Quantitative mass spectrometry-based analysis of proteins related to cattle and their products – focus on cows’ milk beta-casein proteoforms
Publication date: Available online 18 September 2020Source: MethodsAuthor(s): James A. Broadbent, Mark R. Condina, Michelle L. Colgrave (Source: Methods)
Source: Methods - September 19, 2020 Category: Molecular Biology Source Type: research

Detect differentially methylated regions using non-homogeneous hidden Markov model for bisulfite sequencing data
Publication date: Available online 17 September 2020Source: MethodsAuthor(s): Yingyu Chen, Chin Kiu Kwok, Hangjin Jiang, Xiaodan Fan (Source: Methods)
Source: Methods - September 18, 2020 Category: Molecular Biology Source Type: research

A multi-objective optimization method for identification of module biomarkers for disease diagnosis
Publication date: Available online 17 September 2020Source: MethodsAuthor(s): Yansen Su, Xiaochun Su, Qijun Wang, Lejun Zhang (Source: Methods)
Source: Methods - September 18, 2020 Category: Molecular Biology Source Type: research

A novel subnetwork representation learning method for uncovering disease-disease relationships
Publication date: Available online 16 September 2020Source: MethodsAuthor(s): Jiajie Peng, Jiaojiao Guan, Weiwei Hui, Xuequn Shang (Source: Methods)
Source: Methods - September 16, 2020 Category: Molecular Biology Source Type: research

Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications
Publication date: Available online 14 September 2020Source: MethodsAuthor(s): Itika Arora, Trygve O. Tollefsbol (Source: Methods)
Source: Methods - September 16, 2020 Category: Molecular Biology Source Type: research

Deep learning of brain magnetic resonance images: A brief review
Publication date: Available online 12 September 2020Source: MethodsAuthor(s): Xingzhong Zhao, Xing-Ming Zhao (Source: Methods)
Source: Methods - September 13, 2020 Category: Molecular Biology Source Type: research

Detection of changes in the circadian rhythm of cattle in relation to disease, stress, and reproductive events
Publication date: Available online 11 September 2020Source: MethodsAuthor(s): Nicolas Wagner, Marie-Madeleine Mialon, Karen Helle Sloth, Romain Lardy, Dorothée Ledoux, Mathieu Silberberg, Alice De Boyer Des Roches, Isabelle Veissier (Source: Methods)
Source: Methods - September 12, 2020 Category: Molecular Biology Source Type: research

Considerations regarding centromere assembly in plant whole-genome sequencing
Publication date: Available online 11 September 2020Source: MethodsAuthor(s): Miaomiao Han, Yae Yang, Muqing Zhang, Kai Wang (Source: Methods)
Source: Methods - September 12, 2020 Category: Molecular Biology Source Type: research

Methods to quantify heat stress in ruminants: current status and future prospects
Publication date: Available online 11 September 2020Source: MethodsAuthor(s): Gene Wijffels, Megan Sullivan, John Gaughan (Source: Methods)
Source: Methods - September 12, 2020 Category: Molecular Biology Source Type: research

Solid-Supported Lipid Bilayers –a Versatile Tool for the Structural and Functional Characterization of Membrane Proteins
Publication date: Available online 11 September 2020Source: MethodsAuthor(s): Jakob Andersson, Pierluigi Bilotto, Laura L.E. Mears, Stefan Fossati, Ulrich Ramach, Ingo Köper, Markus Valtiner, Wolfgang Knoll (Source: Methods)
Source: Methods - September 12, 2020 Category: Molecular Biology Source Type: research

Structural Biology of Human GPCR Drugs and Endogenous Ligands - Insights from NMR Spectroscopy
Publication date: Available online 8 September 2020Source: MethodsAuthor(s): Guillaume Ferré, Matthew Eddy (Source: Methods)
Source: Methods - September 9, 2020 Category: Molecular Biology Source Type: research

Variability of computed tomography radiomics features of fibrosing interstitial lung disease: A test-retest study
Publication date: Available online 4 September 2020Source: MethodsAuthor(s): Florian Prayer, Johannes Hofmanninger, Michael Weber, Daria Kifjak, Alexander Willenpart, Jeanny Pan, Sebastian Röhrich, Georg Langs, Helmut Prosch (Source: Methods)
Source: Methods - September 6, 2020 Category: Molecular Biology Source Type: research

