21 papers · ranked by Valyu relevance
John H Malone, Brian Oliver
Microarrays first made the analysis of the transcriptome possible, and have produced much important information. Today, however, researchers are increasingly turning to direct high-throughput sequencing - RNA-Seq - which has considerable advantages for examining transcriptome fine structure - for example in the…
Amelia Casamassimi, Antonio Federico, Monica Rienzo, Sabrina Esposito + 1 more
'Sabrina Esposito' 'Alfredo Ciccodicola'] In the last decades, transcriptome profiling has been one of the most utilized approaches to investigate human diseases at the molecular level. Through expression studies, many molecular biomarkers and therapeutic targets have been found for several human pathologies. This…
Nunzio D’Agostino, Wenli Li, Dapeng Wang
High-throughput transcriptomics has revolutionised the field of transcriptome research by offering a cost-effective and powerful screening tool. Standard bulk RNA sequencing (RNA-Seq) enables characterisation of the average expression profiles for individual samples and facilitates identification of the molecular…
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…
Erik Dassi, Alessandro Quattrone
The recent explosion of high-throughput sequencing methods applied to RNA molecules is allowing us to go beyond the description of sequence variants and their relative abundances, as measured by RNA-seq. We can now probe for RNA engagement in polysomes, for ribosomes, RNA binding proteins and microRNAs binding sites…
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…
Adam D Hargreaves, John F Mulley
Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we…
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…
Florian Mair, Jami R. Erickson, Valentin Voillet, Yannick Simoni + 6 more
High throughput single-cell RNA sequencing (sc-RNAseq) has become a frequently used tool to assess immune cell function and heterogeneity. Recently, the combined measurement of RNA and protein expression by sequencing was developed, which is commonly known as CITE-Seq. Acquisition of protein expression data along with…
Wen Jiang, Zhanyong Guo, Nuno Lages, W. Jim Zheng + 3 more
To understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneously measured three parameters – transcription rate (TR), mRNA abundance (RA) and translation activity (TA) – and assessed mRNA stability with the RA to TR ratio. This revealed multiple quantitative insights. First, the…
Dongxue Wang, Basak Eraslan, Thomas Wieland, Björn Hallström + 15 more
Genome-, transcriptome- and proteome-wide measurements provide valuable insights into how biological systems are regulated. However, even fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we have generated a systematic…
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…
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…
Chenchen Zhu, Jingyan Wu, Han Sun, Francesca Briganti + 3 more
Alternative splicing generates differing RNA isoforms that govern phenotypic complexity of eukaryotes. Its malfunction underlies many diseases, including cancer and cardiovascular diseases. Comparative analysis of RNA isoforms at the genome-wide scale has been difficult. Here, we established an experimental and…
Alberto Santos, Kalliopi Tsafou, Christian Stolte, Sune Pletscher-Frankild + 2 more
For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present a comprehensive evaluation…
Joanna Moreton, Abril Izquierdo, Richard D. Emes
De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome.…
Barbara Rakitsch, Christoph Lippert, Hande Topa, Karsten Borgwardt + 3 more
'Antti Honkela' 'Oliver Stegle' 'Eberhard Karls'] Abstract. RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively spliced transcript…
Jorge Ruiz‐Orera, Xavier Messeguer, Juan A. Subirana, M. Mar Albà
1 Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB) - Hospital del Mar Research Institute (IMIM) - Universitat Pompeu Fabra (UPF), Barcelona, Spain. 2 Universitat Politècnica de Catalunya (UPC), Barcelona. 3 Real Academia de Ciències i Arts de Barcelona (RACAB). 4 Catalan Institution for…
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']…
Mark David, Elena Chekmeneva, María Gómez-Romero, Stephane Camuzeaux + 10 more
The chemical analysis of blood products (plasma and serum) is commonplace in metabolic phenotyping studies. The diversity of analytes in blood products characterized by varying physico-chemical properties, stability, and solubility presents an analytical challenge when attempting to achieve comprehensive analyte…