Article
Multidisciplinary Sciences
Nicole DelRosso, Josh Tycko, Peter Suzuki, Cecelia Andrews, Adi Mukund, Ivan Liongson, Connor Ludwig, Kaitlyn Spees, Polly Fordyce, Michael C. Bassik, Lacramioara Bintu
Summary: Human gene expression is regulated by thousands of transcription factors and chromatin regulators. This study systematically measures the activity of over 100,000 protein fragments from these regulators and annotates previously unknown activation and repression domains. The research reveals the necessary residues for activation domain activity and identifies structures or motifs involved in repression. The findings provide valuable insights into the function of transcription factors and chromatin regulators and can aid in gene expression control and predictive modeling of effector domains.
Article
Biochemical Research Methods
Maneesha Aluru, Harsh Shrivastava, Sriram P. Chockalingam, Shruti Shivakumar, Srinivas Aluru
Summary: EnGRaiN is the first supervised ensemble learning method for constructing gene networks, which provides better results and can elucidate complex biological interactions.
Review
Biochemistry & Molecular Biology
Rossin Erbe, Jessica Gore, Kelly Gemmill, Daria A. Gaykalova, Elana J. Fertig
Summary: Biological systems are complex networks of interacting molecules at different scales. High throughput technologies and computational methods enable the study of these interactions. Graphical network modeling is a computational framework that explicitly models molecular interactions within and between cells in biological systems. It allows for the identification of key molecules, generation of hypotheses, and simulation of experimental outcomes.
Article
Biology
Yijie Wang, Hangnoh Lee, Justin M. Fear, Isabelle Berger, Brian Oliver, Teresa M. Przytycka
Summary: NetREX-CF is a computational method that integrates collaborative filtering and a mathematical model of transcriptional regulation to predict gene regulatory networks. By integrating TF binding data and context-specific gene expression, NetREX-CF can obtain a comprehensive regulatory network for Drosophila Schneider 2 cells. This method is important for inferring gene regulatory networks.
COMMUNICATIONS BIOLOGY
(2022)
Article
Oncology
Yumei Wang, Haiyan Wang, Wei Shao, Yuhui Chen, Yu Gui, Chao Hu, Xiaohong Yi, Lijun Huang, Shasha Li, Dong Wang
Summary: This study decoded the intricate regulatory network among hundreds of epigenetic regulators in breast cancer and identified 10 master regulators, offering potential therapeutic targets for breast cancer treatment.
CANCER BIOLOGY & MEDICINE
(2023)
Article
Multidisciplinary Sciences
Francesco Nicola Carelli, Chiara Cerrato, Yan Dong, Alex Appert, Abby Dernburg, Julie Ahringer
Summary: The movement of selfish DNA elements can lead to widespread genomic alterations and rewiring of germline transcriptional regulation. This study found that transposon expansions in Caenorhabditis nematodes led to the acquisition of germline-specific promoters from miniature inverted repeat transposable elements (TEs). These promoters are regulated by a transcription factor related to a transposase. Comparative analyses revealed evolutionary conservation and species-specificity of the co-opted promoters.
Article
Genetics & Heredity
Jiaqi Li, Jingjing Wang, Peijing Zhang, Renying Wang, Yuqing Mei, Zhongyi Sun, Lijiang Fei, Mengmeng Jiang, Lifeng Ma, E. Weigao, Haide Chen, Xinru Wang, Yuting Fu, Hanyu Wu, Daiyuan Liu, Xueyi Wang, Jingyu Li, Qile Guo, Yuan Liao, Chengxuan Yu, Danmei Jia, Jian Wu, Shibo He, Huanju Liu, Jun Ma, Kai Lei, Jiming Chen, Xiaoping Han, Guoji Guo
Summary: This study generated single-cell whole-body expression landscapes of zebrafish, Drosophila, and earthworm using Microwell-seq. By integrating cell landscapes from eight representative species, the researchers developed a deep-learning-based strategy, Nvwa, to predict gene expression and identify regulatory programs. Conserved genetic regulation in vertebrates and invertebrates were revealed through comparison of cell-type-specific transcription factors. This work provides a valuable resource and a new strategy for studying regulatory grammar in diverse biological systems.
Article
Genetics & Heredity
Miles W. DeAngelis, Joseph D. Coolon, Ruth Johnson
Summary: Tissue function relies on proper cellular organization and behavior, with many genes influencing tissue morphogenesis being highly conserved across different phyla. The use of model organisms and developmental systems, such as the Drosophila melanogaster pupal eye with its stereotyped cell arrangement, has advanced our understanding of tissue morphogenesis processes. Analysis of the pupal eye through RNA-sequencing has revealed differential expression of genes involved in various biological processes, potentially suggesting novel patterning factors for tissue morphogenesis.
