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Article ; Online: VariantQC: a visual quality control report for variant evaluation.

Yan, Melissa Y / Ferguson, Betsy / Bimber, Benjamin N

2019 Volume 35, Issue 24, Page(s) 5370–5371

Abstract: Summary: Large scale genomic studies produce millions of sequence variants, generating datasets far too massive for manual inspection. To ensure variant and genotype data are consistent and accurate, it is necessary to evaluate variants prior to ... ...

Abstract	Summary: Large scale genomic studies produce millions of sequence variants, generating datasets far too massive for manual inspection. To ensure variant and genotype data are consistent and accurate, it is necessary to evaluate variants prior to downstream analysis using quality control (QC) reports. Variant call format (VCF) files are the standard format for representing variant data; however, generating summary statistics from these files is not always straightforward. While tools to summarize variant data exist, they generally produce simple text file tables, which still require additional processing and interpretation. VariantQC fills this gap as a user friendly, interactive visual QC report that generates and concisely summarizes statistics from VCF files. The report aggregates and summarizes variants by dataset, chromosome, sample and filter type. The VariantQC report is useful for high-level dataset summary, quality control and helps flag outliers. Furthermore, VariantQC operates on VCF files, so it can be easily integrated into many existing variant pipelines. Availability and implementation: DISCVRSeq's VariantQC tool is freely available as a Java program, with the compiled JAR and source code available from https://github.com/BimberLab/DISCVRSeq/. Documentation and example reports are available at https://bimberlab.github.io/DISCVRSeq/.
MeSH term(s)	Genetic Variation ; Genomics ; Genotype ; Quality Control ; Software
Language	English
Publishing date	2019-07-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btz560
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Article: Rapid, accurate mapping of transgene integration in viable rhesus macaque embryos using enhanced-specificity tagmentation-assisted PCR.

Ryu, Junghyun / Chan, William / Wettengel, Jochen M / Hanna, Carol B / Burwitz, Benjamin J / Hennebold, Jon D / Bimber, Benjamin N

Molecular therapy. Methods & clinical development

2022 Volume 24, Page(s) 241–254

Abstract: Genome engineering is a powerful tool ... ...

Abstract	Genome engineering is a powerful tool for
Language	English
Publishing date	2022-01-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2872938-9
ISSN	2329-0501 ; 2329-0501
ISSN (online)	2329-0501
ISSN	2329-0501
DOI	10.1016/j.omtm.2022.01.009
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Article ; Online: BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data.

Boggy, Gregory J / McElfresh, G W / Mahyari, Eisa / Ventura, Abigail B / Hansen, Scott G / Picker, Louis J / Bimber, Benjamin N

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 10, Page(s) 2791–2801

Abstract: Motivation: Single-cell sequencing methods provide previously impossible resolution into the transcriptome of individual cells. Cell hashing reduces single-cell sequencing costs by increasing capacity on droplet-based platforms. Cell hashing methods ... ...

Abstract	Motivation: Single-cell sequencing methods provide previously impossible resolution into the transcriptome of individual cells. Cell hashing reduces single-cell sequencing costs by increasing capacity on droplet-based platforms. Cell hashing methods rely on demultiplexing algorithms to accurately classify droplets; however, assumptions underlying these algorithms limit accuracy of demultiplexing, ultimately impacting the quality of single-cell sequencing analyses. Results: We present Bimodal Flexible Fitting (BFF) demultiplexing algorithms BFFcluster and BFFraw, a novel class of algorithms that rely on the single inviolable assumption that barcode count distributions are bimodal. We integrated these and other algorithms into cellhashR, a new R package that provides integrated QC and a single command to execute and compare multiple demultiplexing algorithms. We demonstrate that BFFcluster demultiplexing is both tunable and insensitive to issues with poorly behaved data that can confound other algorithms. Using two well-characterized reference datasets, we demonstrate that demultiplexing with BFF algorithms is accurate and consistent for both well-behaved and poorly behaved input data. Availability and implementation: cellhashR is available as an R package at https://github.com/BimberLab/cellhashR. cellhashR version 1.0.3 was used for the analyses in this manuscript and is archived on Zenodo at https://www.doi.org/10.5281/zenodo.6402477. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Algorithms ; Electronic Data Processing ; Sequence Analysis ; Single-Cell Analysis ; Software
Language	English
Publishing date	2022-05-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac213
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Article ; Online: The killer-cell immunoglobulin-like receptors of macaques.

