bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-018-30530-6

Hsa-miR-10a-5p downregulation in mutant UQCRB-expressing cells promotes the cholesterol biosynthesis pathway
Cited by: 8
Author(s): Jeong Eun Kim, Ji Won Hong, Hannah S. Lee, Wankyu Kim, Jae‐Hak Lim, Yoon Shin Cho, Ho Jeong Kwon
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-30873-0

Physiological characterization of the emergence from diapause: A transcriptomics approach
Cited by: 36
Author(s): Vittoria Roncalli, Stephanie A. Sommer, Matthew Cieslak, Cheryl Clarke, Russell R. Hopcroft, Petra H. Lenz
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-30754-6

An Adult Zebrafish Model Reveals that Mucormycosis Induces Apoptosis of Infected Macrophages
Cited by: 29
Author(s): Azucena López-Muñoz, Francisco E. Nicolás, Diana García‐Moreno, Ana B. Pérez-Oliva, María Isabel Navarro-Mendoza, Miguel Ángel Hernández‐Oñate, Alfredo Herrera-Estrella, Santiago Torres-Martı́nez, Rosa M. Ruiz‐Vázquez, Victoriano Mulero
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-30702-4

Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β
Cited by: 10
Author(s): Ahmad M. N. Alhendi, Margaret Patrikakis, Carsten O. Daub, Hideya Kawaji, Masayoshi Itoh, Michiel de Hoon, Piero Carninci, Yoshihide Hayashizaki, Peter Arner, Levon M. Khachigian
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-32266-9

Transcriptional profiling of Zygosaccharomyces bailii early response to acetic acid or copper stress mediated by ZbHaa1
Cited by: 13
Author(s): Miguel Antunes, Margarida Palma, Isabel Sá‐Correia
Software Mentions: 2
Published: almost 8 years ago

10.2196/18387

Personal Health Information Inference Using Machine Learning on RNA Expression Data from Patients With Cancer: Algorithm Validation Study
Cited by: 4
Author(s): Solbi Kweon, Jeong Hoon Lee, Younghee Lee, Yu Rang Park
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-32712-8

Lymphocyte activation gene 3 (Lag3) expression is increased in prion infections but does not modify disease progression
Cited by: 44
Author(s): Yingjun Liu, Silvia Sorce, Mario Nuvolone, Julie Domange, Adriano Aguzzi
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13195-020-00627-0

Differential blood miRNA expression in brain amyloid imaging-defined Alzheimer’s disease and controls
Cited by: 28
Author(s): Helen Zong Ying Wu, Anbupalam Thalamuthu, Lesley Cheng, Christopher Fowler, Colin L. Masters, Perminder S. Sachdev, Karen A. Mather
Software Mentions: 2
Published: over 6 years ago

10.1186/s40478-020-00903-y

Altered secretory and neuroprotective function of the choroid plexus in progressive multiple sclerosis
Cited by: 29
Author(s): Sabela Rodríguez‐Lorenzo, David Francisco, Ricardo Vos, Bert van het Hof, Merel Rijnsburger, Horst Schroten, Hiroshi Ishikawa, Wissam Beaino, Rémy Bruggmann, Gijs Kooij, Helga E. de Vries
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-33928-4

Diet induced obesity is independent of metabolic endotoxemia and TLR4 signalling, but markedly increases hypothalamic expression of the acute phase protein, SerpinA3N
Cited by: 50
Author(s): Matthew J. Dalby, Gabriella Aviello, Alexander Ross, Alan W. Walker, Perry Barrett, Peter J. Morgan
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-34330-w

Differential expression of immune receptors in two marine sponges upon exposure to microbial-associated molecular patterns
Cited by: 37
Author(s): Lucía Pita, Marc P. Hoeppner, Marta Ribes, Ute Hentschel
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-34473-w

Impact of Escherichia coli K12 and O18:K1 on human platelets: Differential effects on platelet activation, RNAs and proteins
Cited by: 8
Author(s): Aniko V. Fejes, Myron G. Best, Wouter A van der Heijden, Adrienne Vancura, Heleen Verschueren, Quirijn de Mast, Thomas Würdinger, Christine Mannhalter
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12951-021-00923-3

Single-cell RNA sequencing reveals the mechanism of sonodynamic therapy combined with a RAS inhibitor in the setting of hepatocellular carcinoma
Cited by: 15
Author(s): Bolin Wu, Yanchi Yuan, Jiayin Liu, Haitao Shang, Jing Dong, Xitian Liang, Dongxu Wang, Yi-Chi Chen, Chunyue Wang, Yang Zhou, Hui Jing, Wen Cheng
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-018-37099-0

