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Search · four archives
18 papers · ranked by Valyu relevance
Yiru Sheng, R. Ayesha Ali, Andreas Heyland
Background Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological experiments, in whole organisms, tissues, and at the single cell level. Collectively, this is a vast comparative…
Marc Robinson‐Rechavi, Julien Roux, Marta Rosikiewicz, Marc Robinson‐Rechavi
'Marc Robinson‐Rechavi'] Title: ABSTRACT Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations.…
Jiyoung Lee, Lenwood S. Heath, Ruth Grene, Song Li
Comparative transcriptome analysis is the comparison of expression patterns between homologous genes in different species. Since most molecular mechanistic studies in plants have been performed in model species including Arabidopsis and rice, comparative transcriptome analysis is particularly important for functional…
Julien Roux, Marta Rosikiewicz, Marc Robinson-Rechavi
Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of…
Wei Vivian Li, Yiling Elaine Chen, Jingyi Jessica Li
Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic data. An important question is to understand the conservation and differentiation…
Yvonne Poeschl, Carolin Delker, Jana Trenner, Kristian Karsten Ullrich + 3 more
'Kristian Karsten Ullrich' 'Marcel Quint' 'Ivo Grosse' 'Ken Mills'] Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence, transcriptomics…
Panpaki Seekaki, N. Ogata
> Abstract. Cells coordinate adjustments in genome expression to accommodate changes in their environment. A drug in culture media for in vitro preclinical testing sometimes cause drastic regime shifting of genome expression system depending on the concentrations; e.g. primary cultured cells exposed to high…
Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo + 5 more
'José F. Muñoz' 'Jonathan Livny' 'Amol C. Shetty' 'Anup Mahurkar' 'Julie C. Dunning Hotopp'] Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to…
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…
Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan + 1 more
'Thomas Shafee'] Transcriptomics technologies are the techniques used to study an organism’s [transcriptome](), the sum of all of its [RNA transcripts](). The information content of an organism is recorded in the DNA of its [genome]() and [expressed]() through [transcription](). Here, [mRNA]() serves as a transient…
Kenneth A. Barr, Yoav Gilad
Comparative functional genomic studies are often affected by biased read mapping across species due to inter-species differences in genome structure, sequence composition, and annotation quality. We developed CrossFilt, a filtering strategy that retains only sequencing reads that map reciprocally between genomes…
Samuel H. Church, Jasmine L. Mah, Casey W. Dunn
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as depicted with phylogenetic trees, that define relationships between species…
Stinus Lindgreen, Sinan U. Umu, Alicia Sook-Wei Lai, Hisham Eldai + 8 more
'Wenting Liu' 'Stephanie McGimpsey' 'Nicole E. Wheeler' 'Patrick J. Biggs' 'Nick Thomson' 'Lars Barquist' 'Anthony M. Poole' 'Paul P. Gardner'] Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While…
Megan Crow, Hamsini Suresh, John Lee, Jesse Gillis
What makes a mouse a mouse, and not a hamster? The answer lies in the genome, and more specifically, in differences in gene regulation between the two organisms: where and when each gene is expressed. To quantify differences, a typical study will either compare functional genomics data from homologous tissues, limiting…
Ping-Han Hsieh, Yen-Jen Oyang, Chien-Yu Chen
Correct quantification of transcript expression is essential to understand the functional products of the genome in different physiological conditions and developmental stages. Recently, the development of high-throughput RNA sequencing (RNA-Seq) allows the researchers to perform transcriptome analysis for the…
Alexander J. Hart, Samuel Ginzburg, Muyang (Sam) Xu, Cera R. Fisher + 4 more
EnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated…
Authors not listed
The WRN helicase has recently emerged as a promising therapeutic target for microsatellite instability (MSI)-high cancers. Here, we report LXW-P1, a potent WRN degrader derived from marine bromotyrosine alkaloids. Its molecular target was identified using an AI-guided, pathway-informed perturbation transcriptomics…
Hunter Dlugas, Xiang Zhang, Seongho Kim
In mass spectrometry (MS)-based metabolomics, compound identification relies on Liquid Chromatography-MS (LC-MS) and Gas Chromatography-MS (GC-MS). The most popular and efficient approach for this purpose is the comparison of similarity scores between experimental spectra and reference spectra. Among the various single…