bioconductor: pathview | Projects

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: almost 11 years ago

10.3389/fgene.2019.00594

BioNetStat: A Tool for Biological Networks Differential Analysis
Cited by: 21
Author(s): Vinícius Carvalho Jardim, Suzana de Siqueira Santos, André Fujita, Marcos Silveira Buckeridge
Software Mentions: 22
Published: over 5 years ago

10.12688/f1000research.8923.2

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Cited by: 105
Author(s): Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D’Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Software Mentions: 17
Published: almost 8 years ago

10.1186/s12859-016-0884-1

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
Cited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: almost 9 years ago

10.3389/fgene.2020.00620

An Analysis Regarding the Association Between the ISLR Gene and Gastric Carcinogenesis
Cited by: 13
Author(s): Shu Li, Wei Zhao, Manyi Sun
Software Mentions: 13
Published: over 4 years ago

10.3389/fimmu.2021.730346

Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens
Cited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: over 3 years ago

10.12688/f1000research.12544.1

Easy and efficient ensemble gene set testing with EGSEA
Cited by: 45
Author(s): Monther Alhamdoosh, Charity W. Law, Tian Li, Julie Sheridan, Milica Ng, Matthew E. Ritchie
Software Mentions: 12
Published: about 7 years ago

10.3390/cancers11091248

Gastric Normal Adjacent Mucosa Versus Healthy and Cancer Tissues: Distinctive Transcriptomic Profiles and Biological Features
Cited by: 28
Author(s): Sabino Russi, Giovanni Calice, Vitalba Ruggieri, Simona Laurino, Francesco La Rocca, Elena Amendola, Cinzia Lapadula, Debora Compare, Gerardo Nardone, Pellegrino Musto, Mario De Felice, Geppino Falco, Pietro Zoppoli
Software Mentions: 12
Published: over 5 years ago

10.3389/fcvm.2021.624714

Identification of Potential Biomarkers and Immune Infiltration Characteristics in Idiopathic Pulmonary Arterial Hypertension Using Bioinformatics Analysis
Cited by: 21
Author(s): Haowei Zeng, Xiaoqin Liu, Yushun Zhang
Software Mentions: 11
Published: almost 4 years ago

10.1186/s12859-020-03846-2

ARPIR: automatic RNA-Seq pipelines with interactive report
Cited by: 10
Author(s): Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini, Maria Paola Martelli
Software Mentions: 11
Published: about 4 years ago

10.1111/jcmm.15615

Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme
Cited by: 15
Author(s): Lan Jiang, Min Zhong, Tianbing Chen, Xiaolong Zhu, Hui Yang, Kun Lv
Software Mentions: 11
Published: over 4 years ago

10.1186/s12859-016-1125-3

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis
Cited by: 3
Author(s): Nathan James Allen Cormier, Tyler Kolisnik, Mark Bieda
Software Mentions: 10
Published: over 8 years ago

10.1186/s12920-020-00754-5

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Cited by: 15
Author(s): Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
Software Mentions: 10
Published: over 4 years ago

10.1186/s13041-020-00681-7

Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer’s disease
Cited by: 22
Author(s): Karissa Barthelson, Stephen Pederson, Morgan Newman, Michael Lardelli
Software Mentions: 9
Published: about 4 years ago

10.3389/fendo.2021.538364

Prognostic Alternative mRNA Splicing in Adrenocortical Carcinoma
Cited by: 4
Author(s): Weiwei Liang, Fangfang Sun
Software Mentions: 9
Published: almost 4 years ago

10.3389/fphar.2021.621359

Compound Dihuang Granule Inhibits Nigrostriatal Pathway Apoptosis in Parkinson’s Disease by Suppressing the JNK/AP-1 Pathway
Cited by: 8
Author(s): Li Wang, Yufang Yang, Long Chen, Zhu-qing He, Dian-yong Bi, Lei Zhang, Yuanfu Xu, Jiancheng He
Software Mentions: 9
Published: over 3 years ago

10.12688/f1000research.18236.1

BioHackathon 2015: Semantics of data for life sciences and reproducible research
Cited by: 5
Author(s): Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Seiichiro Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven Bolleman, Evan Bolton, Raoul J. P. Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, K. Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández‐Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yukiko Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Toshio Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosiñach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Miguel Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12859-020-03703-2

SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o
Cited by: 25
Author(s): Fernando Puente-Sánchez, Natalia García-García, Javier Tamames
Software Mentions: 9
Published: over 4 years ago

10.1128/mSystems.00493-20

Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses
Cited by: 3
Author(s): John L. Chodkowski, Ashley Shade
Software Mentions: 9
Published: about 4 years ago

