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16 papers · ranked by Valyu relevance

01
PPubMed15 Jul 2025
Oarfish : enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification
Zahra Zare Jousheghani, Noor Pratap Singh, Rob Patro
Since the introduction of high-throughput RNA-sequencing (, , , ), the bioinformatics community has invested tremendous effort in the development of methods and software to tackle various challenges related to the analysis of this data. One of the first, and therefore one of the most fundamental challenges, is the…
84relevance
02
PPubMed28 Aug 2025
Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner
Hyun Joo Ji, Mihaela Pertea
Long-read RNA sequencing captures transcripts at full lengths, but existing methods for transcriptome profiling using long-read data often produce inconsistent transcript identification and quantification results. Here, we introduce TranSigner, a tool designed to provide read-level support for transcripts in a given…
83relevance
03
PPubMed30 Jun 2025
A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification
David Wissel, Madison M. Mehlferber, Khue M. Nguyen, Vasilii Pavelko + 3 more
PacBio long-read RNA sequencing resolves transcripts with greater clarity than short-read technologies, yet its quantitative performance remains under-evaluated at scale. Here, we benchmark the high-throughput PacBio Kinnex platform against Illumina short-read RNA-seq using matched, deeply sequenced datasets across a…
81relevance
04
PPubMed25 Feb 2026
A systematic benchmark of high-accuracy PacBio long-read RNA sequencing for transcript-level quantification
David Wissel, Madison M. Mehlferber, Khue M. Nguyen, Vasilii Pavelko + 3 more
Background The assembly of fragmented RNA-sequencing reads into complete transcripts is error-prone, particularly for genes with complex splicing, resulting in ambiguity in transcript discovery and quantification. PacBio long-read RNA sequencing resolves transcripts with greater clarity than short-read technologies.…
81relevance
05
PPubMed7 Jun 2024
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans + 83 more
The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA…
80relevance
06
PPubMed4 Nov 2021
Oxford Nanopore MinION Direct RNA-Seq for Systems Biology
Mikhail A. Pyatnitskiy, Viktoriia A. Arzumanian, Sergey P. Radko, Konstantin G. Ptitsyn + 5 more
Simple Summary A new technology has been recently developed by Oxford Nanopore Technologies, enabling researchers to investigate the structure and relative abundance of specific molecules, ribonucleic acids. The ribonucleic acids carry information from the genes to proteins, which are responsible for virtually every…
80relevance
07
PPubMed2 Jan 2023
Transcriptome-wide profiling and quantification of <i> N </i> 6 -methyladenosine by enzyme-assisted adenosine deamination
Yu-Lan Xiao, Shun Liu, Ruiqi Ge, Yuan Wu + 3 more
'Weixin Tang'] N6-methyladenosine (m6A), the most abundant internal mRNA modification in higher eukaryotes, serves myriad roles in regulating cellular processes. Functional dissection of m6A, however, is hampered in part by the lack of high-resolution and quantitative detection methods. Here, we present evolved…
78relevance
08
PPubMed6 Dec 2024
Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq
Delaney K Sullivan, Kristján Eldjárn Hjörleifsson, Nikhila P Swarna, Conrad Oakes + 3 more
'Nikhila\xa0P Swarna' 'Conrad Oakes' 'Guillaume Holley' 'Páll Melsted' 'Lior Pachter'] Title: Abstract In single-cell and single-nucleus RNA sequencing (RNA-seq), the coexistence of nascent (unprocessed) and mature (processed) messenger RNA (mRNA) poses challenges in accurate read mapping and the interpretation of…
77relevance
09
PPubMed13 Mar 2023
RNA-seq data science: From raw data to effective interpretation Deshpande et al. 10.3389/fgene.2023.997383
Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg + 14 more
'Caitlin Loeffler' 'Jinyang Zhang' 'Agata Muszyńska' 'Viorel Munteanu' 'Harry Yang' 'Jeremy Rotman' 'Laura Tao' 'Brunilda Balliu' 'Elizabeth Tseng' 'Eleazar Eskin' 'Fangqing Zhao' 'Pejman Mohammadi' 'Paweł P. Łabaj' 'Serghei Mangul'] RNA sequencing (RNA-seq) has become an exemplary technology in modern biology and…
76relevance
10
PPubMed12 Oct 2024
The Translatome Map: RNC-Seq vs. Ribo-Seq for Profiling of HBE, A549, and MCF-7 Cell Lines
Anna Kozlova, Elizaveta Sarygina, Ekaterina Ilgisonis, Svetlana Tarbeeva + 1 more
'Svetlana Tarbeeva' 'Elena Ponomarenko'] Gene expression is a tightly regulated process that involves multiple layers of control, including transcriptional, post-transcriptional, and translational regulation. To gain a comprehensive understanding of gene expression dynamics and its functional implications, it is…
75relevance
11
PPubMed3 Oct 2022
From multitude to singularity: An up-to-date overview of scRNA-seq data generation and analysis Carangelo et al. 10.3389/fgene.2022.994069
Giulia Carangelo, Alberto Magi, Roberto Semeraro
Single cell RNA sequencing (scRNA-seq) is today a common and powerful technology in biomedical research settings, allowing to profile the whole transcriptome of a very large number of individual cells and reveal the heterogeneity of complex clinical samples. Traditionally, cells have been classified by their morphology…
74relevance
12
PPubMed1 Mar 2022
Practical bioinformatics pipelines for single-cell RNA-seq data analysis
Jiangping He, Lihui Lin, Jiekai Chen
Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool to explore cells. With an increasing number of scRNA-seq data analysis tools that have been developed, it is challenging for users to choose and compare their performance. Here, we present an overview of the workflow for computational analysis of scRNA-seq…
71relevance
13
PPubMed10 Jun 2024
From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology Hoedjes et al.
Katja M. Hoedjes, Sonja Grath, Nico Posnien, Michael G. Ritchie + 16 more
'Christian Schlötterer' 'Jessica K. Abbott' 'Isabel Almudi' 'Marta Coronado‐Zamora' 'Esra Durmaz Mitchell' 'Thomas Flatt' 'Claudia Fricke' 'Amanda Glaser‐Schmitt' 'Josefa González' 'Luke Holman' 'Maaria Kankare' 'Benedict Lenhart' 'Dorcas J. Orengo' 'Rhonda R. Snook' 'Vera M. Yılmaz' 'Leeban Yusuf'] Title: Abstract RNA…
67relevance
14
PPubMed7 Mar 2022
Obtaining Reliable RT-qPCR Results in Molecular Diagnostics—MIQE Goals and Pitfalls for Transcriptional Biomarker Discovery
Christian Grätz, Maria L. U. Bui, Granit Thaqi, Benedikt Kirchner + 5 more
'Robert P. Loewe' 'Michael W. Pfaffl' 'Stefan Rödiger' 'Andrej-Nikolai Spiess' 'Michał Burdukiewicz'] In this review, we discuss the development pipeline for transcriptional biomarkers in molecular diagnostics and stress the importance of a reliable gene transcript quantification strategy. Hence, a further focus is put…
67relevance
15
PPubMed11 Nov 2023
Workability of mRNA Sequencing for Predicting Protein Abundance
Elena A. Ponomarenko, George S. Krasnov, Olga I. Kiseleva, Polina A. Kryukova + 7 more
'Polina A. Kryukova' 'Viktoriia A. Arzumanian' 'Georgii V. Dolgalev' 'Ekaterina V. Ilgisonis' 'Andrey V. Lisitsa' 'Ekaterina V. Poverennaya' 'Jinghua Zhao' 'Jiadong Ji'] Transcriptomics methods (RNA-Seq, PCR) today are more routine and reproducible than proteomics methods, i.e., both mass spectrometry and…
67relevance
16
PPubMed11 Sep 2024
DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing
Marco Kristen, Marc Lander, Lea-Marie Kilz, Lukas Gleue + 7 more
Due to its high modification content tRNAs are notoriously hard to quantify by reverse transcription and RNAseq. Bypassing numerous biases resulting from concatenation of enzymatic treatments, we here report a hybrid approach that harnesses the advantages of hybridization-based and deep sequencing-based approaches. The…
65relevance

