bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fgene.2019.01175

Conjoint Analysis of SMRT- and Illumina-Based RNA-Sequencing Data of Fenneropenaeus chinensis Provides Insight Into Sex-Biased Expression Genes Involved in Sexual Dimorphism
Cited by: 5
Author(s): Qiong Wang, HE Ya, Jian Li
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-53377-x

Transcriptome analysis of miRNA and mRNA in the livers of pigs with highly diverged backfat thickness
Cited by: 17
Author(s): Kai Xing, Xitong Zhao, Ai Hong, Shaokang Chen, Ting Yang, Zhen Tan, Yuan Wang, Fengxia Zhang, Yibing Liu, Hemin Ni, Yong Guo, Zhuocheng Hou, Chuduan Wang
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/s41598-019-54315-7

Transcriptome profiling reveals transcriptional and alternative splicing regulation in the early embryonic development of hair follicles in the cashmere goat
Cited by: 9
Author(s): Yanjun Zhang, Xun Hu, Zhen Li, Dong Chen, Wenjing Han, Zhihong Wu, Fangzheng Shang, Erhan Hai, Yaxun Wei, Rui Su, Zhihong Liu, Ruijun Wang, Zhiying Wang, Yanhong Zhao, Zhixin Wang, Yi Zhang, Jinquan Li
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-54475-6

LIN28B affects gene expression at the hypothalamic-pituitary axis and serum testosterone levels
Cited by: 5
Author(s): Jaakko T. Leinonen, Yu‐Chia Chen, Jana Pennonen, Leevi Lehtonen, Nella Junna, Taru Tukiainen, Pertti Panula, Elisabeth Widén
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-54076-3

Lithium alters expression of RNAs in a type-specific manner in differentiated human neuroblastoma neuronal cultures, including specific genes involved in Alzheimer’s disease
Cited by: 12
Author(s): Bryan Maloney, Yokesh Balaraman, Yunlong Liu, Nipun Chopra, Howard J. Edenberg, John R. Kelsoe, John I. Nürnberger, Debomoy K. Lahiri
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-54989-z

Species-specific transcriptional profiles of the gut and gut microbiome of Ceratitis quilicii and Ceratitis rosa sensu stricto
Cited by: 1
Author(s): Fathiya M. Khamis, Paul O. Mireji, Fidelis L. O. Ombura, Anna R. Malacrida, Erick O. Awuoche, Martin K. Rono, Samira A. Mohamed, Chrysantus M. Tanga, Sunday Ekesi
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-55409-y

Transcriptome analysis of human brain microvascular endothelial cells response to Neisseria meningitidis and its antigen MafA using RNA-seq
Cited by: 15
Author(s): E. Káňová, Zuzana Tkáčová, Katarína Bhide, Amod Kulkarni, Irene Jiménez-Munguía, Patrícia Mertinková, Monika Drážovská, Punit Tyagi, Mangesh Bhide
Software Mentions: 2
Published: almost 7 years ago

10.1002/cam4.2232

CLEC3A, MMP7, and LCN2 as novel markers for predicting recurrence in resected G1 and G2 pancreatic neuroendocrine tumors
Cited by: 17
Author(s): Masami Minemura, Takamasa Oono, Nao Fujimori, Takehiro Takaoka, Ken Kawabe, Yoshihiro Miyasaka, Takao Ohtsuka, Daisuke Saito, Masafumi Nakamura, Yasuyuki Ohkawa, Yoshinao Oda, Mikita Suyama, Tetsuhide Ito, Yoshihiro Ogawa
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-55454-7

Using mechanistic models for the clinical interpretation of complex genomic variation
Cited by: 14
Author(s): María Peña‐Chilet, Marina Esteban-Medina, Matías M. Falco, Kinza Rian, Marta R. Hidalgo, Carlos Loucera, Joaquı́n Dopazo
Software Mentions: 2
Published: almost 7 years ago

10.18632/oncotarget.8124

Non-invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles
Cited by: 108
Author(s): Danijela Koppers-Lalić, Michael Hackenberg, Renée X. de Menezes, Branislav Mišovic, Magda Wąchalska, Albert A. Geldof, Nicoletta Zini, Theo de Reijke, Thomas Würdinger, Andrè N. Vis, Jeroen van Moorselaar, D. Michiel Pegtel, Irene V. Bijnsdorp
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-019-56030-9