Bimber, Benjamin N / Evans, David T

Immunological reviews

2015 Volume 267, Issue 1, Page(s) 246–258

Abstract: Natural killer (NK) cells play a central role in immune responses through direct cytotoxicity and the release of cytokines that prime adaptive immunity. In simian primates, NK cell responses are regulated by interactions between two highly polymorphic ... ...

Abstract	Natural killer (NK) cells play a central role in immune responses through direct cytotoxicity and the release of cytokines that prime adaptive immunity. In simian primates, NK cell responses are regulated by interactions between two highly polymorphic sets of molecules: the killer-cell immunoglobulin-like receptors (KIRs) and their major histocompatibility complex (MHC) class I ligands. KIR-MHC class I interactions in humans have been implicated in the outcome of a number viral diseases and cancers. However, studies to address the role of KIRs in animal models have been limited by the complex immunogenetics and lack of defined ligands for KIRs in non-human primates. Due to the rapid evolution of KIRs, there is little conservation among the KIR genes of different primate species and it is not possible to predict the specificity of KIRs from known KIR-MHC class I interactions in humans. Hence, the MHC class I ligands for KIRs in species other than humans are poorly defined. Here, we review the KIR genes of the rhesus macaque, an important animal model for human immunodeficiency virus infection and other infectious diseases, and the MHC class I ligands that have been identified for KIRs in this species.
MeSH term(s)	Animals ; Evolution, Molecular ; Genetic Variation/genetics ; Genetic Variation/immunology ; Haplotypes ; Histocompatibility Antigens Class I/genetics ; Histocompatibility Antigens Class I/immunology ; Histocompatibility Antigens Class I/metabolism ; Humans ; Killer Cells, Natural/immunology ; Killer Cells, Natural/metabolism ; Macaca/genetics ; Macaca/immunology ; Macaca/metabolism ; Protein Binding/immunology ; Receptors, KIR/genetics ; Receptors, KIR/immunology ; Receptors, KIR/metabolism
Chemical Substances	Histocompatibility Antigens Class I ; Receptors, KIR
Language	English
Publishing date	2015-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	391796-4
ISSN	1600-065X ; 0105-2896
ISSN (online)	1600-065X
ISSN	0105-2896
DOI	10.1111/imr.12329
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Article ; Online: mGAP: the macaque genotype and phenotype resource, a framework for accessing and interpreting macaque variant data, and identifying new models of human disease.

Bimber, Benjamin N / Yan, Melissa Y / Peterson, Samuel M / Ferguson, Betsy

BMC genomics

2019 Volume 20, Issue 1, Page(s) 176

Abstract: Background: Non-human primates (NHPs), particularly macaques, serve as critical and highly relevant pre-clinical models of human disease. The similarity in human and macaque natural disease susceptibility, along with parallel genetic risk alleles, ... ...

