Article
Genetics & Heredity
Erik K. Zhivkoplias, Oleg Vavulov, Thomas Hillerton, Erik L. L. Sonnhammer
Summary: The regulatory relationships between genes and proteins in a cell form a gene regulatory network (GRN) that controls cellular response. Methods have been developed to reverse engineer GRNs from expression data, but realistic simulations are necessary due to the lack of ground-truth GRNs. Analysis shows that the feed-forward loop (FFL) motif is significantly enriched in real GRNs, leading to the development of a novel preferential attachment algorithm, FFLatt, for network generation.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Anupam Dey, Debashis Barik
Summary: Bistability in living systems is closely related to decision making processes, with the operating principles of a bistable switch from a positive feedback loop well understood. Investigating feed-forward signaling of a positive feedback loop reveals the generation of various emergent bistable switches in hybrid motifs. The emergent behaviors of these switches depend on logic gate configuration and regulatory thresholds, rather than the nature of the positive feedback loop.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Pathology
Margaret A. T. Freeberg, Apostolos Perelas, Jane K. Rebman, Richard P. Phipps, Thomas H. Thatcher, Patricia J. Sime
Summary: Idiopathic pulmonary fibrosis is a progressive disease characterized by accumulation of extracellular matrix in lung tissue, leading to altered mechanical properties. Recent studies suggest that these changes create a feed-forward loop, contributing to fibroblast differentiation and activation. Mechanotransduction pathways, including mechanosensors like integrins and downstream transcription factors, play a role in fibrosis progression.
AMERICAN JOURNAL OF PATHOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Seongho Hong, Dohyun Jeong, Jordan Ryan, Mathias Foo, Xun Tang, Jongmin Kim
Summary: RNA-based regulators are efficient in speed but may lack significant timescale differences in circuit functionality. By incorporating a protein synthesis process, an RNA-protein hybrid IFFL circuit was designed to generate pulses successfully. The agreement between experiments and simulations indicates the usefulness of mechanistic modeling in designing new circuits.
Review
Medicine, Research & Experimental
Zora Baumann, Priska Auf der Maur, Mohamed Bentires-Alj
Summary: Breast cancer is a common cancer among women, and metastasis to distant organs is a major cause of cancer-related deaths. Despite improvements in survival for early-stage breast cancer patients, the survival rate for metastatic patients has not significantly improved. This review explores how the microenvironment of common metastatic sites is influenced by the primary tumor and disseminated tumor cells (DTCs), with a focus on the role of feed-forward loops (FFLs) in the growth and persistence of established metastases. The importance of targeting not only cancer cells but also the tumor microenvironment in novel therapies is discussed.
EMBO MOLECULAR MEDICINE
(2022)
Article
Cell Biology
Yizeng Yang, Dharmendra Bhargava, Xiao Chen, Taicheng Zhou, Gizem Dursuk, Wenpeng Jiang, Jinshen Wang, Zhen Zong, Sharyn I. Katz, Gwen A. Lomberk, Raul A. Urrutia, Jonathan P. Katz
Summary: In non-transformed human squamous epithelial cells, the decision of whether to arrest or undergo apoptosis in response to stress is mediated by the interaction between p53 and the zinc-finger transcription factor KLF5. The levels of cellular stress determine the specific outcome, with moderate stress leading to cell survival and severe stress resulting in apoptosis.
CELL DEATH & DISEASE
(2023)
Article
Computer Science, Artificial Intelligence
Saban Gulcu
Summary: The training algorithm is a crucial component of artificial neural networks (ANN) that affects their performance. This article presents a new hybrid algorithm called DA-MLP, which uses the dragonfly algorithm to train feed-forward multilayer neural networks (MLP). The experimental study shows that the DA-MLP algorithm is more efficient than other algorithms.
APPLIED SOFT COMPUTING
(2022)
Article
Biology
Tobit Dehnen, Josh J. Arbon, Damien R. Farine, Neeltje J. Boogert
Summary: In animal societies, individuals differ in their ability to win agonistic interactions, resulting in dominance hierarchies. Factors such as intrinsic attributes, resource value asymmetry, winner-loser effects, interaction-outcome history, and third-party support can influence interaction outcomes and individuals' positions in dominance hierarchies. These factors are unlikely to act independently, but instead, form feedback loops and feed-forward mechanisms that determine dominance outcomes within and between generations. Understanding these factors and their interactions is crucial for studying dominance dynamics in animal groups.
BIOLOGICAL REVIEWS
(2022)
Article
Cell Biology
Amin R. Mazloom, Huilei Xu, Jaume Reig-Palou, Ana Vasileva, Angel-Carlos Roman, Sonia Mulero-Navarro, Ihor R. Lemischka, Ana Sevilla
Summary: This study describes the transcriptional regulatory circuitry of embryonic stem cells based on miRNA array expression and short transcript sequencing, revealing the regulatory role of Estrogen Related Receptor Beta and its dynamic changes during cell differentiation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Suchana M. Chakravarty, Attila Csikasz-Nagy
Summary: Cells can maintain homeostasis in a noisy environment through their signaling pathways' ability to filter noise. Feed-forward loops, especially when coupled with other motifs, can effectively reduce noise while maintaining signal transduction performance. A combination of specific feed-forward loops, such as coherent 1 and incoherent 4, can provide the best overall performance in noise reduction and signal transduction.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Carrie Easter, Ellouise Leadbeater, Matthew J. Hasenjager
Summary: This study uses an agent-based model to investigate how individual variation in activity and movement shapes the production of feed-forward loops in a simulated insect colony. The findings suggest that individual variation in activity drives the over-representation of feed-forward loops by determining the directionality of interactions. However, activity variation does not promote faster or more efficient information flow. On the other hand, individual variation in movement trajectory, although not involved in generating feed-forward loops, promotes fast and efficient information flow by linking otherwise unconnected regions.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Cell Biology
Myoung Sook Han, Rachel J. Perry, Joao-Paulo Camporez, Philipp E. Scherer, Gerald I. Shulman, Guangping Gao, Roger J. Davis
Summary: This study demonstrates that JNK signaling in adipocytes results in an increased circulating concentration of FGF21, regulating systemic metabolism. This mechanism of organ crosstalk involves a feed-forward regulatory loop mediated by JNK-regulated FGF21 autocrine signaling in adipocytes, promoting the expression of adiponectin and hepatic expression of FGF21. The novel signaling paradigm connects autocrine and endocrine signaling modes of the same hormone in different tissues.