10.15252/msb.20177862

Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases
Cited by: 53
Author(s): Daniela Michlmayr, Theodore R. Pak, Adeeb Rahman, El ad David Amir, Eun Young Kim, Seunghee Kim‐Schulze, Maria Suprun, Michael G. Stewart, Guajira P. Thomas, Ángel Balmaseda, Li Wang, Jun Zhu, Mayte Suárez‐Fariñas, Steven M. Wolinsky, Andrew Kasarskis, Eva Harris
Software Mentions: 9
Published: over 6 years ago

10.3390/cancers11101606

A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning
Cited by: 12
Author(s): Johannes A Vey, Lorenz A. Kapsner, Maximilian Fuchs, Philipp Unberath, Giulia Veronesi, Meik Kunz
Software Mentions: 8
Published: about 5 years ago

10.18632/oncotarget.13467

Effects of <i>Abies sibirica</i> terpenes on cancer- and aging-associated pathways in human cells
Cited by: 9
Author(s): Anna V. Kudryavtseva, George S. Krasnov, Anastasiya V. Lipatova, B. Ya. Alekseev, Faniya Maganova, Mikhail Shaposhnikov, Maria S. Fedorova, Anastasiya V. Snezhkina, Alexey Moskalev
Software Mentions: 8
Published: about 8 years ago

10.3390/ijms22073618

Transcriptome Analyses of Myometrium from Fibroid Patients Reveals Phenotypic Differences Compared to Non-Diseased Myometrium
Cited by: 9
Author(s): Emmanuel N. Paul, Gregory W. Burns, Tyler J. Carpenter, Joshua Grey, Asgerally T. Fazleabas, Jose M. Teixeira
Software Mentions: 8
Published: over 3 years ago

10.18632/oncotarget.24506

Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data
Cited by: 13
Author(s): Mahmoud Ahmed, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang, Deok Ryong Kim
Software Mentions: 8
Published: almost 7 years ago

10.3389/fonc.2021.709796

Helicobacter pylori Infection–Related Long Non-Coding RNA Signatures Predict the Prognostic Status for Gastric Cancer Patients
Cited by: 7
Author(s): Zhuoyuan Xin, Luping Zhang, Mingqing Liu, Yachen Wang, Yingli Zhang, Wenjie Zhao, Yongxiao Sun, Lei Shi, Na Xu, Nan Zhang, Hong Xu
Software Mentions: 7
Published: over 3 years ago

10.3389/fphar.2020.00076

Efficacy of Chinese Herbal Formula Sini Zuojin Decoction in Treating Gastroesophageal Reflux Disease: Clinical Evidence and Potential Mechanisms
Cited by: 10
Author(s): Shaowei Li, Mengfen Huang, Guojing Wu, Wei-Han Huang, Zhanhui Huang, Xiaoqian Yang, Jinming Ou, Qipeng Wei, Chengli Liu, YU Shaoyuan
Software Mentions: 7
Published: almost 5 years ago

10.1093/gigascience/giaa162

Lilikoi V2.0: a deep learning–enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data
Cited by: 10
Author(s): Xinying Fang, Yu Liu, Zhijie Ren, Yuheng Du, Qizhao Huang, Lana X. Garmire
Software Mentions: 7
Published: almost 4 years ago

10.3390/ijms21165923

Oxidant-Induced Alterations in the Adipocyte Transcriptome: Role of the Na,K-ATPase Oxidant Amplification Loop
Cited by: 7
Author(s): Komal Sodhi, James Denvir, Jiang Liu, Juan Sanabria, Yiliang Chen, Roy L. Silverstein, Zijian Xie, Nader G. Abraham, Joseph I. Shapiro
Software Mentions: 7
Published: over 4 years ago

10.1186/s10194-021-01285-9

Identification of disease- and headache-specific mediators and pathways in migraine using blood transcriptomic and metabolomic analysis
Cited by: 13
Author(s): Tímea Aczél, Tamás Körtési, József Kun, Péter Urbán, Witold Bauer, Róbert Herczeg, Robert Farkaš, K Kovács, Barna Vásárhelyi, Gellért Balázs Karvaly, Attila Gyenesei, Bernadett Tuka, János Tajti, László Vécsei, Kata Bölcskei, Zsuzsanna Helyes
Software Mentions: 7
Published: about 3 years ago

10.1038/s41419-020-2477-1

Deficiency in the autophagy modulator Dram1 exacerbates pyroptotic cell death of Mycobacteria-infected macrophages
Cited by: 22
Author(s): Rui Zhang, Mónica Varela, Gabriel Forn-Cuní, Vincenzo Torraca, Michiel van der Vaart, Annemarie H. Meijer
Software Mentions: 7
Published: over 4 years ago