Associating transcriptional regulation for rapid germination of rapeseed (Brassica napus L.) under low temperature stress through weighted gene co-expression network analysis
Cited by: 18
Author(s): Tao Luo, Mengzhu Xian, Chen Zhang, Chenyu Zhang, Liyong Hu, Zhenghua Xu
Software Mentions: 2
Published: over 7 years ago

10.1186/s13195-021-00850-3

Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment
Cited by: 89
Author(s): Yadi Zhou, Jielin Xu, Yuan Hou, James B. Leverenz, Asha R. Kallianpur, Reena Mehra, Yunlong Liu, Haiyuan Yu, Andrew A. Pieper, Lara Jehi, Feixiong Cheng
Software Mentions: 2
Published: about 5 years ago

10.1186/s12951-018-0439-x

Tri-mannose grafting of chitosan nanocarriers remodels the macrophage response to bacterial infection
Cited by: 15
Author(s): Juan Manuel Coya, Laura De Matteis, Alexandre Giraud-Gatineau, Anne Biton, Inés Serrano‐Sevilla, Anne Danckært, Marie‐Agnès Dillies, Brigitte Gicquel, Jesús M. de la Fuente, Ludovic Tailleux
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-38566-y

Anti-microRNA screen uncovers miR-17 family within miR-17~92 cluster as the primary driver of kidney cyst growth
Cited by: 33
Author(s): Matanel Yheskel, Ronak Lakhia, Patricia Cobo-Stark, Andrea Flaten, Vishal Patel
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-38643-2

CXCR4 signaling regulates metastatic onset by controlling neutrophil motility and response to malignant cells
Cited by: 42
Author(s): Claudia Tulotta, Cristina Ştefănescu, Q. Chen, Vincenzo Torraca, Annemarie H. Meijer, B. Ewa Snaar-Jagalska
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-39114-4

How an ancient, salt-tolerant fruit crop, Ficus carica L., copes with salinity: a transcriptome analysis
Cited by: 22
Author(s): Alberto Vangelisti, L. Solorzano Zambrano, Giovanni Caruso, Desiré Macheda, Rodolfo Bernardi, Gabriele Usai, Flavia Mascagni, Tommaso Giordani, Riccardo Gucci, Andrea Cavallini, Lucia Natali
Software Mentions: 2
Published: over 7 years ago

10.1186/s12951-020-00591-9

Proteome interrogation using gold nanoprobes to identify targets of arctigenin in fish parasites
Cited by: 7
Author(s): Xiao Tu, Xiaoping Tan, Xiaozhou Qi, Aiguo Huang, Fei Ling, Gao‐Xue Wang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-39051-2

The susceptibility of sea-island cotton recombinant inbred lines to Fusarium oxysporum f. sp. vasinfectum infection is characterized by altered expression of long noncoding RNAs
Cited by: 17
Author(s): Yao ZhengPei, Quanjia Chen, Dong Chen, Leilei Zhan, Kai Zeng, Aiqin Gu, Jian Zhou, Yu Zhang, Yiwen Zhu, Wenwei Gao, Liping Wang, Yi Zhang, Yanying Qu
Software Mentions: 2
Published: over 7 years ago

10.1007/s11418-018-1270-2

Identification of potential genes involved in triterpenoid saponins biosynthesis in Gleditsia sinensis by transcriptome and metabolome analyses
Cited by: 11
Author(s): Yusuke Kuwahara, D. Nakajima, Sayaka Shinpo, Michimi Nakamura, Noriaki Kawano, Nobuo Kawahara, Mami Yamazaki, Kazuki Saito, Hideyuki Suzuki, Hideki Hirakawa
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-40107-6

Substantial fat mass loss reduces low-grade inflammation and induces positive alteration in cardiometabolic factors in normal-weight individuals
Cited by: 30
Author(s): Heikki V. Sarin, Joseph H. Lee, Matti Jauhiainen, Anni Joensuu, Katja Borodulin, Satu Männistö, Zhi Jin, Joseph D. Terwilliger, Ville Isola, Juha P. Ahtiainen, Keijo Häkkinen, Kati Kristiansson, Juha J. Hulmi, Markus Perola
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-38989-7

Long Non-coding RNAs Coordinate Developmental Transitions and Other Key Biological Processes in Grapevine
Cited by: 29
Author(s): Garima Bhatia, Shailesh Sharma, Santosh Kumar Upadhyay, Kashmir Singh
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-40237-x