Transcriptome analysis-identified long noncoding RNA CRNDE in maintaining endothelial cell proliferation, migration, and tube formation
Cited by: 6
Author(s): Matthew Moran, Xiangdong Cheng, Mohamed Sham Shihabudeen Haider Ali, Nishikant Wase, Nghi M. Nguyen, Wenchao Yang, Chi Zhang, Concetta C. DiRusso, Xinghui Sun
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-55700-y

Transcriptome-wide analysis associates ID2 expression with combined pre- and post-capillary pulmonary hypertension
Cited by: 8
Author(s): Meghan J. Arwood, Nasim Vahabi, Christelle Lteif, Ravindra Sharma, Roberto F. Machado, Julio D. Duarte
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-56566-w

Transcriptome-wide analysis of the SCNT bovine abnormal placenta during mid- to late gestation
Cited by: 8
Author(s): Guang Gao, Shenyuan Wang, Jiaqi Zhang, Guanghua Su, Zhong Zheng, Chunling Bai, Lei Yang, Zhuying Wei, Xiuying Wang, Lanbo Xiao, Ziru Guo, Guangpeng Li, Xianwei Su, Li Zhang
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-56771-7

Molecular mechanisms underlying nuchal hump formation in dolphin cichlid, Cyrtocara moorii
Cited by: 13
Author(s): Laurène Alicia Lecaudey, Christian Sturmbauer, Pooja Singh, Ehsan Pashay Ahi
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-56879-w

Effects of miR-98 in intrauterine extracellular vesicles on maternal immune regulation during the peri-implantation period in cattle
Cited by: 41
Author(s): Keigo Nakamura, Kaoru Kusama, Atsushi Ideta, Koji Kimura, Masaru Hori, Kazuhiko Imakawa
Software Mentions: 2
Published: almost 7 years ago

10.1002/cam4.3361

Identification of potential prognostic small nucleolar RNA biomarkers for predicting overall survival in patients with sarcoma
Cited by: 8
Author(s): Jianwei Liu, Xiwen Liao, Xianze Zhu, Peizhen Lv, Rong Li
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-57495-9

Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data
Cited by: 16
Author(s): Joanna E. Handzlik, Spyros Tastsoglou, Ioannis S. Vlachos, Artemis G. Hatzigeorgiou
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-57512-x

CRL4-Cereblon complex in Thalidomide Embryopathy: a translational investigation
Cited by: 7
Author(s): Thayne Woycinck Kowalski, João Luiz Ellera Gomes, Gabriela Barreto Caldas-Garcia, Lucas Rosa Fraga, Vanessa Rodrigues Paixão‐Côrtes, Mariana Recamonde‐Mendoza, Maria Teresa Vieira Sanseverino, Lavínia Schüler‐Faccini, Fernanda S.L. Vianna
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13058-015-0666-0

ELF5 isoform expression is tissue-specific and significantly altered in cancer
Cited by: 33
Author(s): Catherine Piggin, Daniel Roden, David Gallego‐Ortega, Heather Lee, Samantha Oakes, Christopher J. Ormandy
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-020-58804-y

Identification of gene signature for treatment response to guide precision oncology in clear-cell renal cell carcinoma
Cited by: 15
Author(s): Ninadh Malrina D’Costa, Davide P. Cinà, Raunak Shrestha, Robert H. Bell, Yen-Yi Lin, Hossein Asghari, César Monjarás‐Ávila, Christian Kollmannsberger, Faraz Hach, Claudia Chávez-Muñoz, Alan So
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-59177-y

Physiological and transcriptomic analysis provide novel insight into cobalt stress responses in willow
Cited by: 15
Author(s): Yiming Wang, Qi Yang, Hui Xu, Yan-Jing Liu, Hai-Ling Yang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-59188-9

Restricted immunological and cellular pathways are shared by murine models of chronic alcohol consumption
Cited by: 7
Author(s): Alyx Vogle, Tongqi Qian, Shijia Zhu, Elizabeth B. Burnett, Holger Fey, Zhibin Zhu, Ali Keshavarzian, Maliha Shaikh, Yujin Hoshida, Miran Kim, Costica Aloman
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-59502-5

Deconvoluting Wavelengths Leading to Fluorescent Light Induced Inflammation and Cellular Stress in Zebrafish (Danio rerio)
Cited by: 1
Author(s): Mikki Boswell, William Boswell, Yuan Lu, Markita Savage, Ronald B. Walter
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-59998-x