10.3390/cells10071576

Transcriptomic Profiling of Femoral Veins in Deep Vein Thrombosis in a Porcine Model
Cited by: 7
Author(s): Leszek Gromadziński, Łukasz Paukszto, Agnieszka Skowrońska, Piotr Holak, Michał Smoliński, Elżbieta Łopieńska–Biernat, Ewa Lepiarczyk, Aleksandra Lipka, J Jastrzebski, Marta Majewska
Software Mentions: 7
Published: over 3 years ago

10.3390/cells10071690

Characterisation of Neurospheres-Derived Cells from Human Olfactory Epithelium
Cited by: 1
Author(s): E. A. Zelenova, Nikolay Kondratyev, Т. В. Лежейко, G. Yu. Tsarapkin, A. I. Kryukov, Alexander E Kishinevsky, A.S. Tovmasyan, Ekaterina Momotyuk, Э. Б. Дашинимаев, В. Е. Голимбет
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-020-70173-0

Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers
Cited by: 17
Author(s): Sofia Paraskevopoulou, Alice B. Dennis, Guntram Weithoff, Ralph Tiedemann
Software Mentions: 7
Published: over 4 years ago

10.1155/2021/8897313

Systematic Investigation of the Effect of Powerful Tianma Eucommia Capsule on Ischemic Stroke Using Network Pharmacology
Cited by: 4
Author(s): Pengcheng Feng, Guixia Li, Yuandong Huang, Jinhong Pei
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-021-07509-1

Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis
Cited by: 7
Author(s): Yang Dong, Morgan Newman, Stephen Pederson, Karissa Barthelson, Nhi Hin, Michael Lardelli
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0134011

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.
Cited by: 7
Author(s): Gabriela D. A. Guardia, Luís Ferreira Pires, Ricardo Zorzetto Nicoliello Vêncio, Kelen Cristina Ribeiro Malmegrim, Cléver Ricardo Guareis de Farias
Software Mentions: 6
Published: almost 10 years ago

10.1038/s41598-019-45714-x

Transcriptome Analysis of Long-lived Drosophila melanogaster E(z) Mutants Sheds Light on the Molecular Mechanisms of Longevity
Cited by: 30
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, Nadezhda Zemskaya, Liubov Koval, Eugenia V. Schegoleva, Zulfiya G. Guvatova, George S. Krasnov, Ilya Solovev, Maksim A. Sheptyakov, Alex Zhavoronkov, Anna V. Kudryavtseva
Software Mentions: 6
Published: over 5 years ago

10.1155/2020/5786053

Integrating Network Pharmacology with Molecular Docking to Unravel the Active Compounds and Potential Mechanism of Simiao Pill Treating Rheumatoid Arthritis
Cited by: 16
Author(s): Mengshi Tang, Xiaoqing Xie, Pan Yi, Jin Seok Kang, Jiafen Liao, Wenqun Li, Fen Li
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-016-2483-y

Influenza H3N2 infection of the collaborative cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice
Cited by: 43
Author(s): Sarah R. Leist, Carolin Pilzner, Judith M. A. van den Brand, Leonie Dengler, Robert Geffers, Thijs Kuiken, Rudi Balling, Heike Kollmus, Klaus Schughart
Software Mentions: 6
Published: almost 9 years ago

10.1186/s41065-020-00169-3

Identification of differentially expressed genes, signaling pathways and immune infiltration in rheumatoid arthritis by integrated bioinformatics analysis
Cited by: 8
Author(s): Yanzhi Ge, Li Zhou, Zuxiang Chen, Yingying Mao, Ting Li, Peijian Tong
Software Mentions: 6
Published: almost 4 years ago

10.18632/aging.203448

Effects of Siberian fir terpenes extract Abisil on antioxidant activity, autophagy, transcriptome and proteome of human fibroblasts
Cited by: 1
Author(s): Anastasiya V. Lipatova, George S. Krasnov, Pavel Vorobyov, Pavel Melnikov, Olga N. Alekseeva, Yulia S. Vershinina, Alexander G. Brzhozovskiy, Daria Goliusova, Faniya Maganova, Natalia F. Zakirova, Anna V. Kudryavtseva, Alexey Moskalev
Software Mentions: 6
Published: over 3 years ago

10.1038/srep09549

Difference in microRNA expression and editing profile of lung tissues from different pig breeds related to immune responses to HP-PRRSV
Cited by: 33
Author(s): Jia Li, Zhisheng Chen, Junlong Zhao, Liurong Fang, Rui Fang, Jiang Xiao, Xing Chen, Ao Zhou, Yingyin Zhang, Liming Ren, Xiaoxiang Hu, Yaofeng Zhao, Shujun Zhang, Ning Li
Software Mentions: 6
Published: over 9 years ago