Engraftment and proliferation potential of embryonic lung tissue cells in irradiated mice with emphysema
Cited by: 6
Author(s): Kazushige Shiraishi, Shigeyuki Shichino, Tohru Tsukui, Shinichi Hashimoto, Satoshi Ueha, Kouji Matsushima
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-39919-3

Synchrony and asynchrony between an epigenetic clock and developmental timing
Cited by: 36
Author(s): Akina Hoshino, Steve Horvath, Akshayalakshmi Sridhar, Alex Chitsazan, Thomas A. Reh
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-40886-y

Loss of Neogenin1 in human colorectal carcinoma cells causes a partial EMT and wound-healing response
Cited by: 12
Author(s): Vishal Chaturvedi, Alexandre Fournier‐Level, Helen Cooper, Michael J. Murray
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-41067-7

Differential gene expression in response to eCry3.1Ab ingestion in an unselected and eCry3.1Ab-selected western corn rootworm (Diabrotica virgifera virgifera LeConte) population
Cited by: 12
Author(s): Zhichao Zhao, Lisa N. Meihls, Bruce E. Hibbard, Tieming Ji, Christine G. Elsik, Kent S. Shelby
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-42019-x

Inheritance patterns of the transcriptome in hybrid chickens and their parents revealed by expression analysis
Cited by: 9
Author(s): Hongchang Gu, Xin Qi, Yaxiong Jia, Zebin Zhang, Changsheng Nie, Xinghua Li, Junying Li, Zhihua Jiang, Qiong Wang, Lujiang Qu
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-42436-y

Biomarkers of post-discharge mortality among children with complicated severe acute malnutrition
Cited by: 43
Author(s): James M. Njunge, Agnes Gwela, Nelson Kibinge, Moses Ngari, Lydia Nyamako, Emily Nyatichi, Johnstone Thitiri, Gerard Bryan Gonzales, Robert Bandsma, Judd L. Walson, Evelyn Gitau, James A. Berkley
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-41252-8

Transcriptome Analyses of Heart and Liver Reveal Novel Pathways for Regulating Songbird Migration
Cited by: 13
Author(s): W. J. Horton, Matthew Jensen, Aswathy Sebastian, Craig A. Praul, István Albert, Paul A. Bartell
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-43925-w

Transcriptional profiling of contrasting genotypes revealed key candidates and nucleotide variations for drought dissection in Camellia sinensis (L.) O. Kuntze
Cited by: 26
Author(s): Rajni Parmar, Romit Seth, Pradeep Singh, Gopal Singh, Sanjay Kumar, Ram Kumar Sharma
Software Mentions: 2
Published: over 7 years ago

10.1111/acel.13315

ATF3 drives senescence by reconstructing accessible chromatin profiles
Cited by: 29
Author(s): Chao Zhang, Xuebin Zhang, Li Huang, Yiting Guan, Xiaoke Huang, Xiao-Li Tian, Lijun Zhang, Wei Tao
Software Mentions: 2
Published: over 5 years ago

10.1111/acel.12952

Cell‐type‐specific role of lamin‐B1 in thymus development and its inflammation‐driven reduction in thymus aging
Cited by: 18
Author(s): Sibiao Yue, Xiaobin Zheng, Yixian Zheng
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-021-86049-w

Transcriptomic insight into the translational value of two murine models in human atopic dermatitis
Cited by: 3
Author(s): Young-Won Kim, Eun-A Ko, Sung-Cherl Jung, Dong-Hee Lee, Yelim Seo, Seong-Tae Kim, Jung-Ha Kim, Hyoweon Bang, Tong Zhou, Jae‐Hong Ko
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-86675-4

Delineating proinflammatory microenvironmental signals by ex vivo modeling of the immature intestinal stroma
Cited by: 1
Author(s): Mari Ichinose, Nobumi Suzuki, Tongtong Wang, Josephine Wright, Tamsin R.M. Lannagan, Laura Vrbanac, Hiroki Kobayashi, Krystyna A. Gieniec, Joseph Kim Fai Ng, Souzaburo Ihara, Chris Mavrangelos, Yoku Hayakawa, Patrick A. Hughes, Daniel L. Worthley, Susan L. Woods
Software Mentions: 2
Published: over 5 years ago

