Article
Biochemistry & Molecular Biology
Birgit H. M. Meldal, Livia Perfetto, Colin Combe, Tiago Lubiana, Joao Vitor Ferreira Cavalcante, Hema Bye-A-Jee, Andra Waagmeester, Noemi Del-Toro, Anjali Shrivastava, Elisabeth Barrera, Edith Wong, Bernhard Mlecnik, Gabriela Bindea, Kalpana Panneerselvam, Egon Willighagen, Juri Rappsilber, Pablo Porras, Henning Hermjakob, Sandra Orchard
Summary: Complex Portal is a manually curated database of macromolecular complexes, providing information on complex composition, topology, and function from a range of model organisms. The database has been continuously updated with new information, expanding its collection to include a variety of complex data that users can access, collaborate on, and contribute to through feedback and curation requests.
NUCLEIC ACIDS RESEARCH
(2022)
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
Physics, Multidisciplinary
Giulia Cencetti, Diego Andres Contreras, Marco Mancastroppa, Alain Barrat
Summary: Contagion processes on networks can be described as simple or complex contagion, but it is difficult to determine the underlying mechanism based on empirical data. We propose a strategy to distinguish between these mechanisms by observing the order of node infection and its correlation with local topology. Our results enhance understanding of contagion processes and offer a method to differentiate between different contagion mechanisms with limited information.
PHYSICAL REVIEW LETTERS
(2023)
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.
Article
Chemistry, Multidisciplinary
Amira F. El-Yazbi, Faten M. Aboukhalil, Essam F. Khamis, Mohammed A. W. Elkhatib, Mahmoud A. El-Sayed, Rasha M. Youssef
Summary: A simple and sensitive RP-HPLC method was developed for simultaneous determination of moxifloxacin hydrochloride and metronidazole in biological fluids. The method showed good precision and selectivity, making it suitable for routine therapeutic drug monitoring and pharmacokinetics studies.
Article
Multidisciplinary Sciences
Nikolaj Horsevad, David Mateo, Robert E. Kooij, Alain Barrat, Roland Bouffanais
Summary: In this study, the authors explore the transition from simple to complex contagion in a distributed decision-making model. They find that the nature of contagion is closely related to the intrinsic pace of the spreading behavior, and that network topology plays a significant role in influencing the effectiveness of behavioral transmission.
NATURE COMMUNICATIONS
(2022)
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)
Article
Automation & Control Systems
Jung-Min Yang, Chun-Kyung Lee, Kwang-Hyun Cho
Summary: The study proposes a novel control scheme for achieving global stabilization of complex biological networks by simplifying the Boolean network model and identifying a minimum node set for control inputs. This method does not require structural conditions and ensures global stabilization with modest computational complexity and scalability.
IEEE TRANSACTIONS ON CONTROL OF NETWORK SYSTEMS
(2021)
Article
Mathematics
Nickie Lefevr, Andreas Kanavos, Vassilis C. Gerogiannis, Lazaros Iliadis, Panagiotis Pintelas
Summary: Complex networks, derived from the observation and analysis of real-world networks, include biological networks focusing on connections and interfaces like epidemic models. Fuzzy logic, a powerful mathematical tool, deals with imprecision and aims to provide low-cost solutions to real-world problems. Fuzzy-based simulation scenarios for HIV spreading in a population of needle drug users demonstrate the importance of fuzziness in analyzing disease spread.
Article
Biochemistry & Molecular Biology
Abi S. Ghifari, Aneta Ivanova, Oliver Berkowitz, James Whelan, Monika W. Murcha
Summary: This study describes the mechanism by which the abundance of Complex I (CI) is regulated in a CI-deficient Arabidopsis thaliana mutant. The interaction between the CI subunit PSST and FTSH3 facilitates the disassembly of the CI matrix arm domain for turnover, ensuring protein quality control in the face of oxidative damage. The study reveals the molecular process by which FTSH3 recognizes CI for degradation at the amino acid level.