GENES & DEVELOPMENT
(2021)
Article
Chemistry, Multidisciplinary
Zhengze Lu, Yang Long, Jiaxin Li, Kebai Ren, Wei Zhao, Xuhui Wang, Chunyu Xia, Yashi Wang, Man Li, Zhirong Zhang, Qin He
Summary: The developed LA/DOX NP can inhibit inflammatory cell recruitment in the liver and lungs through multiple mechanisms, block NF-kappa B and STAT3 signaling pathways, thereby shutting down inflammatory feed-forward loops, providing a new therapeutic strategy for breast cancer and its metastasis.
JOURNAL OF CONTROLLED RELEASE
(2021)
Article
Multidisciplinary Sciences
Archishman Ghosh, Divya Kota, Huan-Xiang Zhou
Summary: This study reveals that biomolecular condensates behave as viscoelastic fluids, with shear stress relaxation governing fusion dynamics. These findings have implications for understanding multiphase organization, assembly and disassembly, and aging processes.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Anna Terebus, Farid Manuchehrfar, Youfang Cao, Jie Liang
Summary: The study provides comprehensive characterizations of the stochastic multimodality of feed-forward loops (FFLs), including how switching between different network phenotypes is controlled and the topological sensitivity of the multimodality of the landscapes to regulation intensities. Results show that slow binding and unbinding dynamics of transcription factor to promoter result in strong stochastic behavior of FFLs different from deterministic models, and strong input intensity may lead to up to 6 stable phenotypes.
FRONTIERS IN GENETICS
(2021)
Article
Medicine, Research & Experimental
Kwang-Hyun Cho, Jae Il Joo, Dongkwan Shin, Dongsan Kim, Sang-Min Park
WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE
(2016)
Article
Biochemical Research Methods
Man-Sun Kim, Dongsan Kim, Jeong-Rae Kim
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2019)
Article
Mathematical & Computational Biology
Changki Hong, Minho Lee, Dongsup Kim, Dongsan Kim, Kwang-Hyun Cho, Insik Shin
BMC SYSTEMS BIOLOGY
(2012)
Article
Mathematical & Computational Biology
Man-Sun Kim, Jeong-Rae Kim, Dongsan Kim, Arthur D. Lander, Kwang-Hyun Cho
BMC SYSTEMS BIOLOGY
(2012)
Article
Cell Biology
Tadashi Kaname, Chang-Seok Ki, Norio Niikawa, George S. Baillie, Jonathan P. Day, Ken-ichi Yamamura, Tohru Ohta, Gen Nishimura, Nobuo Mastuura, Ok-Hwa Kim, Young Bae Sohn, Hyun Woo Kim, Sung Yoon Cho, Ah-Ra Ko, Jin Young Lee, Hyun Wook Kim, Sung Ho Ryu, Hwanseok Rhee, Kap-Seok Yang, Keehyoung Joo, Jooyoung Lee, Chi Hwa Kim, Kwang-Hyun Cho, Dongsan Kim, Kumiko Yanagi, Kenji Naritomi, Ko-ichiro Yoshiura, Tatsuro Kondoh, Eiji Nii, Hidefumi Tonoki, Miles D. Houslay, Dong-Kyu Jin
CELLULAR SIGNALLING
(2014)
Article
Biochemistry & Molecular Biology
Dongsan Kim, Walter Kolch, Kwang-Hyun Cho
Article
Biochemistry & Molecular Biology
Dongsan Kim, Man-Sun Kim, Kwang-Hyun Cho
NUCLEIC ACIDS RESEARCH
(2012)
Article
Oncology
Soobeom Lee, Chansu Lee, Chae Young Hwang, Dongsan Kim, Younghyun Han, Sung Noh Hong, Seok-Hyung Kim, Kwang-Hyun Cho
MOLECULAR CANCER RESEARCH
(2020)
Article
Biotechnology & Applied Microbiology
Dongsan Kim, Kwang-Hyun Cho
Summary: This study utilized blind source separation to extract cancer cell-intrinsic gene expression patterns from clinical tumor samples of colorectal cancer. The identified subtypes are independent of biopsy site and provide valuable prognostic information.
CANCER GENE THERAPY
(2023)
Article
Biochemistry & Molecular Biology
Man-Sun Kim, Dongsan Kim, Nam Sook Kang, Jeong-Rae Kim
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2017)
Article
Biochemistry & Molecular Biology
Sung-Young Shin, Sang-Mok Choo, Dongsan Kim, Song Joon Baek, Olaf Wolkenhauer, Kwang-Hyun Cho