10.1038/s41420-021-00547-4

Impairment of neuronal mitochondrial function by l-DOPA in the absence of oxygen-dependent auto-oxidation and oxidative cell damage
Cited by: 5
Author(s): Philipp Hörmann, Sylvie Delcambre, Jasmin E. Hanke, Robert Geffers, Marcel Leist, Karsten Hiller
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-81103-z

Cysteine: an overlooked energy and carbon source
Cited by: 19
Author(s): Luise Göbbels, Anja Poehlein, Albert Dumnitch, Richard Egelkamp, Cathrin Kröger, Johanna Haerdter, Thomas Hackl, Artur Feld, H. Weller, Rolf Daniel, Wolfgang R. Streit, Marie Charlotte Schoelmerich
Software Mentions: 6
Published: almost 4 years ago

10.1111/jcmm.14938

A risk signature with four autophagy‐related genes for predicting survival of glioblastoma multiforme
Cited by: 47
Author(s): Yulin Wang, Wenjin Zhao, Zhe Xiao, Gefei Guan, Xin Liu, Minghua Zhuang
Software Mentions: 6
Published: almost 5 years ago

10.3389/fvets.2019.00214

Transcriptomic Profiling of Duodenal Epithelium Reveals Temporally Dynamic Impacts of Direct Duodenal Starch-Infusion During Dry Period of Dairy Cattle
Cited by: 2
Author(s): Congjun Li, Shudai Lin, María Jose Ranilla-García, VI Ransom L. Baldwin
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-018-0449-9

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool
Cited by: 113
Author(s): Jo De Vrieze, Ameet J. Pinto, William T. Sloan, Umer Zeeshan Ijaz
Software Mentions: 6
Published: over 6 years ago

10.3390/biom9010012

Integrated Transcriptome Analysis Reveals Plant Hormones Jasmonic Acid and Salicylic Acid Coordinate Growth and Defense Responses upon Fungal Infection in Poplar
Cited by: 63
Author(s): Jie Luo, Wenxiu Xia, Pei Cao, Zheng’ang Xiao, Yan Zhang, Meifeng Liu, Chengjun Zhan, Nian Wang
Software Mentions: 6
Published: almost 6 years ago

10.1016/j.isci.2021.103092

The gut microbiota instructs the hepatic endothelial cell transcriptome
Cited by: 11
Author(s): Henning Formes, Joana P. Bernardes, Amrit Mann, Franziska Bayer, Giulia Pontarollo, Klytaimnistra Kiouptsi, Katrin Schäfer, Sebastian Attig, Teodora Nikolova, Thomas G. Hofmann, Jörn M. Schattenberg, Hristo Todorov, Susanne Gerber, Philip Rosenstiel, Tobias Bopp, Felix Sommer, Carsten Reinhardt
Software Mentions: 5
Published: about 3 years ago

10.3390/genes11121430

Distinct Myocardial Transcriptomic Profiles of Cardiomyopathies Stratified by the Mutant Genes
Cited by: 7
Author(s): Katharina Sielemann, Zaher Elbeck, Anna Gärtner, Hendrik Milting, Caroline Stanasiuk, Henrik Fox, Lech Paluszkiewicz, Jens Tiesmeier, Stefan Wlost, Jan Gummert, Stefan P. Albaum, Janik Sielemann, Ralph Knöll
Software Mentions: 5
Published: about 4 years ago

10.3390/pathogens9120997

A Paradox in Bacterial Pathogenesis: Activation of the Local Macrophage Inflammasome Is Required for Virulence of Streptococcus uberis
Cited by: 10
Author(s): Nathan Archer, Sharon A. Egan, Tracey J. Coffey, Richard D. Emes, Maria Filippa Addis, Philip N. Ward, Adam Blanchard, James A. Leigh
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-019-41452-2

Using Bacterial Transcriptomics to Investigate Targets of Host-Bacterial Interactions in Caenorhabditis elegans
Cited by: 21
Author(s): Jason P. Chan, Justin Wright, Hoi Tong Wong, Anastasia Ardasheva, Jamey T. Brumbaugh, Christopher J. McLimans, Regina Lamendella
Software Mentions: 5
Published: over 5 years ago