A network embedding based method for partial multi-omics integration in cancer subtyping
Publication date: Available online 14 August 2020Source: MethodsAuthor(s): Han Xu, Lin Gao, Mingfeng Huang, Ran Duan (Source: Methods)
Source: Methods - August 14, 2020 Category: Molecular Biology Source Type: research

Variational graph auto-encoders for miRNA-disease association prediction
Publication date: Available online 13 August 2020Source: MethodsAuthor(s): Yulian Ding, Li-Ping Tian, Xiujuan Lei, Bo Liao, Fang-Xiang Wu (Source: Methods)
Source: Methods - August 14, 2020 Category: Molecular Biology Source Type: research

Prediction of drug response in multilayer networks based on fusion of multiomics data
Publication date: Available online 13 August 2020Source: MethodsAuthor(s): Liang Yu, Dandan Zhou, Lin Gao, Yunhong Zha (Source: Methods)
Source: Methods - August 14, 2020 Category: Molecular Biology Source Type: research

Large-scale phenotyping in dairy sector using milk MIR spectra: key factors affecting the quality of predictions
Publication date: Available online 4 August 2020Source: MethodsAuthor(s): C. Grelet, P. Dardenne, H. Soyeurt, J.A. Fernandez, A. Vanlierde, F. Steevens, N. Gengler, F. Dehareng (Source: Methods)
Source: Methods - August 13, 2020 Category: Molecular Biology Source Type: research

Integrating Multi-Omics Data by Learning Modality Invariant Representations for Improved Prediction of Overall Survival of Cancer
Publication date: Available online 5 August 2020Source: MethodsAuthor(s): Li Tong, Hang Wu, May D. Wang (Source: Methods)
Source: Methods - August 13, 2020 Category: Molecular Biology Source Type: research

Brain Controllability and Morphometry Similarity of Internet Gaming Addiction
Publication date: Available online 10 August 2020Source: MethodsAuthor(s): Lei Wei, Xu Han, Xuchen Yu, Yawen Sun, Ming Ding, Yasong Du, Wenqing Jiang, Yan Zhou, He Wang (Source: Methods)
Source: Methods - August 13, 2020 Category: Molecular Biology Source Type: research

Mass spectrometric analysis of protein deamidation – a focus on top-down and middle-down mass spectrometry
Publication date: Available online 10 August 2020Source: MethodsAuthor(s): Yutong Jin, Yunyu Yi, Bernice Yeung (Source: Methods)
Source: Methods - August 13, 2020 Category: Molecular Biology Source Type: research

DeepTL-Ubi: a novel deep transfer learning method for effectively predicting ubiquitination sites of multiple species
Publication date: Available online 10 August 2020Source: MethodsAuthor(s): Yu Liu, Ao Li, Xing-Ming Zhao, Minghui Wang (Source: Methods)
Source: Methods - August 13, 2020 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: 1 July 2020Source: Methods, Volume 179Author(s): (Source: Methods)
Source: Methods - August 5, 2020 Category: Molecular Biology Source Type: research

Editorial – Membrane protein tools for drug discovery
Publication date: Available online 28 July 2020Source: MethodsAuthor(s): Anass Jawhari (Source: Methods)
Source: Methods - August 5, 2020 Category: Molecular Biology Source Type: research

Rumen metaproteomics: closer to linking rumen microbial function to animal productivity traits
Publication date: Available online 3 August 2020Source: MethodsAuthor(s): Thea Os Andersen, Benoit J. Kunath, Live H. Hagen, Magnus Ø. Arntzen, Phillip B. Pope (Source: Methods)
Source: Methods - August 5, 2020 Category: Molecular Biology Source Type: research

Identifying and ranking potential cancer drivers using representation learning on attributed network
Publication date: Available online 3 August 2020Source: MethodsAuthor(s): Wei Peng, Sichen Yi, Wei Dai, Jianxin Wang (Source: Methods)
Source: Methods - August 5, 2020 Category: Molecular Biology Source Type: research

Targeted Bisulfite Sequencing for Biomarker Discovery
Publication date: Available online 2 August 2020Source: MethodsAuthor(s): Morselli Marco, Farrell Colin, Rubbi Liudmilla, Heather L. Fehling, Rebecca Henkhaus, Pellegrini Matteo (Source: Methods)
Source: Methods - August 3, 2020 Category: Molecular Biology Source Type: research

Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework
Publication date: Available online 1 August 2020Source: MethodsAuthor(s): Koen J.A. Martens, Abbas Jabermoradi, Suyeon Yang, Johannes Hohlbein (Source: Methods)
Source: Methods - August 1, 2020 Category: Molecular Biology Source Type: research

