Article
Multidisciplinary Sciences
R. Jordan Price, Jahn Davik, Felicidad Fernandez Fernandez, Helen J. Bates, Samantha Lynn, Charlotte F. Nellist, Matteo Buti, Dag Roen, Nada Surbanovski, Muath Alsheikh, Richard J. Harrison, Daniel James Sargent
Summary: In this study, the genome sequences of two red raspberry cultivars ('Autumn Bliss' and 'Malling Jewel') were obtained using long-read Oxford Nanopore Technologies sequencing data. These genome sequences are valuable resources for studying the genetic complexity, functional genomics, evolution, and pan-genomics diversity of red raspberry.
Article
Biochemical Research Methods
Kerr Ding, Sheng Wang, Yunan Luo
Summary: This article introduces a new approach to biological network alignment called GraNA, which utilizes deep learning and functional correspondence between proteins across species to predict functional relatedness. GraNA performs well on multiple tasks and successfully discovers functionally replaceable human-yeast protein pairs documented in previous studies.
Article
Biochemical Research Methods
Hyun-Myung Woo, Byung-Jun Yoon
Summary: MONACO is a novel and versatile network alignment algorithm that achieves highly accurate pairwise and multiple network alignments through iterative optimal matching of 'local' neighborhoods around focal nodes. Extensive performance assessments on real and synthetic networks, where the ground truth is known, show that MONACO consistently outperforms all other state-of-the-art network alignment algorithms in terms of accuracy, coherence, and topological quality of the aligned network regions. Despite the significantly enhanced alignment accuracy, MONACO remains computationally efficient and scales well with increasing size and number of networks.
Review
Biochemistry & Molecular Biology
Leah Schaffer, Trey Ideker
Summary: Biological systems are inherently multiscale, allowing for the application of diverse technologies to characterize units at different levels and create networks of proximities. By using network proximity measures to build hierarchical maps of biological systems, functionalizing them to create predictive models, and addressing challenges in multiscale modeling, a unified hierarchical approach to biological data can be achieved, spanning from the molecular to macroscopic level.
Article
Biochemical Research Methods
Lijia Ma, Shiqiang Wang, Qiuzhen Lin, Jianqiang Li, Zhuhong You, Jiaxiang Huang, Maoguo Gong
Summary: Global Alignment of Biological Networks (GABN) aims to find optimal alignment between proteins across different species, balancing the conservation of biological and topological structures. Existing methods struggle to strike a good balance in conserving both structures. By proposing the CLMNA method, which combines multiple learning algorithms, this problem is addressed, showcasing superior performance in experiments.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Plant Sciences
Abhishek Bohra, Gandam Prasad, Abhishek Rathore, Rachit K. Saxena, Satheesh Naik Sj, Shalini Pareek, Rintu Jha, Lekha Pazhamala, Dibendu Datta, Gaurav Pandey, Abha Tiwari, Alok Kumar Maurya, Khela Ram Soren, Mohd Akram, Rajeev K. Varshney, Narendra P. Singh
Summary: The study identified differences in gene expression between the A(2)-CMS line and its isogenic maintainer line in pigeonpea at the transcriptome level. It revealed candidate genes and metabolic pathways associated with pollen development and male sterility in pigeonpea A(2)-CMS, providing new insights into the molecular mechanism of the CMS trait and accelerating heterosis utilization for enhancing productivity gains in pigeonpea.
Article
Biochemistry & Molecular Biology
Jasmin Adriana Schaefer, Suleyman Bozkurt, Jonas Benjamin Michaelis, Kevin Klann, Christian Muench
Summary: In this study, we introduced a proteomics approach called mePROD(mt), which enables global dynamic analysis of mitochondrial protein uptake. Our results showed that protein uptake into mitochondria is regulated by import and translation machineries, and is influenced by the activation of the integrated stress response.
