bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-61420-5

Eosinophil accumulation in postnatal lung is specific to the primary septation phase of development
Cited by: 17
Author(s): Lucas F. Loffredo, Mackenzie E. Coden, Brian M. Jeong, Matthew T. Walker, Kishore R. Anekalla, Ton C. Doan, Raul I. Rodriguez, M.J. Browning, Ki-Won Nam, James J. Lee, Hiam Abdala‐Valencia, Sergejs Berdnikovs
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-61857-8

De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance
Cited by: 18
Author(s): Soumya Shree Nayak, Seema Pradhan, Dinabandhu Sahoo, Ajay Parida
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-63263-6

Circulating MicroRNA Profiling in Non-ST Elevated Coronary Artery Syndrome Highlights Genomic Associations with Serial Platelet Reactivity Measurements
Cited by: 14
Author(s): Kristian C. Becker, Lydia Coulter Kwee, Megan L. Neely, Elizabeth Grass, Joseph A. Jakubowski, Keith Fox, Harvey D. White, Simon Gregory, Paul A. Gurbel, Leonardo de Pinto Carvalho, Richard C. Becker, E. Magnus Ohman, Matthew T. Roe, Svati H. Shah, Mark Y. Chan
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-62286-3

Fabrication of Perfusable Vascular Channels and Capillaries in 3D Liver-like Tissue
Cited by: 20
Author(s): Nobuhito Mori, Yuka Akagi, Yukiko Imai, Yoichiro Takayama, Yasuyuki S. Kida
Software Mentions: 3
Published: over 6 years ago

10.7150/thno.50051

Adenylosuccinate lyase is oncogenic in colorectal cancer by causing mitochondrial dysfunction and independent activation of NRF2 and mTOR-MYC-axis
Cited by: 17
Author(s): Stephanie Taha‐Mehlitz, Gaia Bianco, Mairene Coto‐Llerena, Venkatesh Kancherla, Glenn R. Bantug, John Gallon, Caner Ercan, Federica Panebianco, Serenella Eppenberger‐Castori, M. Strauß, Sebastian M. Staubli, Martin Bolli, Ralph Peterli, Matthias S. Matter, Luigi Terracciano, Markus von Flüe, Charlotte K.Y. Ng, Savas D. Soysal, Otto Kollmar, Salvatore Piscuoglio
Software Mentions: 3
Published: almost 6 years ago

10.7150/thno.53737

Intratumor heterogeneity of breast cancer detected by epialleles shows association with hypoxic microenvironment
Cited by: 5
Author(s): Yihan Wang, Yan Zhang, Yan Huang, Chuangeng Chen, Xingda Zhang, Ying Xing, Yue Gu, Mengyan Zhang, Li Cai, Shouping Xu, Baoqing Sun
Software Mentions: 3
Published: almost 6 years ago

10.7150/thno.54999

Progressive stretch enhances growth and maturation of 3D stem-cell-derived myocardium
Cited by: 28
Author(s): Kun Lü, Thomas Seidel, Xiaochun Cao-Ehlker, Tatjana Dorn, Aarif M.N. Batcha, Christine Schneider, María Eugenia Aubet Semmler, Tilmann Volk, Alessandra Moretti, Andreas Dendorfer, Roland Tomasi
Software Mentions: 3
Published: almost 6 years ago

10.7150/thno.57237

The metabesity factor HMG20A potentiates astrocyte survival and reactive astrogliosis preserving neuronal integrity
Cited by: 14
Author(s): Petra I. Lorenzo, Eugenia Martin Vázquez, Livia López-Noriega, Esther Fuente-Martín, José Manuel Mellado-Gil, Jaime M. Franco, Nadia Cobo-Vuilleumier, José A. Guerrero-Martínez, Silvana Y. Romero-Zerbo, Jesús A Perez-Cabello, Sabrina Rivero, Antonio Campos‐Caro, Christian Claude Lachaud, Alejandra Crespo Barreda, Manuel Aguilar‐Diosdado, Esther Fuentes, Aléjandro Martín-Montalvo, Manuel Álvarez‐Dolado, Franz Martı́n, Gemma Rojo‐Martínez, David Pozo, Francisco Javier Bermúdez‐Silva, Valentine Comaills, José Carlos Castañeda Reyes, Benoît Gauthier
Software Mentions: 3
Published: almost 6 years ago

10.3390/toxins9060184

Screening of Deoxynivalenol Producing Strains and Elucidation of Possible Toxigenic Molecular Mechanism
Cited by: 13
Author(s): Xizhong Zheng, Xiaoli Zhang, Lina Zhao, Maurice Tibiru Apaliya, Qiya Yang, Wei Sun, Xiaoyun Zhang, Hongyin Zhang
Software Mentions: 3
Published: over 9 years ago

10.3390/toxins12050290

AFB1 Induced Transcriptional Regulation Related to Apoptosis and Lipid Metabolism in Liver of Chicken
Cited by: 27
Author(s): Xueqin Liu, Suchismita Mishra, Tao Wang, Zhongxian Xu, Xiaoling Zhao, Yan Wang, Huadong Yin, Xiaolan Fan, Bo Zeng, Mingyao Yang, Dapeng Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Qing Zhu, Feng Chen, Diyan Li
Software Mentions: 3
Published: over 6 years ago