Article
Computer Science, Information Systems
Tianning Zhang, Chun Yun Kee, Yee Sin Ang, Erping Li, Lay Kee Ang
Summary: This paper presents an improved method for complex metasurface design using a deep learning model and network architecture search method. By combining spatial symmetry information, our method achieves significant improvements in identifying electromagnetic response locations and predicting response curves. It provides a platform for complex metasurface design problems.
Article
Mathematics, Interdisciplinary Applications
Yan Wang, Xinxin Cao, Tongfeng Weng, Huijie Yang, Changgui Gu
Summary: The study introduces a mixed strategy called multi-biased random walk on complex networks, which quantifies the time required to find a target through an analytical expression and reveals that its global mean first passage time follows a specific pattern. These findings are confirmed through numerical and theoretical results on various networks.
CHAOS SOLITONS & FRACTALS
(2021)
Article
Biochemical Research Methods
Alexander Browning, Matthew Simpson
Summary: An enduring challenge in computational biology is to balance data quality and quantity with model complexity. Tools such as identifiability analysis and information criterion have been developed to harmonise this juxtaposition, yet cannot always resolve the mismatch between available data and the granularity required in mathematical models to answer important biological questions. Our study focuses on the interrelationship between the non-identifiable parameters in a complex model and the identifiable parameters in a simple surrogate model, aiming to provide additional biological insights from complex, non-identifiable models.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Computer Science, Hardware & Architecture
Sanjay Kumar, Abhishek Mallik, Sandeep Singh Sengar
Summary: This paper proposes a deep learning approach for community detection in complex networks, combining stacked autoencoders and the Crow Search Algorithm. Experimental results demonstrate that the proposed method achieves excellent performance.
JOURNAL OF SUPERCOMPUTING
(2023)
Article
Multidisciplinary Sciences
Arvind Singh Mer, Emily M. Heath, Seyed Ali Madani Tonekaboni, Nergiz Dogan-Artun, Sisira Kadambat Nair, Alex Murison, Laura Garcia-Prat, Liran Shlush, Rose Hurren, Veronique Voisin, Gary D. Bader, Corey Nislow, Mattias Rantalainen, Soren Lehmann, Mark Gower, Cynthia J. Guidos, Mathieu Lupien, John E. Dick, Mark D. Minden, Aaron D. Schimmer, Benjamin Haibe-Kains
Summary: The molecular heterogeneity of AML poses challenges for prognosis and therapy. NPM1 mutated AML is heterogeneous, with two subtypes exhibiting distinct molecular characteristics, differentiation state, patient survival, and drug response.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Patty Sachamitr, Jolene C. Ho, Felipe E. Ciamponi, Wail Ba-Alawi, Fiona J. Coutinho, Paul Guilhamon, Michelle M. Kushida, Florence M. G. Cavalli, Lilian Lee, Naghmeh Rastegar, Victoria Vu, Maria Sanchez-Osuna, Jasmin Coulombe-Huntington, Evgeny Kanshin, Heather Whetstone, Mathieu Durand, Philippe Thibault, Kirsten Hart, Maria Mangos, Joseph Veyhl, Wenjun Chen, Nhat Tran, Bang-Chi Duong, Ahmed M. Aman, Xinghui Che, Xiaoyang Lan, Owen Whitley, Olga Zaslaver, Dalia Barsyte-Lovejoy, Laura M. Richards, Ian Restall, Amy Caudy, Hannes L. Rost, Zahid Quyoom Bonday, Mark Bernstein, Sunit Das, Michael D. Cusimano, Julian Spears, Gary D. Bader, Trevor J. Pugh, Mike Tyers, Mathieu Lupien, Benjamin Haibe-Kains, H. Artee Luchman, Samuel Weiss, Katlin B. Massirer, Panagiotis Prinos, Cheryl H. Arrowsmith, Peter B. Dirks
