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20 papers · ranked by Valyu relevance

01
PPubMed20 Apr 2023
Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors
Lieke M. J. van Zogchel, Nathalie S. M. Lak, Nina U. Gelineau, Irina Sergeeva + 16 more
'Irina Sergeeva' 'Ellen Stelloo' 'Joost Swennenhuis' 'Harma Feitsma' 'Max van Min' 'Erik Splinter' 'Margit Bleijs' 'Marian Groot Koerkamp' 'Willemijn Breunis' 'Michael Torsten Meister' 'Waleed Hassan Kholossy' 'Frank C. P. Holstege' 'Jan J. Molenaar' 'Wendy W. J. de Leng' 'Janine Stutterheim' 'C. Ellen van der Schoot'…
84relevance
02
PPubMed5 Mar 2019
CRISPR/Cas9 targeted CAPTURE of mammalian genomic regions for characterization by NGS
Alexei Slesarev, Lakshmi Viswanathan, Yitao Tang, Trissa Borgschulte + 5 more
'Katherine Achtien' 'David Razafsky' 'David Onions' 'Audrey Chang' 'Colette Cote'] The robust detection of structural variants in mammalian genomes remains a challenge. It is particularly difficult in the case of genetically unstable Chinese hamster ovary (CHO) cell lines with only draft genome assemblies available. We…
74relevance
03
BbioRxiv20 Jul 2018
Crispr/Cas9 Targeted Capture of Mammalian Genomic Regions for Characterization by NGS
Alexei Slesarev, Lakshmi Viswanathan, Yitao Tang, Trissa Borgschulte + 5 more
The robust detection of structural variants in mammalian genomes remains a challenge. It is particularly difficult in the case of genetically unstable Chinese hamster ovary (CHO) cell lines with only draft genome assemblies available. We explore the potential of the CRISPR/Cas9 system for the targeted capture of…
74relevance
04
PPubMed24 Jun 2022
Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology
Rajesh R. Singh, Mattia Gentile
Screening for genomic sequence variants in genes of predictive and prognostic significance is an integral part of precision medicine. Next-generation sequencing (NGS) technologies are progressively becoming platforms of choice to facilitate this, owing to their massively parallel sequencing capability, which can be…
74relevance
05
AarXiv2021
Optimized protocol for DNA extraction from ancient skeletal human remains using Chelex-100
Wera M. Schmerer
PCR-based analysis of skeletonized human remains is a common aspect in both forensic human identification as well as Ancient DNA research. In this, both areas not merely utilize very similar methodology, but also share the same problems regarding quantity and quality of recovered DNA and presence of inhibitory…
70relevance
06
BbioRxiv7 Mar 2026
MethylHDA: One-pot helicase-dependent amplification with concurrent DNMT1-mediated maintenance of DNA methylation
Kiat Whye Kong, Si En Poh, Fong Tian Wong, Yiqi Seow + 1 more
DNA methylation is an important epigenetic modification involved in gene regulation, genome stability, development, and disease. Analysis of low-abundance methylated DNA often requires DNA amplification. Conventional amplification methods, however, do not preserve methylation marks on newly synthesized DNA, potentially…
68relevance
07
AarXiv2018
Knockdown of Human AMPK Using the CRISPR/Cas9 Genome-Editing System
Adrien Grenier, Pierre Sujobert, Séverine Olivier, Hélène Guermouche + 4 more
'Johanna Mondésir' 'Olivier Kosmider' 'Benoı̂t Viollet' 'Jérôme Tamburini'] AMP activated protein kinase (AMPK) is a critical energy sensor, regulating signaling networks involved in pathology including metabolic diseases and cancer. This increasingly recognized role of AMPK has prompted tremendous research efforts to…
67relevance
08
BbioRxiv22 Feb 2022
Identification of a CCG-enriched expanded allele in DM1 patients using Amplification-free long-read sequencing
Yu-Chi Tsai, Laure de Pontual, Cheryl Heiner, Tanya Stojkovic + 4 more
Myotonic dystrophy type 1 (DM1) exhibits highly heterogeneous clinical manifestations caused by an unstable CTG repeat expansion reaching up to 4,000 CTG. The clinical variability depends on CTG repeat number, CNG repeat interruptions and somatic mosaicism. Currently, none of these factors are simultaneously and…
66relevance
09
BbioRxiv4 Apr 2020
Detecting genetic variation and base modifications together in the same single molecules of DNA and RNA at base pair resolution using a magnetic tweezer platform
Zhen Wang, Jérôme Maluenda, Laurène Giraut, Thibault Vieille + 13 more
Accurate decoding of nucleic acid variation is important to understand the complexity and regulation of genome function. Here we introduce a single-molecule platform based on magnetic tweezer (MT) technology that can identify and map the positions of sequence variation and multiple base modifications together in the…
66relevance
10
AarXiv23 Sep 2014
Deciphering regulation in eukaryotic cell: from sequence to function
Valentina Boeva
| ABSTRACT 4 | | | | | | | | | --- | --- | --- | --- | --- | --- | --- | --- | | RESUMÉ [FRENCH] 5 | | | | | | | | | PREFACE 6 | | | | | | | | | 1 INTRODUCTION 7 | | | | | | | | | 2 PATTERNS IN THE GENOMIC SEQUENCE AND THEIR ROLE IN REGULATION | | | | | | | | | OF GENE EXPRESSION 11 | | | | | | | | | 2.1 detection of…
