RESEARCH ROUNDUP: MAY 7, 2021 Welcome to the May 7, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A protein that helps tumors hide Immune checkpoint inhibitors boost the immune system’s ability to find and destroy tumor cells, but they don’t work for most cancer

patients.

HAPLOVIEW | BROAD INSTITUTESCIENCEABOUT THE BROAD INSTITUTECONTACT AND

SUPPORT

Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, David Bender, Julian Maller, and Jesse Whitworth. The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT MediaLab. Thanks to Andrew Kirby and Hin-Tak Leung for code contributions. HUNG LAB | BROAD INSTITUTE Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

MITOCARTA3.0: AN INVENTORY OF MAMMALIAN MITOCHONDRIAL MitoCarta3.0 is an inventory of 1136 human and 1140 mouse genes encoding proteins with strong support of mitochondrial localization, now with sub-mitochondrial compartment and pathway annotations. To generate this inventory, we performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy,

SINGLE CELL PORTAL

BETA. Reducing barriers and accelerating single-cell research. Featuring 342 studies 13,162,502 cells . COVID-19 Studies CRISPICK - BROAD INSTITUTE CRISPick - Broad Institute

SPLICEAI LOOKUP

To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or

JESSE BOEHM

Jesse Boehm is associate director of the Boehm Group. The Boehm group is focused on bringing the power of functional genomics to bear on living samples from cancer patients. An ultimate goal is to make “precision functional genomics” a reality for patients with rare cancers and rare genotypes. REGISTER - SPECTRUM MILL The current release of Spectrum Mill, v7.07, from the Broad Institute is intended for experienced users of SM with a prior version, v6.0 (released Oct 2016) from Agilent.

GATK

The industry-standard GATK Best Practices. When you're isolating DNA in the lab, you don't treat the work like isolated, disconnected tasks. Every task is a step in a well-documented protocol, carefully developed to optimize yield, purity and to ensure reproducibility as RESEARCH ROUNDUP: MAY 7, 2021 Welcome to the May 7, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A protein that helps tumors hide Immune checkpoint inhibitors boost the immune system’s ability to find and destroy tumor cells, but they don’t work for most cancer

patients.

HAPLOVIEW | BROAD INSTITUTESCIENCEABOUT THE BROAD INSTITUTECONTACT AND

SUPPORT

Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, David Bender, Julian Maller, and Jesse Whitworth. The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT MediaLab. Thanks to Andrew Kirby and Hin-Tak Leung for code contributions. HUNG LAB | BROAD INSTITUTE Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

MITOCARTA3.0: AN INVENTORY OF MAMMALIAN MITOCHONDRIAL MitoCarta3.0 is an inventory of 1136 human and 1140 mouse genes encoding proteins with strong support of mitochondrial localization, now with sub-mitochondrial compartment and pathway annotations. To generate this inventory, we performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy,

SINGLE CELL PORTAL

BETA. Reducing barriers and accelerating single-cell research. Featuring 342 studies 13,162,502 cells . COVID-19 Studies CRISPICK - BROAD INSTITUTE CRISPick - Broad Institute

SPLICEAI LOOKUP

To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or

JESSE BOEHM

Jesse Boehm is associate director of the Boehm Group. The Boehm group is focused on bringing the power of functional genomics to bear on living samples from cancer patients. An ultimate goal is to make “precision functional genomics” a reality for patients with rare cancers and rare genotypes. REGISTER - SPECTRUM MILL The current release of Spectrum Mill, v7.07, from the Broad Institute is intended for experienced users of SM with a prior version, v6.0 (released Oct 2016) from Agilent.

GATK

The industry-standard GATK Best Practices. When you're isolating DNA in the lab, you don't treat the work like isolated, disconnected tasks. Every task is a step in a well-documented protocol, carefully developed to optimize yield, purity and to ensure reproducibility as

BROAD INSTITUTE

Broad Institute is committed to making the extensive data, methods, and technologies it generates rapidly and readily accessible to the scientific community to drive biomedical progress around the world RESEARCH ROUNDUP: JUNE 4, 2021 Welcome to the June 4, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A potential therapeutic approach for sickle cell disease. Sickle cell disease (SCD) is the most common deadly genetic disorder, leading to chronic pain, organ failure, and early death in patients.