Summary: The study suggests that PRMT5 inhibitors can block the growth of patient-derived glioblastoma stem cell cultures in vitro and in vivo, indicating that PRMT5 inhibition may be a useful therapeutic strategy.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Patryk Skowron, Hamza Farooq, Florence M. G. Cavalli, A. Sorana Morrissy, Michelle Ly, Liam D. Hendrikse, Evan Y. Wang, Haig Djambazian, Helen Zhu, Karen L. Mungall, Quang M. Trinh, Tina Zheng, Shizhong Dai, Ana S. Guerreiro Stucklin, Maria C. Vladoiu, Vernon Fong, Borja L. Holgado, Carolina Nor, Xiaochong Wu, Diala Abd-Rabbo, Pierre Berube, Yu Chang Wang, Betty Luu, Raul A. Suarez, Avesta Rastan, Aaron H. Gillmor, John J. Y. Lee, Xiao Yun Zhang, Craig Daniels, Peter Dirks, David Malkin, Eric Bouffet, Uri Tabori, James Loukides, Francois P. Doz, Franck Bourdeaut, Olivier O. Delattre, Julien Masliah-Planchon, Olivier Ayrault, Seung-Ki Kim, David Meyronet, Wieslawa A. Grajkowska, Carlos G. Carlotti, Carmen de Torres, Jaume Mora, Charles G. Eberhart, Erwin G. Van Meir, Toshihiro Kumabe, Pim J. French, Johan M. Kros, Nada Jabado, Boleslaw Lach, Ian F. Pollack, Ronald L. Hamilton, Amulya A. Nageswara Rao, Caterina Giannini, James M. Olson, Laszlo Bognar, Almos Klekner, Karel Zitterbart, Joanna J. Phillips, Reid C. Thompson, Michael K. Cooper, Joshua B. Rubin, Linda M. Liau, Miklos Garami, Peter Hauser, Kay Ka Wai Li, Ho-Keung Ng, Wai Sang Poon, G. Yancey Gillespie, Jennifer A. Chan, Shin Jung, Roger E. McLendon, Eric M. Thompson, David Zagzag, Rajeev Vibhakar, Young Shin Ra, Maria Luisa Garre, Ulrich Schueller, Tomoko Shofuda, Claudia C. Faria, Enrique Lopez-Aguilar, Gelareh Zadeh, Chi-Chung Hui, Vijay Ramaswamy, Swneke D. Bailey, Steven J. Jones, Andrew J. Mungall, Richard A. Moore, John A. Calarco, Lincoln D. Stein, Gary D. Bader, Juri Reimand, Jiannis Ragoussis, William A. Weiss, Marco A. Marra, Hiromichi Suzuki, Michael D. Taylor
Summary: Sonic Hedgehog medulloblastoma (Shh-MB) comprises four subtypes each with distinct clinical traits. The authors characterize the genome, transcriptome, and methylome of Shh-MB subtypes, revealing a complex fusion landscape and the molecular convergence of MYCN and cAMP signaling pathways.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Madonna R. Peter, Misha Bilenky, Alastair Davies, Ruth Isserlin, Gary D. Bader, Neil E. Fleshner, Martin Hirst, Amina Zoubeidi, Bharati Bapat
Summary: Androgens are a major driver of prostate cancer, and resistance to androgen-targeting therapies can lead to metastatic castration-resistant prostate cancer (mCRPC) and treatment-induced neuroendocrine disease (tNEPC). Investigating methylation changes in PCa progression from castration sensitive to tNEPC state can provide insights into novel resistance mechanisms. Analysis on a CRPC xenograft model revealed extensive methylation changes associated with the development of CRPC and tNEPC, highlighting potential therapeutic targets. Moreover, tNEPC-related methylation signals detected in circulating cell-free DNA from mCRPC patients undergoing androgen-targeting therapies were associated with faster clinical progression, suggesting the potential of these biomarkers in identifying aggressive disease.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Yuwei Zhang, Ayden Malekjahani, Buddhisha N. Udugama, Pranav Kadhiresan, Hongmin Chen, Matthew Osborne, Max Franz, Mike Kucera, Simon Plenderleith, Lily Yip, Gary D. Bader, Vanessa Tran, Jonathan B. Gubbay, Allison McGeer, Samira Mubareka, Warren C. W. Chan
Summary: The study developed a portable smartphone-based quantum barcode serological assay device with high clinical sensitivity, enabling real-time surveillance of patients infected with SARS-CoV-2. Compared to lateral flow assays, this device showed significantly higher diagnostic performance and provided instantaneous results for informing patients, physicians, and public health agencies.