Abstract	Background: Non-human primates (NHPs), particularly macaques, serve as critical and highly relevant pre-clinical models of human disease. The similarity in human and macaque natural disease susceptibility, along with parallel genetic risk alleles, underscores the value of macaques in the development of effective treatment strategies. Nonetheless, there are limited genomic resources available to support the exploration and discovery of macaque models of inherited disease. Notably, there are few public databases tailored to searching NHP sequence variants, and no other database making use of centralized variant calling, or providing genotype-level data and predicted pathogenic effects for each variant. Results: The macaque Genotype And Phenotype (mGAP) resource is the first public website providing searchable, annotated macaque variant data. The mGAP resource includes a catalog of high confidence variants, derived from whole genome sequence (WGS). The current mGAP release at time of publication (1.7) contains 17,087,212 variants based on the sequence analysis of 293 rhesus macaques. A custom pipeline was developed to enable annotation of the macaque variants, leveraging human data sources that include regulatory elements (ENCODE, RegulomeDB), known disease- or phenotype-associated variants (GRASP), predicted impact (SIFT, PolyPhen2), and sequence conservation (Phylop, PhastCons). Currently mGAP includes 2767 variants that are identical to alleles listed in the human ClinVar database, of which 276 variants, spanning 258 genes, are identified as pathogenic. An additional 12,472 variants are predicted as high impact (SnpEff) and 13,129 are predicted as damaging (PolyPhen2). In total, these variants are predicted to be associated with more than 2000 human disease or phenotype entries reported in OMIM (Online Mendelian Inheritance in Man). Importantly, mGAP also provides genotype-level data for all subjects, allowing identification of specific individuals harboring alleles of interest. Conclusions: The mGAP resource provides variant and genotype data from hundreds of rhesus macaques, processed in a consistent manner across all subjects ( https://mgap.ohsu.edu ). Together with the extensive variant annotations, mGAP presents unprecedented opportunity to investigate potential genetic associations with currently characterized disease models, and to uncover new macaque models based on parallels with human risk alleles.
MeSH term(s)	Animals ; Computational Biology/methods ; Disease Models, Animal ; Genetic Variation ; Genotype ; Humans ; Information Storage and Retrieval ; Internet ; Macaca mulatta ; Phenotype
Language	English
Publishing date	2019-03-06
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-019-5559-7
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Article ; Online: A Multifunctional and Highly Adaptable Reporter System for CRISPR/Cas Editing.

Wettengel, Jochen M / Hansen-Palmus, Lea / Yusova, Sofiya / Rust, Lauren / Biswas, Sreya / Carson, Julien / Ryu, Junghyun / Bimber, Benjamin N / Hennebold, Jon D / Burwitz, Benjamin J

International journal of molecular sciences

2023 Volume 24, Issue 9

Abstract: CRISPR/Cas systems are some of the most promising tools for therapeutic genome editing. The use of these systems is contingent on the optimal designs of guides and homology-directed repair (HDR) templates. While this design can be achieved in silico, ... ...

Abstract	CRISPR/Cas systems are some of the most promising tools for therapeutic genome editing. The use of these systems is contingent on the optimal designs of guides and homology-directed repair (HDR) templates. While this design can be achieved in silico, validation and further optimization are usually performed with the help of reporter systems. Here, we describe a novel reporter system, termed BETLE, that allows for the fast, sensitive, and cell-specific detection of genome editing and template-specific HDR by encoding multiple reporter proteins in different open-reading frames. Out-of-frame non-homologous end joining (NHEJ) leads to the expression of either secretable NanoLuc luciferase, enabling a highly sensitive and low-cost analysis of editing, or fluorescent mTagBFP2, allowing for the enumeration and tissue-specific localization of genome-edited cells. BETLE includes a site to validate CRISPR/Cas systems for a sequence-of-interest, making it broadly adaptable. We evaluated BETLE using a defective moxGFP with a 39-base-pair deletion and showed spCas9, saCas9, and asCas12a editing as well as sequence-specific HDR and the repair of moxGFP in cell lines with single and multiple reporter integrants. Taken together, these data show that BETLE allows for the rapid detection and optimization of CRISPR/Cas genome editing and HDR in vitro and represents a state-of the art tool for future applications in vivo.
MeSH term(s)	CRISPR-Cas Systems/genetics ; DNA Breaks, Double-Stranded ; Gene Editing ; DNA End-Joining Repair ; Genome
Language	English
Publishing date	2023-05-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24098271
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Article ; Online: Epigenetic MLH1 silencing concurs with mismatch repair deficiency in sporadic, naturally occurring colorectal cancer in rhesus macaques.

