JournalFeeds

Analyzing histone ChIP-seq data with a bin-based probability of being signal

Authors: Vivian Hecht, et al. Abstract Histone ChIP-seq is one of the primary methods for charting the cellular epigenomic landscape, the components of which play a critical regulatory role in gene expression. Analyzing the activity of regulatory elements across datasets and cell types can be challenging due to shifting peak positions and normalization artifacts resulting…

Read More
JournalFeeds

The circadian clock is disrupted in pancreatic cancer

Authors: Patrick B. Schwartz, et al. Citation: Schwartz PB, Nukaya M, Berres ME, Rubinstein CD, Wu G, Hogenesch JB, et al. (2023) The circadian clock is disrupted in pancreatic cancer. PLoS Genet 19(6): e1010770. https://doi.org/10.1371/journal.pgen.1010770 Editor: Robert Dallmann, University of Warwick, UNITED KINGDOM Received: November 23, 2022; Accepted: May 1, 2023; Published: June 1, 2023…

Read More
JournalFeeds

Mutual repression between JNK/AP-1 and JAK/STAT stratifies senescent and proliferative cell behaviors during tissue regeneration

Authors: Janhvi Jaiswal, et al. Citation: Jaiswal J, Egert J, Engesser R, Peyrotón AA, Nogay L, Weichselberger V, et al. (2023) Mutual repression between JNK/AP-1 and JAK/STAT stratifies senescent and proliferative cell behaviors during tissue regeneration. PLoS Biol 21(5): e3001665. https://doi.org/10.1371/journal.pbio.3001665 Academic Editor: Philipp Niethammer, Harvard Medical School, UNITED STATES Received: April 26, 2022; Accepted:…

Read More
JournalFeeds

Understanding the medication experience of patients with advanced non-small cell lung cancer taking epidermal growth factor receptor-tyrosine kinase inhibitors: A phenomenological study

Authors: Meng-Jung Wen, et al. Abstract Background and objective Patients with cancer taking oral antineoplastic medications may encounter problems including suboptimal adherence as well as physical and psychological disease burden. Despite increase in the use of oncology pharmacy services, there are wide variations between healthcare professionals and patient perceptions of patients’ medication experiences. The objective…

Read More
JournalFeeds

Bacteria in the oral cavity of individuals consuming intoxicating substances

Authors: Reyaz Ahmad Khan, et al. Abstract Food habits and oral hygiene are critical attributes for physiochemical environment of the oral cavity. Consumption of intoxicating substances such as betel nut (’Tamul’), alcohol, smoking and chewing tobacco may strongly influence the oral ecosystem including commensal microbes. Therefore, a comparative assessment of microbes in the oral cavity…

Read More
JournalFeeds

Domain-specific transfer learning in the automated scoring of tumor-stroma ratio from histopathological images of colorectal cancer

Authors: Liisa Petäinen , et al. Abstract Tumor-stroma ratio (TSR) is a prognostic factor for many types of solid tumors. In this study, we propose a method for automated estimation of TSR from histopathological images of colorectal cancer. The method is based on convolutional neural networks which were trained to classify colorectal cancer tissue in…

Read More
JournalFeeds

Prevalence of psychological distress, quality of life, and satisfaction among patients and family members following comprehensive genomic profiling testing: Protocol of the Quality of life for Cancer genomics and Advanced Therapeutics (Q-CAT) study

Authors: Makoto Nishino, et al. Abstract Precision medicine is rapidly changing the diagnostic and treatment spectrum of oncology. In May 2019, comprehensive genomic profiling (CGP) (somatic and/or germline) was approved for reimbursement in Japan. While the promise of novel and targeted therapies has elevated hopes for the benefits of CGP, the lack of relevant genomic…

Read More
JournalFeeds

Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression

Authors: Kexin Huang , et al. Abstract Lung adenocarcinoma (LUAD) is a deadly tumor with dynamic evolutionary process. Although much endeavors have been made in identifying the temporal patterns of cancer progression, it remains challenging to infer and interpret the molecular alterations associated with cancer development and progression. To this end, we developed a computational…

Read More
JournalFeeds

Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data

Authors: David Augustin , et al. Citation: Augustin D, Lambert B, Wang K, Walz A-C, Robinson M, Gavaghan D (2023) Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data. PLoS Comput Biol 19(5): e1011135. https://doi.org/10.1371/journal.pcbi.1011135 Editor: Jason M. Haugh, North Carolina State University, UNITED STATES Received: November 1, 2022; Accepted:…

Read More

Structure Learning for Gene Regulatory Networks

Authors: Anthony Federico, et al. Abstract Inference of biological network structures is often performed on high-dimensional data, yet is hindered by the limited sample size of high throughput “omics” data typically available. To overcome this challenge, often referred to as the “small n, large p problem,” we exploit known organizing principles of biological networks that…

Read More