Article
Biochemical Research Methods
Nadezhda T. Doncheva, John H. Morris, Henrietta Holze, Rebecca Kirsch, Katerina C. Nastou, Yesid Cuesta-Astroz, Thomas Rattei, Damian Szklarczyk, Christian von Mering, Lars J. Jensen
Summary: Biological networks can represent complex biological systems, and Cytoscape software tool and its many apps support the analysis and visualization of such networks. The new stringApp 2.0 improves support for heterogeneous networks and allows the creation of networks containing proteins, interactions, and other biological entities from different sources.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Narmada Sambaturu, Vaidehi Pusadkar, Sridhar Hannenhalli, Nagasuma Chandra
Summary: PathExt is a computational tool that can identify differentially active paths with a control, or most active paths without one, in an omics-integrated biological network. It can extract characteristic genes and pathways for studying systems effectively.
Review
Computer Science, Artificial Intelligence
Lijia Ma, Zengyang Shao, Lingling Li, Jiaxiang Huang, Shiqiang Wang, Qiuzhen Lin, Jianqiang Li, Maoguo Gong, Asoke K. Nandi
Summary: In this paper, a comprehensive review of heuristic and metaheuristic biological network alignment methods is presented. Comparative analyses of alignment models, datasets, evaluation metrics, and experimental results are provided, along with conclusions and possible future directions for BNAs.
Article
Computer Science, Artificial Intelligence
Xuefeng Zhang, Richong Zhang, Junfan Chen, Jaein Kim, Yongyi Mao
Summary: This study proposes a model called GALA to address the limitation of existing entity alignment models in exploring the topology information of unaligned entities. By constructing global features and aggregating local information, GALA aligns entities from different knowledge graphs and achieves promising results.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Bo-Kai Ge, Geng-Ming Hu, Rex Chen, Chi-Ming Chen
Summary: MSClustering is an efficient software package used in Cytoscape for visualizing and analyzing complex networks. It automatically displays the minimum span clustering (MSC) of the network based on the input distance matrix, and organizes the multi-level results into an MSC tree. The package performs well in studying the evolutionary relationships of complex systems and clustering large systems.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Biochemical Research Methods
Prashant S. Emani, Jonathan Warrell, Alan Anticevic, Stefan Bekiranov, Michael Gandal, Michael J. McConnell, Guillermo Sapiro, Alan Aspuru-Guzik, Justin T. Baker, Matteo Bastiani, John D. Murray, Stamatios N. Sotiropoulos, Jacob Taylor, Geetha Senthil, Thomas Lehner, Mark B. Gerstein, Aram W. Harrow
Summary: Quantum computing, leveraging the unique properties of quantum mechanics, addresses the challenges of scale and complexity in biological sciences and facilitates the integration of insights across different areas.
Article
Biology
Anurag Chaturvedi, Joaquim Cruz Corella, Chanz Robbins, Anita Loha, Laure Menin, Natalia Gasilova, Frederic G. Masclaux, Soon-Jae Lee, Ian R. Sanders
Summary: Early-diverging fungi exhibit high levels of N6-methyldeoxyadenine (6mA) content, distinct from Dikarya and other eukaryotes. Arbuscular mycorrhizal fungi have evolved a symbiotic lifestyle with 80% of plant species worldwide, showing unique 5mC and 6mA methylation characteristics. The model AMF, R. irregularis, demonstrates differential methylation profiles, particularly in genes related to phosphate regulation, highlighting their adaptation for symbiotic relationships with important plant species.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemical Research Methods
Anna Paola Muntoni, Andrea Pagnani
Summary: DCAlign is a new alignment method that can handle the conservation and the co-evolution signals in the columns of multiple sequence alignments of homologous sequences. By including an empirical prior over variables reflecting the presence of insertions and deletions, the overall computing time can be dramatically reduced.
Article
Medicine, General & Internal
Michelle Bous, Erol Tutdibi, Nasenien Nourkami-Tutdibi, Elisabeth Kaiser, Regine Stutz, Sascha Meyer, Jorg Ingo Baumbach, Michael Zemlin, Sybelle Goedicke-Fritz
Summary: This study successfully analyzed the volatile organic compound (VOC) profiles in diapers of premature infants using ion mobility spectrometry coupled with multi-capillary columns. Further research is needed to identify specific VOC profiles in infections and other diseases of premature infants in order to establish quick and noninvasive diagnostics.