Editorial - Membrane Protein tools for drug discovery
Publication date: Available online 28 July 2020Source: MethodsAuthor(s): Anass Jawhari (Source: Methods)
Source: Methods - July 30, 2020 Category: Molecular Biology Source Type: research

Sizing, stabilising, and cloning repeat-expansions for gene targeting constructs
Publication date: Available online 25 July 2020Source: MethodsAuthor(s): Remya R. Nair, Charlotte Tibbit, David Thompson, Ross McLeod, Asif Nakhuda, Michelle M. Simon, Robert H. Baloh, Elizabeth M.C. Fisher, Adrian M. Isaacs, Thomas J. Cunningham (Source: Methods)
Source: Methods - July 27, 2020 Category: Molecular Biology Source Type: research

Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies
Publication date: Available online 25 July 2020Source: MethodsAuthor(s): Loic Lindner, Pauline Cayrou, Sylvie Jacquot, Marie-Christine Birling, Yann Herault, Guillaume Pavlovic (Source: Methods)
Source: Methods - July 27, 2020 Category: Molecular Biology Source Type: research

Efficient allele conversion in mouse zygotes and primary cells based on electroporation of Cre protein
Publication date: Available online 24 July 2020Source: MethodsAuthor(s): Irena Jenickova, Petr Kasparek, Silvia Petrezselyova, Jan Elias, Jan Prochazka, Jana Kopkanova, Michal Navratil, Cyril Barinka, Radislav Sedlacek (Source: Methods)
Source: Methods - July 25, 2020 Category: Molecular Biology Source Type: research

Reinventing Radiation Therapy with Machine Learning and Imaging Bio-markers (Radiomics): state-of-the-art, challenges and perspectives
Publication date: Available online 19 July 2020Source: MethodsAuthor(s): Laurent Dercle, Theophraste Henry, Alexandre Carré, Nikos Paragios, Eric Deutsch, Charlotte Robert (Source: Methods)
Source: Methods - July 20, 2020 Category: Molecular Biology Source Type: research

FreeHi-C Spike-in Simulations for Benchmarking Differential Chromatin Interaction Detection
Publication date: Available online 12 July 2020Source: MethodsAuthor(s): Ye Zheng, Peigen Zhou, Sündüz Keleş (Source: Methods)
Source: Methods - July 13, 2020 Category: Molecular Biology Source Type: research

Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map
Publication date: Available online 9 July 2020Source: MethodsAuthor(s): Timothy Kunz, Lila Rieber, Shaun Mahony (Source: Methods)
Source: Methods - July 10, 2020 Category: Molecular Biology Source Type: research

An open-access computer image analysis (CIA) method to predict meat and fat content from an android smartphone-derived picture of the bovine 5th-6th rib
Publication date: Available online 7 July 2020Source: MethodsAuthor(s): Bruno Meunier, Jérôme Normand, Benjamin Albouy-Kissi, Didier Micol, Mohammed El Jabri, Muriel Bonnet (Source: Methods)
Source: Methods - July 8, 2020 Category: Molecular Biology Source Type: research

Free energy-based model of CTCF-mediated chromatin looping in the human genome
Publication date: Available online 6 July 2020Source: MethodsAuthor(s): Wayne Dawson, Michal Lazniewski, Dariusz Plewczynski (Source: Methods)
Source: Methods - July 7, 2020 Category: Molecular Biology Source Type: research

Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition
Publication date: Available online 6 July 2020Source: MethodsAuthor(s): Sebastian Raschka, Benjamin Kaufman (Source: Methods)
Source: Methods - July 7, 2020 Category: Molecular Biology Source Type: research

Modern Epigenetics Methods in Biological Research
Publication date: Available online 6 July 2020Source: MethodsAuthor(s): Yuanyuan Li (Source: Methods)
Source: Methods - July 7, 2020 Category: Molecular Biology Source Type: research

Methods for analysis of specific DNA methylation status
Publication date: Available online 5 July 2020Source: MethodsAuthor(s): María J. Pajares, Cora Palanca-Ballester, Raquel Urtasun, Ester Alemany-Cosme, Agustin Lahoz, Juan Sandoval (Source: Methods)
Source: Methods - July 7, 2020 Category: Molecular Biology Source Type: research

Validation of two laboratory methods for beef intramuscular fat quantification
Publication date: Available online 5 July 2020Source: MethodsAuthor(s): Sylvie Bardou-Valette, Carole Delavaud, Agnès Thomas, Donato Andueza, Denis Durand, Dominique Gruffat (Source: Methods)
Source: Methods - July 7, 2020 Category: Molecular Biology Source Type: research

