21 papers · ranked by Valyu relevance
Julian Wolf, Stefaniya Boneva, Anja Schlecht, Thabo Lapp + 6 more
The applications of deep sequencing technologies in life science research and clinical diagnostics have increased rapidly over the last decade. Although fast algorithms for data processing exist, intuitive, portable solutions for data analysis are still rare. For this purpose, we developed a web-based transcriptome…
Anna V. Klepikova, Artem S. Kasianov, Margarita A. Ezhova, Aleksey A. Penin + 2 more
'Aleksey A. Penin' 'Maria D. Logacheva' 'Francisco Balao'] The vast diversity of Orchidaceae together with sophisticated adaptations to pollinators and other unique features make this family an attractive model for evolutionary and functional studies. The sequenced genome of Phalaenopsis equestris facilitates…
Sergio Alan Cervantes-Pérez, Sandra Thibivilliers, Sahand Amini, Julie M. Pelletier + 14 more
Soybean (Glycine max) is an essential source of protein and oil with high nutritional value for human and animal consumption. To enhance our understanding of soybean biology, it is essential to have accurate information regarding the expression of each of its 55,897 protein-coding genes. Here, we present “Tabula…
Jiexue Pan, Yuejiao Li, Zhongliang Lin, Qing Lan + 35 more
The spatial and temporal atlas of gene expression in the human embryo at early gestation is critical in understanding embryo development, organogenesis, and disease origins. We obtained the spatiotemporal transcriptome from 90 sagittal sections of 16 whole human embryos from 3 to 8 post-conception weeks by Stereo-seq…
Evelyn Kulesza, Patrick Thomas, Sarah F. Prewitt, Akiva Shalit-Kaneh + 11 more
'Eric Wafula' 'Benjamin Knollenberg' 'Noah Winters' 'Eddi Esteban' 'Asher Pasha' 'Nicholas Provart' 'Craig Praul' 'Lena Landherr' 'Claude dePamphilis' 'Siela N. Maximova' 'Mark J. Guiltinan'] Background Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the…
Fang Ye, Jingjing Wang, Jiaqi Li, Yuqing Mei + 1 more
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts…
Muhammad-Redha Abdullah-Zawawi, Nisha Govender, Sarahani Harun, Nor Azlan Nor Muhammad + 4 more
'Nor Azlan Nor Muhammad' 'Zamri Zainal' 'Zeti-Azura Mohamed-Hussein' 'Noe Fernandez-Pozo' 'M. Gonzalo Claros'] In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive…
Piotr Kica, Sabina Lichołai, Michał Orzechowski, M. Malawski
In this work, we explore the Transcriptomics Atlas pipeline adapted for cost-efficient and high-throughput computing in the cloud. We propose a scalable, cloud-native architecture designed for running a resource-intensive aligner – STAR – and processing tens or hundreds of terabytes of RNA-sequencing data. We implement…
Matthew Adams, Christopher Vollmers
Generating an accurate and complete genome annotation for an organism is complex because the cells within each tissue can express a unique set of transcript isoforms from a unique set of genes. A comprehensive genome annotation should contain information on what tissues express what transcript isoforms at what level.…
Xuanxuan Zou, Xi Dai, Alexios-Fotios A Mentis, Miguel A Esteban + 2 more
The cell is the fundamental constituent unit of a mammal which, in turn, depends on the cooperative work of various cells to compose intricate life activities. Cells harbor diverse features, such as genome sequence (including genetic mutations that may be present only in cellular subpopulations), epigenetic changes…
Piotr Kica, Sabina Lichołai, Michał Orzechowski, M. Malawski
—We propose a scalable, cloud-native architecture designed for Transcriptomics Atlas Pipeline, using a resourceintensive STAR aligner and processing tens or hundreds of terabytes of RNA-seq data. We implement the pipeline using AWS cloud services, introduce performance optimizations and perform experimental evaluation…
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…
Ross Laidlaw, Marta Garcia Sanchez, Juliana Da Silva Pacheco, Luciana De Sousa Paradela + 2 more
Trypanosoma cruzi, the causative agent of Chagas disease, exhibits a complex life cycle with multiple hosts, stages and differentiation steps. We present a complete cell atlas for the T. cruzi life cycle, based on single cell transcriptomes for over 31,000 cells and population-based transcriptomics. The atlas reveals…
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…
Martin Hemberg, Fédérico Marini, Shila Ghazanfar, Ahmad Al Ajami + 26 more
'Najla Abassi' 'Benedict Anchang' 'Bérénice A. Benayoun' 'Yue Cao' 'Ken Chen' 'Yesid Cuesta-Astroz' 'Zach DeBruine' 'Calliope A. Dendrou' 'Iwijn De Vlaminck' 'Katharina Imkeller' 'Ilya Korsunsky' 'Alex R. Lederer' 'Pieter Meysman' 'Clint Miller' 'Kerry A. Mullan' 'Uwe Ohler' 'Nikolaos Patikas' 'Jonas Schuck'…
Timothy R. Fallon, Tereza Čalounová, Martin Mokrejš, Jing-Ke Weng + 1 more
'Tomáš Pluskal'] Background RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore…
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…
Alexander J. Brown, Stephanie N. Seifert
Many transcriptome creation workflows are not standardized, are difficult to install or share, prone to breaking as dependencies update or cease to be maintained and are resource intensive. Due to a lack of authoritative literature, many also overlook potentially important steps, such as thinning contig over-assembly…
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…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…