G3-GENES GENOMES GENETICS
(2021)
Article
Astronomy & Astrophysics
S. G. Shulman, V. P. Grinin
Summary: We simulate the polarized radiative transfer during the minima of UX Ori type stars and investigate the influence of perturbation extensions on eclipse depth and linear polarization parameters. Our results show that large-scale azimuthally extended perturbations can cause deeper eclipses with greater linear polarization. The extension of perturbations and puffing-up of the disk also strongly affect the polarization and color index of the star during the eclipse.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2022)
Article
Astronomy & Astrophysics
G. A. Pena, G. N. Candlish
Summary: The late-time effect of primordial non-Gaussianity in the early Universe is studied in this work. By generating multiple realizations of cosmological structure and analyzing the matter power spectrum, bispectrum, and trispectrum, it is found that the initial non-Gaussianity has only a small imprint on the first three polyspectra. Some models show interesting scale-dependent deviations from the Gaussian case in the bispectrum and trispectrum, although the signal is at most at the per cent level.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2022)
Article
Biochemical Research Methods
Softya Sebastian, Swarup Roy, Jugal Kalita
Summary: The inference of large-scale gene regulatory networks is important for understanding interactions among genes. Existing methods can only reconstruct limited networks, so parallel computing paradigms are necessary. We propose a generic parallel framework that allows any existing method to infer large networks in parallel without compromising quality. We test the framework on 15 inference methods using benchmarks and real-world expression matrices, and it successfully constructs a large network related to Alzheimer's Disease.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Softya Sebastian, Swarup Roy, Jugal Kalita
Summary: Inference of large-scale gene regulatory networks is crucial for understanding gene interactions. Existing methods are limited to small networks, so parallel computing is proposed to construct large networks. A generic parallel framework is proposed which can infer large networks without re-engineering existing methods, and has been tested on various inference methods with good results. Finally, a gene network associated with Alzheimer's Disease was successfully inferred using the framework, revealing hub genes related to the disease.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Computer Science, Artificial Intelligence
Nisar Wani, Khalid Raza
Summary: The study introduces a gene regulatory network inference method based on multiple kernel learning, which can run on multi-processor machines and learn large-scale GRNs from multiple heterogeneous datasets. This approach demonstrates superior classification accuracy and enhanced speedup potential compared to other state-of-the-art methods.
PEERJ COMPUTER SCIENCE
(2021)
Article
Biochemical Research Methods
Lujing Zheng, Zhenhuan Liu, Yang Yang, Hong-Bin Shen
Summary: This study introduces a new method, ConGRI, for identifying gene regulatory interactions from gene expression images using contrastive learning and deep neural network technology. The method outperforms traditional and deep learning methods on a Drosophila embryogenesis dataset, achieving high prediction accuracy.
Article
Biochemical Research Methods
Sugyun An, So-Yeong Jang, Sang-Min Park, Chun-Kyung Lee, Hoon-Min Kim, Kwang-Hyun Cho
Summary: Researchers have discovered that optimal global stabilizing control targets can be identified by analyzing the dynamics between structurally identified control targets. Based on this discovery, they developed a scalable global stabilizing control framework using both structural and dynamic information. They found that the proposed global stabilizing control is superior in terms of the number of control target nodes, scalability, and computational complexity.
Article
Multidisciplinary Sciences
Jasper Janssens, Sara Aibar, Ibrahim Ihsan Taskiran, Joy N. Ismail, Alicia Estacio Gomez, Gabriel Aughey, Katina Spanier, Florian De Rop, Carmen Bravo Gonzalez-Blas, Marc Dionne, Krista Grimes, Xiao Jiang Quan, Dafni Papasokrati, Gert Hulselmans, Samira Makhzami, Maxime De Waegeneer, Valerie Christiaens, Tony Southall, Stein Aerts
Summary: The study reveals the diversity of neuronal and glial cell types in the Drosophila brain and identifies gene regulatory networks (GRNs) controlling their identities. By analyzing chromatin accessibility and transcriptome data, the researchers identified thousands of regulatory regions and created enhancer GRNs for different cell types.
Article
Biotechnology & Applied Microbiology
Amin R. Mohamed, Marina Naval-Sanchez, Moira Menzies, Bradley Evans, Harry King, Antonio Reverter, James W. Kijas
Summary: This study successfully documented the transcriptome and epigenome changes in key genes and pathways involved in sexual maturation in Atlantic salmon. Using a Systems Biology approach, regulatory networks and important genes were identified, revealing the crucial factors in the onset of maturation. The results provide a comprehensive view of the spatiotemporal changes in a complex trait and offer new insights for manipulating puberty in economically important aquaculture species.