10.1111/acel.13180

Impaired phagocytic function in CX3CR1 <sup>+</sup> tissue‐resident skeletal muscle macrophages prevents muscle recovery after influenza A virus‐induced pneumonia in old mice
Cited by: 17
Author(s): Constance E. Runyan, Lynn C. Welch, Emilia Lecuona, Masahiko Shigemura, Luciano Amarelle, Hiam Abdala‐Valencia, Nikita Joshi, Ziyan Lu, Ki-Won Nam, Nikolay S. Markov, Alexandra C. McQuattie‐Pimentel, Raul Piseaux‐Aillon, Yuliya Politanska, Lango Sichizya, Satoshi Watanabe, Kibileri Williams, G. R. Scott Budinger, Jacob I. Sznajder, Alexander V. Misharin
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-021-87048-7

Genome-wide identification and analysis of long non-coding RNAs involved in fatty acid biosynthesis in young soybean pods
Cited by: 9
Author(s): Ben Ma, Aijing Zhang, Qiuzhu Zhao, Zeyuan Li, Abraham Lamboro, Haobo He, Yue Li, Suqi Jiao, Shuyan Guan, Siyan Liu, Dan Yao, Jun Zhang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-87420-7

Molecular mechanisms detected in yak lung tissue via transcriptome-wide analysis provide insights into adaptation to high altitudes
Cited by: 8
Author(s): Qian Ge, Yongbo Guo, Wangshan Zheng, Shengguo Zhao, Yuan Cai, Xuebin Qi
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-87526-y

A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling
Cited by: 7
Author(s): Jeremy Roy, Catherine A. Taylor, Annie P. Beauregard, Surendar Reddy Dhadi, D. Craig Ayre, Sheena Fry, Simi Chacko, Gabriel Wajnberg, Andrew P. Joy, Ngoc-Nu Mai-Thi, Nicolas Crapoulet, David A. Barnett, Anirban Ghosh, Stephen M. Lewis, Rodney J. Ouellette
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-87970-w

Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends
Cited by: 1
Author(s): Wojciech Rosikiewicz, J. Sikora, Tomasz Skrzypczak, Magdalena Regina Kubiak, Izabela Makałowska
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-89921-x

Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells
Cited by: 5
Author(s): Regan J. Hayward, Michael S. Humphrys, Wilhelmina M. Huston, Garry S. A. Myers
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-90011-1

De novo transcriptome assembly and comparative transcriptomic analysis provide molecular insights into low temperature stress response of Canarium album
Cited by: 4
Author(s): Ruilian Lai, Xin Feng, Jin Chen, Yongyan Zhang, Xiaoxia Wei, Yi-Ting Chen, Chunzhen Cheng, Rujian Wu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-90212-8

Health monitoring in birds using bio-loggers and whole blood transcriptomics
Cited by: 9
Author(s): Elinor Jax, Inge Müller, Stefan T. Börno, Hanna Borlinghaus, Gustaw Eriksson, Evi Fricke, Bernd Timmermann, Helene Pendl, Wolfgang Fiedler, Karsten Klein, Falk Schreiber, Martin Wikelski, Katharine E. Magor, Robert H. S. Kraus
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-90548-1

Comprehensive profiling analysis of the N6-methyladenosine-modified circular RNA transcriptome in cultured cells infected with Marek’s disease virus
Cited by: 7
Author(s): Aijun Sun, Rui Wang, Shuaikang Yang, Xiaojing Zhu, Ying Liu, Maikun Teng, Luping Zheng, Jun Luo, Gaiping Zhang, Guoqing Zhuang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-90932-x

Comparative analyses of transcriptional responses of Dectes texanus LeConte (Coleoptera: Cerambycidae) larvae fed on three different host plants and artificial diet
Cited by: 4
Author(s): Lina Maria Aguirre-Rojas, Erin D. Scully, Harold N. Trick, Kun Yan Zhu, C. Michael Smith
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-90174-x

In vitro responses to platelet-rich-plasma are associated with variable clinical outcomes in patients with knee osteoarthritis
Cited by: 8
Author(s): Habib Zahir, Bijan Dehghani, Xianglin Yuan, Yurii Chinenov, Christine Kim, Alissa J. Burge, Reyna Bandhari, Daniel Nemirov, Patrick Fava, Peter J. Moley, Hollis G. Potter, Joseph Nguyen, Brian Halpern, Laura T. Donlin, Lionel B. Ivashkiv, Scott A. Rodeo, Miguel Otero
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-91317-w

Comparative analysis of phenotypic plasticity sheds light on the evolution and molecular underpinnings of locust phase polyphenism
Cited by: 10
Author(s): Bert Foquet, Adrian A. Castellanos, Ho‐Jun Song
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-91951-4

Photoperiodically driven transcriptome-wide changes in the hypothalamus reveal transcriptional differences between physiologically contrasting seasonal life-history states in migratory songbirds
Cited by: 5
Author(s): Aakansha Sharma, Subhajit Das, Sayantan Sur, Jyoti Tiwari, Khushboo Chaturvedi, Neha Agarwal, Shalie Malik, Sangeeta Rani, Vinod Kumar
Software Mentions: 2
Published: about 5 years ago

10.1186/s12974-020-02026-6

Crosstalk between microglia and patient-derived glioblastoma cells inhibit invasion in a three-dimensional gelatin hydrogel model
Cited by: 17
Author(s): Jee Wei Emily Chen, Jan Lumibao, Sarah Leary, Jann N. Sarkaria, Andrew J. Steelman, H. Rex Gaskins, Brendan A.C. Harley
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-93606-w

Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress
Cited by: 13
Author(s): Laura Entrambasaguas, Miriam Ruocco, Koen Verhoeven, Gabriele Procaccini, Lázaro Marín-Guirao
Software Mentions: 2
Published: about 5 years ago

10.18632/aging.202168

Plasma cytokines for predicting diabetic retinopathy among type 2 diabetic patients via machine learning algorithms
Cited by: 3
Author(s): Bin Cao, Ning Zhang, Yuanyuan Zhang, Ying Fu, Dong Zhao
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-94641-3

Transcriptome-level assessment of the impact of deformed wing virus on honey bee larvae
Cited by: 4
Author(s): Zih-Ting Chang, Yu-Feng Huang, Yuewen Chen, Ming‐Ren Yen, Po‐Ya Hsu, Tzu-Han Chen, Yi-Hsuan Li, King-Wah Chiu, Yu‐Shin Nai
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-94314-1

Extracellular NLRP3 inflammasome particles are internalized by human coronary artery smooth muscle cells and induce pro-atherogenic effects
Cited by: 7
Author(s): Susanne Gaul, Karen Marie Schaeffer, Lena Opitz, Christina Maeder, Alexander Kögel, Luisa Uhlmann, Hermann Kalwa, Ulf Wagner, Jan Haas, Amirhossein Behzadi, Pablo Pelegrı́n, Jes‐Niels Boeckel, Ulrich Laufs
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-95224-y

Patrolling human SLE haematopoietic progenitors demonstrate enhanced extramedullary colonisation; implications for peripheral tissue injury
Cited by: 4
Author(s): Ioannis Kokkinopoulos, Aggelos Banos, Maria Grigoriou, Anastasia Filia, Theodora Manolakou, Themis Alissafi, Nikolaos Malissovas, Ioannis Mitroulis, Panayotis Verginis, Dimitrios T. Boumpas
Software Mentions: 2
Published: about 5 years ago

10.18632/aging.202373

Microglia exosomal miRNA-137 attenuates ischemic brain injury through targeting Notch1
Cited by: 46
Author(s): Dianquan Zhang, Guoliang Cai, Kai Li, Zhe Zhuang, Kunping Jia, Siying Pei, Xiuzhen Wang, Hong Wang, Shengnan Xu, Cheng Cui, Manchao Sun, Sihui Guo, Wenli Song, Guofeng Cai
Software Mentions: 2
Published: over 5 years ago

10.1186/s40478-019-0855-7

Molecular signature of different lesion types in the brain white matter of patients with progressive multiple sclerosis
Cited by: 47
Author(s): Maria L. Elkjaer, Tobias Frisch, Richard Reynolds, Tim Kacprowski, Mark Burton, Torben A. Kruse, Mads Thomassen, Jan Baumbach, Zsolt Illés
Software Mentions: 2
Published: almost 7 years ago

10.1523/JNEUROSCI.2571-18.2019

The Spinal Transcriptome after Cortical Stroke: In Search of Molecular Factors Regulating Spontaneous Recovery in the Spinal Cord
Cited by: 22
Author(s): Julia Kaiser, Martina A. Maibach, Iris Salpeter, Niels Hagenbuch, Vladimir B. C. de Souza, Mark D. Robinson, Martin E. Schwab
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-021-97765-8

A forward genetic screen identifies modifiers of rocaglate responsiveness
Cited by: 2
Author(s): Leo Shen, Lauren Pugsley, Regina Cencic, HanChen Wang, Françis Robert, Sai Kiran Naineni, Ananya Sahni, Geneviève Morin, Wenhan Zhang, Anastasia Nijnik, John A. Porco, David Langlais, Sidong Huang, Jerry Pelletier
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-021-98777-0

ZBED6 regulates Igf2 expression partially through its regulation of miR483 expression
Cited by: 4
Author(s): Rakan Naboulsi, Mårten Larsson, Leif Andersson, Shady Younis
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-021-99139-6

Efflux transporters in rat placenta and developing brain: transcriptomic and functional response to paracetamol
Cited by: 6
Author(s): Liam M. Koehn, Yifan Huang, Mark D. Habgood, Shuai Nie, SheneYi-Shiuan Chiou, Richard B. Bánati, Katarzyna M. Dzięgielewska, Norman Saunders
Software Mentions: 2
Published: almost 5 years ago

10.1080/14686996.2019.1614980

Ozone ultrafine bubble water induces the cellular signaling involved in oxidative stress responses in human periodontal ligament fibroblasts
Cited by: 13
Author(s): Anongwee Leewananthawet, Shin’ichi Arakawa, Tokuju Okano, Ryô Kinoshita, Hiroshi Ashida, Yuichi Izumi, Toshihiko Suzuki
Software Mentions: 2
Published: about 7 years ago

10.1126/scitranslmed.abf7872

SARS-CoV-2 infection of human iPSC–derived cardiac cells reflects cytopathic features in hearts of patients with COVID-19
Cited by: 127
Author(s): Juan A. Pérez-Bermejo, Serah S Kang, Sarah J. Rockwood, Camille R. Simoneau, David A Joy, Ana C. Silva, Gokul N. Ramadoss, Will Flanigan, Parinaz Fozouni, Huihui Li, Peiyi Chen, Ken Nakamura, Jeffrey D. Whitman, P. J. Hanson, Bruce M. McManus, Mélanie Ott, Bruce R. Conklin, Todd C. McDevitt
Software Mentions: 2
Published: over 5 years ago

10.1038/s41392-020-00382-6

Molecular characteristics of primary pulmonary lymphoepithelioma-like carcinoma based on integrated genomic analyses
Cited by: 18
Author(s): Bojiang Chen, Yu Zhang, Shenyu Dai, Ping Zhou, Wenxin Luo, Zhoufeng Wang, Xuping Chen, Cheng Peng, Guoya Zheng, Jing Ren, Xiaodong Yang, Weimin Li
Software Mentions: 2
Published: over 5 years ago

10.1038/s41392-021-00709-x

Multimodal single-cell omics analysis identifies epithelium–immune cell interactions and immune vulnerability associated with sex differences in COVID-19
Cited by: 13
Author(s): Yuan Hou, Yadi Zhou, Michaela U. Gack, Justin D. Lathia, Asha R. Kallianpur, Reena Mehra, Timothy A. Chan, Jae U. Jung, Lara Jehi, Charis Eng, Feixiong Cheng
Software Mentions: 2
Published: about 5 years ago

10.1186/1758-907X-2-2

Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments
Cited by: 83
Author(s): Kevin McCormick, Matthew R. Willmann, Blake C. Meyers
Software Mentions: 2
Published: over 15 years ago

10.1016/j.stemcr.2018.03.001

Heterogeneity of Human Breast Stem and Progenitor Cells as Revealed by Transcriptional Profiling
Cited by: 99
Author(s): Justin A. Colacino, Ebrahim Azizi, Michael Brooks, Ramdane Harouaka, Shamileh Fouladdel, Sean McDermott, Michael Lee, David R. Hill, Julie Madden, Julie L. Boerner, Michele L. Coté, Maureen A. Sartor, Laura S. Rozek, Max S. Wicha
Software Mentions: 2
Published: over 8 years ago

10.1016/j.stemcr.2018.03.011

HDAC1 and HDAC2 Modulate TGF-β Signaling during Endothelial-to-Hematopoietic Transition
Cited by: 25
Author(s): Roshana Thambyrajah, Muhammad Zaki Hidayatullah Fadlullah, Martin Proffitt, Rahima Patel, Shaun M. Cowley, Valérie Kouskoff, Georges Lacaud
Software Mentions: 2
Published: over 8 years ago

10.1186/s13287-018-1095-7

Does osteogenic potential of clonal human bone marrow mesenchymal stem/stromal cells correlate with their vascular supportive ability?
Cited by: 7
Author(s): Alison T. Merryweather‐Clarke, David Cook, Barbara Joo Lara, Peng Hua, Emmanouela Repapi, Neil Ashley, Shiang Y. Lim, Suzanne M. Watt
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-019-6001-x

Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa
Cited by: 5
Author(s): Libin Zhang, Jun Zou, Shisheng Li, Baoshan Wang, Nadia Raboanatahiry, Maoteng Li
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-020-07074-z

Differentially expressed genes in cotyledon of ewes fed mycotoxins
Cited by: 1
Author(s): Jessica Britt, Rooksana E. Noorai, S. K. Duckett
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-017-3699-1

Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range
Cited by: 48
Author(s): Cecilia Deng, Kim M. Plummer, Darcy A. B. Jones, Carl H. Mesarich, Jason Shiller, Adam P. Taranto, Andrew Robinson, P. Kastner, Nathan E. Hall, Matthew D. Templeton, Joanna K. Bowen
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-15-400

Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata
Cited by: 69
Author(s): Eshita Sharma, Axel Künstner, Bonnie A. Fraser, Gideon Zipprich, Verena A. Kottler, Stefan R. Henz, Detlef Weigel, Christine Dreyer
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-015-1778-8

A comparative analysis of host responses to avian influenza infection in ducks and chickens highlights a role for the interferon-induced transmembrane proteins in viral resistance
Cited by: 83
Author(s): Jacqueline Smith, Nikki Smith, Yu Lan, Ian R. Paton, Maria Weronika Gutowska, H. S. Forrest, Angela Danner, J. Seiler, Paul Digard, Robert G. Webster, David W. Burt
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-016-3154-8

High-resolution analysis of multi-copy variant surface glycoprotein gene expression sites in African trypanosomes
Cited by: 22
Author(s): Sebastian Hutchinson, Lucy Glover, David Horn
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-016-3360-4

Dhurrin metabolism in the developing grain of Sorghum bicolor (L.) Moench investigated by metabolite profiling and novel clustering analyses of time-resolved transcriptomic data
Cited by: 51
Author(s): Lasse Nielsen, Peter Stuart, Martina Pičmanová, Simon Rasmussen, Carl Erik Olsen, Jesper Harholt, Birger Lindberg Møller, Nanna Bjarnholt
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-15-305

A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines
Cited by: 12
Author(s): Zhilin Qu, Geoffrey E. Hill, Scott V. Edwards, Niclas Backström
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-015-1967-5

Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis
Cited by: 34
Author(s): Cathriona Foley, Aspinas Chapwanya, John J. Callanan, Ronan Whiston, Raúl Miranda-CasoLuengo, Junnan Lu, Wim G. Meijer, David J. Lynn, Cliona O’Farrelly, Kieran G. Meade
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-020-6584-2

Sirt2-associated transcriptome modifications in cisplatin-induced neuronal injury
Cited by: 4
Author(s): Xin Zhao, Wei Du, Manchao Zhang, Zainab Atiq, Fang Xia
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-015-1399-2

Genome wide comparative analysis of the effects of PRMT5 and PRMT4/CARM1 arginine methyltransferases on the Arabidopsis thaliana transcriptome
Cited by: 36
Author(s): Carlos Esteban Hernando, Sabrina E. Sanchez, Estefanía Mancini, Marcelo J. Yanovsky
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-14-797

The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios
Cited by: 53
Author(s): Damian Kao, Daniel A. Felix, A. Aziz Aboobaker
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12864-015-2186-9

Transcriptome profiling of differentially expressed genes in floral buds and flowers of male sterile and fertile lines in watermelon
Cited by: 53
Author(s): Sun-Ju Rhee, Minseok Seo, Yoonjeong Jang, Seoae Cho, Gung Pyo Lee
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-018-5261-1

RNA-Seq transcriptome analysis of breast muscle in Pekin ducks supplemented with the dietary probiotic Clostridium butyricum
Cited by: 12
Author(s): Yanhan Liu, Yaxiong Jia, Cun Liu, Limin Ding, Zhaofei Xia
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13287-019-1163-7

A scalable solution for isolating human multipotent clinical-grade neural stem cells from ES precursors
Cited by: 28
Author(s): Dáša Bohačiaková, Marián Hruška-Plocháň, Rachel Tsunemoto, Wesley D. Gifford, Shawn P. Driscoll, Thomas D. Glenn, Stephanie Wu, Silvia Marsala, Michael Navarro, Takahiro Tadokoro, Štefan Juhás, Jana Juhásová, Oleksandr Platoshyn, David R. Piper, Vickie Sheckler, Dara Ditsworth, Samuel L. Pfaff, Martin Mars̆ala
Software Mentions: 2
Published: over 7 years ago

10.18632/oncotarget.7781

Identification of a six microRNA signature as a novel potential prognostic biomarker in patients with head and neck squamous cell carcinoma
Cited by: 27
Author(s): Hao Shi, Jian Chen, Yuncheng Li, Guojun Li, Rong Zhong, Dandan Du, Mengqi Wang, Weijia Kong, Meixia Lü
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-017-4256-7

Comparative transcriptome analysis of soybean response to bean pyralid larvae
Cited by: 18
Author(s): Weiying Zeng, Zheng Sun, Zheng-Li Cai, Huaizhu Chen, Zhenguang Lai, Shou-Zhen Yang, Xiangmin Tang
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-017-3902-4

Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls
Cited by: 34
Author(s): Colleen MacMillan, Hannah Birke, Aaron Chuah, Elizabeth Brill, Yukiko Tsuji, John Ralph, Elizabeth S. Dennis, Danny Llewellyn, Filomena Pettolino
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-020-07104-w

Construction of an 11-microRNA-based signature and a prognostic nomogram to predict the overall survival of head and neck squamous cell carcinoma patients
Cited by: 13
Author(s): Yu‐Sheng Huang, Zhiguo Liu, Zhong Li, Yi Wen, Qixiang Ye, Deliang Cao, Peiwu Li, Yufeng Liu
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-020-06866-7

Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala × Culter alburnus
Cited by: 9
Author(s): Li Ren, Xiaojing Yan, Xin Gao, Jialin Cui, Peiyao Yan, Chang Wu, Wuhui Li, Shaojun Liu
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-018-4911-7

Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops
Cited by: 18
Author(s): Karl R. Franke, Skye Schmidt, Sunhee Park, Dong‐Hoon Jeong, Monica Accerbi, Pamela J. Green
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-15-4

Specific gene-regulation networks during the pre-implantation development of the pig embryo as revealed by deep sequencing
Cited by: 108
Author(s): Suying Cao, Jun Wu, Qiuyan Li, Zhong Hua Liu, Wei Zhang, Yangli Pei, Xiaoan Ruan, Xumin Wang, Bing Lim, Ning Li
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-15-1052

Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress
Cited by: 64
Author(s): Nedeljka Rosic, Paulina Kaniewska, Chon‐Kit Kenneth Chan, Edmund Y. S. Ling, David Edwards, Sophie Dove, Ove Høegh-Guldberg
Software Mentions: 2
Published: over 12 years ago

10.1186/s13287-020-01650-6

PI3K/Akt signaling pathway is essential for de novo hair follicle regeneration
Cited by: 41
Author(s): Yu Chen, Zhimeng Fan, Xiaoxiao Wang, Miaohua Mo, Siyuan Zeng, Ren‐He Xu, Xusheng Wang, Yaojiong Wu
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-020-07349-5

IRLnc: a novel functional noncoding RNA contributes to intramuscular fat deposition
Cited by: 9
Author(s): Ligang Wang, Zhongyin Zhou, Tian Zhang, Longchao Zhang, Xinhua Hou, Yan Hua, Lixian Wang
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-13-364

Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection
Cited by: 56
Author(s): Bala R. Thumma, Naveen Sharma, Simon G. Southerton
Software Mentions: 2
Published: over 14 years ago

10.1186/s12864-015-1392-9

NMDA receptor activation upstream of methyl farnesoate signaling for short day-induced male offspring production in the water flea, Daphnia pulex
Cited by: 41
Author(s): Kenji Toyota, Hitoshi Miyakawa, Katsushi Yamaguchi, Shuji Shigenobu, Yukiko Ogino, Norihisa Tatarazako, Shinichi Miyagawa, Taisen Iguchi
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-15-189

Using RNA sequencing to characterize female reproductive genes between Z and E Strains of European Corn Borer moth (Ostrinia nubilalis)
Cited by: 22
Author(s): Nooria Al‐Wathiqui, Sara M. Lewis, Erik B. Dopman
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-018-4657-2

Co-sequencing and novel delayed anti-correlation identify function for pancreatic enriched microRNA biomarkers in a rat model of acute pancreatic injury
Cited by: 4
Author(s): Zhihua Li, Rodney Rouse
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-017-3963-4

Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing
Cited by: 48
Author(s): Bin Tian, Shichen Wang, T. C. Todd, Charles D. Johnson, Guiliang Tang, Harold N. Trick
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-020-07048-1

Multiple omics analysis reveals that high fiber diets promote gluconeogenesis and inhibit glycolysis in muscle
Cited by: 8
Author(s): Jianghong Wu, Yang Ding, Husile Gong, Yunxia Qi, Huichao Sun, Yongbin Liu, Yahong Liu, Qiu Xiao
Software Mentions: 2
Published: almost 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568