Review
Biochemical Research Methods
Surui Pei, Tao Liu, Xue Ren, Weizhong Li, Chongjian Chen, Zhi Xie
Summary: DNA variants are important sources of genetic variation among individuals. Next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies are widely used for genome-wide variant calling. Different variant callers show varying performance on NGS and TGS data, with TGS detecting more variants, particularly in complex and repetitive regions. Careful selection of tools and parameters is essential for accurate variant calling under different scenarios.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Shuo Shi, Qi Wang, Yunfei Shang, Congfan Bu, Mingming Lu, Meiye Jiang, Hao Zhang, Shuhuan Yu, Jingyao Zeng, Zaichao Zhang, Zhenglin Du, Jingfa Xiao
Summary: This article introduces a new method for identifying somatic and germline variants using tumor samples. The method shows higher accuracy and better capability in detecting somatic variants, and accurately identifies germline variants in tumor samples.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Hye Lim Choi, Ha Rim Yang, Ha Gyeong Shin, Kyusang Hwang, Ji Woong Kim, Ji Hyun Lee, Taehoon Ryu, Yushin Jung, Sukmook Lee
Summary: Antibody phage display is a crucial technology for discovering and developing target-specific monoclonal antibodies. This study constructed a large human combinatorial single-chain variable fragment library with high diversity, which can be used for the rapid development of recombinant human monoclonal antibodies for therapeutic and diagnostic applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Sanjay Joshi, Hadia Awan, Priyanka Paul, Ran Tian, Sharyn E. Perry
Summary: AGL15, a member of the MADS-domain transcription factor family, primarily accumulates in plant embryos and promotes plant regeneration. Through the use of different technological platforms, researchers have identified an interaction between AGL15 and the brassinosteroid hormone signaling pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Oncology
Youngjun Park, Dominik Heider, Anne-Christin Hauschild
Summary: In recent years, advancements in next-generation sequencing and artificial intelligence have led to the development of various algorithms and applications. Integrating systems biology and machine learning has been crucial in addressing challenges posed by big data. Machine learning algorithms and network-based models play a key role in analyzing NGS data effectively.
Article
Oncology
Minghan Jia, Ning Liao, Bo Chen, Guochun Zhang, Yulei Wang, Xuerui Li, Li Cao, Hsiaopei Mok, Chongyang Ren, Kai Li, Cheukfai Li, Lingzhu Wen, Jiali Lin, Guangnan Wei, Charles M. Balch
Summary: PIK3CA alterations are prevalent in Chinese breast cancer patients with different molecular features compared to Caucasians. These findings provide valuable insights for the application of PIK3CA inhibitors in Chinese patients.
Article
Multidisciplinary Sciences
Lyora A. Cohen-Aharonov, Annie Rebibo-Sabbah, Adar Yaacov, Roy Z. Granit, Merav Strauss, Raul Colodner, Ori Cheshin, Shai Rosenberg, Ronen Eavri
Summary: In this study, the researchers proposed a solution for large-scale viral screening and specific variant analysis by integrating DNA barcoding technology, sample pooling, and Next Generation Sequencing (NGS) methods. The solution allows high throughput testing with high sensitivity and specificity, and enables variant analysis at a single nucleotide resolution.
Article
Multidisciplinary Sciences
Duo Wang, Yuanfeng Zhang, Rui li, Jinming Li, Rui Zhang
Summary: This study developed paired tumor-normal reference materials using CRISPR-Cas9 technology and evaluated the performance of 56 panels in detecting somatic mutations. The results showed variations in accuracy and reproducibility among different panels, with filtering errors, low-quality detection, cross-contamination, and other sequencing errors as major sources of false discoveries. The study provides an integrated practice to assess onco-panels and quantitatively reveals the sources of detection errors.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Engineering, Environmental
Yuanyan Jiang, Jiawei Huang, Wei Luo, Kejin Chen, Wenrou Yu, Wenjun Zhang, Chuan Huang, Junjun Yang, Yingzhou Huang
Summary: In this study, machine learning models (Random Forest, XGBoost, LightGBM) were established to predict the production of odors from domestic waste based on four factors (weight, wet composition, temperature, and fermentation time). The Random Forest model showed the highest accuracy with a R2 value of 0.8958. Furthermore, the impact of microbial fermentation on odor production from domestic waste was discussed.