Article
Multidisciplinary Sciences
Ryohei Iwata, Pierre Casimir, Emir Erkol, Leila Boubakar, Melanie Planque, Isabel M. Gallego Lopez, Martyna Ditkowska, Vaiva Gaspariunaite, Sofie Beckers, Daan Remans, Katlijn Vints, Anke Vandekeere, Suresh Poovathingal, Matthew Bird, Ine Vlaeminck, Eline Creemers, Keimpe Wierda, Nikky Corthout, Pieter Vermeersch, Sebastien Carpentier, Kristofer Davie, Massimiliano Mazzone, Natalia V. Gounko, Stein Aerts, Bart Ghesquiere, Sarah-Maria Fendt, Pierre Vanderhaeghen
Summary: Compared with other mammals, the development of neuronal in the human cerebral cortex takes longer. We investigated the impact of mitochondria on the species-specific timing of cortical neuron maturation. Through comparing the maturation of human and mouse cortical neurons, we found that the mitochondria development in human cortical neurons was slower, accompanied by lower mitochondria metabolic activity, especially oxidative phosphorylation. Stimulating mitochondria metabolism in human neurons accelerated their development in vitro and in vivo, enabling them to mature weeks ahead of time, while inhibiting mitochondria in mouse neurons resulted in decreased rates of maturation. Therefore, mitochondria play a crucial role in regulating the pace of neuronal development underlying human-specific brain neoteny.
Article
Neurosciences
Sara Calafate, Gokhan Ozturan, Nicola Thrupp, Jeroen Vanderlinden, Luisa Santa-Marinha, Rafaela Morais-Ribeiro, Antonella Ruggiero, Ivan Bozic, Thomas Rusterholz, Blanca Lorente-Echeverria, Marcelo Dias, Wei-Ting Chen, Mark Fiers, Ashley Lu, Ine Vlaeminck, Eline Creemers, Katleen Craessaerts, Joris de Wit, Luuk van Boekholdt, Suresh Poovathingal, Kristofer Davie, Dietmar Rudolf Thal, Keimpe Wierda, Tiago Gil Oliveira, Inna Slutsky, Antoine Adamantidis, Bart De Strooper, Joris de Wit
Summary: Early AD is characterized by hippocampal hyperactivity and decreased sleep quality. The MCH system is involved in neuronal homeostasis but fails in the early stages of AD, leading to aberrant excitatory drive and sleep defects that compromise hippocampus-dependent functions.
NATURE NEUROSCIENCE
(2023)
Article
Neurosciences
Roman Praschberger, Sabine Kuenen, Nils Schoovaerts, Natalie Kaempf, Jeevanjot Singh, Jasper Janssens, Jef Swerts, Eliana Nachman, Carles Calatayud, Stein Aerts, Suresh Poovathingal, Patrik Verstreken
Summary: In this study, we investigated the vulnerability of different neuronal subtypes to a-synuclein and tau toxicity. We found that the susceptibility to these toxic proteins is not solely determined by their expression levels, but also by the intrinsic characteristics of the cells.
Article
Biology
Swann Floc'hlay, Ramya Balaji, Dimitrije Stankovic, Valerie M. Christiaens, Carmen Bravo Gonzalez-Blas, Seppe De Winter, Gert J. Hulselmans, Maxime De Waegeneer, Xiaojiang Quan, Duygu Koldere, Mardelle Atkins, Georg Halder, Mirka Uhlirova, Anne-Kathrin Classen, Stein Aerts
Summary: This study provides important insights into the wound response and its relationship to malignancy. By using a systems biology approach, the authors demonstrate the dual use of regulatory sequences in achieving context dependence for wound repair and tumor growth. This research is valuable for researchers in the fields of gene regulation, developmental biology, and cancer research.
Article
Medicine, General & Internal
Matthias Van Gils, Justin Depauw, Paul J. J. Coucke, Shari Aerts, Shana Verschuere, Lukas Nollet, Olivier M. M. Vanakker
Summary: Pseudoxanthoma elasticum (PXE) is a rare calcification disorder caused by ABCC6 mutations. Reduced levels of PPi were found in PXE patients and carriers, but it is not a predictive biomarker for disease severity and progression.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Cell Biology
Evelyne Naus, Marleen Derweduwe, Youlia Lampi, Annelies Claeys, Jarne Pauwels, Tobias Langenberg, Filip Claes, Jie Xu, Veerle Haemels, Zeynep Kalender Atak, Rob van der Kant, Joost Van Durme, Greet De Baets, Keith L. Ligon, Mark Fiers, Kris Gevaert, Stein Aerts, Frederic Rousseau, Joost Schymkowitz, Frederik De Smet
Summary: Induction of a heat shock-related stress response mediated by Foldlin reduces the levels of misfolded/aggregated mutant p53 and prevents the formation of stress-induced p53 nuclear inclusion bodies. The proteasome inhibitor Bortezomib has similar cellular effects as Foldlin. Induction of a cellular heat shock response seems to be an effective strategy to deal with pathological protein aggregation.