Article
Multidisciplinary Sciences
Farshad Nassiri, Jeff Liu, Vikas Patil, Yasin Mamatjan, Justin Z. Wang, Rupert Hugh-White, Andrew M. Macklin, Shahbaz Khan, Olivia Singh, Shirin Karimi, Rosario I. Corona, Lydia Y. Liu, Caroline Y. Chen, Ankur Chakravarthy, Qingxia Wei, Bharati Mehani, Suganth Suppiah, Andrew Gao, Adriana M. Workewych, Ghazaleh Tabatabai, Paul C. Boutros, Gary D. Bader, Daniel D. de Carvalho, Thomas Kislinger, Kenneth Aldape, Gelareh Zadeh
Summary: Meningiomas, the most common primary intracranial tumor in adults, often require surgery due to lack of effective medical therapies. This study introduced four consensus molecular groups of meningioma, which accurately predicted clinical outcomes and informed therapeutic options. Single-cell RNA sequencing revealed inter-individual variations in meningioma biology, highlighting the importance of molecular classification in guiding treatment strategies.
Article
Multidisciplinary Sciences
Shunsuke Funakoshi, Ian Fernandes, Olya Mastikhina, Dan Wilkinson, Thinh Tran, Wahiba Dhahri, Amine Mazine, Donghe Yang, Benjamin Burnett, Jeehoon Lee, Stephanie Protze, Gary D. Bader, Sara S. Nunes, Michael Laflamme, Gordon Keller
Summary: The study established a differentiation strategy for generating structurally, metabolically, and functionally mature compact ventricular cardiomyocytes from human pluripotent stem cells. These cardiomyocytes exhibited metabolic changes indicative of heart failure when challenged with pathological stimuli.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Maria Abou Chakra, Ruth Isserlin, Thinh N. Tran, Gary D. Bader
Summary: The duration of the cell cycle changes dramatically during development, acting as a transcriptional filter to control gene transcript expression, cell diversity, and the number of different cell types. Fast-developing organisms have a narrow genomic distribution of gene lengths while slower developers have more long genes. These findings support the importance of cell cycle dynamics in controlling gene transcript expression and cell fate across multicellular animals.
Article
Oncology
Martine Dumont, Nana Weber-Lassalle, Charles Joly-Beauparlant, Corinna Ernst, Arnaud Droit, Bing-Jian Feng, Stephane Dubois, Annie-Claude Collin-Deschesnes, Penny Soucy, Maxime Vallee, Frederic Fournier, Audrey Lemacon, Muriel A. Adank, Jamie Allen, Janine Altmueller, Norbert Arnold, Margreet G. E. M. Ausems, Riccardo Berutti, Manjeet K. Bolla, Shelley Bull, Sara Carvalho, Sten Cornelissen, Michael R. Dufault, Alison M. Dunning, Christoph Engel, Andrea Gehrig, Willemina R. R. Geurts-Giele, Christian Gieger, Jessica Green, Karl Hackmann, Mohamed Helmy, Julia Hentschel, Frans B. L. Hogervorst, Antoinette Hollestelle, Maartje J. Hooning, Judit Horvath, M. Arf An Ikram, Silke Kaulfuss, Renske Keeman, Da Kuang, Craig Luccarini, Wolfgang Maier, John W. M. Martens, Dieter Niederacher, Peter Nurnberg, Claus-Eric Ott, Annette Peters, Paul D. P. Pharoah, Alfredo Ramirez, Juliane Ramser, Steffi Riedel-Heller, Gunnar Schmidt, Mitul Shah, Martin Scherer, Antje Stabler, Tim M. Strom, Christian Sutter, Holger Thiele, Christi J. van Asperen, Lizet van der Kolk, Rob B. van der Luijt, Alexander E. Volk, Michael Wagner, Quinten Waisfisz, Qin Wang, Shan Wang-Gohrke, Bernhard H. F. Weber, Peter Devilee, Sean Tavtigian, Gary D. Bader, Alfons Meindl, David E. Goldgar, Irene L. Andrulis, Rita K. Schmutzler, Douglas F. Easton, Marjanka K. Schmidt, Eric Hahnen, Jacques Simard
Summary: This study aimed to identify new genes associated with breast cancer risk through whole-exome sequencing. The results revealed 20 novel genes with evidence of association, but larger studies are needed for confirmation. Additionally, known genes such as BRCA1, BRCA2, PALB2, ATM, and CHEK2 were found to be associated with increased risk of breast cancer, although they only explain a fraction of the familial aggregation of the disease.
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
Biochemical Research Methods
Max Franz, Christian T. Lopes, Dylan Fong, Mike Kucera, Manfred Cheung, Metin Can Siper, Gerardo Huck, Yue Dong, Onur Sumer, Gary D. Bader
Summary: Cytoscape.js is an open-source graph library implemented in JavaScript. It can be used as a visualization software component to render interactive graphs in web browsers, or in a headless manner for server-side graph operations with Node.js.
Article
Oncology
Laura M. Richards, Owen K. N. Whitley, Graham MacLeod, Florence M. G. Cavalli, Fiona J. Coutinho, Julia E. Jaramillo, Nataliia Svergun, Mazdak Riverin, Danielle C. Croucher, Michelle Kushida, Kenny Yu, Paul Guilhamon, Naghmeh Rastegar, Moloud Ahmadi, Jasmine K. Bhatti, Danielle A. Bozek, Naijin Li, Lilian Lee, Clare Che, Erika Luis, Nicole I. Park, Zhiyu Xu, Troy Ketela, Richard A. Moore, Marco A. Marra, Julian Spears, Michael D. Cusimano, Sunit Das, Mark Bernstein, Benjamin Haibe-Kains, Mathieu Lupien, H. Artee Luchman, Samuel Weiss, Stephane Angers, Peter B. Dirks, Gary D. Bader, Trevor J. Pugh
Summary: The study revealed that glioblastomas contain diverse cell populations, with GSCs showing high transcriptional heterogeneity associated with normal neural development and inflammatory wound response. Genome-wide CRISPR-Cas9 dropout screens validated this observation. Additionally, the majority of malignant cells were found to organize along an orthogonal astrocyte maturation gradient while retaining founder GSC transcriptional programs.
Article
Biochemical Research Methods
Brenda L. K. Coles, Mahmoud Labib, Mahla Poudineh, Brendan T. Innes, Justin Belair-Hickey, Surath Gomis, Zongjie Wang, Gary D. Bader, Edward H. Sargent, Shana O. Kelley, Derek van der Kooy
Summary: This study introduces a microfluidic platform that efficiently enriches retinal stem cells (RSCs) by combining nickel micromagnets, herringbone structures, and variable flow velocities. Utilizing an affinity enrichment strategy based on cell-surface markers, researchers successfully separated RSCs from adult ciliary epithelium and identified four differentially expressed cell surface markers that can be targeted simultaneously. This innovative approach allows for an unprecedented enrichment of RSCs compared to unsorted cells.
Meeting Abstract
Ophthalmology
Brian G. Ballios, Justin Belair-Hickey, Saeed Khalili, Kenneth Grise, Brenda Blk Coles, Jeff Liu, Gilbert Bernier, Valerie Wallace, Gary Bader, Molly S. Shoichet, Derek Van der Kooy
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Meeting Abstract
Oncology
Geethu Emily Thomas, Grace Egan, Laura Gracia Prat, Aaron Botham, Veronique Voisin, Elias Orouji, Jordan Chin, Boaz Nachmias, Kerstin B. Kaufmann, Neil Maclean, Rose Hurren, Marcela Gronda, Xiaoming Wang, Dilshad H. Khan, Rashim P. Singh, Andrea Arruda, Mark Minden, Gary D. Bader, John E. Dick, Aaron D. Schimmer