66relevance
11
BbioRxiv21 Sep 2018
Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers
Joel Pel, Amy Leung, Wendy W. Y. Choi, Milenko Despotovic + 4 more
Targeted Next Generation Sequencing (NGS) is being adopted increasingly broadly in many research, commercial and clinical settings. Currently used target capture methods, however, typically require complex and lengthy (sometimes multi-day) workflows that complicates their use in certain applications. In addition, small…
66relevance
12
PPubMed29 Jan 2021
Detection of genetic variation and base modifications at base-pair resolution on both DNA and RNA
Zhen Wang, Jérôme Maluenda, Laurène Giraut, Thibault Vieille + 13 more
'Andréas Lefevre' 'David Salthouse' 'Gaël Radou' 'Rémi Moulinas' 'Sandra Astete' 'Pol D’Avezac' 'Geoff Smith' 'Charles André' 'Jean-François Allemand' 'David Bensimon' 'Vincent Croquette' 'Jimmy Ouellet' 'Gordon Hamilton'] Accurate decoding of nucleic acid variation is critical to understand the complexity and…
64relevance
13
BbioRxiv1 Jan 2026
Restriction-site-based enrichment coupled to adaptive sampling enables long-read transposon-insertion sequencing
Christian Jonas Lapp, Janek Weiler, Johannes Gescher
Long-read Transposon insertion sequencing is essential for linking genotypes to phenotypes, as short-read approaches struggle with complex genomic regions. Long-read sequencing demands high sequencing depth or targeted sequencing, which either requires extensive sample preparation or suffer from low net efficiency. We…
62relevance
14
PPubMed29 Oct 2021
Locus-Specific DNA Methylation Editing in Melanoma Cell Lines Using a CRISPR-Based System
Jim Smith, Rakesh Banerjee, Reema Waly, Arthur Urbano + 6 more
'Gregory Gimenez' 'Robert Day' 'Michael R. Eccles' 'Robert J. Weeks' 'Aniruddha Chatterjee' 'Luis Franco'] Simple Summary DNA methylation is an important modification of the genome that is implicated in the pathogenesis of numerous human diseases, including cancer. DNA methylation changes can alter the expression of…
61relevance
15
AarXiv2022
Enriching and Characterizing T-Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products
Tasneem Jivanjee, Samira Ibrahim, Sarah K. Nyquist, G. James Gatter + 6 more
'Joshua D. Bromley' 'Swati Jaiswal' 'Bonnie Berger' 'Samuel M. Behar' 'J. Christopher Love' 'Alex K. Shalek'] - 1. Institute for Medical Engineering & Science and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA - 2. Koch Institute for Integrative Cancer Research, Massachusetts Institute of…
60relevance
16
AarXiv18 Feb 2025
Fast Antibiotic resistance-Based gene editing of mammalian cells with CRISPR-Cas9 (FAB-CRISPR)
Petia Adarska, Eleanor Fox, Joshua R. Heyza, Carlo Barnaba + 2 more
CRISPR-Cas9 (FAB-CRISPR) Authors: ['Petia Adarska' 'Eleanor Fox' 'Joshua R. Heyza' 'Carlo Barnaba' 'Jens C. Schmidt' 'Francesca Bottanelli'] Protein tagging with CRISPR-Cas9 enables the investigation of protein function in its native environment but is limited by low homology-directed repair (HDR) efficiency causing…
58relevance
17
PPubMed24 Sep 2015
Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research
Toshitsugu Fujita, Hodaka Fujii, Qiang “Shawn” Chen
Engineered DNA-binding molecules such as transcription activator-like effector (TAL or TALE) proteins and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) (CRISPR/Cas) system have been used extensively for genome editing in cells of various types and species.…
58relevance
18
BbioRxiv1 Jun 2023
Miniaturized CAR knocked onto CD3ε extends TCR function with CAR specificity under control of endogenous TCR signaling cascade
Katrin Manske, Lisa Dressler, Simon P. Fräßle, Manuel Effenberger + 10 more
Immunotherapy using TCR and especially CAR transgenic T cells is a rapidly advancing field with the potential to become standard of care for the treatment of multiple diseases. While all current FDA approved CAR T cell products are generated using lentiviral gene transfer, extensive work is put into CRISPR/Cas mediated…
56relevance
19
CchemRxiv26 Oct 2021
Exponential Amplification by Redox Cross-Catalysis and Unmasking of Doubly Protected Molecular Probes
Justine Pallu, Charlie Rabin, Pan Hui, Thamires Moreira + 4 more
The strength of autocatalytic reactions lies in their ability to provide a powerful means of molecular amplification, which can be very useful for improving the analytical performances of a multitude of analytical and bioanalytical methods. However, one of the major difficulties in designing an efficient autocatalytic…
52relevance
20
AarXiv13 Jul 2026
Targeting DNA Methylation: New Paradigms and the Advent of Gene-Selective Tools
Julie Gilbert, Francesco Calzaferri
DNA methylation can function as a toxic alkylation reaction exploited by chemotherapeutic agents to induce cancer cell death. However, finely tuned DNA methylation plays a fundamental role in cellular physiology, particularly in the epigenetic regulation of gene expression. Once thought to act solely as a repressor of…
51relevance