Results for transcriptome quantification

Oarfish : enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification

Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner

A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification

A systematic benchmark of high-accuracy PacBio long-read RNA sequencing for transcript-level quantification

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Oxford Nanopore MinION Direct RNA-Seq for Systems Biology

Transcriptome-wide profiling and quantification of <i> N </i> 6 -methyladenosine by enzyme-assisted adenosine deamination

Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq

RNA-seq data science: From raw data to effective interpretation Deshpande et al. 10.3389/fgene.2023.997383

The Translatome Map: RNC-Seq vs. Ribo-Seq for Profiling of HBE, A549, and MCF-7 Cell Lines

From multitude to singularity: An up-to-date overview of scRNA-seq data generation and analysis Carangelo et al. 10.3389/fgene.2022.994069

Practical bioinformatics pipelines for single-cell RNA-seq data analysis

From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology Hoedjes et al.

Obtaining Reliable RT-qPCR Results in Molecular Diagnostics—MIQE Goals and Pitfalls for Transcriptional Biomarker Discovery

Workability of mRNA Sequencing for Predicting Protein Abundance

DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing

Oarfish : enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification

Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner

A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification

A systematic benchmark of high-accuracy PacBio long-read RNA sequencing for transcript-level quantification

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Oxford Nanopore MinION Direct RNA-Seq for Systems Biology

Transcriptome-wide profiling and quantification of <i> N </i> 6 -methyladenosine by enzyme-assisted adenosine deamination

Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq

RNA-seq data science: From raw data to effective interpretation Deshpande et al. 10.3389/fgene.2023.997383

The Translatome Map: RNC-Seq vs. Ribo-Seq for Profiling of HBE, A549, and MCF-7 Cell Lines

From multitude to singularity: An up-to-date overview of scRNA-seq data generation and analysis Carangelo et al. 10.3389/fgene.2022.994069

Practical bioinformatics pipelines for single-cell RNA-seq data analysis

From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology Hoedjes et al.

Obtaining Reliable RT-qPCR Results in Molecular Diagnostics—MIQE Goals and Pitfalls for Transcriptional Biomarker Discovery

Workability of mRNA Sequencing for Predicting Protein Abundance

DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing