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| Open AccessSARS-CoV-2 potential drugs, drug targets, and biomarkers: a viral-host interaction network-based analysis
- Asmaa Samy
- , Mohamed A. Maher
- & Eman Badr
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| Open AccessA novel approach GRNTSTE to reconstruct gene regulatory interactions applied to a case study for rat pineal rhythm gene
- Zhenyu Liu
- , Jing Gao
- & Junjie Chen
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| Open AccessConstruction and analysis of a ceRNA network and patterns of immune infiltration in chronic rhinosinusitis with nasal polyps: based on data mining and experimental verification
- Jing-cai Chen
- , Qi-long Xing
- & Yan-jun Wang
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| Open AccessClassification of triple negative breast cancer by epithelial mesenchymal transition and the tumor immune microenvironment
- Francesc Font-Clos
- , Stefano Zapperi
- & Caterina A. M. La Porta
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| Open AccessiTRAQ-based quantitative proteomic analysis provides insight into the drought-stress response in maize seedlings
- Wen Ren
- , Zi Shi
- & Jiuran Zhao
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| Open AccessSeasonal and sex-dependent gene expression in emu (Dromaius novaehollandiae) fat tissues
- Kristina Wright
- , Ka Ming Nip
- & Inanc Birol
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| Open AccessMALAT1 as master regulator of biomarkers predictive of pan-cancer multi-drug resistance in the context of recalcitrant NRAS signaling pathway identified using systems-oriented approach
- Santosh Kumar
- & Seema Mishra
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| Open AccessGlobal coordination level in single-cell transcriptomic data
- Guy Amit
- , Dana Vaknin Ben Porath
- & Amir Bashan
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| Open AccessInterpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data
- Sara A. Yones
- , Alva Annett
- & Jan Komorowski
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| Open AccessNetwork analysis reveals dysregulated functional patterns in type II diabetic skin
- Chunan Liu
- , Sudha Ram
- & Bonnie L. Hurwitz
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| Open AccessUnveiling OASIS family as a key player in hypoxia–ischemia cases induced by cocaine using generative adversarial networks
- Kyoungmin Lee
- , Taehyeong Kim
- & Wookyung Yu
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| Open AccessDynamical modeling of miR-34a, miR-449a, and miR-16 reveals numerous DDR signaling pathways regulating senescence, autophagy, and apoptosis in HeLa cells
- Shantanu Gupta
- , Pritam Kumar Panda
- & Rajeev Ahuja
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| Open AccessShear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites
- Roman Tsaryk
- , Nora Yucel
- & Arndt F. Siekmann
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| Open AccessIntegrative analysis reveals the functional implications and clinical relevance of pyroptosis in low-grade glioma
- Lin Shen
- , Yanyan Li
- & Zhanzhan Li
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| Open AccessComputation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome
- Micha Sam Brickman Raredon
- , Junchen Yang
- & Laura E. Niklason
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| Open AccessPromoter/enhancer-based controllability of regulatory networks
- Prajwal Devkota
- & Stefan Wuchty
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| Open AccessTranscriptome analysis reveals the potential roles of long non-coding RNAs in feed efficiency of chicken
- Parastoo Karimi
- , Mohammad Reza Bakhtiarizadeh
- & Hamid Reza Izadnia
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| Open AccessCharacterization of influenza A virus induced transposons reveals a subgroup of transposons likely possessing the regulatory role as eRNAs
- Steven S. Shen
- , Hezkiel Nanda
- & Ryan A. Langlois
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| Open AccessPredicting clinical outcomes of cancer patients with a p53 deficiency gene signature
- Evelien Schaafsma
- , Eric M. Takacs
- & Manabu Kurokawa
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| Open AccessPetri nets and ODEs as complementary methods for comprehensive analysis on an example of the ATM–p53–NF-\(\kappa\)B signaling pathways
- Kaja Gutowska
- , Daria Kogut
- & Krzysztof Puszynski
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| Open AccessConstruction of a potential microRNA and messenger RNA regulatory network of acute lung injury in mice
- Yufeng Zhang
- , Weilong Jiang
- & Xudong Han
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| Open AccessThree topological features of regulatory networks control life-essential and specialized subsystems
- Ivan Rodrigo Wolf
- , Rafael Plana Simões
- & Guilherme Targino Valente
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| Open AccessIdentification of transcriptional regulatory network associated with response of host epithelial cells to SARS-CoV-2
- Chen Su
- , Simon Rousseau
- & Amin Emad
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| Open AccessNovel cancer subtyping method based on patient-specific gene regulatory network
- Mai Adachi Nakazawa
- , Yoshinori Tamada