USER ACCOUNT

Enter the password that accompanies your username. Or log in with Login with Google. Twitter; Facebook; YouTube; Instagram STUDY OF SEVERE COVID-19 HELPS UNCOVER THE ROOTS OF SEPSIS Sepsis is a dreaded, life-threatening condition that can occur when an infection spins out of control. Like a tsunami after an earthquake, sepsis occurs when an infection triggers a dysregulation of the immune system, which leads to widespread organ damage and even death. RESEARCHERS IDENTIFY POTENTIAL NEW TARGETS FOR NEXT Current COVID-19 vaccines are effective at preventing severe disease, including infection caused by known variants of concern. But new variants of the SARS-CoV-2 virus could potentially evade immunity, so vaccine makers have already started developing next-generation

vaccines.

HUNG LAB | BROAD INSTITUTE Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

STUDY LINKS BLOOD CELL MUTATIONS TO INCREASED INFECTION Zekavat S. et al. Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection. Nature Medicine.Online June 7, 2021. DOI: 10.1038/s41591-021-01371-0. GENETIC BASE EDITING TREATS SICKLE CELL DISEASE IN MICE Newby GA, Yen JS, Woodard KJ, Mayuranathan T et al. Base editing of haematopoietic stem cells rescues sickle cell disease in mice. Nature.Online June 2, 2021. DOI: 10.1038/s41586-021-03609-w

RAVI THADHANI

Ravi Thadhani is the chief academic officer of Mass General Brigham (MGB). He manages a roughly $2 billion research enterprise. He oversees several key system-wide departments at MGB, including human subjects affairs, the clinical trials office, research management, the MGB Biobank, and graduate medical education across MGB. Thadhani managed a research laboratory for 25 years,

SPLICEAI LOOKUP

To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or RESEARCH ROUNDUP: MAY 7, 2021 Welcome to the May 7, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A protein that helps tumors hide Immune checkpoint inhibitors boost the immune system’s ability to find and destroy tumor cells, but they don’t work for most cancer

patients.

HAPLOVIEW | BROAD INSTITUTESCIENCEABOUT THE BROAD INSTITUTECONTACT AND

SUPPORT

Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, David Bender, Julian Maller, and Jesse Whitworth. The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT MediaLab. Thanks to Andrew Kirby and Hin-Tak Leung for code contributions. HUNG LAB | BROAD INSTITUTE Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

MITOCARTA3.0: AN INVENTORY OF MAMMALIAN MITOCHONDRIAL MitoCarta3.0 is an inventory of 1136 human and 1140 mouse genes encoding proteins with strong support of mitochondrial localization, now with sub-mitochondrial compartment and pathway annotations. To generate this inventory, we performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy,

SINGLE CELL PORTAL

BETA. Reducing barriers and accelerating single-cell research. Featuring 342 studies 13,162,502 cells . COVID-19 Studies CRISPICK - BROAD INSTITUTE CRISPick - Broad Institute

SPLICEAI LOOKUP

To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or

JESSE BOEHM

Jesse Boehm is associate director of the Boehm Group. The Boehm group is focused on bringing the power of functional genomics to bear on living samples from cancer patients. An ultimate goal is to make “precision functional genomics” a reality for patients with rare cancers and rare genotypes. REGISTER - SPECTRUM MILL The current release of Spectrum Mill, v7.07, from the Broad Institute is intended for experienced users of SM with a prior version, v6.0 (released Oct 2016) from Agilent.

GATK

The industry-standard GATK Best Practices. When you're isolating DNA in the lab, you don't treat the work like isolated, disconnected tasks. Every task is a step in a well-documented protocol, carefully developed to optimize yield, purity and to ensure reproducibility as RESEARCH ROUNDUP: MAY 7, 2021 Welcome to the May 7, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A protein that helps tumors hide Immune checkpoint inhibitors boost the immune system’s ability to find and destroy tumor cells, but they don’t work for most cancer

patients.

