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View article: A Multi-Omics Framework for Decoding Disease Mechanisms: Insights From Methylmalonic Aciduria
A Multi-Omics Framework for Decoding Disease Mechanisms: Insights From Methylmalonic Aciduria Open
View article: Melanin and Neurotransmitter Signalling Genes Are Differentially Co‐Expressed in Growing Feathers of White and Rufous Barn Owls
Melanin and Neurotransmitter Signalling Genes Are Differentially Co‐Expressed in Growing Feathers of White and Rufous Barn Owls Open
Regulation of melanin‐based pigmentation is complex, involving multiple genes. Because different genes can contribute to the same pigmentation phenotype, the genes identified in model organisms may not necessarily apply to wild species. In…
View article: Integrating knowledge, omics and AI to develop patient-specific virtual avatars
Integrating knowledge, omics and AI to develop patient-specific virtual avatars Open
We propose a method for creating personalized regulatory networks, enabling the development of virtual avatars for cancer patients, with patient-derived xenograft (PDX) models as a test case. Starting from a Prior Knowledge Network (PKN) b…
View article: Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms
Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms Open
Antibodies have emerged as the leading class of biotherapeutics, yet traditional screening methods face significant time and resource challenges in identifying lead candidates. Integrating high-throughput sequencing with computational appr…
View article: AI-accelerated therapeutic antibody development: practical insights
AI-accelerated therapeutic antibody development: practical insights Open
Antibodies represent the largest class of biotherapeutics thanks to their high target specificity, binding affinity and versatility. Recent breakthroughs in Artificial Intelligence (AI) have enabled information-rich in silico representatio…
View article: Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms
Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms Open
Antibodies have emerged as the leading class of biotherapeutics, yet traditional screening methods face significant time and resource challenges in identifying lead candidates. Integrating highthroughput sequencing with computational appro…
View article: Improving population scale statistical phasing with whole-genome sequencing data
Improving population scale statistical phasing with whole-genome sequencing data Open
Haplotype estimation, or phasing, has gained significant traction in large-scale projects due to its valuable contributions to population genetics, variant analysis, and the creation of reference panels for imputation and phasing of new sa…
View article: Improving population scale statistical phasing with whole-genome sequencing data
Improving population scale statistical phasing with whole-genome sequencing data Open
Haplotype estimation, or phasing, has gained significant traction in large-scale projects due to its valuable contributions to population genetics, variant analysis, and the creation of reference panels for imputation and phasing of new sa…
View article: Reference genomes for BALB/c Nude and NOD/SCID mouse models
Reference genomes for BALB/c Nude and NOD/SCID mouse models Open
Mouse xenograft models play a vital role in tumor studies for research as well as for screening of drugs for the pharmaceutical industry. In particular, models with compromised immunity are favorable to increase the success of transplantat…
View article: Data from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors
Data from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors Open
Purpose: Tumor-associated TIE-2–expressing monocytes (TEM) are highly proangiogenic cells critical for tumor vascularization. We previously showed that, in human breast cancer, TIE-2 and VEGFR pathways control proangiogenic activity…
View article: Supplementary figures from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors
Supplementary figures from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors Open
Supplementary figures - PDF file 1536K, Figure S1. Proliferation of tumor-specific CD4 T cells by matured DC pulsed with autologous tumor lysate; Figure S2. In breast tumors TEM and CD11c+ are distinct cell subsets
View article: Supplementary figures from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors
Supplementary figures from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors Open
Supplementary figures - PDF file 1536K, Figure S1. Proliferation of tumor-specific CD4 T cells by matured DC pulsed with autologous tumor lysate; Figure S2. In breast tumors TEM and CD11c+ are distinct cell subsets
View article: Supplementary Information from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors
Supplementary Information from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors Open
Supplementary Information - PDF file 145K, Supplementary Material and Methods; Supplementary Figure Legend S1 (Proliferation of tumor-specific CD4 T cells by matured DC pulsed with autologous tumor lysate.); Supplementary Figure Legend S2 …
View article: Data from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors
Data from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors Open