Article
Engineering, Multidisciplinary
Maira Alvi, Khamael M. Abualnaja, Waqas Tariq Toor, Muhammad Saadi
Summary: The study analyzed the ACB factor in LTE-A and its selection criteria show that the optimal selection of the ACB factor is crucial for achieving the maximum throughput of the system.
ALEXANDRIA ENGINEERING JOURNAL
(2021)
Article
Food Science & Technology
Francesca Ghilardelli, Mario Barbato, Antonio Gallo
Summary: In this study, corn silage samples were analyzed for mycotoxin concentrations and scanned using a NIR spectrometer. Random Forest classification models were developed to classify samples based on mycotoxin concentration or count. Different cut-off values were applied to achieve accurate classification.
Article
Pediatrics
Yi-Sheng Chang, Chang-Wei Li, Ling Chen, Xing-An Wang, Maw-Sheng Lee, Yu-Hua Chao
Summary: The development of the gut microbiome during early life has long-term effects on health. This study analyzed the microbiota profile of the first-pass meconium in healthy neonates and found a similar composition, with Pseudomonas being the most abundant genus. The diversity of the microbial communities in the first-pass meconium was extremely poor. Primigravidae babies had a higher diversity index, and the Bacteroidales order was a biomarker for their meconium. Delivery mode, maternal antibiotic treatment, rupture of membranes, and birth weight did not affect the diversity index.
Article
Computer Science, Artificial Intelligence
Yu Chen
Summary: This paper examines the prediction of college English level 4 pass rate using machine learning algorithms. The random forest algorithm is applied for prediction, and through preprocessing, feature extraction, and dimensionality reduction, high prediction accuracy is achieved.
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Genetics & Heredity
Maria Plesa, Vincent Gagne, Sanja Glisovic, Melissa Younan, Bahram Sharif-Askari, Caroline Laverdiere, Nathalie Alos, Jean-Marie Leclerc, Stephen E. Sallan, Donna Neuberg, Jeffery L. Kutok, Lewis B. Silverman, Daniel Sinnett, Maja Krajinovic
PHARMACOGENOMICS JOURNAL
(2019)
Article
Nutrition & Dietetics
E. Delvin, N. Alos, F. Rauch, V. Marcil, S. Morel, M. Boisvert, M. -A. Lecours, C. Laverdiere, D. Sinnett, M. Krajinovic, J. Dubois, S. Drouin, G. Lefebvre, M. Samoilenko, C. Nyalendo, E. Cavalier, E. Levy
CLINICAL NUTRITION
(2019)
Article
Cardiac & Cardiovascular Systems
Maxime Caru, Denis Corbin, Delphine Perie, Valerie Lemay, Jacques Delfrate, Simon Drouin, Laurence Bertout, Maja Krajinovic, Caroline Laverdiere, Gregor Andelfinger, Daniel Sinnett, Daniel Curnier
CLINICAL RESEARCH IN CARDIOLOGY
(2019)
Article
Genetics & Heredity
Yosr Hamdi, Martin Leclerc, Martine Dumont, Stephane Dubois, Martine Tranchant, Guy Reimnitz, Penny Soucy, Pauline Cassart, Manon Ouimet, Daniel Sinnett, M'Hamed Lajmi Lakhal Chaieb, Jacques Simard
Meeting Abstract
Sport Sciences
Maxime Caru, Valerie Lemay, Mariia Samoilenko, Simon Drouin, Nathalie Alos, Genevieve Lefebvre, Emile Levy, Sarah Lippe, Valerie Marcil, Serge Sultan, Laurence Bertout, Maja Krajinovic, Caroline Laverdiere, Marie-Josee Raboisson, Daniel Sinnett, Gregor Andelfinger, Daniel Sinnett, Daniel Curnier
MEDICINE AND SCIENCE IN SPORTS AND EXERCISE
(2019)
Meeting Abstract
Sport Sciences
