9, we discussed why we need Read More...

To proceed with converting the bedGraph files to bigWig, we need to first create an index of our genome using SAMTOOLS and it's faidx feature. Where faidx will index/extract FASTA. samtools faidx refs/22. Read More...

After assessing the quality of our raw sequencing data and performing cleanup if necessary the step that follows alignment the raw sequencing data to a genome or transcriptome. What tools can we use? {{Sdet}} Answer{{ Read More...

Now that we have downloaded the Golden Snidget reference files let's take a moment to get to know the references. First, change into the refs folder. How do we do this from the ~/biostar_ Read More...

One of the things we will be doing quite often is to visualize genomics data using some sort of genome browser. In this course series, we will use a popular one called Integrative Genome Viewer( Read More...

One of the things we will be doing quite often is to visualize genomics data using some sort of genome browser. In this course series, we will use a popular one called Integrative Genome Viewer( Read More...

Get to know the HBR and UHR dataset Introduce ourselves to the concept of reference genomes Provide a brief introduction to the Integrative Genome Viewer - will focus on visualizing our reference and annotation files

07/13/2023 - The Comparative Genome Viewer (CGV) is a visualization tool that helps you quickly compare two genomes based on assembly-assembly alignments provided by NCBI. CGV includes eukaryotic (animal, plant and fungal) assemblies, and many cross-species Read More...

06/06/2023 - Dr. Maximilian Haeussler is the co-PI for the  UCSC Genome Browser , an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with Read More...

01/24/2022 - Please plan to attend the Earl Stadtman Investigator Program search seminar by: Elizabeth Finn, Ph.D. Laboratory of Receptor Biology and Gene Expression, CCR Dr. Finn studies the large-scale features of genome organization within Read More...

05/26/2021 - Register This month’s Cancer Genomics Cloud (CGC) webinar welcomes Dr. Wenming Xiao, a lead bioinformatics scientist at the U.S. Food and Drug Administration. Dr. Xiao specializes in researching how computational, technical, and Read More...

04/14/2021 - Registration: https://cbiit.webex.com/cbiit/onstage/g.php?MTID=ec198bc69667ba131397fb48e0c9b9708 Presenter: Christian Zinser PhD Head of Bioinformativs at Precigen Bioinformatics Germany Description: This presentation will give you Read More...

08/20/2020 - Single nucleotide polymorphism (SNP) & Variation Suite (SVS) is an analytic tool created to empower researchers to perform complex analyses and visualizations on genomic and phenotypic data. Genome-Wide Association Studies (GWAS) continues to be Read More...

05/09/2018 - Driven by the decreasing costs and increasing performance of next-generation sequencing (NGS) technologies, the amount of publicly available genomic data has grown exponentially in recent years.  While most of the analyses of these data Read More...

12/13/2016 - Driven by the decreasing costs and increasing performance of next-generation sequencing (NGS) technologies, the amount of publicly available genomic data has grown exponentially in recent years.  While most of the analyses of these data Read More...

The reference genome is a completely assembled sequence (ie. the order in which the nucleotides are arranged is known). For high throughput sequencing, the known sequence help scientists find out where in the genome each Read More...

The UCSC Genome Browser is the "goto tool" for viewing sequence data in a genomic context. It's wide variety of supported organisms and data types, coupled with its responsive performance make it Read More...

04/22/2021 - Meeting link: https://cbiit.webex.com/cbiit/j.php?MTID=m2e54a1e4fca4e029e3691210f2422599 Meeting number: 160 936 5213 Password: Please obtain your meeting password from your host. Cohost: Leonard Freedman Presenter: Justin Read More...

02/27/2025 - NGS produces millions of sequences per sample and the challenge is to identify where in the genome each sequence came from. Fortunately, there are aligners that help scientists with this task. After this class, Read More...

Now that we have downloaded the HBR and UHR dataset and know where analysis tools are, let's start learning about RNA sequencing, by first learning about our reference genome and annotation files. Let's Read More...

Now that we have downloaded the HBR and UHR dataset and know where analysis tools are, let's start learning about RNA sequencing, by first learning about our reference genome and annotation files. Let's Read More...

The bowtie2-build indexer builds a Bowtie index from a set of DNA sequences ([ref]. "bowtie2-build" builds a Bowtie index from a set of DNA sequences. "bowtie2-build" outputs a Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinfo environment. conda activate bioinfo Then create a new directory for files we will be working with today in Read More...

Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...

Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...

Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, Read More...

Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, Read More...

06/07/2023 - Join us for the upcoming CCR Fellows & Young Investigators-Seminar Series ( CCR FYI-SS 2022/2023 )  which is being held as a ‘ virtual ’ seminar that is open to everyone!  Julianna King , Laboratory Animal Sciences Program (LASP) “Genome-wide Read More...

07/27/2022 - Many recent studies highlighted the improved capability of long-read sequencing to detect structural variation in the human genome. For example, these technologies was also recently utilized to produce the first complete assembly of the Read More...

06/06/2022 - Are you a cancer researcher or bioinformatician wanting to learn more about how the experts at NCI’s  Genomic Data Commons  (GDC) process a variety of molecular data types? This month’s GDC support Read More...

01/12/2021 - Please plan to attend the Earl Stadtman Investigator Program search seminar by: Mikhail Kolmogorov, Ph.D. University of California, San Diego Dr. Kolmogorov's research focus is bioinformatics. Particularly, he is interested in algorithms Read More...

11/17/2020 - Register The goal of this meeting is to critically address the wealth of new data generated by bulk and single-cell molecular, imaging and computational approaches that are increasingly revealing how the genome folds to Read More...

11/16/2020 - Register The goal of this meeting is to critically address the wealth of new data generated by bulk and single-cell molecular, imaging and computational approaches that are increasingly revealing how the genome folds to Read More...

08/28/2020 - Speaker: Dr. Christian Zinser, Precigen Bioinformatics Registration The Genomatix Genome Analyzer (GGA) aids in analyzing next generation sequencing (NGS) data from ChIP, RNA, DNA, methylation, or small RNA sequencing. This introductory webinar gives an Read More...

07/27/2020 - The GDC RNA-Seq Analysis pipeline quantifies protein-coding gene expression. RNA-Seq data is aligned to the reference genome to detect splice junctions and then re-aligned to increase quality. Gene expression quantification and fusion detection are Read More...

BOWTIE2 is a non-splice aware aligner that is used for analyzing DNA sequences. The hcc1395 FASTQ files will be aligned to the human chromosome 22 reference genome to compare the differences between the alignment outcome obtained Read More...

To view genomic alignment output using IGV, an index for the reference needs to be created. samtools can be used to create the index. Recall that reference genome is located in the references folder and Read More...

After QC as well as quality and/or adapter trimming, it is time to map the sequences in the FASTQ files to the reference genome. RNA sequencing analysis requires the use of a splice aware Read More...

10/27/2021 - Wrapping up its final webinar of 2021, the NCI Cancer Research Data Commons (CRDC) Cancer Genomics Cloud (CGC) welcomes Cold Spring Harbor Laboratory fellow Dr. Pascal Belleau. He will share his findings from recent work Read More...

02/24/2021 - Register/Join Dennis A. Dean II. Ph.D.  serves as a Principle Investigator at Seven Bridges. In this upcoming Cancer Genome Cloud (CGC) monthly webinar, Dr. Dennis Dean will share his experience working with Read More...

07/11/2025 - SIG Website : https://oir.nih.gov/ sig s/ long-read Agenda: https://docs.google.com/document/d/1ytKXJa17vRyq9FnooW4Bs9gTiAJbOccZM6XLoI1SAgA/edit?usp=sharing Signup to the mailing list: https://list.nih. Read More...

11/21/2024 - Dear FNL colleagues,   It’s time once again for our last in 2024 Biotech Connector event!!   The Frederick National Laboratory for Cancer Research together with the Frederick County Chamber of Commerce organizes the quarterly Biotech Read More...

Let's open IGV locally on our computer. Then we will copy the Golden Snidget refs folder to our public directory so we can download and use these locally. Remember the location on your computer Read More...

Before getting started, remember to be signed on to the DNAnexus GOLD environment.

Before getting started, remember to be signed on to the DNAnexus GOLD environment.

Before getting started, remember to be signed on to the DNAnexus GOLD environment.

Before getting started, remember to be signed on to the DNAnexus GOLD environment.

Go to your biostar_class directory. cd biostar_class Create a new directory named "refs" and go to that directory. mkdir refs cd refs Use the following command to retrieve data from NCBI. Read More...

04/15/2021 - Presenter: Ichiro Hiratani, Ph.D. Team Leader Laboratory for Developmental Epigenetics RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), Japan JOIN WEBEX MEETING https://cbiit.webex.com/cbiit/j.php?MTID=m13d114a534 Read More...

01/23/2020 - Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power WGS/WES Pipelines at NIH Pipeline performance Using Pipeliner for internal and external data Variant QC, Annotation Read More...

The tool HISAT2 will be used to align the trimmed hcc1395 FASTQ files to the human chromosome 22 reference. RNA sequencing analyses require the use of splice aware aligners in order to map sequences that span Read More...

Learn to align the sequencing reads to reference Familiarize ourselves with the content of alignment output files (SAM) Learn to use SAMTOOLS to work with alignment output

10/24/2019 - https://videocast.nih.gov/summary.asp?live=34578 NIH Users please connect via VPN to view this video Presenter: Steven Salzberg, Ph.D. Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science and Biostatistics and Director Read More...

09/10/2019 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/aa908acc7fd64f3fac4579bc3b69725d/playback

2016-2024 Publications using images obtained in OMC

2025 Sebastian R, Sun EG, Fedkenheuer M, Fu H, Jung S, Thakur BL, Redon CE, Pegoraro G, Tran AD, Gross JM, Mosavarpour S, Kusi NA, Ray A, Dhall A, Pongor LS, Casellas R, Aladjem MI. Mechanism Read More...

07/21/2025 - Profe or Angela Brook i a leader in the development and application of high-throughput genomic and computational approache to inve tigate gene regulation. Her re earch focu e on characterizing mutation impacting RNA expre Read More...

05/22/2025 - It took over $3 billion and 13 years to sequence the first human genome. Today, we can sequence a genome in a single day for less than $1,000.  That incredible technological advancement has led to the generation Read More...

03/13/2025 - UCSC Xena showcases seminal cancer genomics datasets from The Cancer Genome Atlas (TCGA) and the Pan-Cancer Atlas, as well as the Genomic Data Commons, Pan-cancer Atlas of Whole Genomes, and the International Cancer Genome Read More...

01/27/2025 - NCI CCR Liver Cancer Program Seminar Series Dr. Sethupathy is professor of physiological genomics and chair of the Department of Biomedical Sciences at Cornell University. He leads a research lab focused on genome-scale and Read More...

12/02/2025 - The SeqSPACE Planning Committee is pleased to announce a two-part webinar series highlighting the work of four junior investigators selected through our recent call for abstracts. Part 1 will feature presentations by Dr. Jing Dong Read More...

10/29/2025 - The Buenrostro lab is broadly dedicated to advancing our knowledge of gene regulation and the downstream consequences on cell fate decisions. To do this, the Buenrostro lab develops new technologies utilizing molecular biology, microscopy Read More...

07/01/2025 - Learn how to vi ualize equencing and analy i re ult effectively. Thi e ion de cribe the application of the web-ba ed interactive OmicCirco in R hiny to con truct circular plot with Read More...

06/17/2025 - Explore tran cription factor binding ite analy i and peak calling. Thi training will introduce ChIP- eq data analy i followed by a tep-by- tep live demon tration of a ChIP- eq analy i Read More...

06/10/2025 - Under tand how to identify and interpret variant . Thi training will introduce Exome equencing data analy i followed by a tep-by- tep live demon tration of an exome equencing analy i workflow u ing Read More...

nf-core is a community effort to generate a curated set of standardized, best-practice, reproducible, documented, NGS analysis pipelines. All these workflows are built using the versatile workflow manager, Nextflow , and have been released under the Read More...

Long read sequencing was recently named 2022’s method of the year by Nature Methods . Long read sequencing technologies, those that generate sequence reads with lengths of 10s of kilobases or longer have several advantages over Read More...

03/04/2025 - Alignment of RNA sequencing data enables researchers to identify where in the genome each sequence came from. However, it does not inform of how many sequences aligned to each genomic feature such as a Read More...

01/10/2025 - NIH DIRECTORS SEMINAR SERIES In this presentation, Dr. Scholz will discuss the approach to tackling complex neurodegenerative diseases using modern genomic tools, focusing on Lewy body dementia, a major research area in her lab. Read More...

10/24/2024 - Recent advances in artificial intelligence (AI) have revolutionized the use of hematoxylin and eosin (H&E)-stained tumor slides for precision oncology, enabling data-driven approaches to predict molecular characteristics and therapeutic outcomes. In Read More...

09/13/2024 - Reverse-phase protein arrays (RPPAs) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and develop novel cancer therapies.   To facilitate community-based investigation of the large-scale protein expression data generated by Read More...

08/29/2024 - Dr. Mardis is an internationally recognized expert in cancer genomics, with ongoing interests in the integrated characterization of cancer genomes, defining DNA-based somatic and germline interactions and RNA-based pathways, and immune microenvironments that lead Read More...

08/23/2024 - In this webinar, Dr. Carey will provide an introduction to Bioconductor for genomic data science.   Bioconductor.org enters its third decade as an NHGRI/NCI-funded resource for many aspects of genomic data Read More...

01/13/2026 - The past decade has witnessed thriving cell atlas research activities in elucidating human cell types and their organization principles. The NIH BRAIN Initiative launched a pilot 3-year BRAIN Initiative Cell Census Consortium (BICCC) in 2014, Read More...

This is part II of the article highlighting nf-core pipelines and specifically addresses the use of these pipelines in the DNAnexus cloud environment. Part I of the article can be found in the October 2023 topic Read More...

04/16/2025 - Updated Location: ATRF, Frederick MD, Main Auditorium What to bring:  Laptop capable of connecting to internet via NIH wifi For questions or to register, please contact Amy Stonelake ( amy.stonelake@nih.gov ) Read More...

04/15/2025 - What to bring:  Laptop capable of connecting to internet via NIH  wifi Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?& Read More...

General questions or comments about the BTEP program or classes should be addressed to: NCIBTEP@nih.gov Amy Stonelake, Ph.D . BTEP Program Manager and Bioinformatics Analyst amy.stonelake@nih.gov I am an experienced Read More...

01/22/2025 - This three hour online training covers QIAGEN’s CLC Genomics Workbench enables researchers to analyze NGS data without the use of command line and is a powerful tool for determining differential expression. Read More...

Listed below are the video recordings of past BTEP events (classes, seminars, workshops). Videos are hosted on various servers and may play slightly differently. Some videos may be downloaded for local viewing. Recorded Videos of Read More...

10/24/2024 - NIH Text Mining and Natural Language Processing SIG is pleased to welcome you to this special event featuring two extraordinary speakers focused on the applications of Deep Learning in Computational Biology.  & Read More...

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