HAPLOVIEW | BROAD INSTITUTESCIENCEABOUT THE BROAD INSTITUTECONTACT AND

SUPPORT

Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, David Bender, Julian Maller, and Jesse Whitworth. The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT MediaLab. Thanks to Andrew Kirby and Hin-Tak Leung for code contributions. HUNG LAB | BROAD INSTITUTE Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

MITOCARTA3.0: AN INVENTORY OF MAMMALIAN MITOCHONDRIAL MitoCarta3.0 is an inventory of 1136 human and 1140 mouse genes encoding proteins with strong support of mitochondrial localization, now with sub-mitochondrial compartment and pathway annotations. To generate this inventory, we performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy,

SINGLE CELL PORTAL

BETA. Reducing barriers and accelerating single-cell research. Featuring 342 studies 13,162,502 cells . COVID-19 Studies CRISPICK - BROAD INSTITUTE CRISPick - Broad Institute

SPLICEAI LOOKUP

To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or

JESSE BOEHM

Jesse Boehm is associate director of the Boehm Group. The Boehm group is focused on bringing the power of functional genomics to bear on living samples from cancer patients. An ultimate goal is to make “precision functional genomics” a reality for patients with rare cancers and rare genotypes. REGISTER - SPECTRUM MILL The current release of Spectrum Mill, v7.07, from the Broad Institute is intended for experienced users of SM with a prior version, v6.0 (released Oct 2016) from Agilent.

GATK

The industry-standard GATK Best Practices. When you're isolating DNA in the lab, you don't treat the work like isolated, disconnected tasks. Every task is a step in a well-documented protocol, carefully developed to optimize yield, purity and to ensure reproducibility as

BROAD INSTITUTE

Broad Institute is committed to making the extensive data, methods, and technologies it generates rapidly and readily accessible to the scientific community to drive biomedical progress around the world RESEARCH ROUNDUP: JUNE 4, 2021 Welcome to the June 4, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A potential therapeutic approach for sickle cell disease. Sickle cell disease (SCD) is the most common deadly genetic disorder, leading to chronic pain, organ failure, and early death in patients.

USER ACCOUNT

Enter the password that accompanies your username. Or log in with Login with Google. Twitter; Facebook; YouTube; Instagram STUDY OF SEVERE COVID-19 HELPS UNCOVER THE ROOTS OF SEPSIS Sepsis is a dreaded, life-threatening condition that can occur when an infection spins out of control. Like a tsunami after an earthquake, sepsis occurs when an infection triggers a dysregulation of the immune system, which leads to widespread organ damage and even death. RESEARCHERS IDENTIFY POTENTIAL NEW TARGETS FOR NEXT Current COVID-19 vaccines are effective at preventing severe disease, including infection caused by known variants of concern. But new variants of the SARS-CoV-2 virus could potentially evade immunity, so vaccine makers have already started developing next-generation

vaccines.

HUNG LAB | BROAD INSTITUTE Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

STUDY LINKS BLOOD CELL MUTATIONS TO INCREASED INFECTION Zekavat S. et al. Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection. Nature Medicine.Online June 7, 2021. DOI: 10.1038/s41591-021-01371-0. GENETIC BASE EDITING TREATS SICKLE CELL DISEASE IN MICE Newby GA, Yen JS, Woodard KJ, Mayuranathan T et al. Base editing of haematopoietic stem cells rescues sickle cell disease in mice. Nature.Online June 2, 2021. DOI: 10.1038/s41586-021-03609-w

RAVI THADHANI

Ravi Thadhani is the chief academic officer of Mass General Brigham (MGB). He manages a roughly $2 billion research enterprise. He oversees several key system-wide departments at MGB, including human subjects affairs, the clinical trials office, research management, the MGB Biobank, and graduate medical education across MGB. Thadhani managed a research laboratory for 25 years,

SPLICEAI LOOKUP

To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or RESEARCH ROUNDUP: MAY 7, 2021 Welcome to the May 7, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A protein that helps tumors hide Immune checkpoint inhibitors boost the immune system’s ability to find and destroy tumor cells, but they don’t work for most cancer

patients.