EUROPEAN JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Neurosciences
Shraddha Pai, Shirley Hui, Philipp Weber, Soumil Narayan, Owen Whitley, Peipei Li, Viviane Labrie, Jan Baumbach, Anne L. Wheeler, Gary D. Bader
Summary: An open challenge in human genetics is to understand the impact of genotype variation on developmental cognition. In this study, the genetic underpinnings of cognitive tasks were analyzed in the Philadelphia Neurodevelopmental Cohort. A significant region of the Fibulin-1 gene was associated with nonverbal reasoning accuracy and white matter fractional anisotropy. This research advances the understanding of cognition and provides a framework for using systems-level data in biomedical domains.
Article
Plant Sciences
Parvinderdeep S. Kahlon, Andrea Foerner, Michael Muser, Mhaned Oubounyt, Michael Gigl, Richard Hammerl, Jan Baumbach, Ralph Hueckelhoven, Corinna Dawid, Remco Stam
Summary: Natural plant populations show polymorphism and intraspecific variation in resistance against pathogens. Perception of pathogen-associated molecular patterns or elicitors can activate defence responses, and this variation was evaluated in the wild tomato species Solanum chilense. The diversity in basal and elicitor-induced levels of reactive oxygen species and phytohormones was measured in 83 plants from nine populations. Geographical origin influenced the effect of individual components on infection frequency of Phytophthora infestans, with a direct correlation found between ethylene responses and resistance in the southern coastal region.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Health Care Sciences & Services
Alissa Brauneck, Louisa Schmalhorst, Mohammad Mahdi Kazemi Majdabadi, Mohammad Bakhtiari, Uwe Voelker, Jan Baumbach, Linda Baumbach, Gabriele Buchholtz
Summary: This article summarizes the legal questions and concerns related to federated learning (FL) systems in medical research. The study found that FL can meet the legal requirements of the General Data Protection Regulation (GDPR) by combining secure multiparty computation (SMPC) and differential privacy (DP) as privacy-enhancing technologies, providing a secure technical solution.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2023)
Letter
Biotechnology & Applied Microbiology
Sebastian Lobentanzer, Patrick Aloy, Jan Baumbach, Balazs Bohar, Vincent J. Carey, Pornpimol Charoentong, Katharina Danhauser, Tunca Dogan, Johann Dreo, Ian Dunham, Elias Farr, Adria Fernandez-Torras, Benjamin M. Gyori, Michael Hartung, Charles Tapley Hoyt, Christoph Klein, Tamas Korcsmaros, Andreas Maier, Matthias Mann, David Ochoa, Elena Pareja-Lorente, Ferdinand Popp, Martin Preusse, Niklas Probul, Benno Schwikowski, Buenyamin Sen, Maximilian T. Strauss, Denes Turei, Erva Ulusoy, Dagmar Waltemath, Judith A. H. Wodke, Julio Saez-Rodriguez
NATURE BIOTECHNOLOGY
(2023)
Review
Cell Biology
Aylin Del Moral-Morales, Marisol Salgado-Albarran, Yesennia Sanchez-Perez, Nina Kerstin Wenke, Jan Baumbach, Ernesto Soto-Reyes
Summary: Architectural proteins such as CTCF are crucial for chromatin organization and gene expression control. CTCF functions as a key player in maintaining complex chromatin structure due to its ability to bind various sequences. However, the exact mechanisms of its versatility are still not fully understood. This review focuses on CTCF's interactions with other epigenetic molecules, including histone and DNA demethylases, as well as long non-coding RNAs that recruit CTCF. Understanding the partners of CTCF is essential for unraveling chromatin regulation and investigating the finely-tuned role of CTCF as a master regulator of chromatin.
Article
Biochemical Research Methods
Mhaned Oubounyt, Lorenz Adlung, Fabio Patroni, Nina Kerstin Wenke, Andreas Maier, Michael Hartung, Jan Baumbach, Maria L. Elkjaer
Summary: This study presents a novel approach to reconstruct complex regulatory networks from single-cell transcriptome data, aiming to explain the differences in cell development. The method not only provides insights into the mechanisms underlying diseases, but also offers potential drug targets for therapeutic intervention.
