Article
Multidisciplinary Sciences
Takeshi Yoshihara, Nathan D. Miller, Fernando A. Rabanal, Hannah Myles, Il-Youp Kwak, Karl W. Broman, Boris Sadkhin, Ivan Baxter, Brian P. Dilkes, Matthew E. Hudson, Edgar P. Spalding
Summary: By conducting large-scale experiments on two plant species, we have discovered four naturally varying components of a conserved process in gravitropism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Environmental Sciences
Aude Ratier, Virgile Baudrot, Milena Kaag, Aurelie Siberchicot, Christelle Lopes, Sandrine Charles
Summary: This paper introduces the functions and applications of the R-package rbioacc, which can be used to analyze data from bioaccumulation tests. The package provides TK parameter estimates, bioaccumulation metrics, and supports environmental risk assessment, in compliance with regulatory requirements.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Microbiology
Jiajia Li, Tania Chroumpi, Sandra Garrigues, Roland S. Kun, Jiali Meng, Sonia Salazar-Cerezo, Maria Victoria Aguilar-Pontes, Yu Zhang, Sravanthi Tejomurthula, Anna Lipzen, Vivian Ng, Chaevien S. Clendinen, Nikola Tolic, Igor Grigoriev, Adrian Tsang, Miia R. Makela, Berend Snel, Mao Peng, Ronald P. de Vries
Summary: Fungi play a critical role in the global carbon cycle by degrading plant polysaccharides to small sugars and metabolizing them as carbon and energy sources. This study mapped the sugar metabolic network of Aspergillus niger to other fungi species and found that the diversity of sugar metabolism is correlated with taxonomic distance. Integrative analysis of transcriptome, proteome, and metabolome confirmed these results and provided a valuable resource for rational metabolic engineering.
Article
Computer Science, Interdisciplinary Applications
Laura Florez-Perez, Zhiyuan Song, Jean C. Cortissoz
Summary: This article proposes a machine learning-based approach to predict task productivity in construction by considering subjective measure (compatibility of personality), external and site conditions, and other workers' characteristics. The results test rules in the masonry industry and find that crew size, task difficulty, and the relevance of experience depend on productivity.
COMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING
(2022)
Article
Multidisciplinary Sciences
Zhu Han, Weizhi Zhang, Wanshan Ning, Chenwei Wang, Wankun Deng, Zhidan Li, Zehua Shang, Xiaofei Shen, Xiaohui Liu, Otto Baba, Tsuyoshi Morita, Lu Chen, Yu Xue, Da Jia
Summary: This study establishes a pipeline integrating computational and experimental approaches to demonstrate the frequent occurrence of altered autophagy selectivity in cancer cells and to link glycogen autophagy with tumourigenesis.
NATURE COMMUNICATIONS
(2021)
Article
Mathematics, Interdisciplinary Applications
Yunjing Zhou, Shouxin Zong, Run Cao, Miguel-Angel Gomez, Chuqi Chen, Yixiong Cui
Summary: This research aimed to study the stroke patterns of professional tennis players by constructing a complex network based on ball bounce locations. Data from 127 Australian Open matches played by 128 male tennis players were analyzed to create the tennis stroke network. The results showed that certain court zones were more frequently used and had shorter path lengths. The study also found that rally lengths and tournament rounds influenced stroke patterns.
CHAOS SOLITONS & FRACTALS
(2023)
Article
Chemistry, Medicinal
Raghad Al-Jarf, Alex G. C. de Sa, Douglas E. Pires, David B. Ascher
Summary: The development of a novel predictive tool, pdCSM-cancer, provides an accurate way to predict molecules likely to be active against one or multiple cancer cell lines by using graph-based chemical structure signatures. This tool includes trained and validated models on data from over 18,000 compounds on 9 tumor types and 74 distinct cancer cell lines, achieving successful predictive performance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Sung-Bae Cho, Jin-Young Kim
Summary: This study proposes a method based on deep learning to analyze urban mobility by clustering and embedding mobility patterns to reveal their implicit meanings, enabling more effective analysis of mobility patterns.