HAPLOVIEW | BROAD INSTITUTESCIENCEABOUT THE BROAD INSTITUTECONTACT AND

SUPPORT

Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, David Bender, Julian Maller, and Jesse Whitworth. The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT MediaLab. Thanks to Andrew Kirby and Hin-Tak Leung for code contributions. HUNG LAB | BROAD INSTITUTE Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

MITOCARTA3.0: AN INVENTORY OF MAMMALIAN MITOCHONDRIAL MitoCarta3.0 is an inventory of 1136 human and 1140 mouse genes encoding proteins with strong support of mitochondrial localization, now with sub-mitochondrial compartment and pathway annotations. To generate this inventory, we performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy,

SINGLE CELL PORTAL

BETA. Reducing barriers and accelerating single-cell research. Featuring 342 studies 13,162,502 cells . COVID-19 Studies CRISPICK - BROAD INSTITUTE CRISPick - Broad Institute

SPLICEAI LOOKUP

To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or

JESSE BOEHM

Jesse Boehm is associate director of the Boehm Group. The Boehm group is focused on bringing the power of functional genomics to bear on living samples from cancer patients. An ultimate goal is to make “precision functional genomics” a reality for patients with rare cancers and rare genotypes. REGISTER - SPECTRUM MILL The current release of Spectrum Mill, v7.07, from the Broad Institute is intended for experienced users of SM with a prior version, v6.0 (released Oct 2016) from Agilent.

GATK

The industry-standard GATK Best Practices. When you're isolating DNA in the lab, you don't treat the work like isolated, disconnected tasks. Every task is a step in a well-documented protocol, carefully developed to optimize yield, purity and to ensure reproducibility as RESEARCH ROUNDUP: MAY 7, 2021 Welcome to the May 7, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A protein that helps tumors hide Immune checkpoint inhibitors boost the immune system’s ability to find and destroy tumor cells, but they don’t work for most cancer

patients.

HAPLOVIEW | BROAD INSTITUTESCIENCEABOUT THE BROAD INSTITUTECONTACT AND

SUPPORT

Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, David Bender, Julian Maller, and Jesse Whitworth. The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT MediaLab. Thanks to Andrew Kirby and Hin-Tak Leung for code contributions. HUNG LAB | BROAD INSTITUTE Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

MITOCARTA3.0: AN INVENTORY OF MAMMALIAN MITOCHONDRIAL MitoCarta3.0 is an inventory of 1136 human and 1140 mouse genes encoding proteins with strong support of mitochondrial localization, now with sub-mitochondrial compartment and pathway annotations. To generate this inventory, we performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy,

SINGLE CELL PORTAL

BETA. Reducing barriers and accelerating single-cell research. Featuring 342 studies 13,162,502 cells . COVID-19 Studies CRISPICK - BROAD INSTITUTE CRISPick - Broad Institute

SPLICEAI LOOKUP

To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or

JESSE BOEHM

Jesse Boehm is associate director of the Boehm Group. The Boehm group is focused on bringing the power of functional genomics to bear on living samples from cancer patients. An ultimate goal is to make “precision functional genomics” a reality for patients with rare cancers and rare genotypes. REGISTER - SPECTRUM MILL The current release of Spectrum Mill, v7.07, from the Broad Institute is intended for experienced users of SM with a prior version, v6.0 (released Oct 2016) from Agilent.

GATK

The industry-standard GATK Best Practices. When you're isolating DNA in the lab, you don't treat the work like isolated, disconnected tasks. Every task is a step in a well-documented protocol, carefully developed to optimize yield, purity and to ensure reproducibility as

BROAD INSTITUTE

Broad Institute is committed to making the extensive data, methods, and technologies it generates rapidly and readily accessible to the scientific community to drive biomedical progress around the world RESEARCH ROUNDUP: JUNE 4, 2021 Welcome to the June 4, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A potential therapeutic approach for sickle cell disease. Sickle cell disease (SCD) is the most common deadly genetic disorder, leading to chronic pain, organ failure, and early death in patients.

USER ACCOUNT

Enter the password that accompanies your username. Or log in with Login with Google. Twitter; Facebook; YouTube; Instagram RESEARCHERS IDENTIFY POTENTIAL NEW TARGETS FOR NEXT Current COVID-19 vaccines are effective at preventing severe disease, including infection caused by known variants of concern. But new variants of the SARS-CoV-2 virus could potentially evade immunity, so vaccine makers have already started developing next-generation

vaccines.

HUNG LAB | BROAD INSTITUTE Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

GENETIC BASE EDITING TREATS SICKLE CELL DISEASE IN MICE Newby GA, Yen JS, Woodard KJ, Mayuranathan T et al. Base editing of haematopoietic stem cells rescues sickle cell disease in mice. Nature.Online June 2, 2021. DOI: 10.1038/s41586-021-03609-w STUDY LINKS BLOOD CELL MUTATIONS TO INCREASED INFECTION Zekavat S. et al. Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection. Nature Medicine.Online June 7, 2021. DOI: 10.1038/s41591-021-01371-0.