10.18632/aging.202446

A novel five-lncRNA signature panel improves high-risk survival prediction in patients with cholangiocarcinoma
Cited by: 11
Author(s): Xiaozai Xie, Yi Wang, Sina Zhang, Jialiang Li, Zhengping Yu, Xiwei Ding, Long‐Yun Ye, Peirong Gong, Qing Zhu, Junjian Li, Zi-Yan Chen, Xinfei Yao, Zhifeng Du, Qian Zeng, Hanbin Chen, Zhen Yang, Gang Chen
Software Mentions: 5
Published: almost 4 years ago

10.1007/s11103-020-01041-8

Integrative transcriptomics reveals genotypic impact on sugar beet storability
Cited by: 7
Author(s): Silvia Madritsch, Svenja Bomers, Alexandra Posekany, Agnes Burg, Rebekka Birke, Florian Emerstorfer, Reinhard Turetschek, Sandra Otte, Herbert Eigner, Eva Maria Sehr
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-018-5411-5

Bacterial and viral pathogen-associated molecular patterns induce divergent early transcriptomic landscapes in a bovine macrophage cell line
Cited by: 6
Author(s): Felix N. Toka, Kiera Dunaway, Felicia Smaltz, Lidia Szulc-Dąbrowska, Jenny Drnevich, Matylda Barbara Mielcarska, Magdalena Bossowska-Nowicka, Matthias Schweizer
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13068-018-1215-8

The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973
Cited by: 42
Author(s): Xiaoming Tan, Songjun Hou, Kuo Song, Jens Georg, Stephan Klähn, Xuefeng Lü, Wolfgang R. Hess
Software Mentions: 5
Published: over 6 years ago

10.1038/s41392-020-00457-4

Longitudinal transcriptome analyses show robust T cell immunity during recovery from COVID-19
Cited by: 55
Author(s): Hong Zheng, Min Xu, Cui Xian Yang, Ren Rong Tian, Mi Zhang, Jian Jian Li, Xi Cheng Wang, Zhao Ding, Gui Mei Li, Xiaolu Li, Yu He, Xing-qi Dong, Yong Yao, Yong Zheng
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-017-14650-z

Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females
Cited by: 18
Author(s): Louise Pease, Peter Clegg, Carole J. Proctor, Daryl P. Shanley, Simon Cockell, Mandy J. Peffers
Software Mentions: 5
Published: about 7 years ago

10.1186/s40170-020-00216-7

Fine-tuning the metabolic rewiring and adaptation of translational machinery during an epithelial-mesenchymal transition in breast cancer cells
Cited by: 3
Author(s): Tamara Fernández-Calero, Marcos Davyt, Karen Perelmuter, Cora Chalar, Giovana Bavia Bampi, Helena Persson, Juan Pablo Tosar, Völundur Hafstað, Hugo Naya, Carlos Rovira, Mariela Bollati-Fogolín, Ricardo Ehrlich, Gilles Flouriot, Zoya Ignatova, Mónica Marı́n
Software Mentions: 5
Published: over 4 years ago

10.3389/fnins.2016.00071

BBBomics-Human Blood Brain Barrier Transcriptomics Hub
Cited by: 28
Author(s): Krishna R. Kalari, Kevin J. Thompson, Asha Nair, Xiaojia Tang, Matthew A. Bockol, Navya Jhawar, Suresh Kumar Swaminathan, Val J. Lowe, Karunya K. Kandimalla
Software Mentions: 5
Published: almost 9 years ago

10.3390/cells8091092

Expression of FGF8, FGF18, and FGFR4 in Gastroesophageal Adenocarcinomas
Cited by: 13
Author(s): Gerd Jomrich, Xenia Hudec, Felix Harpain, Daniel Winkler, Gerald Timelthaler, Thomas Mohr, Brigitte Marian, Sebastian F. Schoppmann
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2925-6

Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi
Cited by: 74
Author(s): S. Matić, Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Greice Amaral Carneiro, Ilenia Siciliano, Giampiero Valè, M. L. Gullino, D. Spadaro
Software Mentions: 4
Published: over 8 years ago

10.7717/peerj.6848

Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish (<i>Danio rerio</i>)
Cited by: 5
Author(s): Matthew Tuttle, Mark Dalman, Qin Liu, Richard L. Londraville
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-4168-6

TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms
Cited by: 7
Author(s): Daniela Beißer, Nadine Graupner, Lars Großmann, Henning Timm, Jens Boenigk, Sven Rahmann
Software Mentions: 4
Published: about 7 years ago

10.1186/s13287-020-02111-w

Radiation-induced toxicity in rectal epithelial stem cell contributes to acute radiation injury in rectum
Cited by: 11
Author(s): Felipe Rodriguez-Tirado, Payel Bhanja, Eduardo Castro-Nallar, Ximena Diaz Olea, Catalina Salamanca, Subhrajit Saha
Software Mentions: 4
Published: almost 4 years ago