Bacterial Flagellar Motor as a Multimodal Biosensor
Publication date: Available online 5 July 2020Source: MethodsAuthor(s): Ekaterina Krasnopeeva, Uriel E. Barboza-Perez, Jerko Rosko, Teuta Pilizota, Chien-Jung Lo (Source: Methods)
Source: Methods - July 7, 2020 Category: Molecular Biology Source Type: research

Functional Imaging using Radiomic Features in Assessment of Lymphoma
Publication date: Available online 4 July 2020Source: MethodsAuthor(s): Marius E. Mayerhoefer, Lale Umutlu, Heiko Schöder (Source: Methods)
Source: Methods - July 5, 2020 Category: Molecular Biology Source Type: research

Methods in isolation and characterization of bovine monocytes and macrophages
Publication date: Available online 2 July 2020Source: MethodsAuthor(s): F. Ceciliani, G. Ávila Morales, G. De Matteis, F. Grandoni, R. Furioso Ferreira, P. Roccabianca, C. Lecchi (Source: Methods)
Source: Methods - July 3, 2020 Category: Molecular Biology Source Type: research

GCN-BMP: Investigating Graph Representation Learning for DDI Prediction Task
Publication date: Available online 3 July 2020Source: MethodsAuthor(s): Xin Chen, China Xien Liu, China Ji Wu (Source: Methods)
Source: Methods - July 3, 2020 Category: Molecular Biology Source Type: research

Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment
Publication date: Available online 2 July 2020Source: MethodsAuthor(s): Christina Haddad, Jesse Davila-Calderon, Blanton S. Tolbert (Source: Methods)
Source: Methods - July 2, 2020 Category: Molecular Biology Source Type: research

Automation of data analysis in molecular cancer imaging and its potential impact on future clinical practice
Publication date: Available online 29 June 2020Source: MethodsAuthor(s): Benjamin Theek, Zuzanna Magnuska, Felix Gremse, Horst Hahn, Volkmar Schulz, Fabian Kiessling (Source: Methods)
Source: Methods - June 30, 2020 Category: Molecular Biology Source Type: research

PrGeFNE: Predicting disease-related genes by fast network embedding
Publication date: Available online 28 June 2020Source: MethodsAuthor(s): Ju Xiang, Ning-Rui Zhang, Jia-Shuai Zhang, Xiao-Yi Lv, Min Li (Source: Methods)
Source: Methods - June 30, 2020 Category: Molecular Biology Source Type: research

Estimation of dairy goat body composition: A direct calibration and comparison of eight methods
Publication date: Available online 27 June 2020Source: MethodsAuthor(s): Sylvain Lerch, Anne De La Torre, Christophe Huau, Mathieu Monziols, Caroline Xavier, Loïc Louis, Yannick Le Cozler, Philippe Faverdin, Philippe Lamberton, Isabelle Chery, Dominique Heimo, Christelle Loncke, Philippe Schmidely, Jose A.A. Pires (Source: Methods)
Source: Methods - June 28, 2020 Category: Molecular Biology Source Type: research

Stereological estimation of cardiomyocyte number and proliferation
Publication date: Available online 27 June 2020Source: MethodsAuthor(s): Vasco Sampaio-Pinto, Elsa D. Silva, Tiago L. Laundos, Paula da Costa Martins, Perpétua Pinto-do-Ó, Diana S. Nascimento (Source: Methods)
Source: Methods - June 28, 2020 Category: Molecular Biology Source Type: research

Universal Southern blot protocol with cold or radioactive probes for the validation of alleles obtained by homologous recombination
Publication date: Available online 26 June 2020Source: MethodsAuthor(s): Gemma F. Codner, Valerie Erbs, Jorik Loeffler, Lauren Chessum, Adam Caulder, Nicolas Jullien, Sara Wells, Marie-Christine Birling, Lydia Teboul (Source: Methods)
Source: Methods - June 27, 2020 Category: Molecular Biology Source Type: research

Optimized sensitive and inexpensive method to measure D-lactate as a surrogate marker of methylglyoxal fluxes in metabolically relevant contexts
Publication date: Available online 23 June 2020Source: MethodsAuthor(s): Alejandro Gugliucci, Russell Caccavello (Source: Methods)
Source: Methods - June 24, 2020 Category: Molecular Biology Source Type: research