Article
Multidisciplinary Sciences
Mahsa Saliani, Razieh Jalal, Ali Javadmanesh
Summary: This study analyzed the transcriptional profiles of KRAS mutant and wild-type cell lines using RNA-seq data and bioinformatics methods. The results showed that KRAS signaling is an oncogenic signature in KRAS mutant cells. Furthermore, differentially-expressed genes were found to be involved in cancer-associated signal transduction pathways. Additionally, several differentially-expressed lncRNAs potentially regulate genes in the Rap1 and RAS signaling pathways.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Yao Shen, Zhipeng Yan
Summary: In this study, multiple large-scale public data sets were leveraged to predict drug resistance caused by transporters using machine learning models. Novel drug-transporter interactions were discovered, and features selected by the models were significantly enriched in known drug transporters.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Physical
Esmaeil Zarei, Faisal Khan, Mohammad Yazdi
Summary: This paper introduces a dynamic and holistic risk model to address significant shortcomings of current hydrogen risk analysis models, using improved techniques such as Bow-tie and Dynamic Bayesian Network. The model helps analyze uncertainty in factors and barriers while demonstrating its application in a water electrolysis process. The proposed model serves as a useful tool for operational safety management in complex engineering systems.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2021)
Article
Biochemical Research Methods
Haijian Zhang, Joel R. Steele, Hossein Valipour Kahrood, Deanna Deveson Lucas, Anup D. Shah, Ralf B. Schittenhelm
Summary: Phosphoproteomics is a comprehensive method for identifying and quantifying phosphorylated peptides and their associated proteins. Phospho-Analyst is an easy-to-use web application that simplifies the statistical analysis and interpretation of phosphoproteomic data. It also automatically normalizes the results to protein abundance levels, ensuring the consideration of genuine phosphorylation changes.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Microbiology
Laura Munoz-Baena, Art F. Y. Poon
Summary: This study conducts a global comparative study of overlapping open reading frames (OvRFs) of 12,609 virus reference genomes in the NOBI database. Results show that the number of OvRFs increases with genome length, but they tend to be shorter in longer genomes. Majority of overlaps involve +2 frameshifts and antisense overlaps tend to be longer. The study also develops a new graph-based representation to visualize the distribution of overlaps among genomes in a virus family.
Article
Biochemical Research Methods
Keilash Chirom, Md Zubbair Malik, Irengbam Rocky Mangangcha, Pallavi Somvanshi, R. K. Brojen Singh
Summary: This study investigates the topological properties of ovarian cancer network (OCN) and the roles of hubs to understand OCN organization and disease complexity. The OCN exhibits self-organizing behavior with fractal properties and follows scaling laws at all levels of organization. The key regulators, including provincial and connector hubs, are responsible for maintaining the integrity and organization of the network. These key regulators are overexpressed and positively correlated with immune infiltrates. Additionally, potential drugs related to the key regulators are identified.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Sucharita Dey, Jaime Prilusky, Emmanuel D. Levy
Summary: The QSalign web server allows users to submit homo-oligomeric structures and predict their physiological relevance by searching for homologs based on sequence similarity and PFAM domain architecture. Representative QSs in the protein family of the query are also provided for further analysis and homology modeling.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Editorial Material
Oncology
Neshika Wijewardhane, Lisa Dressler, Francesca D. Ciccarelli
Summary: Gene alterations play a crucial role in driving cancer initiation and progression, but the genetic events occurring in normal cells prior to tumorigenesis remain unknown. Recent studies have started mapping somatic mutations in normal human tissues, shedding light on our understanding of tumorigenesis.
Article
Genetics & Heredity
Marc Jan Bonder, Craig Smail, Michael J. Gloudemans, Laure Fresard, David Jakubosky, Matteo D'Antonio, Xin Li, Nicole M. Ferraro, Ivan Carcamo-Orive, Bogdan Mirauta, Daniel D. Seaton, Na Cai, Dara Vakili, Danilo Horta, Chunli Zhao, Diane B. Zastrow, Devon E. Bonner, Matthew T. Wheeler, Helena Kilpinen, Joshua W. Knowles, Erin N. Smith, Kelly A. Frazer, Stephen B. Montgomery, Oliver Stegle
Summary: By integrating data from 1,367 human iPSC lines, researchers comprehensively mapped common and rare regulatory variants in human pluripotent cells, identified new colocalization events specific to iPSCs, and demonstrated the utility of iPSCs in identifying causal genes for rare diseases.
Article
Genetics & Heredity
Joel Nulsen, Hrvoje Misetic, Christopher Yau, Francesca D. Ciccarelli
Summary: sysSVM2 is a machine learning software that integrates cancer genetic alterations with gene systems-level properties to predict driver genes in individual patients, showing low false-positive rate and stability, with applicability to rare cancer types. It can be used to identify driver alterations in patients lacking sufficient canonical drivers, furthering the goals of precision oncology.
Article
Multidisciplinary Sciences
Soohwan Oh, Jiaofang Shao, Joydeep Mitra, Feng Xiong, Matteo D'Antonio, Ruoyu Wang, Ivan Garcia-Bassets, Qi Ma, Xiaoyu Zhu, Joo-Hyung Lee, Sreejith J. Nair, Feng Yang, Kenneth Ohgi, Kelly A. Frazer, Zhengdong D. Zhang, Wenbo Li, Michael G. Rosenfeld
Summary: The study shows that when a preferred promoter is functionally lost, its partner enhancer may be released and activate another nearby promoter. This process of target-switching may be determined by CTCF binding at promoters, in line with the model of 'enhancer scanning'. Additionally, the mechanism of enhancer release and retargeting is found to underlie the activation of disease-susceptibility genes.
Article
Multidisciplinary Sciences
Michele Bortolomeazzi, Lucia Montorsi, Damjan Temelkovski, Mohamed Reda Keddar, Amelia Acha-Sagredo, Michael J. Pitcher, Gianluca Basso, Luigi Laghi, Manuel Rodriguez-Justo, Jo Spencer, Francesca D. Ciccarelli
Summary: SIMPLI is a flexible and technology-agnostic software for multiplexed imaging data analysis, allowing single-cell analysis and quantification of marker expression while preserving spatial information. Its customizability and parallel processing capabilities make it suitable for large datasets.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Nicola Lockwood, Silvia Martini, Ainara Lopez-Pardo, Katharina Deiss, Hendrika A. Segeren, Robert K. Semple, Ian Collins, Dimitra Repana, Mathias Cobbaut, Tanya Soliman, Francesca Ciccarelli, Peter J. Parker
Summary: G2 arrest is crucial for the faithful segregation of sister chromatids, and the p53-p21 signaling pathway plays an essential role in cell lines, patient-derived cells, and colorectal cancer organoids. In arrest-defective hTERT-positive cells, the PKC epsilon failsafe mechanism is engaged. In ALT-dependent cancer cells, a distinct form of p53-independent G2 arrest is mediated by BLM and Chk1.
Review
Cell Biology
Felipe S. Rodrigues, Francesca D. Ciccarelli, Ilaria Malanchi
Summary: The activation of developmental programmes by mutant cells is a fundamental requirement for cancer initiation. Oncogenic signals confer undifferentiated, stem cell-like properties to cancer cells, supporting their long-term proliferative potential. While mutations in cancer-driver genes alone are insufficient for tumor formation, the proliferation of cells with oncogenic mutations depends on their microenvironment. This Opinion article discusses how the reprogrammed status of cancer cells represents their tumorigenicity and triggers 'reflected stemness' in surrounding normal cells, contributing to the establishment of the tumor microenvironment (TME).
TRENDS IN CELL BIOLOGY
(2022)
Article
Biochemical Research Methods
Matteo D'Antonio, Jennifer P. Nguyen, Timothy D. Arthur, Hiroko Matsui, Margaret K. R. Donovan, Agnieszka D'Antonio-Chronowska, Kelly A. Frazer
Summary: Reactivation of fetal-specific genes and isoforms occurs during heart failure, suggesting a stricter transcriptional regulation in fetal cardiac tissue.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biology
Alvin Wei Tian Ng, Gianmarco Contino, Sarah Killcoyne, Ginny Devonshire, Ray Hsu, Sujath Abbas, Jing Su, Aisling M. Redmond, Jamie M. J. Weaver, Matthew D. Eldridge, Simon Tavare, Paul A. W. Edwards, Rebecca C. Fitzgerald
Summary: This study categorizes genomic structural variants (SVs) in 383 cases of oesophageal cancer, uncovering mutational patterns and new disease drivers. Identification of SV events in OAC is crucial for targeted therapies.
COMMUNICATIONS BIOLOGY
(2022)
Article
Oncology
Jessica Marinello, Andrea Arleo, Marco Russo, Maria Delcuratolo, Francesca Ciccarelli, Yves Pommier, Giovanni Capranico
Summary: This study used molecular, genetic, and bioinformatic approaches to investigate the mechanism of micronuclei formation induced by TOP1 poisons in different cancer cells. The results revealed an immune signaling mechanism activated by TOP1 poisons, which is often impaired in human small-cell lung cancer tumors.
BRITISH JOURNAL OF CANCER
(2022)
Review
Oncology
A. Acha-Sagredo, P. Ganguli, F. D. Ciccarelli
Summary: Somatic variation is an important factor in cancer initiation and early detection. The extent of somatic variation varies across tissues depending on their intrinsic features and exposure to endogenous and exogenous insults. Mutations in tumor suppressor genes involved in chromatin modification and cell growth signaling are tissue-specific drivers of clonal expansion. Understanding the factors triggering the transformation of somatic variation into malignant clones is crucial for cancer prevention and early detection.
ANNALS OF ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Matteo P. D'Antonio, Jennifer P. D. Nguyen, Timothy D. Arthur, Hiroko A. Matsui, Agnieszka D'Antonio-Chronowska, Kelly A. Frazer
Summary: This study identifies 2,578 eQTLs associated with specific developmental stages, tissues, and cell types using spatiotemporal information of 966 RNA-seq cardiac samples. The colocalization between eQTLs and GWAS signals reveals the impact of genetic variants on cardiac traits and diseases. These findings shed light on the specific effects of cardiac GWAS variants on developmental stages, tissues, and cell types.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Hrvoje Misetic, Mohamed Reda Keddar, Jean-Pierre Jeannon, Francesca D. D. Ciccarelli
Summary: In this study, the significant interactions between cancer-specific genetic drivers and anti- and pro-tumour features of the tumour immune microenvironment (TIME) were computed using Lasso regularised ordinal regression in 32 cancer types. The functional networks linking specific TIME driver alterations to the associated TIME state were reconstructed for head and neck squamous cancer (HNSC). The study identified 477 TIME drivers that are multifunctional genes, predicted the immune profiles of HNSC molecular subtypes, and provided insights into the immune-regulatory role of TIME drivers.
Article
Evolutionary Biology
Ella F. Gunady, Kathryn E. Ware, Sarah Hoskinson Plumlee, Nicolas Devos, David Corcoran, Joseph Prinz, Hrvoje Misetic, Francesca D. Ciccarelli, Tara M. Harrison, Jeffrey L. Thorne, Robert Schopler, Jeffrey Everitt, William C. Eward, Jason A. Somarelli
Summary: The mutational landscape of hepatocellular carcinoma in lemurs shows similarities and unique features compared to human hepatocellular carcinomas, suggesting potential differences in the etiology and progression of this cancer in lemurs and humans.
EVOLUTION MEDICINE AND PUBLIC HEALTH
(2022)
Article
Biotechnology & Applied Microbiology
Lisa Dressler, Michele Bortolomeazzi, Mohamed Reda Keddar, Hrvoje Misetic, Giulia Sartini, Amelia Acha-Sagredo, Lucia Montorsi, Neshika Wijewardhane, Dimitra Repana, Joel Nulsen, Jacki Goldman, Marc Pollitt, Patrick Davis, Amy Strange, Karen Ambrose, Francesca D. Ciccarelli
Summary: This study compiled a literature-based repertoire of 3355 well-known or predicted drivers of cancer and non-cancer somatic evolution in 122 cancer types and 12 non-cancer tissues. The analysis of these genes revealed that the known compendium of drivers is still incomplete and biased towards frequently occurring coding mutations. There is a high overlap between drivers of cancer and non-cancer somatic evolution, although significant differences exist in their recurrence. Additionally, a set of evolutionarily conserved and essential genes were identified, and alteration in even one of these genes is sufficient to drive clonal expansion but not malignant transformation.