10.1186/s40035-018-0135-7

GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis
Cited by: 11
Author(s): William R. Swindell, Krzysztof Bojanowski, Mark S. Kindy, R.M.W. Chau, Dorothy Ko
Software Mentions: 3
Published: almost 8 years ago

10.1186/s40035-021-00249-y

Several miRNAs derived from serum extracellular vesicles are potential biomarkers for early diagnosis and progression of Parkinson’s disease
Cited by: 31
Author(s): Shulei He, Lu Huang, Ci Shao, Tiejian Nie, Xia Li, Bozhou Cui, Fangfang Lu, Lin Zhu, Bolin Chen, Qian Yang
Software Mentions: 3
Published: over 5 years ago

10.1038/tp.2016.229

Transcriptome sequencing of the choroid plexus in schizophrenia
Cited by: 42
Author(s): S Kim, Young Sun Hwang, Doheon Lee, Maree J. Webster
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41398-018-0355-8

Cell type-specific gene expression patterns associated with posttraumatic stress disorder in World Trade Center responders
Cited by: 79
Author(s): Pei‐Fen Kuan, Xiaohua Yang, Sean Clouston, Ruwei Xu, Roman Kotov, Monika A. Waszczuk, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41398-019-0610-7

Protein expression of prenyltransferase subunits in postmortem schizophrenia dorsolateral prefrontal cortex
Cited by: 8
Author(s): Anita Pinner, Toni Mueller, Khaled Alganem, Robert E. McCullumsmith, James H. Meador‐Woodruff
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41398-021-01435-2

Convergent and distributed effects of the 3q29 deletion on the human neural transcriptome
Cited by: 8
Author(s): Esra Sefik, Ryan H. Purcell, q Emory, Elaine F. Walker, Gary J. Bassell, Jennifer G. Mullé
Software Mentions: 3
Published: over 5 years ago

10.1186/s13063-021-05442-y

Does intervention with GLP-1 receptor agonist semaglutide modulate perception of sweet taste in women with obesity: study protocol of a randomized, single-blinded, placebo-controlled clinical trial
Cited by: 3
Author(s): Mojca Jensterle, Simona Ferjan, Tadej Battelino, Jernej Kovač, Saba Battelino, Dušan Šuput, Andrej Vovk, Andrej Janež
Software Mentions: 3
Published: over 5 years ago

10.1101/2021.01.19.427194

BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2
Cited by: 7
Author(s): Ruilin Tian, Avi J. Samelson, Veronica V. Rezelj, Merissa Chen, Gokul N. Ramadoss, Xiaoyan Guo, Alice Mac Kain, Quang Tran, Shion A. Lim, Irene Lui, James K. Nuñez, Sarah J. Rockwood, Na Liu, Jared Carlson-Stevermer, Jennifer Oki, Travis J. Maures, Kevin Holden, Jonathan S. Weissman, James A. Wells, Bruce R. Conklin, Marco Vignuzzi, Martin Kampmann
Software Mentions: 3
Published: almost 6 years ago

10.1101/2021.01.19.426885

Rapid protection from COVID-19 in nonhuman primates vaccinated intramuscularly but not intranasally with a single dose of a recombinant vaccine
Cited by: 14
Author(s): Wakako Furuyama, Kyle Shifflett, Amanda N Pinksi, Amanda Griffin, Friederike Feldmann, Atsushi Okumura, Tylisha Gourdine, Allen Jankeel, Jamie Lovaglio, Patrick W. Hanley, Tina Thomas, Chad S. Clancy, Ilhem Messaoudi, Andrea Marzi
Software Mentions: 3
Published: almost 6 years ago

10.1101/2021.07.11.451964

Pathogenic and transcriptomic differences of emerging SARS-CoV-2 variants in the Syrian golden hamster model
Cited by: 3
Author(s): Kyle L. O’Donnell, Amanda N. Pinski, Chad S. Clancy, Tylisha Gourdine, Kyle Shifflett, Paige Fletcher, Ilhem Messaoudi, Andrea Marzi
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.00813-16

Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung
Cited by: 24
Author(s): Jozef Dingemans, Pieter Monsieurs, Sung-Huan Yu, Aurélie Crabbé, Konrad U. Förstner, Anne Malfroot, Pierre Cornélis, Rob Van Houdt
Software Mentions: 3
Published: about 10 years ago

10.1128/mBio.01950-18

Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
Cited by: 8
Author(s): James T. Van Leuven, Meng Mao, Denghui Xing, Gordon M. Bennett, John P. McCutcheon
Software Mentions: 3
Published: over 7 years ago

10.1128/mBio.00215-20

Norovirus Replication in Human Intestinal Epithelial Cells Is Restricted by the Interferon-Induced JAK/STAT Signaling Pathway and RNA Polymerase II-Mediated Transcriptional Responses
Cited by: 56
Author(s): Myra Hosmillo, Yasmin Chaudhry, Komal Nayak, Frédéric Sorgeloos, Bon‐Kyoung Koo, Alessandra Merenda, Reidun Lillestøl, Lydia N Drumright, Matthias Zilbauer, Ian Goodfellow
Software Mentions: 3
Published: over 6 years ago

10.1128/mBio.01628-20

Pathogenesis of Human Papillomaviruses Requires the ATR/p62 Autophagy-Related Pathway
Cited by: 11
Author(s): Siqi Hong, Yan Li, Paul J. Kaminski, Jorge Andrade, Laimonis A. Laimins
Software Mentions: 3
Published: about 6 years ago

10.1128/mBio.03533-20

In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses
Cited by: 23
Author(s): Carl J. Yeoman, Christopher J. Fields, Pascale Lepercq, Philippe Ruiz, Evelyne Forano, Bryan A. White, Pascale Mosoni
Software Mentions: 3
Published: over 5 years ago

10.1128/mSphere.00378-19

Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats
Cited by: 15
Author(s): Julia M. McGonigle, Jeremiah A. Bernau, Brenda B. Bowen, William J. Brazelton
Software Mentions: 3
Published: about 7 years ago

10.1128/mSphere.00065-20

Convergence between Regulation of Carbon Utilization and Catabolic Repression in Xanthophyllomyces dendrorhous
Cited by: 3
Author(s): Pilar Martínez-Moya, Sebastián Campusano, Pamela Córdova, Alberto Paradela, Dionisia Sepúlveda, Jennifer Alcaı́no, Marcelo Baeza, Víctor Cifuentes
Software Mentions: 3
Published: over 6 years ago

10.1128/mSphere.00659-20

MARTX Toxin-Stimulated Interplay between Human Cells and Vibrio vulnificus
Cited by: 8
Author(s): Byoung Sik Kim, Jong-Hwan Kim, Sunghee Choi, Shinhye Park, Eun-Young Lee, Sung-Cheol Koh, Choong‐Min Ryu, Seon‐Young Kim, Myung Hee Kim
Software Mentions: 3
Published: about 6 years ago

10.1128/mSystems.00216-19

Dual RNA-seq in Streptococcus pneumoniae Infection Reveals Compartmentalized Neutrophil Responses in Lung and Pleural Space
Cited by: 19
Author(s): Neil D. Ritchie, Tom Evans
Software Mentions: 3
Published: about 7 years ago

10.1128/mSystems.00416-19

Genomewide Analysis of Mode of Action of the S -Adenosylmethionine Analogue Sinefungin in Leishmania infantum
Cited by: 13
Author(s): Arijit Bhattacharya, Meenakshi Sharma, Charles Packianathan, Barry P. Rosen, Philippe Leprohon, Marc Ouellette
Software Mentions: 3
Published: about 7 years ago

10.1128/mSystems.00451-19

Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer
Cited by: 24
Author(s): Sarah Tomkovich, Raad Z. Gharaibeh, Christine M. Dejea, Jillian L. Pope, Jinmai Jiang, Kathryn Winglee, Josée Gauthier, Rachel C. Newsome, Ye Yang, Anthony A. Fodor, Thomas D. Schmittgen, Cynthia L. Sears, Christian Jobin
Software Mentions: 3
Published: over 6 years ago

10.1128/mSystems.00358-21

Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments
Cited by: 16
Author(s): Sean Ting-Shyang Wei, Yi Lung Chen, Yu Wei Wu, Tien Yu Wu, Yi Li Lai, Po Hsiang Wang, Wael Ismail, Tzong‐Huei Lee, Yin-Ru Chiang
Software Mentions: 3
Published: over 5 years ago

10.1186/s40246-019-0199-1

Transcriptome-wide analysis of differentially expressed chemokine receptors, SNPs, and SSRs in the age-related macular degeneration
Cited by: 22
Author(s): Madhu Sudhana Saddala, Anton Lennikov, Anthony Mukwaya, Lijuan Fan, Zhengmao Hu, Huang Hu
Software Mentions: 3
Published: over 7 years ago

10.1038/s41396-020-0693-4

Changes in the transcriptome, ploidy, and optimal light intensity of a cryptomonad upon integration into a kleptoplastic dinoflagellate
Cited by: 10
Author(s): Ryo Onuma, Shunsuke Hirooka, Yu Kanesaki, Takayuki Fujiwara, Hideki Yoshikawa, Shin-ya Miyagishima
Software Mentions: 3
Published: over 6 years ago

10.1038/s41396-017-0039-z

Identifying metabolic pathways for production of extracellular polymeric substances by the diatom Fragilariopsis cylindrus inhabiting sea ice
Cited by: 34
Author(s): Shazia Aslam, Jan Strauss, David N. Thomas, Thomas Möck, Graham J. C. Underwood
Software Mentions: 3
Published: almost 9 years ago

10.7150/ijbs.49243

Deciphering the genomic and lncRNA landscapes of aerobic glycolysis identifies potential therapeutic targets in pancreatic cancer
Cited by: 14
Author(s): Lili Zhu, Zheng Wu, Rongkun Li, Xin Xing, Yongsheng Jiang, Jun Li, Yahui Wang, Li-Peng Hu, Xu Wang, Weiting Qin, Yongwei Sun, Zhigang Zhang, Qin Yang, Shu‐Heng Jiang
Software Mentions: 3
Published: almost 6 years ago

10.7150/ijbs.57802

Downregulation of ACE2 expression by SARS-CoV-2 worsens the prognosis of KIRC and KIRP patients via metabolism and immunoregulation
Cited by: 14
Author(s): Qian Tang, Yue Wang, Ling Ou, Jieling Li, Kai Zheng, Hui Zhan, Jiayu Gu, Guibao Zhou, Shouqi Xie, Jianping Zhang, Wei Huang, Shaoxiang Wang, Wang Xiao
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13046-019-1239-3

RETRACTED ARTICLE: Down-regulated lncRNA DLX6-AS1 inhibits tumorigenesis through STAT3 signaling pathway by suppressing CADM1 promoter methylation in liver cancer stem cells
Cited by: 64
Author(s): Dongmei Wu, Zihui Zheng, Yingbo Zhang, Shao‐Hua Fan, Zi-Feng Zhang, Yongjian Wang, Yuxin Zheng, Jun Lü
Software Mentions: 3
Published: over 7 years ago

10.1002/jev2.12110

Extracellular Vesicle Capture by AnTibody of CHoice and Enzymatic Release (EV‐CATCHER): A customizable purification assay designed for small‐RNA biomarker identification and evaluation of circulating small‐EVs
Cited by: 23
Author(s): Megan I. Mitchell, Iddo Z. Ben‐Dov, Christina Liu, Kenny Ye, Kar Fai Chow, Y.G. Kramer, Anju Gangadharan, Steven Park, Sean Fitzgerald, Andrew Ramnauth, David S. Perlin, Michèle Donato, Emily Bhoy, Ehsan Manouchehri Doulabi, Michael G. Poulos, Masood Kamali‐Moghaddam, Olivier Loudig
Software Mentions: 3
Published: over 5 years ago

10.1002/ijc.33270

Association between breast cancer risk and disease aggressiveness: Characterizing underlying gene expression patterns
Cited by: 2
Author(s): Emilio Ugalde-Morales, Felix Graßmann, Keith Humphreys, Jingmei Li, Mikael Eriksson, Nicholas P. Tobin, Åke Borg, Johan Vallon‐Christersson, Per Hall, Kamila Czene
Software Mentions: 3
Published: about 6 years ago

10.3390/jof6040311

Transcriptional Remodeling Patterns in Murine Dendritic Cells Infected with Paracoccidioides brasiliensis: More Is Not Necessarily Better
Cited by: 1
Author(s): Calliandra Maria de-Souza-Silva, Fabián Andrés Hurtado, Aldo Henrique Tavares, Getúlio Pereira de Oliveira Júnior, Tainá Raiol, Christiane Nishibe, Daniel Paiva Agustinho, Nalvo F. Almeida, Maria Tereza Machado Teles Walter, André Moraes Nicola, Anamélia Lorenzetti Bocca, Patrícia Albuquerque, Ildinete Silva-Pereira
Software Mentions: 3
Published: almost 6 years ago

10.1099/jgv.0.000744

Differentially expressed genes during spontaneous lytic switch of Marek's disease virus in lymphoblastoid cell lines determined by global gene expression profiling
Cited by: 9
Author(s): William Mwangi, Deepali Vasoya, Lydia Kgosana, Michael Watson, Venugopal Nair
Software Mentions: 3
Published: over 9 years ago

10.1155/2021/3984463

Identification of Potential lncRNAs and miRNAs as Diagnostic Biomarkers for Papillary Thyroid Carcinoma Based on Machine Learning
Cited by: 14
Author(s): Fei Yang, Jie Zhang, Baokun Li, Zhao Zhi-gang, Yan Liu, Zhen Zhao, Jing Shao, Guiying Wang
Software Mentions: 3
Published: over 5 years ago

10.1155/2017/8027626

Transcriptome Analysis of Two Different Developmental Stages of Paeonia lactiflora Seeds
Cited by: 7
Author(s): Yong-Lei Ma, Jinqiu Cui, Xiujun Lu, Lijie Zhang, Zhijing Chen, Riwen Fei, Xiulan Sun
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13045-021-01155-6

Combine and conquer: manganese synergizing anti-TGF-β/PD-L1 bispecific antibody YM101 to overcome immunotherapy resistance in non-inflamed cancers
Cited by: 46
Author(s): Ming Yi, Mengke Niu, Jing Zhang, Shiyu Li, Shuangli Zhu, Yongxiang Yan, Ning Li, Pengfei Zhou, Qian Chu, Kongming Wu
Software Mentions: 3
Published: about 5 years ago

10.4049/jimmunol.1901072

CXCR3 Identifies Human Naive CD8+ T Cells with Enhanced Effector Differentiation Potential
Cited by: 30
Author(s): Gabriele De Simone, Emilia Maria Cristina Mazza, Antonino Cassotta, Alexey N. Davydov, Mirela Kuka, Veronica Zanon, Fédérica De Paoli, Eloise Scamardella, Maria Metsger, Alessandra Roberto, Karolina Pilipow, Federico Colombo, Elena Tenedini, Enrico Tagliafico, Luca Gattinoni, Domenico Mavilio, Clelia Peano, David A. Price, Satya P. Singh, Joshua M. Farber, Valentina Serra, Francesco Cucca, Francesco Ferrari, Valeria Orrù, Edoardo Fiorillo, Matteo Iannacone, Dmitriy M. Chudakov, Federica Sallusto, Enrico Lugli
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41388-019-0845-z

The protein secretion modulator TMED9 drives CNIH4/TGFα/GLI signaling opposing TMED3-WNT-TCF to promote colon cancer metastases
Cited by: 34
Author(s): Sasmita Mishra, Carolina Bernal, Marianna Silvano, Santosh Anand, Ariel Ruiz i Altaba
Software Mentions: 3
Published: over 7 years ago

10.1038/s41388-020-01435-4

The proapoptotic gene interferon regulatory factor-1 mediates the antiproliferative outcome of paired box 2 gene and tamoxifen
Cited by: 2
Author(s): Shixiong Wang, Venkata S. Somisetty, Baoyan Bai, Igor Chernukhin, Henri Niskanen, Minna U. Kaikkonen, Meritxell Bellet, Jason S. Carroll, Antoni Hurtado
Software Mentions: 3
Published: about 6 years ago

10.1038/s41389-018-0083-1

The FAK inhibitor BI 853520 exerts anti-tumor effects in breast cancer
Cited by: 49
Author(s): Stefanie Tiede, Nathalie Meyer-Schaller, Ravi Kiran Reddy Kalathur, Robert Ivánek, Ernesta Fagiani, Philip Schmassmann, Patrick Stillhard, Simon Häfliger, Norbert Kraut, Norbert Schweifer, Irene C. Waizenegger, Ruben Bill, Gerhard Christofori
Software Mentions: 3
Published: about 8 years ago

10.1038/s41389-020-0204-5

Transglutaminase-2 facilitates extracellular vesicle-mediated establishment of the metastatic niche
Cited by: 79
Author(s): Aparna Shinde, Juan Sebastian Paez, Sarah Libring, Kelsey Hopkins, Luis Solorio, Michael K. Wendt
Software Mentions: 3
Published: over 6 years ago

10.1038/s41389-021-00338-7

USP29-mediated HIF1α stabilization is associated with Sorafenib resistance of hepatocellular carcinoma cells by upregulating glycolysis
Cited by: 29
Author(s): Ruize Gao, David Buechel, Ravi Kiran Reddy Kalathur, Marco Morini, Mairene Coto‐Llerena, Caner Ercan, Salvatore Piscuoglio, Qian Chen, Tanja Blumer, Xueya Wang, Eva Dazert, Markus H. Heim, Michael N. Hall, Fengyuan Tang, Gerhard Christofori
Software Mentions: 3
Published: over 5 years ago

10.1515/jib-2020-0031

Differentially methylated CpG sites associated with the high-risk group of prostate cancer
Cited by: 2
Author(s): Anastasiya A. Kobelyatskaya, Elena A. Pudova, Maria Fedorova, K. M. Nyushko, B. Ya. Alekseev, А. Д. Каприн, Д. Ю. Трофимов, Г. Т. Сухих, Anastasiya V. Snezhkina, George S. Krasnov, S. V. Razin, Anna V. Kudryavtseva
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.37182

A selective gut bacterial bile salt hydrolase alters host metabolism
Cited by: 156
Author(s): Lina Yao, Sarah C. Seaton, Sula Ndousse-Fetter, Arijit A. Adhikari, Nicholas DiBenedetto, Amir I. Mina, Alexander S. Banks, Lynn Bry, A. Sloan Devlin
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms21218269

ITGA6+ Human Testicular Cell Populations Acquire a Mesenchymal Rather than Germ Cell Transcriptional Signature during Long-Term Culture
Cited by: 1
Author(s): Robert B. Struijk, Callista L Mulder, Saskia K.M. van Daalen, Cindy M de Winter-Korver, Aldo Jongejan, Sjoerd Repping, Ans M.M. van Pelt
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms21228430

Complementary Transcriptome and Proteome Analyses Provide Insight into the Floral Transition in Bamboo (Dendrocalamus latiflorus Munro)
Cited by: 3
Author(s): Xiaoyan Wang, Yujiao Wang, Guoqian Yang, Lei Zhao, Xuemei Zhang, Li D, Zhenhua Guo
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms21239198

Multi-Omics Analysis Provides Novel Insight into Immuno-Physiological Pathways and Development of Thermal Resistance in Rainbow Trout Exposed to Acute Thermal Stress
Cited by: 18
Author(s): HyeongJin Roh, Ahran Kim, Nameun Kim, Yoonhang Lee, Do-Hyung Kim
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms22031252

Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean
Cited by: 7
Author(s): Jamie A. O’Rourke, Michelle A. Graham
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms22083982

The MarR-Type Regulator PA3458 Is Involved in Osmoadaptation Control in Pseudomonas aeruginosa
Cited by: 10
Author(s): Karolina Kotecka, Adam Kawałek, Kamil Kobyłecki, Aneta Agnieszka Bartosik
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22105231

Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge
Cited by: 12
Author(s): Cristina Zamora-Ballesteros, Glória Pinto, Joana Amaral, Luís Valledor, Artur Alves, Julio J. Diez, Jorge Martín‐García
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22115798

Genome-Wide Role of HSF1 in Transcriptional Regulation of Desiccation Tolerance in the Anhydrobiotic Cell Line, Pv11
Cited by: 6
Author(s): Shoko Tokumoto, Yugo Miyata, Ruslan Deviatiiarov, Takahiro Yamada, Yusuke Hiki, О. С. Козлова, Yuki Yoshida, Richard Cornette, Akira Funahashi, Elena Shagimardanova, Oleg Gusev, Takahiro Kikawada
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22126437

BrPP5.2 Overexpression Confers Heat Shock Tolerance in Transgenic Brassica rapa through Inherent Chaperone Activity, Induced Glucosinolate Biosynthesis, and Differential Regulation of Abiotic Stress Response Genes
Cited by: 5
Author(s): Muthusamy Muthusamy, Jong Hee Kim, Suk Hee Kim, So Young Park, Soo In Lee
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22126467

Molecular and Functional Analysis of Sunitinib-Resistance Induction in Human Renal Cell Carcinoma Cells
Cited by: 10
Author(s): Magdalena Rausch, Adriano Rutz, Pierre‐Marie Allard, Céline Delucinge-Vivier, Mylène Docquier, Olivier Dormond, Jean‐Luc Wolfender, Patrycja Nowak-Śliwińska
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22136799

Chrysomycin A Attenuates Neuroinflammation by Down-Regulating NLRP3/Cleaved Caspase-1 Signaling Pathway in LPS-Stimulated Mice and BV2 Cells
Cited by: 16
Author(s): Man Liu, Shanshan Zhang, Dong-Ni Liu, Yinglin Yang, Yue-Hua Wang, Guanhua Du
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22158072

LOXL3 Silencing Affected Cell Adhesion and Invasion in U87MG Glioma Cells
Cited by: 6
Author(s): Talita de Sousa Laurentino, Roseli da Silva Soares, Antônio M. Lerário, Suely Kazue Nagahashi Marie, Sueli Mieko Oba-Shinjo
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22179120

Identifying the Main Functional Pathways Associated with Cognitive Resilience to Alzheimer’s Disease
Cited by: 11
Author(s): Marta Pérez-González, Sara Badesso, Elena Lorenzo, Elizabeth Guruceaga, Alberto Pérez-Mediavilla, Ana Garcı́a-Osta, Mar Cuadrado‐Tejedor
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22189799

Identification of miR-199a-5p, miR-214-3p and miR-99b-5p as Fibrosis-Specific Extracellular Biomarkers and Promoters of HSC Activation
Cited by: 7
Author(s): Catherine Jane Messner, Saskia Schmidt, Dilek Özkul, Carine Gaiser, Luigi Terracciano, Stephan Krähenbühl, Laura Suter‐Dick
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22189693

Fetal Brain Elicits Sexually Conflicting Transcriptional Response to the Ablation of Uterine Forkhead Box A2 (Foxa2) in Mice
Cited by: 5
Author(s): Pramod Dhakal, Monica Strawn, Ananya Samal, Susanta K. Behura
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22189719

Genome-Wide Analysis of LncRNA in Bovine Mammary Epithelial Cell Injuries Induced by Escherichia Coli and Staphylococcus Aureus
Cited by: 11
Author(s): Changjie Lin, Yifan Zhu, Zhiyu Hao, Haojun Xu, Ting Li, Jinghan Yang, Xi Chen, Yingyu Chen, Aizhen Guo, Changmin Hu
Software Mentions: 3
Published: about 5 years ago

10.1186/s12974-020-02011-z

Complement peptide C3a receptor 1 promotes optic nerve degeneration in DBA/2J mice
Cited by: 27
Author(s): Jeffrey M. Harder, Pete A. Williams, Catherine E. Braine, Hongtian Yang, Jocelyn M. Thomas, Nicole E. Foxworth, Simon W. M. John, Gareth R. Howell
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12974-021-02191-2

Microglia RAGE exacerbates the progression of neurodegeneration within the SOD1G93A murine model of amyotrophic lateral sclerosis in a sex-dependent manner
Cited by: 13
Author(s): Michael MacLean, Judyta K. Juranek, Swetha Cuddapah, Raquel López‐Díez, Henry H. Ruiz, Jiyuan Hu, Laura Frye, Huilin Li, Paul F. Gugger, Ann Marie Schmidt
Software Mentions: 3
Published: over 5 years ago

10.1186/s12974-020-01900-7

A1 reactive astrocytes and a loss of TREM2 are associated with an early stage of pathology in a mouse model of cerebral amyloid angiopathy
Cited by: 30
Author(s): Xavier Taylor, Pablo Cisternas, Yanwen You, Yingjian You, Shunian Xiang, Yamil Marambio, Jie Zhang, Rubén Vidal, Cristian A. Lasagna‐Reeves
Software Mentions: 3
Published: over 6 years ago

10.1186/s12974-019-1628-8

Midbrain microglia mediate a specific immunosuppressive response under inflammatory conditions
Cited by: 28
Author(s): Miguel A. Abellanas, Marta Zamarbide, Leyre Basurco, Esther Luquin, Marta Garcı́a-Granero, Pedro Clavero, Patxi San Martín-Úriz, Amaia Vilas, Elisa Mengual, Sandra Hervás-Stubbs, Marta Aymerich
Software Mentions: 3
Published: almost 7 years ago

10.1523/JNEUROSCI.1163-18.2018

A Multicomponent Neuronal Response Encodes the Larval Decision to Pupariate upon Amino Acid Starvation
Cited by: 19
Author(s): Siddharth Jayakumar, Shlesha Richhariya, Bipan Kumar Deb, Gaiti Hasan
Software Mentions: 3
Published: about 8 years ago

10.1155/2020/9235101

Identification of Key Differentially Expressed Transcription Factors in Glioblastoma
Cited by: 8
Author(s): Gang Qin, Beiquan Hu, Xianfeng Li, Rongjie Li, Youshi Meng, Yimei Wang, Donghua Zou, Feng Wang
Software Mentions: 3
Published: over 6 years ago

10.1155/2020/8841622

Cancer Stem Cell Characteristics by Network Analysis of Transcriptome Data Stemness Indices in Breast Carcinoma
Cited by: 2
Author(s): Zeng-Hong Wu, Youjing Zhang, Changli Jia
Software Mentions: 3
Published: about 6 years ago

10.1016/j.isci.2021.102741

Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra syndrome
Cited by: 3
Author(s): Ayumi Yamada, Takae Hirasawa, Kayako Nishimura, Chikako Shimura, Naomi Kogo, Kei Fukuda, Madoka Kato, Masaki Yokomori, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Yoichiro Iwakura, Itoshi Nikaido, Shigeyoshi Itohara, Yoichi Shinkai
Software Mentions: 3
Published: over 5 years ago

10.1186/s13048-020-00712-w

A novel signature of two long non-coding RNAs in BRCA mutant ovarian cancer to predict prognosis and efficiency of chemotherapy
Cited by: 4
Author(s): Yinglian Pan, Jia Li, Yuzhu Liu, Yiyu Han, Qian Li, Qin Zou, Zhongpei Zhang, Jin Long Huang, Qingchun Deng
Software Mentions: 3
Published: about 6 years ago

10.18632/oncotarget.20013

An integrated lncRNA, microRNA and mRNA signature to improve prognosis prediction of colorectal cancer
Cited by: 31
Author(s): Yong Xiong, Rong Wang, Linglong Peng, Wenxian You, Jinlai Wei, Shouru Zhang, Xingye Wu, Jun Guo, Jiaman Xu, Zhenbing Lv, Zhongxue Fu
Software Mentions: 3
Published: about 9 years ago

10.3389/fgene.2021.743786

SOCS3 is Related to Cell Proliferation in Neuronal Tissue: An Integrated Analysis of Bioinformatics and Experiments
Cited by: 4
Author(s): Yeuni Yu, Soon Ki Sung, Chi Hyung Lee, Mihyang Ha, Junmo Kang, Eun Jung Kwon, Ji Wan Kang, Youngjoo Kim, Ga Hyun Kim, Hye Jin Heo, Hansong Lee, Tae Woo Kim, Yoonsung Lee, Kyungjae Myung, Chang‐Kyu Oh, Yun Hak Kim
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2019.01410

A Novel Method to Efficiently Highlight Nonlinearly Expressed Genes
Cited by: 3
Author(s): Qifei Wang, Haojian Zhang, Yuqing Liang, Huichuan Jiang, Siqiao Tan, Feng Luo, Zheming Yuan, Yuan Chen
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2019.00916

An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Treatment of Heart Failure
Cited by: 3
Author(s): Guodong Yang, Aiqun Ma, Zhaohui S. Qin
Software Mentions: 3
Published: about 7 years ago

10.3389/fgene.2021.619857

Identification of Predictor Genes for Feed Efficiency in Beef Cattle by Applying Machine Learning Methods to Multi-Tissue Transcriptome Data
Cited by: 14
Author(s): Wei-Hao Chen, Pâmela Almeida Alexandre, Gabriela de Cássia Ribeiro, Heidge Fukumasu, Wei Sun, Antônio Reverter, Yutao Li
Software Mentions: 3
Published: over 5 years ago

10.1128/JVI.00969-19

Differentiation into an Effector Memory Phenotype Potentiates HIV-1 Latency Reversal in CD4+T Cells
Cited by: 67
Author(s): Deanna A. Kulpa, Aarthi Talla, Jessica H. Brehm, Susan Pereira Ribeiro, Sally Yuan, Anne-Gaelle Bebin-Blackwell, Michael D. Miller, Richard Barnard, Steven G. Deeks, Daria J. Hazuda, Nicolas Chomont, Rafick‐Pierre Sékaly
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2019.00408

Identification of Hub Genes Associated With Progression and Prognosis in Patients With Bladder Cancer
Cited by: 18
Author(s): Xin Yan, Xiaoping Li, Zixin Guo, Tong-Zu Liu, Sheng Li
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2020.586658

Cardiac Regeneration and Tumor Growth—What Do They Have in Common?
Cited by: 1
Author(s): Severin Dicks, Lonny Jürgensen, Florian Leuschner, David Hassel, Geoffroy Andrieux, Melanie Boerries
Software Mentions: 3
Published: almost 6 years ago

10.3389/fimmu.2019.00280

Studies Into β-Glucan Recognition in Fish Suggests a Key Role for the C-Type Lectin Pathway
Cited by: 49
Author(s): Jules Petit, Erin C. Bailey, Robert T. Wheeler, Carlos Alberto Ferreira de Oliveira, Maria Forlenza, G.F. Wiegertjes
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2021.725323

Non-Coding RNAs in Human Breast Milk: A Systematic Review
Cited by: 29
Author(s): Lina Tingö, Emelie Ahlberg, Lars-Åke Johansson, Sindre Andre Pedersen, Konika Chawla, Pål Sætrom, Erika Cione, Melanie Rae Simpson
Software Mentions: 3
Published: about 5 years ago

10.3389/fimmu.2020.00708

Transcriptome Profiling of Lung Innate Immune Responses Potentially Associated With the Pathogenesis of Acinetobacter baumannii Acute Lethal Pneumonia
Cited by: 10
Author(s): Xi Zeng, Hao Gu, Peng Li, Yang Yao, Ning Wang, Yun Shi, Quanming Zou
Software Mentions: 3
Published: over 6 years ago

10.26508/lsa.202001000

IL-13 deficiency exacerbates lung damage and impairs epithelial-derived type 2 molecules during nematode infection
Cited by: 11
Author(s): Alistair Chenery, Silvia Rosini, JE Parkinson, Jesuthas Ajendra, Jeremy Herrera, Craig Lawless, Brian H. K. Chan, P’ng Loke, Andrew S. MacDonald, Karl E. Kadler, Tara E. Sutherland, Judith E. Allen
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms21010364

Global Gene Expression Analysis Identifies Age-Related Differences in Knee Joint Transcriptome during the Development of Post-Traumatic Osteoarthritis in Mice
Cited by: 25
Author(s): Aimy Sebastian, Deepa K. Murugesh, Melanie E. Mendez, Nicholas R. Hum, Naiomy Deliz Rios‐Arce, Jillian L. McCool, Blaine A. Christiansen, Gabriela G. Loots
Software Mentions: 3
Published: almost 7 years ago

10.3389/fimmu.2019.00120

Vaccine-Induced Protection Against Furunculosis Involves Pre-emptive Priming of Humoral Immunity in Arctic Charr
Cited by: 14
Author(s): Laura M. Braden, S. K. Whyte, Alyson Brown, Carter Van Iderstine, Corinne Letendre, David B. Groman, J. Lewis, Sara L. Purcell, Tiago S. Hori, Mark D. Fast
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2019.02016

Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4+ T Cells
Cited by: 10
Author(s): Stephanie D. Byrum, Charity L. Washam, John M. Patterson, Kanan K. Vyas, Kathleen M. Gilbert, Sarah J. Blossom
Software Mentions: 3
Published: about 7 years ago

10.1128/JVI.01010-21

Kinetic Multi-omic Analysis of Responses to SARS-CoV-2 Infection in a Model of Severe COVID-19
Cited by: 19
Author(s): Angelene M. Cantwell, Harinder Singh, Maryann P. Platt, Yonghao Yu, Yi‐Han Lin, Yuji Ikeno, Gene B. Hubbard, Yan Xiang, Norberto González-Juarbe, Peter H. Dube
Software Mentions: 3
Published: about 5 years ago

10.26508/lsa.201900441

Essential functions of Runx/Cbfβ in gut conventional dendritic cells for priming Rorγt+ T cells
Cited by: 7
Author(s): Mari Tenno, Alicia Yoke Wei Wong, Mika Ikegaya, Eiji Miyauchi, Wooseok Seo, Peter See, Tamotsu Kato, Takashi Taida, Michiko Ohno-Oishi, Hiroshi Ohno, Hideyuki Yoshida, Florent Ginhoux, Ichiro Taniuchi
Software Mentions: 3
Published: almost 7 years ago

10.3389/fimmu.2017.00335

CD103+ CD8 T Cells in the Toxoplasma-Infected Brain Exhibit a Tissue-Resident Memory Transcriptional Profile
Cited by: 45
Author(s): Tyler Landrith, Suhas Sureshchandra, Andrea Rivera, Jessica Jang, Maham Rais, Meera G. Nair, Ilhem Messaoudi, Emma H. Wilson
Software Mentions: 3
Published: over 9 years ago

10.3389/fimmu.2021.611656

IL-12p40/IL-23p40 Blockade With Ustekinumab Decreases the Synovial Inflammatory Infiltrate Through Modulation of Multiple Signaling Pathways Including MAPK-ERK and Wnt
Cited by: 16
Author(s): Renée H Fiechter, Henriëtte M. de Jong, Leonieke J J van Mens, Inka A. Fluri, Sander W. Tas, Dominique Baeten, Nataliya Yeremenko, Marleen G H van de Sande
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2019.02484

Gut Antibody Deficiency in a Mouse Model of CVID Results in Spontaneous Development of a Gluten-Sensitive Enteropathy
Cited by: 18
Author(s): Ahmed Dawood Mohammed, M.A. Wadud Khan, Ioulia Chatzistamou, Douja Chamseddine, Katie N. Kang, Mason Perry, Reilly T. Enos, Angela Murphy, Gregorio Gomez, Ahmed Al-Adhami, Carole A. Oskeritzian, Amy Jolly, Yan Chang, Siying He, Zui Pan, Jason L. Kubinak
Software Mentions: 3
Published: about 7 years ago

10.3389/fimmu.2020.595877

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors
Cited by: 5
Author(s): Vladimir A. Veselovsky, Marina S. Dyachkova, Egor Menyailo, Polina S. Polyaeva, Evgenii I. Olekhnovich, Egor Shitikov, Dmitry Bespiatykh, Tatiana A. Semashko, Artem S. Kasianov, Elena N. Ilina, В Н Даниленко, Ksenia M. Klimina
Software Mentions: 3
Published: almost 6 years ago

10.26508/lsa.202000810

DGCR8 deficiency impairs macrophage growth and unleashes the interferon response to mycobacteria
Cited by: 0
Author(s): Barbara Killy, Barbara Bodendorfer, Jörg Mages, Kristina Ritter, Jonathan Schreiber, Christoph Hölscher, Katharina Pracht, Arif B. Ekici, Hans‐Martin Jäck, Roland Lang
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2018.01344

Common Features of Regulatory T Cell Specialization During Th1 Responses
Cited by: 37
Author(s): Katharina Littringer, Claudia Moresi, Nikolas Rakebrandt, Xiaobei Zhou, Michelle Schorer, Tamas Dolowschiak, Florian Kirchner, Felix Rost, Christian W. Keller, Donal McHugh, Salomé LeibundGut‐Landmann, Mark D. Robinson, Nicole Joller
Software Mentions: 3
Published: over 8 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568