Search Our Scientific Publications & Authors

Nat Commun 2021 Apr 16;12(1):2301. Epub 2021 Apr 16.

Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark.

The molecular landscape in non-muscle-invasive bladder cancer (NMIBC) is characterized by large biological heterogeneity with variable clinical outcomes. Here, we perform an integrative multi-omics analysis of patients diagnosed with NMIBC (n = 834). Transcriptomic analysis identifies four classes (1, 2a, 2b and 3) reflecting tumor biology and disease aggressiveness. Read More

Cell 2021 Apr 14. Epub 2021 Apr 14.

Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:

Precision oncology has made significant advances, mainly by targeting actionable mutations in cancer driver genes. Aiming to expand treatment opportunities, recent studies have begun to explore the utility of tumor transcriptome to guide patient treatment. Here, we introduce SELECT (synthetic lethality and rescue-mediated precision oncology via the transcriptome), a precision oncology framework harnessing genetic interactions to predict patient response to cancer therapy from the tumor transcriptome. Read More

J Proteome Res 2021 Apr 15. Epub 2021 Apr 15.

Division of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden.

Proteogenomic approaches have enabled the generat̲ion of novel information levels when compared to single omics studies although burdened by extensive experimental efforts. Here, we improved a data-independent acquisition mass spectrometry proteogenomic workflow to reveal distinct molecular features related to mammographic appearances in breast cancer. Our results reveal splicing processes detectable at the protein level and highlight quantitation and pathway complementarity between RNA and protein data. Read More

Environ Sci Pollut Res Int 2021 Apr 12. Epub 2021 Apr 12.

National Centre for Cell Science, Ganeshkhind, Pune, 411007, India.

Microbial activities within oil reservoirs have adversely impacted the world's majority of oil by lowering its quality, thereby increasing its recovery and refining cost. Moreover, conventional method of extraction leaves behind nearly two-thirds of the fossil fuels in the oil fields. This huge potential can be extracted if engineered methanogenic consortium is adapted to convert the hydrocarbons into natural gas. Read More

Parasite 2021 12;28:36. Epub 2021 Apr 12.

CONACYT-Instituto Tecnológico de Sonora, Ciudad Obregón, 85000 Sonora, México.

In this review, we focus on the sequenced genomes of the pathogens Naegleria fowleri, Acanthamoeba spp. and Balamuthia mandrillaris, and the remarkable discoveries regarding the pathogenicity and genetic information of these organisms, using techniques related to the various omics branches like genomics, transcriptomics, and proteomics. Currently, novel data produced through comparative genomics analyses and both differential gene and protein expression in these free-living amoebas have allowed for breakthroughs to identify genes unique to N. Read More

Front Physiol 2021 25;12:638983. Epub 2021 Mar 25.

Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.

Skeletal muscle is the most abundant type of tissue in human body, being involved in diverse activities and maintaining a finely tuned metabolic balance. Autophagy, characterized by the autophagosome-lysosome system with the involvement of evolutionarily conserved autophagy-related genes, is an important catabolic process and plays an essential role in energy generation and consumption, as well as substance turnover processes in skeletal muscles. Autophagy in skeletal muscles is finely tuned under the tight regulation of diverse signaling pathways, and the autophagy pathway has cross-talk with other pathways to form feedback loops under physiological conditions and metabolic stress. Read More

Semin Immunopathol 2021 Apr 9. Epub 2021 Apr 9.

Faculty of Medicine, Heidelberg University, Heidelberg, Germany.

IgA nephropathy (IgAN) is the most common glomerulonephritis. It is characterized by the deposition of immune complexes containing immunoglobulin A (IgA) in the kidney's glomeruli, triggering an inflammatory process. In many patients, the disease has a progressive course, eventually leading to end-stage kidney disease. Read More

Appl Microbiol Biotechnol 2021 Apr 9;105(8):3027-3043. Epub 2021 Apr 9.

Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa.

The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. Read More

Brief Bioinform 2021 Apr 5. Epub 2021 Apr 5.

Department of Entomology and Plant Pathology, University of Tennessee, USA.

