Review
Oncology
Leandro Jonata Carvalho Oliveira, Larissa Costa Amorim, Thais Baccili Cury Megid, Cristiano Augusto Andrade De Resende, Max S. Mano
Summary: We comprehensively review the clinical data of 5 common gene expression signatures (GES) in breast cancer, discussing their roles in special histologic subtypes, premenopausal women, late recurrence, and adjuvant treatment de-escalation.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2022)
Article
Gastroenterology & Hepatology
Virginia Diez-Obrero, Christopher H. Dampier, Ferran Moratalla-Navarro, Matthew Devall, Sarah J. Plummer, Anna Diez-Villanueva, Ulrike Peters, Stephanie Bien, Jeroen R. Huyghe, Anshul Kundaje, Gemma Ibanez-Sanz, Elisabeth Guino, Mireia Obon-Santacana, Robert Carreras-Torres, Graham Casey, Victor Moreno
Summary: This study characterized gene expression and splicing profiles across different colon subsites, identified numerous expression and splicing QTLs, proposed candidate effector genes for diseases affecting colon tissue and other tissues, and developed the Colon Transcriptome Explorer web application for visualization. The findings provide valuable insights into the genetic underpinnings of complex traits and diseases influenced by transcriptomic changes in colon tissue.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2021)
Article
Multidisciplinary Sciences
Daisuke Kasugai, Masayuki Ozaki, Kazuki Nishida, Yukari Goto, Kunihiko Takahashi, Shigeyuki Matsui, Naoyuki Matsuda
Summary: The study suggests that larger platelet reductions in sepsis patients are associated with increased in-hospital mortality risk, independent from absolute platelet counts. This finding may provide a better signature of coagulopathies in sepsis and could be a plausible criterion for sepsis-associated coagulopathies.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Tzu-Hsien Yang, Yu-Hsuan Chiang, Sheng-Cian Shiue, Po-Heng Lin, Ya-Chiao Yang, Kai-Chi Tu, Yan-Yuan Tseng, Joseph T. Tseng, Wei-Sheng Wu
Summary: The transcript isoforms regulated by alternative splicing play a significant role in carcinogenesis. The Cancer DEIso database was constructed to facilitate in-depth analysis of gene-level and isoform-level human cancer studies, allowing for searches of differentially expressed genes/isoforms, expression survival analysis, and visualization of gene/isoform stage expression comparisons.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Nicole E. James, Morgan Woodman, Jennifer R. Ribeiro
Summary: EOC patients have low response rates to immunotherapies, but evidence suggests ovarian tumors are immunogenic and immune-related genomic profiles can serve as prognostic markers. Specific research areas that need to be addressed include developing immune-based prognostic signatures and driving advancements in this field.
Article
Oncology
Xiaoqing Yu, Ling Cen, Y. Ann Chen, Joseph Markowitz, Timothy Shaw, Kenneth Y. Tsai, Jose R. Conejo-Garcia, Xuefeng Wang
Summary: DNA methylation signatures can be used as reliable biomarkers to predict patient prognosis and immune status in tumors. This study introduces the concept of tumor-based expression quantitative trait methylation (eQTM) for the identification of predictive biomarkers. eQTM CpGs and genes represent new and efficient candidate targets for prognosis and immune status monitoring.
Article
Biochemical Research Methods
Martin Pirkl, Niko Beerenwinkel
Summary: A novel mathematical method has been developed to analyze cancer driver genes and patient-specific perturbation profiles by combining genetic aberrations with gene expression data in a causal network derived across patients to infer unobserved perturbations. The method has been shown to predict perturbations in simulations, CRISPR perturbation screens, and breast cancer samples from The Cancer Genome Atlas.
Article
Biotechnology & Applied Microbiology
Euphy Y. Y. Wu, Noor P. P. Singh, Kwangbom Choi, Mohsen Zakeri, Matthew Vincent, Gary A. A. Churchill, Cheryl L. L. Ackert-Bicknell, Rob Patro, Michael I. I. Love
Summary: SEESAW is a new method that uses Salmon and Swish to detect allelic imbalance. It allows analysis at various levels of resolution, including gene, isoform, and aggregates isoforms to groups. The method has higher power compared to other methods for detecting isoform-level allelic imbalance.
Article
Biochemistry & Molecular Biology
Allison Creason, David Haan, Kristen Dang, Kami E. Chiotti, Matthew Inkman, Andrew Lamb, Thomas Yu, Yin Hu, Thea C. Norman, Alex Buchanan, Marijke J. van Baren, Ryan Spangler, M. Rick Rollins, Paul T. Spellman, Dmitri Rozanov, Jin Zhang, Christopher A. Maher, Cristian Caloian, John D. Watson, Sebastian Uhrig, Brian J. Haas, Miten Jain, Mark Akeson, Mehmet Eren Ahsen, Gustavo Stolovitzky, Justin Guinney, Paul C. Boutros, Joshua M. Stuart, Kyle Ellrott
Summary: The ICGC-TCGA DREAM Somatic Mutation Calling in RNA (SMC-RNA) challenge aimed to benchmark methods for RNA isoform quantification and fusion detection from bulk cancer RNA sequencing data, which is crucial for analyzing the cancer transcriptome. The evaluation compared 77 fusion detection entries and 65 isoform quantification entries on 51 synthetic tumors and 32 cell lines with spiked-in fusion constructs.
Article
Biochemical Research Methods
Hong-Dong Li, Changhuo Yang, Zhimin Zhang, Mengyun Yang, Fang-Xiang Wu, Gilbert S. Omenn, Jianxin Wang
Summary: IsoResolve is a novel approach for isoform function prediction that leverages gene function prediction models with domain adaptation to improve performance. It treats gene-level and isoform-level features as source and target domains respectively, and uses domain adaptation to project them into a latent variable space for more accurate predictions.
Article
Biochemistry & Molecular Biology
Mikhail Raevskiy, Maxim Sorokin, Galina Zakharova, Victor Tkachev, Nicolas Borisov, Denis Kuzmin, Kristina Kremenchutckaya, Alexander Gudkov, Dmitry Kamashev, Anton Buzdin
Summary: Analyzing data at the pathway activation level can yield more consistent results when comparing RNA and protein expression profiles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Pankaj Ahluwalia, Ravindra Kolhe, Gagandeep K. Gahlay
Summary: This review emphasizes composite prognostic scores from diverse resources with clinical utility in CRC, highlighting the importance of gene-expression based prognostic risk scores in improving the management of the disease.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2021)
Article
Environmental Sciences
Samantha H. Hartke, Daniel B. Wright
Summary: This study compares the performance of interpolated gauge estimates and satellite precipitation data under different gauge densities, finding that satellite precipitation data shows similar accuracy to interpolated gauge data at very low gauge densities.
Article
Biochemical Research Methods
Fei Wang, Yulian Ding, Xiujuan Lei, Bo Liao, Fangxiang Wu
Summary: Drug repositioning is crucial for drug discovery, and this study proposes a new method, GS4CDRSC, based on sample clustering to identify gene signatures for cancer drug repositioning, which outperforms existing methods in predicting known drugs for specific cancers.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Chemistry, Analytical
Jialing Zhao, Hui He, Zhanchen Guo, Zhen Liu
Summary: Phosphorylation is a common post-translational modification in mammals and is related to various diseases. Molecularly imprinted polymers (MIPs) show unique advantages as phosphorylation recognition reagents, but their performance is currently not ideal. The new approach RMTD-SIC allows for the preparation of monodispersed imprinted nanoparticles for improved phosphorylation recognition.
ANALYTICAL CHEMISTRY
(2021)