Purpose: Tumor-associated TIE-2–expressing monocytes (TEM) are highly proangiogenic cells critical for tumor vascularization. We previously showed that, in human breast cancer, TIE-2 and VEGFR pathways control proangiogenic activity…
View article: Supplementary Information from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors
Supplementary Information from TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors Open
Supplementary Information - PDF file 145K, Supplementary Material and Methods; Supplementary Figure Legend S1 (Proliferation of tumor-specific CD4 T cells by matured DC pulsed with autologous tumor lysate.); Supplementary Figure Legend S2 …
View article: PAPET: a collection of performant algorithms to identify 5-methyl cytosine from PacBio SequelII data
PAPET: a collection of performant algorithms to identify 5-methyl cytosine from PacBio SequelII data Open
Background Cytosine followed by guanine (CpG) rich genomic regions are known important regulatory sequences among vertebrates. Their cytosines can be subjected to a variety of chemical modifications, one of which being 5-methylcytosine (5m…
View article: Reference mouse strain assemblies for BALB/c Nude and NOD/SCID mouse models
Reference mouse strain assemblies for BALB/c Nude and NOD/SCID mouse models Open
Mouse xenograft models play a vital role in tumor studies for research as well as for screening of drugs for the pharmaceutical industry. In particular, models with compromised immunity are favorable to increase the success of transplantat…
View article: Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency
Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency Open
View article: Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large European metropolitan region
Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large European metropolitan region Open
View article: Exploiting parallelization in positional Burrows–Wheeler transform (PBWT) algorithms for efficient haplotype matching and compression
Exploiting parallelization in positional Burrows–Wheeler transform (PBWT) algorithms for efficient haplotype matching and compression Open
Summary The positional Burrows–Wheeler transform (PBWT) data structure allows for efficient haplotype data matching and compression. Its performance makes it a powerful tool for bioinformatics. However, existing algorithms do not exploit p…
View article: Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing
Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing Open
Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and preclinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leadin…
View article: Towards mouse genetic-specific RNA-sequencing read mapping
Towards mouse genetic-specific RNA-sequencing read mapping Open
Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the tr…
View article: An anti-influenza combined therapy assessed by single cell RNA-sequencing
An anti-influenza combined therapy assessed by single cell RNA-sequencing Open
Figures source data
View article: An anti-influenza combined therapy assessed by single cell RNA-sequencing
An anti-influenza combined therapy assessed by single cell RNA-sequencing Open
Figures source data
View article: Dissection of the macrophage response towards infection by the Leishmania-viral endosymbiont duo and dynamics of the type I interferon response
Dissection of the macrophage response towards infection by the Leishmania-viral endosymbiont duo and dynamics of the type I interferon response Open
Leishmania RNA virus 1 (LRV1) is a double-stranded RNA virus found in some strains of the human protozoan parasite Leishmania , the causative agent of leishmaniasis, a neglected tropical disease. Interestingly, the presence of LRV1 inside …
View article: XSI—a genotype compression tool for compressive genomics in large biobanks
XSI—a genotype compression tool for compressive genomics in large biobanks Open
Motivation Generation of genotype data has been growing exponentially over the last decade. With the large size of recent datasets comes a storage and computational burden with ever increasing costs. To reduce this burden, we propose XSI, …
View article: Sex-Biased Control of Inflammation and Metabolism by a Mitochondrial Nod-Like Receptor
Sex-Biased Control of Inflammation and Metabolism by a Mitochondrial Nod-Like Receptor Open
Mitochondria regulate steroid hormone synthesis, and in turn sex hormones regulate mitochondrial function for maintaining cellular homeostasis and controlling inflammation. This crosstalk can explain sex differences observed in several pat…
View article: Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing
Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing Open
Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and pre-clinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leadi…
View article: Integrated multi-omics reveals anaplerotic insufficiency in methylmalonyl-CoA mutase deficiency
Integrated multi-omics reveals anaplerotic insufficiency in methylmalonyl-CoA mutase deficiency Open
Multi-layered omics approaches can help define relationships between genetic factors, biochemical processes and phenotypes thus extending research of inherited diseases beyond identifying their monogenic cause 1 . We implemented a multi-la…
View article: External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories
External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories Open
This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID…