Search · four archives
Search · four archives
20 papers · ranked by Valyu relevance
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…
Hyun Joo Ji, Mihaela Pertea
Recently developed long-read RNA sequencing technologies promise to provide a more accurate and comprehensive view of transcriptomes compared to short-read sequencers, primarily due to their capability to achieve full-length sequencing of transcripts. However, realizing this potential requires computational tools…
Boxiang Liu, Yanjun Li, Liang Zhang
Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of spatial information. Spatial transcriptomics is a recent technological innovation…
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…
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.…
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…
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…
James Titus‐McQuillan, Adalena V. Nanni, Lauren M. McIntyre, Rebekah L. Rogers
'Rebekah L. Rogers'] Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable…
Ying Chen, Andre Sim, Yuk Kei Wan, Keith Yeo + 4 more
Most approaches to transcript quantification rely on fixed reference annotations. However, the transcriptome is dynamic, and depending on the context, such static annotations contain inactive isoforms for some genes while they are incomplete for others. To address this, we have developed Bambu, a method that performs…
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…
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 6 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
Amir Asiaee, Zachary B. Abrams, Heather H. Pua, Kevin R. Coombes
Transcription factors (TFs) and microRNAs (miR-NAs) are fundamental regulators of gene expression, cell state, and biological processes. This study investigated whether a small subset of TFs and miRNAs could accurately predict genome-wide gene expression. We analyzed 8895 samples across 31 cancer types from The Cancer…
O.G. Akintunde, Trichina Tucker, Valerie J. Carabetta
The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to elucidate the exact composition and sequence of DNA molecules. Discoveries and the…
N. Ogata, Aoi Hosaka
—Many studies used the Shannon entropy of transcriptome data to determine cell dedifferentiation and differentiation. The collection of evidence has strengthened the certainty that the transcriptome's Shannon entropy may be used to quantify cellular dedifferentiation and differentiation. Quantifying this cellular…
B.L. Draper, Mark Dunning, David C. James
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed examination of their statistical methods, case applications, and benefits. A…
Hyeongseon Jeon, Juan Xie, Yeseul Jeon, Kyeong Joo Jung + 3 more
'Arkobrato Gupta' 'Won Chang' 'Dongjun Chung'] Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct…
Jafar Isbarov, Elmir Mahammadov
analysis Authors: ['Jafar Isbarov' 'Elmir Mahammadov'] Single-cell analysis is an increasingly relevant approach in "omics" studies. In the last decade, it has been applied to various fields, including cancer biology, neuroscience, and, especially, developmental biology. This rise in popularity has been accompanied…
Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek, Bogdan Budnik
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling…
Authors not listed
Large-scale de novo nucleic acid synthesis is a powerful tool enabling researchers to better understand and engineer biological systems. Fields ranging from genomics to nucleic acid therapeutics to synthetic biology make use of high-throughput experimental approaches requiring access to large pools or libraries of DNA…
Mingze Bai, Jingwen Deng, Chengxin Dai, Julianus Pfeuffer + 1 more
Testing for significant differences in quantities on protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a fixed proteomics quantification software, there exists a multitude of tools and R packages to perform the…