Next-generation sequencing (NGS) enables massively parallel acquisition of large-scale omics data; however, objective data quality filtering parameters are lacking. Although a useful metric, evidence reveals that platform-generated Phred values overestimate per-base quality scores. We have developed novel and empirically based algorithms that streamline NGS data quality filtering. Read More

PeerJ Comput Sci 2021 28;7:e363. Epub 2021 Jan 28.

Department of Computer Science, Jamia Millia Islamia, New Delhi, India.

High throughput multi-omics data generation coupled with heterogeneous genomic data fusion are defining new ways to build computational inference models. These models are scalable and can support very large genome sizes with the added advantage of exploiting additional biological knowledge from the integration framework. However, the limitation with such an arrangement is the huge computational cost involved when learning from very large datasets in a sequential execution environment. Read More

Philos Trans R Soc Lond B Biol Sci 2021 May 5;376(1825):20200162. Epub 2021 Apr 5.

Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87112, USA.

Traditional molecular methods and omics-techniques across molluscan taxonomy increasingly inform biology of Mollusca. Recovery of DNA and RNA for such studies is challenged by common biological properties of the highly diverse molluscs. Molluscan biomineralization, adhesive structures and mucus involve polyphenolic proteins and mucopolysaccharides that hinder DNA extraction or copurify to inhibit enzyme-catalysed molecular procedures. Read More

Viruses 2021 Mar 5;13(3). Epub 2021 Mar 5.

Department of Agriculture and Environmental Sciences, National Institute of Food Technology Entrepreneurship & Management (NIFTEM), Industrial Estate, Kundli 131028, India.

Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. Read More

Biomedicines 2021 Mar 31;9(4). Epub 2021 Mar 31.

Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal.

In the wake of the 'omics' explosion of data, reverse vaccinology approaches are being applied more readily as an alternative for the discovery of candidates for next generation diagnostics and vaccines. Promising protective antigens for the control of ticks and tick-borne diseases can be discovered by mining available omics data for immunogenic epitopes. The present study aims to explore the previously obtained sialotranscriptome during both feeding and infection, to select antigenic targets that are either membrane-associated or a secreted protein, as well as unique to the ectoparasite and not present in the mammalian host. Read More

Cells 2021 Mar 13;10(3). Epub 2021 Mar 13.

Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA.

Pulmonary arterial hypertension (PAH) is a rare and chronic lung disease characterized by progressive occlusion of the small pulmonary arteries, which is associated with structural and functional alteration of the smooth muscle cells and endothelial cells within the pulmonary vasculature. Excessive vascular remodeling is, in part, responsible for high pulmonary vascular resistance and the mean pulmonary arterial pressure, increasing the transpulmonary gradient and the right ventricular "pressure overload", which may result in right ventricular (RV) dysfunction and failure. Current technological advances in multi-omics approaches, high-throughput sequencing, and computational methods have provided valuable tools in molecular profiling and led to the identification of numerous genetic variants in PAH patients. Read More

Genes (Basel) 2021 Mar 9;12(3). Epub 2021 Mar 9.

Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA.

The promise of personalized medicine is a therapeutic advance where tumor signatures obtained from different omics platforms, such as genomics, transcriptomics, proteomics, and metabolomics, in addition to environmental factors including metals and metalloids, are used to guide the treatments. Clear cell renal carcinoma (ccRCC), the most common type of kidney cancer, can be sporadic (frequently) or genetic (rare), both characterized by loss of the von Hippel-Lindau (VHL) gene that controls hypoxia inducible factors. Recently, several genomic subtypes were identified with different prognoses. Read More

Int J Mol Sci 2021 Mar 10;22(6). Epub 2021 Mar 10.

Medical Informatics for Translational Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

Recent advances in sequencing and biotechnological methodologies have led to the generation of large volumes of molecular data of different omics layers, such as genomics, transcriptomics, proteomics and metabolomics. Integration of these data with clinical information provides new opportunities to discover how perturbations in biological processes lead to disease. Using data-driven approaches for the integration and interpretation of multi-omics data could stably identify links between structural and functional information and propose causal molecular networks with potential impact on cancer pathophysiology. Read More

Anticancer Agents Med Chem 2021 Apr 1. Epub 2021 Apr 1.

Department of Biology, University of Pisa, Pisa. Italy.

Background: Zebrafish (Danio rerio) is a vertebrate that has become a popular alternative model for the cellular and molecular study of human tumors and for drug testing and validating approaches. Notably, zebrafish embryos, thanks to their accessibility, allow rapid collection of in vivo results prodromal to validation in the murine models in respect to the 3R principles. The generation of tumor xenograft in zebrafish embryos and larvae, or zebrafish avatar, represents a unique opportunity to study tumor growth, angiogenesis, cell invasion and metastatic dissemination, interaction between tumor and host in vivo avoiding immunogenic rejection, representing a promising platform for the translational research and personalized therapies. Read More

J Cell Sci 2021 Apr 1;134(7). Epub 2021 Apr 1.

Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel

Cell imaging has entered the 'Big Data' era. New technologies in light microscopy and molecular biology have led to an explosion in high-content, dynamic and multidimensional imaging data. Similar to the 'omics' fields two decades ago, our current ability to process, visualize, integrate and mine this new generation of cell imaging data is becoming a critical bottleneck in advancing cell biology. Read More

Cell Prolif 2021 Apr 1:e13038. Epub 2021 Apr 1.

State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Objectives: Organic Selenium (Se) compounds such as L-Se-methylselenocysteine (L-SeMC/SeMC) have been employed as a class of anti-oxidant to protect normal tissues and organs from chemotherapy-induced systemic toxicity. However, their comprehensive effects on cancer cell proliferation and tumour progression remain elusive.

Materials And Methods: CCK-8 assays were conducted to determine the viabilities of cancer cells after exposure to SeMC, chemotherapeutics or combined treatment. Read More

Brief Funct Genomics 2021 Apr 1. Epub 2021 Apr 1.

Cancer is one of the most prevailing, deadly and challenging diseases worldwide. The advancement in technology led to the generation of different types of omics data at each genome level that may potentially improve the current status of cancer patients. These data have tremendous applications in managing cancer effectively with improved outcome in patients. Read More

Best Pract Res Clin Endocrinol Metab 2021 Feb 17:101504. Epub 2021 Feb 17.

Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708, WE, Wageningen, the Netherlands; Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. Electronic address:

The human gut microbiota has appeared as an important factor affecting host health and intestinal bacteria have recently emerged as potential therapeutics to treat diabetes and other endocrine diseases. These mainly anaerobic bacteria have been identified either via comparative "omics" analysis of the intestinal microbiota in healthy and diseased subjects or of data collected by fecal microbiota transplantation studies. Both approaches require advanced and in-depth sequencing technologies to perform massive genomic screening to select bacteria with potential benefits. Read More

Sheng Wu Gong Cheng Xue Bao 2021 Mar;37(3):806-815

State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.

Yeast are comprised of diverse single-cell fungal species including budding yeast Saccharomyces cerevisiae and various nonconventional yeasts. Budding yeast is well known as an important industrial microorganism, which has been widely applied in various fields, such as biopharmaceutical and health industry, food, light industry and biofuels production. In the recent years, various yeast strains from different ecological environments have been isolated and characterized. Read More

Curr Ophthalmol Rep 2020 Dec 2;8(4):216-225. Epub 2020 Sep 2.

Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA 30912.

Purpose Of Review: To summarize the recent advances in transcriptomics and proteomics studies of keratoconus using advanced genome-wide gene and protein expression profiling techniques.

Recent Findings: Second-generation sequencing including RNA sequencing has been widely used to characterize the genome-wide gene expression in corneal tissues or cells affected by keratoconus. Due to different sample types, sequencing platforms, and analysis pipeline, different lists of genes have been identified to be differentially expressed in KC-affected samples. Read More

Nat Commun 2021 03 25;12(1):1850. Epub 2021 Mar 25.

Cell Signalling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK.