10.3390/genes11090983

MicroRNAs Modulate the Pathogenesis of Alzheimer’s Disease: An In Silico Analysis in the Human Brain
Cited by: 12
Author(s): Agnese Gugliandolo, Luigi Chiricosta, Virginia Boccardi, Patrizia Mecocci, Placido Bramantı, Emanuela Mazzon
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0148818

Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis
Cited by: 14
Author(s): Wonjun Lee, Sang Cheol Kim, Jong Ho Yoon, Sang Jun Yoon, Jong-Tae Lim, You Sun Kim, Sung Won Kwon, Jeong Hill Park
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0232189

Investigating the epithelial barrier and immune signatures in the pathogenesis of equine insect bite hypersensitivity
Cited by: 10
Author(s): Iva Cvitaš, Simone Oberhänsli, Tosso Leeb, Martina Dettwiler, Eliane J. Müller, Rémy Bruggman, Eliane Marti
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers12061535

TP53 Status, Patient Sex, and the Immune Response as Determinants of Lung Cancer Patient Survival
Cited by: 21
Author(s): Donald Freudenstein, Cassandra Litchfield, Franco Caramia, Gavin Wright, Benjamin Solomon, David Ball, Simon P. Keam, Paul J. Neeson, Ygal Haupt, Sue Haupt
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers13102306

Evidence of Cooperation between Hippo Pathway and RAS Mutation in Thyroid Carcinomas
Cited by: 3
Author(s): Thaise Nayane Ribeiro Carneiro, Larissa Valdemarin Bim, Vanessa Candiotti Buzatto, Vanessa Galdeno, Paula Fontes Asprino, Eunjung Alice Lee, Pedro A. F. Galante, Janete M. Cerutti
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers12092433

Oncogenic Orphan Nuclear Receptor NR4A3 Interacts and Cooperates with MYB in Acinic Cell Carcinoma
Cited by: 11
Author(s): David Y. Lee, Kathryn J. Brayer, Yoshitsugu Mitani, Eric A Burns, Pulivarthi H. Rao, Diana Bell, Michelle D. Williams, Renata Ferrarotto, Kristen B. Pytynia, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers13163954

Prognostication of Primary Tumor Location in Early-Stage Nodal Diffuse Large B-Cell Lymphoma: An Analysis of the SEER Database
Cited by: 2
Author(s): Yi Xia, Silan Huang, Yu Wang, Dexin Lei, Yanlou Wang, Hang Yang, Yan Gao, Panpan Li
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-91534-3

A defective interleukin-17 receptor A1 causes weight loss and intestinal metabolism-related gene downregulation in Japanese medaka, Oryzias latipes
Cited by: 4
Author(s): Yo Okamura, Hiroshi Miyanishi, Masato Kinoshita, Tomoya Kono, Masahiro Sakai, Jun-ichi Hikima
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2019.00149

The Neuronal Overexpression of Gclc in Drosophila melanogaster Induces Life Extension With Longevity-Associated Transcriptomic Changes in the Thorax
Cited by: 8
Author(s): Alexey Moskalev, Zulfiya G. Guvatova, Mikhail Shaposhnikov, Ekaterina Lashmanova, Ekaterina Proshkina, Liubov Koval, Alex Zhavoronkov, George S. Krasnov, Anna V. Kudryavtseva
Software Mentions: 4
Published: almost 6 years ago

10.3390/cells7120275

Activation of Polyamine Catabolism by N1,N11-Diethylnorspermine in Hepatic HepaRG Cells Induces Dedifferentiation and Mesenchymal-Like Phenotype
Cited by: 12
Author(s): О. Н. Иванова, Anastasiya V. Snezhkina, George S. Krasnov, Vladimir T. Valuev-Elliston, Olga A. Khomich, Alexey Khomutov, Tuomo A. Keinänen, Leena Alhonen, Birke Bartosch, Anna V. Kudryavtseva, Sergey N. Kochetkov, Alexander Ivanov
Software Mentions: 4
Published: about 6 years ago

10.1186/s13018-021-02552-w

Study on the potential active components and molecular mechanism of Xiao Huoluo Pills in the treatment of cartilage degeneration of knee osteoarthritis based on bioinformatics analysis and molecular docking technology
Cited by: 13
Author(s): Weijian Chen, Tianye Lin, Qi He, Peng Yang, Gangyu Zhang, Fayi Huang, Zihao Wang, Hao Peng, Baolin Li, Liqing Du, Haibin Wang
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2018.03137

The Schistosomiasis SpleenOME: Unveiling the Proteomic Landscape of Splenomegaly Using Label-Free Mass Spectrometry
Cited by: 6
Author(s): Miguel Cosenza-Contreras, Renata Alves de Oliveira e Castro, Bruno Mattei, Jonatan Marques Campos, Gustavo Gonçalves Silva, Nívia Carolina Nogueira de Paiva, Rodrigo Dian de Oliveira Aguiar-Soares, Cláudia Martins Carneiro, Luís Afonso, William Castro-Borges
Software Mentions: 4
Published: almost 6 years ago

10.18632/oncotarget.16118

Whole-genome expression analyses of type 2 diabetes in human skin reveal altered immune function and burden of infection
Cited by: 23
Author(s): Wang Chun, Xiaopan Chen, Jing Shu, Chun-Ting Lee
Software Mentions: 4
Published: almost 8 years ago

10.3389/fonc.2020.574977

Serum RNA Profiling in the 10-Years Period Prior to Diagnosis of Testicular Germ Cell Tumor
Cited by: 6
Author(s): Joshua Burton, Sinan Uğur Umu, Hilde Langseth, Tom Grotmol, Tom Kristian Grimsrud, Trine B. Haugen, Trine B. Rounge
Software Mentions: 4
Published: about 4 years ago

10.18632/oncotarget.14286

Comprehensive tissue-specific gene set enrichment analysis and transcription factor analysis of breast cancer by integrating 14 gene expression datasets
Cited by: 23
Author(s): Wen‐Xing Li, Kan He, Ling Tang, Shao‐Xing Dai, Gong‐Hua Li, Wen Lv, Yicheng Guo, Sanqi An, Guoying Wu, Dahai Liu, Jing‐Fei Huang
Software Mentions: 4
Published: about 8 years ago

10.3389/fnmol.2018.00375

L-Lactate Regulates the Expression of Synaptic Plasticity and Neuroprotection Genes in Cortical Neurons: A Transcriptome Analysis
Cited by: 57
Author(s): Michael B. Margineanu, Hanan Mahmood, Hubert Fiumelli, Pierre J. Magistretti
Software Mentions: 4
Published: about 6 years ago

10.3389/fmolb.2021.696072

Decreased Expression of PACSIN1 in Brain Glioma Samples Predicts Poor Prognosis
Cited by: 6
Author(s): Zimu Zhou, Zhiyuan Jia, Xi-an Fu, Rui Ma, Ren Yuting, Yuan Wang, Tao Wen, Ming Ma, Yinlong Liu, Enfang Shan
Software Mentions: 4
Published: over 3 years ago

10.3390/jcm8050639

The Role of MicroRNAs in the Regulation of Gastric Cancer Stem Cells: A Meta-Analysis of the Current Status
Cited by: 22
Author(s): Vitalba Ruggieri, Sabino Russi, Pietro Zoppoli, Francesco La Rocca, Tiziana Angrisano, Geppino Falco, Giovanni Calice, Simona Laurino
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22052481

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species
Cited by: 5
Author(s): Jodi B Callwood, Kalpalatha Melmaiee, Krishnanand P. Kulkarni, Amaranatha R. Vennapusa, Diarra Aicha, Michael J. Moore, Nicholi Vorsa, Purushothaman Natarajan, Umesh K. Reddy, Sathya Elavarthi
Software Mentions: 4
Published: almost 4 years ago

10.3390/metabo11070414

Analysis of Host Jejunum Transcriptome and Associated Microbial Community Structure Variation in Young Calves with Feed-Induced Acidosis
Cited by: 3
Author(s): Gaowa Naren, Wenli Li, S.L. Gelsinger, Brianna Murphy, Shengli Li
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2021.684664

Basidiomycetes Are Particularly Sensitive to Bacterial Volatile Compounds: Mechanistic Insight Into the Case Study of Pseudomonas protegens Volatilome Against Heterobasidion abietinum
Cited by: 12
Author(s): Maria Isabella Prigigallo, A. De Stradis, Abhishek Anand, Francesco Mannerucci, Floriane L’Haridon, Laure Weisskopf, Giovanni Bubici
Software Mentions: 3
Published: over 3 years ago

10.18632/aging.102300

COL6A6 interacted with P4HA3 to suppress the growth and metastasis of pituitary adenoma via blocking PI3K-Akt pathway
Cited by: 26
Author(s): Ruiqing Long, Zhuohui Liu, Jinghui Li, Hualin Yu
Software Mentions: 3
Published: about 5 years ago

10.3390/antibiotics9060343

Studying the Gene Expression of Penicillium rubens Under the Effect of Eight Essential Oils
Cited by: 2
Author(s): Zuzana Kisová, Andrea Šoltýsová, Mária Bučková, Gábor Beke, Andrea Puškárová, Domenico Pangallo
Software Mentions: 3
Published: over 4 years ago

10.1186/s12906-021-03215-3

A network pharmacology perspective for deciphering potential mechanisms of action of Solanum nigrum L. in bladder cancer
Cited by: 17
Author(s): Yun Dong, Lin Hao, Kun Fang, Xing Han, Hui Yu, Jianjun Zhang, Longjun Cai, Tao Fan, Wen-da Zhang, Kun Pang, Weiming Ma, Xitao Wang, Conghui Han
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-015-1644-8

Non-thermal plasma treatment altered gene expression profiling in non-small-cell lung cancer A549 cells
Cited by: 49
Author(s): Jue Hou, Jie Ma, K.N. Yu, Wei Li, Cheng Cheng, Lingzhi Bao, Wei Han
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-019-6233-9

Transcriptomic analyses suggest a dominant role of insulin in the coordinated control of energy metabolism and ureagenesis in goat liver
Cited by: 5
Author(s): Zhongyan Lu, Zhihui Xu, Zongzhuan Shen, Hong Shen, Jörg R. Aschenbach
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-016-3356-0

The influence of pro-longevity gene Gclc overexpression on the age-dependent changes in Drosophila transcriptome and biological functions
Cited by: 17
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, Ekaterina Proshkina, А. С. Белый, Alexander Fedintsev, Svetlana Zhikrivetskaya, Zulfiya G. Guvatova, А. Ф. Садритдинова, А. В. Снежкина, George S. Krasnov, Anna V. Kudryavtseva
Software Mentions: 3
Published: about 8 years ago

10.1155/2021/5089371

CXCL1 Clone Evolution Induced by the HDAC Inhibitor Belinostat Might Be a Favorable Prognostic Indicator in Triple-Negative Breast Cancer
Cited by: 4
Author(s): Xinle Han, Jun Du, Yadan Zheng, Jingbo Dai, Su-Wen Lin, Bingyue Zhang, Fubo Zhong, Zhe-Guang Lin, Shuhan Jiang, Wei Wei, Zhengyu Fang
Software Mentions: 3
Published: over 3 years ago

10.3390/molecules25163609

Involvement of Differentially Expressed microRNAs in the PEGylated Liposome Encapsulated 188Rhenium-Mediated Suppression of Orthotopic Hypopharyngeal Tumor
Cited by: 5
Author(s): Bei Lin, Shen-Ying Wan, Lin Ma, Cheng-Yen Chang, Ting-Wen Chen, Muh‐Hwa Yang, Yi Jang Lee
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pntd.0005461

Modulation of the immune response by Fonsecaea pedrosoi morphotypes in the course of experimental chromoblastomycosis and their role on inflammatory response chronicity
Cited by: 26
Author(s): Isaque Medeiros Siqueira, Raffael Júnio Araújo de Castro, Luiza Chaves de Miranda Leonhardt, Márcio Sousa Jerônimo, A.J.M. Soares, Tainá Raiol, Christiane Nishibe, Nalvo F. Almeida, Aldo Henrique Tavares, Christian Hoffmann, Anamélia Lorenzetti Bocca
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0207799

Subgrouping breast cancer patients based on immune evasion mechanisms unravels a high involvement of transforming growth factor-beta and decoy receptor 3
Cited by: 19
Author(s): Mayassa J. Bou‐Dargham, Yuhang Liu, Qing‐Xiang Amy Sang, Jinfeng Zhang
Software Mentions: 3
Published: about 6 years ago

10.3389/fcvm.2021.655869

AMPA-Type Glutamate Receptors Associated With Vascular Smooth Muscle Cell Subpopulations in Atherosclerosis and Vascular Injury
Cited by: 5
Author(s): Alessandro L Gallina, Urszula Rykaczewska, Robert Wirka, April S. Caravaca, Vladimir S. Shavva, Mohamad Youness, Glykeria Karadimou, Mariette Lengquist, Anton Razuvaev, Gabrielle Paulsson-Berne, Thomas Quertermous, Anton Gisterå, Stephen Malin, Laura Tarnawski, Ljubica Matic, Peder S. Olofsson
Software Mentions: 3
Published: over 3 years ago

10.3389/fcell.2020.00807

The Pathogenic Effects of Fusobacterium nucleatum on the Proliferation, Osteogenic Differentiation, and Transcriptome of Osteoblasts
Cited by: 8
Author(s): Hui Gao, Tianyong Sun, Fanghong Yang, Jiakan Yuan, Mei Yang, Wenyan Kang, Di Tang, Jun Zhang, Qiang Feng
Software Mentions: 3
Published: over 4 years ago

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