23 papers · ranked by Valyu relevance
Yongqing Zhang, Qingyuan Chen, Meiqin Gong, Yuanqi Zeng + 1 more
'Dongrui Gao'] Background Recently, erdafitinib (Balversa), the first targeted therapy drug for genetic alteration, was approved to metastatic urothelial carcinoma. Cancer genomics research has been greatly encouraged. Currently, a large number of gene regulatory networks between different states have been constructed…
Miriam Shiffman, Ryan Giordano, Tamara Broderick
C O U L D D R O P P I N G A F E W C E L L S C H A N G E T H E TA K E A W AY S F R O M D I F F E R E N T I A L E X P R E S S I O N ?
Vaibhav B. Sinha, Siladitya Dash, Nazma Naskar, Sk Md Mosaddek Hossain
'Sk Md Mosaddek Hossain'] Abstract—In this work, we study and analyze different feature selection algorithms that can be used to classify cancer subtypes in case of highly varying high-dimensional data. We apply three different feature selection methods on five different types of cancers having two separate omics each.…
Dominik J. Otto, Erica Arriaga-Gomez, Elana Thieme, Ruijin Yang + 2 more
Kompot is a statistical framework for holistic comparison of multi-condition single-cell datasets, supporting both differential abundance and differential expression. Differential abundance captures changes in how cells populate the phenotypic manifold across conditions, while differential expression identifies…
Franziska Hoerbst, Gurpinder Singh Sidhu, Thelonious Omori, Melissa Tomkins + 1 more
Advances in sequencing technologies have revolutionised our ability to capture the complete RNA profile in tissue samples, allowing for comparative analyses of RNA levels between developmental processes, environmental responses, or treatments. However, quantifying changes in gene expression remains challenging, given…
Daigo Okada, Cheng Zheng, Jian Hao Cheng
Title: Graphical abstract
Mykhaylo M. Malakhov, Ben Dai, Xiaotong T. Shen, Wei Pan
Understanding how genetic variation affects gene expression is essential for a complete picture of the functional pathways that give rise to complex traits. Although numerous studies have established that many genes are differentially expressed in distinct human tissues and cell types, no tools exist for identifying…
Pedro L. Baldoni, Lizhong Chen, Mengbo Li, Yunshun Chen + 1 more
Differential transcript usage (DTU) refers to changes in the relative abundance of transcript isoforms of the same gene between experimental conditions, even when the total expression of the gene doesn’t change. DTU analysis requires the quantification of individual isoforms from RNA-seq data, which has a high level of…
Nufar Grinshpan, Faiza A.A. Abayed, Melody Wahl, Hadas Ner-Gaon + 3 more
'Rivka Manor' 'Amir Sagi' 'Tal Shay'] The giant freshwater prawn pjMacrobrachium rosenbergii is one of the best studied species in aquaculture. However, the transcriptional changes associated with embryonic development and the sexual differentiation mechanism of M. rosenbergii remain to be elucidated. To characterize…
Yunyi Lan, Wei Tao, Luyao Ma, Xiaoxiong Wang + 8 more
Background Peripheral T-cell lymphoma (PTCL) is a subtype of non-Hodgkin's lymphoma that occurs primarily at extranodal sites and is commonly treated using chemotherapy and radiotherapy. PTCL is more malignant than other lymphoid tumors, resulting in a poor prognosis.The 5-year recurrence rate remains high, and there…
Juliana Costa-Silva, David Menotti, Fabricio M. Lopes
Motivation: Bulk RNA-Seq is a widely used method for studying gene expression across a variety of contexts. The significance of RNA-Seq studies has grown with the advent of high-throughput sequencing technologies. Computational methods have been developed for each stage of the identification of differentially expressed…
Christophe Le Priol, Chloé-Agathe Azencott, Xavier Gidrol, Saurabh Sinha
'Saurabh Sinha'] The majority of gene expression studies focus on the search for genes whose mean expression is different between two or more populations of samples in the so-called “differential expression analysis” approach. However, a difference in variance in gene expression may also be biologically and…
Chloe J. Bennett, Rodolfo Aramayo
RNA sequencing (RNA-seq) is a commonly used method to identify changes in gene expression between two conditions. The analysis of RNA-seq output is complicated, with the possibility of getting different results from the same raw data. We developed and deployed four parallel pipelines to reanalyze an existing dataset of…
Franziska Hoerbst, G. S. Sidhu, Melissa Tomkins, Richard J. Morris
in Gene Expression using Bayes Factors Authors: ['Franziska Hoerbst' 'G. S. Sidhu' 'Melissa Tomkins' 'Richard J. Morris'] Sequencing technologies have revolutionised the field of molecular biology. We now have the ability to routinely capture the complete RNA profile in tissue samples. This wealth of data allows for…
Tinghua Huang, Siqi Niu, Fanghong Zhang, Binyu Wang + 3 more
'Guoping Liu' 'Min Yao'] Identification of key transcription factors from transcriptome data by correlating gene expression levels with transcription factor binding sites is important for transcriptome data analysis. In a typical scenario, we always set a threshold to filter the top ranked differentially expressed…
Samuel Khodursky, Caroline S. Jiang, Eric B. Zheng, Roger Vaughan + 2 more
Understanding phenotypic sex differences has long been a goal of biology from both a medical and evolutionary perspective. Although much attention has been paid to mean differences in phenotype between the sexes, little is known about sex differences in phenotypic variability. To gain insight into sex differences in…
Erik Bot, Jose Davila-Velderrain
Gene expression specificity is a biological parameter relevant for understanding the molecular basis of evolutionary constraints and tissue-selective pathogenesis. Many efforts have tried to quantify the degree of tissue specificity of individual genes. The growing availability of single-cell transcriptomic data…
Fadi Alharbi, Aleksandar Vakanski
Cancer is a term that denotes a group of diseases caused by abnormal growth of cells that can spread in different parts of the body. According to the World Health Organization (WHO), cancer is the second major cause of death after cardiovascular diseases. Gene expression can play a fundamental role in the early…
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…
Alicia Nieto-Reyes, Javier Cabrera
Normalization and outlier detection belong to the preprocessing of gene expression data. We propose a natural normalization procedure based on statistical data depth which normalizes to the distribution of gene expressions of the most representative gene expression of the group. This differ from the standard method of…
Authors not listed
Chinese hamster ovary (CHO) cells are the industrial workhorse for manufacturing biopharmaceuticals, including monoclonal antibodies. CHO cell line development requires a more data-driven approach for the accelerated identification of hyper-productive cell lines. Traditional methods, which rely on time-consuming…
Guy Quanrud, Sunil Balamurugan, Carolina Canizal, Joseph Genereux
Herbicides in the popular chloroacetanilide class harbor a potent electrophilic moiety, which can damage proteins through nucleophilic substitution. In general, damaged proteins are subject to misfolding. Accumulation of misfolded proteins compromises cellular integrity by disrupting cellular proteostasis networks…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…