Article
Multidisciplinary Sciences
Hannah Walgrave, Amber Penning, Giorgia Tosoni, Sarah Snoeck, Kristofer Davie, Emma Davis, Leen Wolfs, Annerieke Sierksma, Mayte Mars, Taofeng Bu, Nicola Thrupp, Lujia Zhou, Diederik Moechars, Renzo Mancuso, Mark Fiers, Andrew J. M. Howden, Bart De Strooper, Evgenia Salta
Summary: miR-132 is significantly downregulated in the brain of Alzheimer's disease patients. Increasing miR-132 levels can improve amyloid and Tau pathologies, as well as restore neurogenesis and memory deficits. However, further analysis is needed to understand the full effects of miR-132 supplementation before it can be used for AD therapy.
Article
Biotechnology & Applied Microbiology
Florian V. De Rop, Gert Hulselmans, Chris Flerin, Paula Soler-Vila, Albert Rafels, Valerie Christiaens, Carmen Bravo Gonzalez-Blas, Domenica Marchese, Ginevra Caratu, Suresh Poovathingal, Orit Rozenblatt-Rosen, Michael Slyper, Wendy Luo, Christoph Muus, Fabiana Duarte, Rojesh Shrestha, S. Tansu Bagdatli, M. Ryan Corces, Lira Mamanova, Andrew Knights, Kerstin B. Meyer, Ryan Mulqueen, Akram Taherinasab, Patrick Maschmeyer, Jorn Pezoldt, Camille Lucie Germaine Lambert, Marta Iglesias, Sebastian R. Najle, Zain Y. Dossani, Luciano G. Martelotto, Zach Burkett, Ronald Lebofsky, Jose Ignacio Martin-Subero, Satish Pillai, Arnau Sebe-Pedros, Bart Deplancke, Sarah A. Teichmann, Leif S. Ludwig, Theodore P. Braun, Andrew C. Adey, William J. Greenleaf, Jason D. Buenrostro, Aviv Regev, Stein Aerts, Holger Heyn
Summary: This study benchmarks the performance of eight scATAC-seq methods by conducting 47 experiments on human PBMCs. Significant differences in sequencing library complexity and tagmentation specificity were found, which impact various downstream analyses. The findings underscore the importance of sample extraction, method selection, data processing, and total cost of experiments, offering valuable guidance for future research.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Carmen Bravo Gonzalez-Blas, Seppe De Winter, Gert Hulselmans, Nikolai Hecker, Irina Matetovici, Valerie Christiaens, Suresh Poovathingal, Jasper Wouters, Sara Aibar, Stein Aerts
Summary: SCENIC+ is a method for inferring enhancer-driven gene regulatory networks, which predicts genomic enhancers and their connections with candidate upstream transcription factors and target genes. Through evaluation and analysis of diverse datasets, it can also study conserved transcription factors, enhancers, and gene regulatory networks between human and mouse cell types in the cerebral cortex, as well as the dynamics of gene regulation along differentiation trajectories and the effect of transcription factor perturbations on cell state.
Meeting Abstract
Clinical Neurology
Pegah Masrori, Baukje Bijnens, Kristofer Davie, Suresh Kumar Poovathingal, Annet Storm, Nicole Hersmus, Laura Fumagalli, Ludo Van Den Bosch, Mark Fiers, Dietmar Thal, Renzo Mancuzo, Philip Van Damme
Article
Hematology
Elisa Gabinaud, Laurent Hannouche, Elisa Andersen, Delphine Bastelica, Denis Bernot, Manal Ibrahim-Kosta, Pierre-Emmanuel Morange, Marie Loosveld, Paul Saultier, Dominique Payet-Bornet, Marie-Christine Alessi, Delphine Potier, Marjorie Poggi
Summary: Using single-cell RNA sequencing, researchers have discovered a link between ETV6 germline mutations and thrombocytopenia through the highly deregulated core ribosome biogenesis pathway.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2023)
Article
Biotechnology & Applied Microbiology
Viacheslav Mylka, Irina Matetovici, Suresh Poovathingal, Jeroen Aerts, Niels Vandamme, Ruth Seurinck, Kevin Verstaen, Gert Hulselmans, Silvie van den Hoecke, Isabelle Scheyltjens, Kiavash Movahedi, Hans Wils, Joke Reumers, Jeroen Van Houdt, Stein Aerts, Yvan Saeys
Summary: This study compares the performance of different hashing strategies in single-cell RNA-seq and single-nucleus RNA-seq, and evaluates their applications in clinical samples. The results show that both lipid- and antibody-hashing can achieve correct demultiplexing, but their performance varies in different cell types and tissues.