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SPLICEAI LOOKUP

To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or

RAVI THADHANI

Ravi Thadhani is the chief academic officer of Mass General Brigham (MGB). He manages a roughly $2 billion research enterprise. He oversees several key system-wide departments at MGB, including human subjects affairs, the clinical trials office, research management, the MGB Biobank, and graduate medical education across MGB. Thadhani managed a research laboratory for 25 years, RESEARCH ROUNDUP: MAY 7, 2021 Welcome to the May 7, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A protein that helps tumors hide Immune checkpoint inhibitors boost the immune system’s ability to find and destroy tumor cells, but they don’t work for most cancer

patients.

MITOCARTA3.0: AN INVENTORY OF MAMMALIAN MITOCHONDRIAL MitoCarta3.0 is an inventory of 1136 human and 1140 mouse genes encoding proteins with strong support of mitochondrial localization, now with sub-mitochondrial compartment and pathway annotations. To generate this inventory, we performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy, HAPLOVIEW | BROAD INSTITUTE Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, David Bender, Julian Maller, and Jesse Whitworth. The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT MediaLab. Thanks to Andrew Kirby and Hin-Tak Leung for code contributions. HUNG LAB | BROAD INSTITUTEBROAD INSTITUTE CAMBRIDGEBROAD INSTITUTE INCBROAD INSTITUTE NEWSBROAD INSTITUTE ORGBROAD INSTITUTE STOCK Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

SINGLE CELL PORTAL

BETA. Reducing barriers and accelerating single-cell research. Featuring 342 studies 13,162,502 cells . COVID-19 Studies CRISPICK - BROAD INSTITUTE CRISPick - Broad Institute SPLICEAI LOOKUPGITHUB SPLICEAI To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or

JESSE BOEHM

Jesse Boehm is associate director of the Boehm Group. The Boehm group is focused on bringing the power of functional genomics to bear on living samples from cancer patients. An ultimate goal is to make “precision functional genomics” a reality for patients with rare cancers and rare genotypes. REGISTER - SPECTRUM MILLSPECTRUM SOFTWARE CONSTRUCTIONSPECTRUM SOFTWARE DOWNLOADMASS SPECTRUM DATABASESPECTRUM DATABASE SYSTEMSPECTRUM SOFTWARE SYSTEMSPECTRUM SOFTWARE TECHNOLOGY The current release of Spectrum Mill, v7.07, from the Broad Institute is intended for experienced users of SM with a prior version, v6.0 (released Oct 2016) from Agilent.

GATK

The industry-standard GATK Best Practices. When you're isolating DNA in the lab, you don't treat the work like isolated, disconnected tasks. Every task is a step in a well-documented protocol, carefully developed to optimize yield, purity and to ensure reproducibility as RESEARCH ROUNDUP: MAY 7, 2021 Welcome to the May 7, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A protein that helps tumors hide Immune checkpoint inhibitors boost the immune system’s ability to find and destroy tumor cells, but they don’t work for most cancer

patients.

MITOCARTA3.0: AN INVENTORY OF MAMMALIAN MITOCHONDRIAL MitoCarta3.0 is an inventory of 1136 human and 1140 mouse genes encoding proteins with strong support of mitochondrial localization, now with sub-mitochondrial compartment and pathway annotations. To generate this inventory, we performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy, HAPLOVIEW | BROAD INSTITUTE Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, David Bender, Julian Maller, and Jesse Whitworth. The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT MediaLab. Thanks to Andrew Kirby and Hin-Tak Leung for code contributions. HUNG LAB | BROAD INSTITUTEBROAD INSTITUTE CAMBRIDGEBROAD INSTITUTE INCBROAD INSTITUTE NEWSBROAD INSTITUTE ORGBROAD INSTITUTE STOCK Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

SINGLE CELL PORTAL

BETA. Reducing barriers and accelerating single-cell research. Featuring 342 studies 13,162,502 cells . COVID-19 Studies CRISPICK - BROAD INSTITUTE CRISPick - Broad Institute SPLICEAI LOOKUPGITHUB SPLICEAI To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or