Gabrielle E. Duhamel, Maxime Caru, Valerie Lemay, Simon Drouin, Nathalie Alos, Laurence Bertout, Maja Krajinovic, Caroline Laverdiere, Marie-Josee Raboisson, Daniel Sinnett, Gregoir Andelfinger, Daniel Curnier
MEDICINE AND SCIENCE IN SPORTS AND EXERCISE
(2019)
Article
Multidisciplinary Sciences
Kateryna Petrykey, Sarah Lippe, Philippe Robaey, Serge Sultan, Julie Laniel, Simon Drouin, Laurence Bertout, Patrick Beaulieu, Pascal St-Onge, Aubree Boulet-Craig, Aziz Rezgui, Yutaka Yasui, Yadav Sapkota, Kevin R. Krull, Melissa M. Hudson, Caroline Laverdiere, Daniel Sinnett, Maja Krajinovic
Article
Oncology
Maxime Caru, Mariia Samoilenko, Simon Drouin, Valerie Lemay, Laurence Kern, Lucia Romo, Laurence Bertout, Genevieve Lefebvre, Gregor Andelfinger, Maja Krajinovic, Caroline Laverdiere, Daniel Sinnett, Daniel Curnier
JOURNAL OF ADOLESCENT AND YOUNG ADULT ONCOLOGY
(2019)
Article
Nutrition & Dietetics
Sophie Berard, Sophia Morel, Emma Teasdale, Nitin Shivappa, James R. Hebert, Caroline Laverdiere, Daniel Sinnett, Emile Levy, Valerie Marcil
Article
Pediatrics
Johanne Kerba, Catherine Demers, Veronique Belanger, Melanie Napartuk, Isabelle Bouchard, Caroline Meloche, Sophia Morel, Nicolas Prud'homme, Isabelle Gelinas, Johanne Higgins, Daniel Curnier, Serge Sultan, Caroline Laverdiere, Daniel Sinnett, Valerie Marcil
Summary: This study aims to assess the needs, barriers and facilitators to healthy lifestyle promotion interventions for adolescents with cancer. The findings suggest that adolescents with cancer need activities adapted to their age, peer support, and support to maintain their education and friendships. Lack of motivation, fatigue, and treatment side effects are reported as barriers to intervention.
Article
Pediatrics
Melanie Napartuk, Veronique Belanger, Isabelle Bouchard, Caroline Meloche, Daniel Curnier, Serge Sultan, Caroline Laverdiere, Daniel Sinnett, Valerie Marcil
Summary: This study examined the changes in diet and anthropometric and cardiometabolic profiles of children and adolescents undergoing cancer treatments after a one-year nutritional intervention. It found that the intervention improved diet quality and adherence, as well as weight, BMI, HDL-C levels, and vitamin D levels.
Article
Medicine, General & Internal
Fida Khater, Stephanie Vairy, Sylvie Langlois, Sophie Dumoucel, Thomas Sontag, Pascal St-Onge, Henrique Bittencourt, Dorothee Dal Soglio, Josette Champagne, Michel Duval, Jean-Marie Leclerc, Caroline Laverdiere, Thai Hoa Tran, Natalie Patey, Benjamin Ellezam, Sebastien Perreault, Nelson Piche, Yvan Samson, Pierre Teira, Nada Jabado, Bruno Michon, Josee Brossard, Monia Marzouki, Sonia Cellot, Daniel Sinnett
Article
Nutrition & Dietetics
E. Delvin, V Marcil, N. Alos, C. Laverdiere, D. Sinnett, M. Krajinovic, V Belanger, S. Drouin, C. Nyalendo, E. Levy
CLINICAL NUTRITION ESPEN
(2019)
Article
Pharmacology & Pharmacy
Genevieve Nadeau, Erika Ouimet-Grennan, Michelle Aaron, Simon Drouin, Laurence Bertout, Albert Shalmiev, Patrick Beaulieu, Pascal St-Onge, Louis-Nicolas Veilleux, Frank Rauch, Kateryna Petrykey, Caroline Laverdiere, Daniel Sinnett, Nathalie Alos, Maja Krajinovic
PHARMACOGENOMICS & PERSONALIZED MEDICINE
(2019)
Article
Multidisciplinary Sciences
Maryse Fournier, Eric Bonneil, Carole Garofalo, Guy Grimard, Caroline Laverdiere, Maja Krajinovic, Simon Drouin, Daniel Sinnett, Valerie Marcil, Emile Levy
SCIENTIFIC REPORTS
(2019)