- & Yasushi Okuno
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| Open AccessExploring the mechanism of Yixinyin for myocardial infarction by weighted co-expression network and molecular docking
- Mengqi Huo
- , Lina Ma
- & Guoguo Liu
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| Open AccessCapturing hidden regulation based on noise change of gene expression level from single cell RNA-seq in yeast
- Thoma Itoh
- & Takashi Makino
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| Open AccessNkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness
- Nasibeh Khayer
- , Maryam Jalessi
- & Mehdi Mirzaie
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| Open AccessIntegrated computational analyses reveal novel insights into the stromal microenvironment of SHH-subtype medulloblastoma
- Alexander P. Landry
- , Nardin Samuel
- & Zsolt Zador
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| Open AccessComparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice
- Muhammad-Redha Abdullah-Zawawi
- , Nur-Farhana Ahmad-Nizammuddin
- & Zeti-Azura Mohamed-Hussein
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| Open AccessSingle-cell and bulk transcriptomics of the liver reveals potential targets of NASH with fibrosis
- Zhong-Yi Wang
- , Adrian Keogh
- & Florian Nigsch
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| Open AccessSystems biology analysis of lung fibrosis-related genes in the bleomycin mouse model
- Dmitri Toren
- , Hagai Yanai
- & Vadim E Fraifeld
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| Open AccessSex-dependent gene co-expression in the human body
- Robin J. G. Hartman
- , Michal Mokry
- & Hester M. den Ruijter
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| Open AccessNovel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
- Cristina Cheroni
- , Lara Manganaro
- & Raffaele De Francesco
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| Open AccessPan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.)
- Cesar Augusto Medina
- , Deborah A. Samac
- & Long-Xi Yu
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| Open AccessGenome-wide comparative analyses of GATA transcription factors among seven Populus genomes
- Mangi Kim
- , Hong Xi
- & Jongsun Park
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| Open AccessThe switch of DNA states filtering the extrinsic noise in the system of frequency modulation
- Shih-Chiang Lo
- , Chao-Xuan You
- & Che-Chi Shu
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| Open Accessk-core genes underpin structural features of breast cancer
- Rodrigo Dorantes-Gilardi
- , Diana García-Cortés
- & Jesús Espinal-Enríquez
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| Open AccessUnderstanding the impact of SNPs associated with autism spectrum disorder on biological pathways in the human fetal and adult cortex
- E. Golovina
- , T. Fadason
- & J. M. O’Sullivan
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| Open AccessTranscriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer
- Dilara Uzuner
- , Yunus Akkoç
- & Tunahan Çakır
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| Open AccessKBoost: a new method to infer gene regulatory networks from gene expression data
- Luis F. Iglesias-Martinez
- , Barbara De Kegel
- & Walter Kolch
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| Open AccessUntangling the genetic link between type 1 and type 2 diabetes using functional genomics
- Denis M. Nyaga
- , Mark H. Vickers
- & Justin M. O’Sullivan
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| Open Accesshsp-90 and unc-45 depletion induce characteristic transcriptional signatures in coexpression cliques of C. elegans
- Lukas Schmauder
- & Klaus Richter
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| Open AccessTranscriptional response to prolonged perchlorate exposure in the methanogen Methanosarcina barkeri and implications for Martian habitability
- Rachel L. Harris
- , Andrew C. Schuerger
- & Tullis C. Onstott
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| Open AccessIdentifying molecular targets for reverse aging using integrated network analysis of transcriptomic and epigenomic changes during aging
- Hwang-Yeol Lee
- , Yeonsu Jeon
- & Kwang-Hyun Cho
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| Open AccessIdentification of Nrf2-responsive microRNA networks as putative mediators of myocardial reductive stress
- Justin M. Quiles
- , Mark E. Pepin
- & Namakkal S. Rajasekaran
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| Open AccessChamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction
- Xin Luo
- , Jun Yin
- & Marina Stolina
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| Open AccessEvolutionary history expands the range of signaling interactions in hybrid multikinase networks
- Philippe Ortet
- , Sylvain Fochesato
- & Mohamed Barakat
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| Open AccessImmunological and hematological outcomes following protracted low dose/low dose rate ionizing radiation and simulated microgravity
- Amber M. Paul
- , Eliah G. Overbey
- & Xiao Wen Mao
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| Open AccessRelationship between gene regulation network structure and prediction accuracy in high dimensional regression
- Yuichi Okinaga
- , Daisuke Kyogoku
- & Kei Hirose