Deycmar, Simon / Johnson, Brendan J / Ray, Karina / Schaaf, George W / Ryan, Declan Patrick / Cullin, Cassandra / Dozier, Brandy L / Ferguson, Betsy / Bimber, Benjamin N / Olson, John D / Caudell, David L / Whitlow, Christopher T / Solingapuram Sai, Kiran Kumar / Romero, Emily C / Villinger, Francois J / Burgos, Armando G / Ainsworth, Hannah C / Miller, Lance D / Hawkins, Gregory A /

Chou, Jeff W / Gomes, Bruno / Hettich, Michael / Ceppi, Maurizio / Charo, Jehad / Cline, J Mark

Journal of translational medicine

2024 Volume 22, Issue 1, Page(s) 292

Abstract: Background: Naturally occurring colorectal cancers (CRC) in rhesus macaques share many features with their human counterparts and are useful models for cancer immunotherapy; but mechanistic data are lacking regarding the comparative molecular ... ...

Abstract	Background: Naturally occurring colorectal cancers (CRC) in rhesus macaques share many features with their human counterparts and are useful models for cancer immunotherapy; but mechanistic data are lacking regarding the comparative molecular pathogenesis of these cancers. Methods: We conducted state-of-the-art imaging including CT and PET, clinical assessments, and pathological review of 24 rhesus macaques with naturally occurring CRC. Additionally, we molecularly characterized these tumors utilizing immunohistochemistry (IHC), microsatellite instability assays, DNAseq, transcriptomics, and developed a DNA methylation-specific qPCR assay for MLH1, CACNA1G, CDKN2A, CRABP1, and NEUROG1, human markers for CpG island methylator phenotype (CIMP). We furthermore employed Monte-Carlo simulations to in-silico model alterations in DNA topology in transcription-factor binding site-rich promoter regions upon experimentally demonstrated DNA methylation. Results: Similar cancer histology, progression patterns, and co-morbidities could be observed in rhesus as reported for human CRC patients. IHC identified loss of MLH1 and PMS2 in all cases, with functional microsatellite instability. DNA sequencing revealed the close genetic relatedness to human CRCs, including a similar mutational signature, chromosomal instability, and functionally-relevant mutations affecting KRAS (G12D), TP53 (R175H, R273), APC, AMER1, ALK, and ARID1A. Interestingly, MLH1 mutations were rarely identified on a somatic or germline level. Transcriptomics not only corroborated the similarities of rhesus and human CRCs, but also demonstrated the significant downregulation of MLH1 but not MSH2, MSH6, or PMS2 in rhesus CRCs. Methylation-specific qPCR suggested CIMP-positivity in 9/16 rhesus CRCs, but all 16/16 exhibited significant MLH1 promoter hypermethylation. DNA hypermethylation was modelled to affect DNA topology, particularly propeller twist and roll profiles. Modelling the DNA topology of a transcription factor binding motif (TFAP2A) in the MLH1 promoter that overlapped with a methylation-specific probe, we observed significant differences in DNA topology upon experimentally shown DNA methylation. This suggests a role of transcription factor binding interference in epigenetic silencing of MLH1 in rhesus CRCs. Conclusions:* These data indicate that epigenetic silencing suppresses MLH1 transcription, induces the loss of MLH1 protein, abrogates mismatch repair, and drives genomic instability in naturally occurring CRC in rhesus macaques. We consider this spontaneous, uninduced CRC in immunocompetent, treatment-naïve rhesus macaques to be a uniquely informative model for human CRC.
MeSH term(s)	Humans ; Animals ; Macaca mulatta/genetics ; Macaca mulatta/metabolism ; Microsatellite Instability ; MutL Protein Homolog 1/genetics ; Mismatch Repair Endonuclease PMS2/genetics ; Mismatch Repair Endonuclease PMS2/metabolism ; Colorectal Neoplasms/pathology ; DNA Methylation/genetics ; Epigenesis, Genetic ; Transcription Factors/genetics ; Transcription Factors/metabolism ; DNA/metabolism ; DNA Mismatch Repair/genetics ; Brain Neoplasms ; Neoplastic Syndromes, Hereditary
Chemical Substances	MutL Protein Homolog 1 (EC 3.6.1.3) ; Mismatch Repair Endonuclease PMS2 (EC 3.6.1.3) ; Transcription Factors ; DNA (9007-49-2) ; MLH1 protein, human
Language	English
Publishing date	2024-03-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2118570-0
ISSN	1479-5876 ; 1479-5876
ISSN (online)	1479-5876
ISSN	1479-5876
DOI	10.1186/s12967-024-04869-6
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Article ; Online: JBrowse 2: a modular genome browser with views of synteny and structural variation.

Genome biology

2023 Volume 24, Issue 1, Page(s) 74

Abstract: We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, ... ...

Abstract	We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.
MeSH term(s)	Genomics ; Software ; Synteny ; Genome ; Biological Evolution ; Web Browser ; Internet
Language	English
Publishing date	2023-04-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-023-02914-z
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Article: Whole genome sequencing predicts novel human disease models in rhesus macaques

Bimber, Benjamin N / Betsy Ferguson / Ranjani Ramakrishnan / Ravi Madhira / Rita Cervera-Juanes / Robert B. Norgren / Samuel M. Peterson

Elsevier Inc. Genomics. 2017 July, v. 109, no. 3-4

2017

Abstract: Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, ... ...

Abstract	Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, validated with Mendelian inheritance. Next, we used alignment data from our cohort to detect genomic regions likely to produce inaccurate genotypes, potentially due to either gene duplication or structural variation between individuals. We generated a final dataset of >16 million high confidence variants, including 13 million in Chinese-origin rhesus macaques, an increasingly important disease model. We detected an average of 131 mutations predicted to severely alter protein coding per animal, and identified 45 such variants that coincide with known pathogenic human variants. These data suggest that expanded screening of existing breeding colonies will identify novel models of human disease, and that increased genomic characterization can help inform research studies in macaques.
Keywords	breeding ; data collection ; disease models ; gene duplication ; genetic variation ; genotype ; human diseases ; humans ; Macaca mulatta ; Mendelian inheritance ; mutation ; screening ; sequence analysis
Language	English
Dates of publication	2017-07
Size	p. 214-220.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2017.04.001
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Long-term hepatitis B virus infection of rhesus macaques requires suppression of host immunity.

Nature communications

2022 Volume 13, Issue 1, Page(s) 2995

Abstract: Hepatitis B virus has infected a third of the world's population, and 296 million people are living with chronic infection. Chronic infection leads to progressive liver disease, including hepatocellular carcinoma and liver failure, and there remains no ... ...

Abstract	Hepatitis B virus has infected a third of the world's population, and 296 million people are living with chronic infection. Chronic infection leads to progressive liver disease, including hepatocellular carcinoma and liver failure, and there remains no reliable curative therapy. These gaps in our understanding are due, in large part, to a paucity of animal models of HBV infection. Here, we show that rhesus macaques regularly clear acute HBV infection, similar to adult humans, but can develop long-term infection if immunosuppressed. Similar to patients, we longitudinally detected HBV DNA, HBV surface antigen, and HBV e antigen in the serum of experimentally infected animals. In addition, we discovered hallmarks of HBV infection in the liver, including RNA transcription, HBV core and HBV surface antigen translation, and covalently closed circular DNA biogenesis. This pre-clinical animal model will serve to accelerate emerging HBV curative therapies into the clinic.
MeSH term(s)	Animals ; Antigens, Surface ; Hepatitis B ; Hepatitis B virus/genetics ; Hepatitis B, Chronic ; Humans ; Liver Neoplasms ; Macaca mulatta
Chemical Substances	Antigens, Surface
Language	English
Publishing date	2022-05-30
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-30593-0
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