Article
Mathematical & Computational Biology
Klaudia Adamowicz, Lis Arend, Andreas Maier, Johannes R. Schmidt, Bernhard Kuster, Olga Tsoy, Olga Zolotareva, Jan Baumbach, Tanja Laske
Summary: Proteomics technologies are important for biomarker identification and disease mechanism research. However, leveraging publicly available proteomics data for these purposes is challenging due to the heterogeneity of data generated by different research groups using different organisms and assay systems. To address this issue, researchers have developed ProHarMeD, a tool that harmonizes and compares proteomics data from multiple studies and extracts disease mechanisms and drug repurposing candidates.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Biochemical Research Methods
Chit Tong Lio, Gordon Grabert, Zakaria Louadi, Amit Fenn, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy
Summary: In this study, a novel framework called Spycone is proposed for time course data analysis, taking alternative splicing into consideration. Spycone utilizes a new algorithm for alternative splicing detection and provides downstream analysis like network and gene set enrichment. The performance of Spycone is demonstrated using simulated and real-world data of SARS-CoV-2 infection.
Article
Biochemical Research Methods
Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, Markus List
Summary: Cancer is a major cause of death globally, and there is a need for innovative methods to stratify patients and identify biomarkers using molecular data. spongEffects is a novel method that infers subnetworks from ceRNA networks and calculates patient- or sample-specific scores related to their regulatory activity.
Article
Biochemical Research Methods
Suryadipto Sarkar, Marta Lucchetta, Andreas Maier, Mohamed M. Abdrabbou, Jan Baumbach, Markus List, Martin H. Schaefer, David B. Blumenthal
Summary: ROBUST-Web is a user-friendly web application that implements our recently presented ROBUST disease module mining algorithm. It enables seamless downstream disease module exploration through integrated gene set enrichment analysis, tissue expression annotation, and visualization of drug-protein and disease-gene links. Furthermore, ROBUST-Web introduces bias-aware edge costs for the underlying Steiner tree model, which helps correct for study bias in protein-protein interaction networks and enhances the robustness of computed modules.
Article
Genetics & Heredity
Amit Fenn, Olga Tsoy, Tim Faro, Fanny L. M. Roessler, Alexander Dietrich, Johannes Kersting, Zakaria Louadi, Chit Tong Lio, Uwe Voelker, Jan Baumbach, Tim Kacprowski, Markus List
Summary: Alternative splicing is a diverse phenomenon in transcriptome and proteome, and various tools have been developed to study it. However, previous benchmarks focused on certain aspects and neglected event detection tools. This study presents a comprehensive framework called DICAST, which integrates multiple mapping and event detection tools for alternative splicing analysis. The performance of different tools was evaluated on simulated and real RNA-seq data, and STAR and HISAT2 were identified as the most balanced tools. Furthermore, the study proposes a reporting standard to unify formats and guide future tool development.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Mhaned Oubounyt, Maria L. Elkjaer, Tanja Laske, Alexander G. B. Gronning, Marcus J. Moeller, Jan Baumbach
Summary: Single-cell RNA sequencing (scRNA-seq) technology allows us to understand gene functions and interactions at a single-cell level. However, current methods lack the ability to directly learn differential regulatory disease mechanisms from single-cell data. In this study, we present a new methodology called DiNiro, which can uncover and interpret small transcriptional regulatory network modules to explain differential cellular gene expression programs.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Article
Pharmacology & Pharmacy
Julian Spaeth, Rui-Sheng Wang, Maeve Humphrey, Jan Baumbach, Joseph Loscalzo
Summary: This study presents a machine learning framework that integrates various target network features and physicochemical properties of compounds to analyze their influence on the therapeutic effects for SARS-CoV-2 infection and host cell cytotoxic effects. The models achieve a reasonable mean area under the receiver operating characteristic curve (ROC-AUC) of 0.73 on an unseen validation set, providing insights into the determinants of drug efficacy and cytotoxicity.
CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Julian Matschinske, Tobias Frisch, Markus List, Julian Spaeth, Stefan Weiss, Uwe Voelker, Esa Pitkaenen, Dominik Heider, Nina Kerstin Wenke, Georgios Kaissis, Daniel Rueckert, Tim Kacprowski, Jan Baumbach
Summary: sPLINK is a hybrid federated and user-friendly tool that performs privacy-aware GWAS on distributed datasets while preserving the accuracy of the results.