Results for Targeted Locus Amplification

Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors

CRISPR/Cas9 targeted CAPTURE of mammalian genomic regions for characterization by NGS

Crispr/Cas9 Targeted Capture of Mammalian Genomic Regions for Characterization by NGS

Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology

Optimized protocol for DNA extraction from ancient skeletal human remains using Chelex-100

MethylHDA: One-pot helicase-dependent amplification with concurrent DNMT1-mediated maintenance of DNA methylation

Knockdown of Human AMPK Using the CRISPR/Cas9 Genome-Editing System

Identification of a CCG-enriched expanded allele in DM1 patients using Amplification-free long-read sequencing

Detecting genetic variation and base modifications together in the same single molecules of DNA and RNA at base pair resolution using a magnetic tweezer platform

Deciphering regulation in eukaryotic cell: from sequence to function

Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers

Detection of genetic variation and base modifications at base-pair resolution on both DNA and RNA

Restriction-site-based enrichment coupled to adaptive sampling enables long-read transposon-insertion sequencing

Locus-Specific DNA Methylation Editing in Melanoma Cell Lines Using a CRISPR-Based System

Enriching and Characterizing T-Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products

Fast Antibiotic resistance-Based gene editing of mammalian cells with CRISPR-Cas9 (FAB-CRISPR)

Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research

Miniaturized CAR knocked onto CD3ε extends TCR function with CAR specificity under control of endogenous TCR signaling cascade

Exponential Amplification by Redox Cross-Catalysis and Unmasking of Doubly Protected Molecular Probes

Targeting DNA Methylation: New Paradigms and the Advent of Gene-Selective Tools

Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors

CRISPR/Cas9 targeted CAPTURE of mammalian genomic regions for characterization by NGS

Crispr/Cas9 Targeted Capture of Mammalian Genomic Regions for Characterization by NGS

Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology

Optimized protocol for DNA extraction from ancient skeletal human remains using Chelex-100

MethylHDA: One-pot helicase-dependent amplification with concurrent DNMT1-mediated maintenance of DNA methylation

Knockdown of Human AMPK Using the CRISPR/Cas9 Genome-Editing System

Identification of a CCG-enriched expanded allele in DM1 patients using Amplification-free long-read sequencing

Detecting genetic variation and base modifications together in the same single molecules of DNA and RNA at base pair resolution using a magnetic tweezer platform

Deciphering regulation in eukaryotic cell: from sequence to function

Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers

Detection of genetic variation and base modifications at base-pair resolution on both DNA and RNA

Restriction-site-based enrichment coupled to adaptive sampling enables long-read transposon-insertion sequencing

Locus-Specific DNA Methylation Editing in Melanoma Cell Lines Using a CRISPR-Based System

Enriching and Characterizing T-Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products

Fast Antibiotic resistance-Based gene editing of mammalian cells with CRISPR-Cas9 (FAB-CRISPR)

Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research

Miniaturized CAR knocked onto CD3ε extends TCR function with CAR specificity under control of endogenous TCR signaling cascade

Exponential Amplification by Redox Cross-Catalysis and Unmasking of Doubly Protected Molecular Probes

Targeting DNA Methylation: New Paradigms and the Advent of Gene-Selective Tools