JESSE BOEHM

Jesse Boehm is associate director of the Boehm Group. The Boehm group is focused on bringing the power of functional genomics to bear on living samples from cancer patients. An ultimate goal is to make “precision functional genomics” a reality for patients with rare cancers and rare genotypes. REGISTER - SPECTRUM MILLSPECTRUM SOFTWARE CONSTRUCTIONSPECTRUM SOFTWARE DOWNLOADMASS SPECTRUM DATABASESPECTRUM DATABASE SYSTEMSPECTRUM SOFTWARE SYSTEMSPECTRUM SOFTWARE TECHNOLOGY The current release of Spectrum Mill, v7.07, from the Broad Institute is intended for experienced users of SM with a prior version, v6.0 (released Oct 2016) from Agilent.

GATK

The industry-standard GATK Best Practices. When you're isolating DNA in the lab, you don't treat the work like isolated, disconnected tasks. Every task is a step in a well-documented protocol, carefully developed to optimize yield, purity and to ensure reproducibility as

BROAD INSTITUTE

Broad Institute is committed to making the extensive data, methods, and technologies it generates rapidly and readily accessible to the scientific community to drive biomedical progress around the world RESEARCH ROUNDUP: JUNE 4, 2021 Welcome to the June 4, 2021 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.. A potential therapeutic approach for sickle cell disease. Sickle cell disease (SCD) is the most common deadly genetic disorder, leading to chronic pain, organ failure, and early death in patients.

USER ACCOUNT

Enter the password that accompanies your username. Or log in with Login with Google. Twitter; Facebook; YouTube; Instagram RESEARCHERS IDENTIFY POTENTIAL NEW TARGETS FOR NEXT Current COVID-19 vaccines are effective at preventing severe disease, including infection caused by known variants of concern. But new variants of the SARS-CoV-2 virus could potentially evade immunity, so vaccine makers have already started developing next-generation

vaccines.

HUNG LAB | BROAD INSTITUTE Hung Lab. The Hung laboratory combines chemical and genomic approaches to define host-pathogen interactions and to reveal the critical pressure points of infectious disease. By using small organic molecules and applying systematic genetic perturbations, the lab hopes to gain new insight into bacterial responses to host immunity and

chemotherapy

GENETIC BASE EDITING TREATS SICKLE CELL DISEASE IN MICE Newby GA, Yen JS, Woodard KJ, Mayuranathan T et al. Base editing of haematopoietic stem cells rescues sickle cell disease in mice. Nature.Online June 2, 2021. DOI: 10.1038/s41586-021-03609-w STUDY LINKS BLOOD CELL MUTATIONS TO INCREASED INFECTION Zekavat S. et al. Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection. Nature Medicine.Online June 7, 2021. DOI: 10.1038/s41591-021-01371-0.

SINGLE CELL PORTAL

BETA. Reducing barriers and accelerating single-cell research. Featuring 342 studies 13,162,502 cells . COVID-19 Studies

RAVI THADHANI

Ravi Thadhani is the chief academic officer of Mass General Brigham (MGB). He manages a roughly $2 billion research enterprise. He oversees several key system-wide departments at MGB, including human subjects affairs, the clinical trials office, research management, the MGB Biobank, and graduate medical education across MGB. Thadhani managed a research laboratory for 25 years,

SPLICEAI LOOKUP

To post issues or feature requests, please use SpliceAI-lookup/issues June 2, 2021 - show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or Skip to main content ×

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Empowering scientists Broad Institute fosters an environment in which scientists can take risks on bold ideas with transformative potential

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Broad Institute is committed to addressing medical challenges across the world, including collaborating with scientists and public health experts to address important needs in developing countries Collaborating deeply Broad Institute is a mission-driven community that brings together researchers in medicine, biology, chemistry, computation, engineering, and mathematics from across MIT, Harvard, and Harvard-affiliated hospitals, along with collaborators around the world Propelling the understanding and treatment of disease Broad Institute of MIT and Harvard is empowering a revolution in biomedicine to accelerate the pace at which the world conquers disease Responding to COVID19 Learn how the Broad community is contributing to the global pandemic

