20 papers · ranked by Valyu relevance
Alexandra Lee, Taylor Reiter, Georgia Doing, Julia Oh + 2 more
'Deborah A. Hogan' 'Casey S. Greene'] A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a tremendous opportunity for gaining a systems…
Tanner Stokes, Haoning Howard Cen, Philipp Kapranov, Iain J Gallagher + 7 more
'Iain J Gallagher' 'Andrew A. Pitsillides' 'Claude‐Henry Volmar' 'William E Kraus' 'James D. Johnson' 'Stuart M. Phillips' 'Claes Wahlestedt' 'James A. Timmons'] Title: Abstract Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug…
Hongfei Li, Jiechen Wang, Qing Liu, Quan Zou + 1 more
Joint profiling technologies combining single-cell chromatin accessibility (CA) and transcriptome sequencing enable cellular heterogeneity analysis from both gene and cis-regulatory element perspectives, greatly advancing molecular biology at a cellular resolution. These techniques have been used to construct gene…
Florian Bernard, Emma Kandel, Delphine Dargere, Eric Cornes + 1 more
Single-cell RNA sequencing technology dramatically changed the way we investigate transcriptomes. However, the amount and complexity of data generated by such methods poses new challenges for biologists who are trying to extract detailed insights into the genetic programs that drive cellular functions and…
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…
Hao Yuan, Christopher A Mancuso, Kayla A Johnson, Ingo Braasch + 1 more
'Arjun Krishnan'] - Hao Yuan 0000-0002-8848-1595 · yhadevol · yhbioinfo Genetics and Genome Science Program; Ecology, Evolution, and Behavior Program, Michigan State University - Christopher A. Mancuso 0000-0003-3081-2758 · ChristopherMancuso · ChrisAMancuso Department of Biostatistics & Informatics, University of…
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…
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…
Kevin Vo, Ryan Mohamadi, Yashica Sharma, Amelia Mohamadi + 2 more
RNA sequencing (RNA-Seq) has become a widely adopted genome-wide technique for investigating gene expression patterns. However, conventional RNA-Seq analyses typically rely on gene expression (GE) values that aggregate all the transcripts produced by a gene under a single identifier, overlooking the complexity of…
Molly Martorella, Silva Kasela, Renee Garcia-Flores, Alper Gokden + 2 more
Transcriptomic studies lend insight into the biology of genetic regulation and bear promise in furthering the goals of precision medicine. However, the cost of RNA-sequencing and types of tissues currently assayed pose major limitations to study expansion and disease-relevant discovery. Here, we develop methods for…
Nurul Arneida Husin
Durio zibethinus is a popular seasonal fruit among the Asian population and is frequently associated with economic losses due to a rapid post-harvest process. To identify novel transcripts and characterize D. zibethinus transcriptome, we employed high throughput RNA-Seq analysis. In this study, we characterized the…
Marina Reixachs‐Solé, Eduardo Eyras
The high-throughput sequencing of cellular RNAs has underscored a broad effect of isoform diversification through alternative splicing on the transcriptome. Moreover, the differential production of transcript isoforms from gene loci has been recognized as a critical mechanism in cell differentiation, organismal…
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…
Ya-Hui Lin, Jennifer E. Dodd, Luisa Cutillo, Lydia M. Castelli + 14 more
Transcriptomes and translatomes measure genome-wide levels of total and ribosome-associated RNAs. A few hundred translatomes were reported over >250,000 transcriptomes highlighting the challenges of identifying translating RNAs. Here, we used a human isogenic inducible model of TDP-43-linked amyotrophic lateral…
Juan Ochoteco Asensio, Jos Kleinjans, Florian Caiment
Transcriptomics is nowadays frequently used as an analytical tool to study the extent of cell expression changes between two phenotypes or between different conditions. However, an important portion of the significant changes observed in transcriptomics at the gene level is usually not consistently detected at the…
Vighnesh Ghatpande, Uma Paul, MacKenzie A Howard, Can Cenik
In the last decade, an unexpectedly large number of translated regions (translons) have been discovered using ribosome profiling and proteomics. Translons can regulate mRNA translation and encode micropeptides that contribute to multiprotein complex formation, Ca^2+^ regulation in muscle, and signaling during embryonic…
Isaac Adeyemi Babarinde, Andrew Paul Hutchins
Investigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts. The heterogeneity of the assembled transcript sets might…
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…
Paulo Amaral, Sílvia Carbonell Sala, Francisco M. De La Vega, Tiago Faial + 17 more
'Tiago Faial' 'Adam Frankish' 'T Gingeras' 'Roderic Guigó' 'Jennifer Harrow' 'Artemis G. Hatzigeorgiou' 'Rory Johnson' 'Terence D. Murphy' 'Mihaela Pertea' 'Kim D. Pruitt' 'Shashikant Pujar' 'Hazuki Takahashi' 'Igor Ulitsky' 'Ales Varabyou' 'Christine A. Wells' 'Mark Yandell' 'Piero Carninci' 'Steven L. Salzberg']…
Matthew Lewis, Elena Chekmeneva, Stephane Camuzeaux, Caroline Sands + 11 more
Metabolomics utilising liquid chromatography mass spectrometry (LC-MS) offers biomedical researchers a powerful means of assessing and comparing human phenotypes via measurement of the metabolome in biological samples. Platforms for LC-MS-based global profiling quantify hundreds or thousands of small molecule…