Artificial intelligence and machine learning (ML) promise to transform cancer therapies by accurately predicting the most appropriate therapies to treat individual patients. Here, we present an approach, named Drug Ranking Using ML (DRUML), which uses omics data to produce ordered lists of >400 drugs based on their anti-proliferative efficacy in cancer cells. To reduce noise and increase predictive robustness, instead of individual features, DRUML uses internally normalized distance metrics of drug response as features for ML model generation. Read More

Cell Commun Signal 2021 Mar 24;19(1):39. Epub 2021 Mar 24.

Department of Urology, Fujian Province, Fujian Medical University Union Hospital, Gulou District, 29 Xinquan Road, Fuzhou, 200001, People's Republic of China.

Background: Tumor angiogenesis, an essential process for cancer proliferation and metastasis, has a critical role in prognostic of kidney renal clear cell carcinoma (KIRC), as well as a target in guiding treatment with antiangiogenic agents. However, tumor angiogenesis subtypes and potential epigenetic regulation mechanisms in KIRC patient remains poorly characterized. System evaluation of angiogenesis subtypes in KIRC patient might help to reveal the mechanisms of KIRC and develop more target treatments for patients. Read More

Bioinformatics 2021 Mar 4. Epub 2021 Mar 4.

Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada.

Motivation: The growing production of massive heterogeneous biological data offers opportunities for new discoveries. However, performing multi-omics data analysis is challenging, and researchers are forced to handle the ever-increasing complexity of both data management and evolution of our biological understanding. Substantial efforts have been made to unify biological datasets into integrated systems. Read More

iScience 2021 Mar 20;24(3):102219. Epub 2021 Feb 20.

BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China.

In this study, six bacterial isolates with variable GC, including as mesophilic reference strain, were selected to compare hybrid assembly strategies based on next-generation sequencing (NGS) of short reads, single-tube long-fragment reads (stLFR) sequencing, and Oxford Nanopore Technologies (ONT) sequencing platforms. We obtained the complete genomes using the hybrid assembler Unicycler based on the NGS and ONT reads; others were assembled using NGS, stLFR, and ONT reads by using different strategies. The contiguity, accuracy, completeness, sequencing costs, and DNA material requirements of the investigated strategies were compared systematically. Read More

Front Genet 2021 4;12:620453. Epub 2021 Mar 4.

Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain.

Technologies for profiling samples using different omics platforms have been at the forefront since the human genome project. Large-scale multi-omics data hold the promise of deciphering different regulatory layers. Yet, while there is a myriad of bioinformatics tools, each multi-omics analysis appears to start from scratch with an arbitrary decision over which tools to use and how to combine them. Read More

BMC Genomics 2021 Mar 20;22(1):198. Epub 2021 Mar 20.

Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic.

Background: Lineage-specific gene expansions represent one of the driving forces in the evolutionary dynamics of unique phylum traits. Myxozoa, a cnidarian subphylum of obligate parasites, are evolutionarily altered and highly reduced organisms with a simple body plan including cnidarian-specific organelles and polar capsules (a type of nematocyst). Minicollagens, a group of structural proteins, are prominent constituents of nematocysts linking Myxozoa and Cnidaria. Read More

mSystems 2021 Mar 16;6(2). Epub 2021 Mar 16.

Center for Experimental and Molecular Medicine, Amsterdam UMC, Location AMC, Amsterdam Infection and Immunity Institute, Amsterdam, The Netherlands.

Bacterial microbiota play a critical role in mediating local and systemic immunity, and shifts in these microbial communities have been linked to impaired outcomes in critical illness. Emerging data indicate that other intestinal organisms, including bacteriophages, viruses of eukaryotes, fungi, and protozoa, are closely interlinked with the bacterial microbiota and their host, yet their collective role during antibiotic perturbation and critical illness remains to be elucidated. We employed multi-omics factor analysis (MOFA) to systematically integrate the bacterial (16S rRNA), fungal (intergenic transcribed spacer 1 rRNA), and viral (virus discovery next-generation sequencing) components of the intestinal microbiota of 33 critically ill patients with and without sepsis and 13 healthy volunteers. Read More