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Broad Institute believes that progress in biomedical research requires a fully inclusive community across sex, race, ethnicity, sexual orientation, age, and gender identity Sharing data and knowledge Broad Institute is committed to making the extensive data, methods, and technologies it generates rapidly and readily accessible to the scientific community to drive biomedical progress around the world Building partnerships Broad Institute works to build and sustain international consortia to speed discovery in areas including psychiatric research, infectious disease, cardiovascular disease, and cancer Empowering scientists Broad Institute fosters an environment in which scientists can take risks on bold ideas with transformative potential

Reaching globally

Broad Institute is committed to addressing medical challenges across the world, including collaborating with scientists and public health experts to address important needs in developing countries Collaborating deeply Broad Institute is a mission-driven community that brings together researchers in medicine, biology, chemistry, computation, engineering, and mathematics from across MIT, Harvard, and Harvard-affiliated hospitals, along with collaborators around the world Propelling the understanding and treatment of disease Broad Institute of MIT and Harvard is empowering a revolution in biomedicine to accelerate the pace at which the world conquers disease Responding to COVID19 Learn how the Broad community is contributing to the global pandemic

response

Promoting inclusion

Broad Institute believes that progress in biomedical research requires a fully inclusive community across sex, race, ethnicity, sexual orientation, age, and gender identity Sharing data and knowledge Broad Institute is committed to making the extensive data, methods, and technologies it generates rapidly and readily accessible to the scientific community to drive biomedical progress around the world Building partnerships Broad Institute works to build and sustain international consortia to speed discovery in areas including psychiatric research, infectious disease, cardiovascular disease, and cancer

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Blog / 06.4.20

Introduction and spread of SARS-CoV-2 in the greater Boston area New data from the Broad Institute of MIT and Harvard, Massachusetts General Hospital, and the Massachusetts Department of Public Health provides insights into the entry of SARS-CoV-2 virus in the Boston area, and epidemiological events that shaped the trajectory of the epidemic in the region.Read more

News / 06.4.20

Single-cell map of the heart reveals wide cellular diversity The largest single-nucleus survey of the human heart to date uncovers several new cell types and a variety of gene expression patterns.Read

more

News / 06.4.20

Researchers discover new member of novel drug family for ‘undruggable’ targets Findings offer a roadmap for how to build compounds to target proteins for degradation by the cell’s recycling system.Read more

News / 06.3.20

How DNA crossovers can drive both healthy and abnormal sperm

formation

A single biological process may regulate key aspects of how parents' DNA recombines in sperm developmentRead more

News / 05.27.20

How Broad Institute is ramping up on-site scientific activity Scientists are returning to on-site lab work with new health and safety protocolsRead more

News / 06.5.20

Research Roundup: June 5, 2020 Helping deaf mice hear, understanding meiosis mistakes, making sense of TB evolution, and moreRead more

News / 05.27.20

International gnomAD Consortium releases its first major studies of human genetic variation Analyses of the largest publicly available catalog of human genomic data reveal new details on rare types of genetic variation and provide better tools for genetic disease diagnosis and drug development.Read

more

News / 06.3.20

Base editing restores partial hearing in mice By showing they could repair a single recessive mutation behind a form of hearing loss, researchers open the door to using base editing to address a broader range of conditionsRead more

Blog / 05.21.20

Researchers study single cells to ask why children generally fare better against COVID-19 In #WhyIScience Q&A, medical engineer Alex K. Shalek and biologist Jose Ordovas-Montanes talk about their work on pediatric COVID-19 patient samples and how they quickly pivoted their research to respond to the pandemic.Read more

Blog / 05.12.20

Combing through old drugs to find new ones for COVID-19 The Broad Institute’s Drug Repurposing Hub has opened its repository of nearly 7,000 drug compounds to help scientists discover COVID-19 treatments.Read more Spotlight / 05.18.20 Get Broad Institute news in your inbox Sign up for the Broad’s regular email newsletter to stay up-to-date on the latest news, research, and eventsRead more Spotlight / 05.21.20

COVID-19

Learn about COVID-19 clinical testing and research activities at Broad, as well as data and resources for scientists studying

COVID-19.Read more

Spotlight / 05.12.20

Broad@15

Experience the entire Broad@15 talk series.Read more

Blog / 02.3.20

#WhyIScience Q&A: A software engineer tells her story of moving from finance to biomedical research Eno-Abasi Augustine-Akpan talks about her career shift and her passion for mentoring young girls of color in science.Read more

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