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host
Cited by: 47
Author(s): Megha Hastantram Sampangi-Ramaiah, Jagadheesh, Prajjal Dey, Shridhar Jambagi, Meenu Kumari, Ralf Oelmüller, K. Nataraja, K. V. Ravishankar, G. Ravikanth, R. Uma Shaanker
Software Mentions: 2
Published: over 6 years ago

10.1002/cam4.3122

Identification of the key genes associated with chemotherapy sensitivity in ovarian cancer patients
Cited by: 4
Author(s): Hui Zheng, Meiqin Zhang, Shuang Ma, Wenting Yang, Shuanshuan Xie, Yanchun Wang, Yixuan Liu, Jinyan Kai, Qian Ma, Renquan Lu, Lin Guo
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-60558-6

Endothelin-1 Mediated Decrease in Mitochondrial Gene Expression and Bioenergetics Contribute to Neurodegeneration of Retinal Ganglion Cells
Cited by: 20
Author(s): Renuka Chaphalkar, Dorota Stankowska, Shuning He, Bindu Kodati, Nicole Phillips, Jude Prah, Shaohua Yang, Raghu R. Krishnamoorthy
Software Mentions: 2
Published: over 6 years ago

10.1002/cam4.4095

Immunophenotype‐associated gene signature in ductal breast tumors varies by receptor subtype, but the expression of individual signature genes remains consistent
Cited by: 4
Author(s): Michael Behring, Yuanfan Ye, Amr Elkholy, Prachi Bajpai, Sumit Agarwal, Hyung‐Gyoon Kim, Akinyemi I. Ojesina, Howard W. Wiener, Upender Manne, Sadeep Shrestha, Ana I. Vázquez
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-60761-5

TREM-1 activation is a potential key regulator in driving severe pathogenesis of enterovirus A71 infection
Cited by: 10
Author(s): Siti Naqiah Amrun, Jeslin J. L. Tan, Natasha Y. Rickett, Jonathan Cox, Bernett Lee, Michael J. Griffiths, Tom Solomon, David Perera, Mong How Ooi, Julian A. Hiscox, Lisa F. P. Ng
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-61017-y

Transcriptomic and computational analysis identified LPA metabolism, KLHL14 and KCNE3 as novel regulators of Epithelial-Mesenchymal Transition
Cited by: 7
Author(s): Valeria Di Lollo, Angelo Canciello, Massimiliano Orsini, Nicola Bernabò, Massimo Ancora, Marta Di Federico, Valentina Curini, Mauro Mattioli, Valentina Russo, Annunziata Mauro, Cesare Cammà, Barbara Barboni
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-61723-7

Evaluation of bile salt hydrolase inhibitor efficacy for modulating host bile profile and physiology using a chicken model system
Cited by: 9
Author(s): Wenjing Geng, Sarah L. Long, Yun‐Juan Chang, Arnold M. Saxton, Susan A. Joyce, Jun Lin
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-62194-6

Janus effect of glucocorticoids on differentiation of muscle fibro/adipogenic progenitors
Cited by: 15
Author(s): Andrea Cerquone Perpetuini, Giulio Giuliani, Alessio Reggio, Mauro Cerretani, Marisabella Santoriello, Roberta Stefanelli, Alessandro Palma, Simone Vumbaca, Steven J. Harper, Luisa Castagnoli, Alberto Bresciani, Gianni Cesareni
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-62584-w

Germline-dependent transmission of male reproductive traits induced by an endocrine disruptor, di-2-ethylhexyl phthalate, in future generations
Cited by: 17
Author(s): Radwa Barakat, Po Ching Lin, Chan Jin Park, Mohamed Zeineldin, Sherry Zhou, Saniya Rattan, Emily Brehm, Jodi A. Flaws, Che Myong Ko
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-62458-1

Genome-wide identification and expression analysis of the CBF/DREB1 gene family in lettuce
Cited by: 22
Author(s): Sunchung Park, Ainong Shi, Beiquan Mou
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-63023-6

Skin transcriptome profiling of Changthangi goats highlights the relevance of genes involved in Pashmina production
Cited by: 17
Author(s): Sonika Ahlawat, Reena Arora, Rekha Sharma, Upasna Sharma, Manpreet Kaur, Ashok Kumar, Kritika Singh, Manoj Kumar Singh, R. K. Vijh
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-63085-6

Alpha-tocopherol exerts protective function against the mucotoxicity of particulate matter in amphibian and human goblet cells
Cited by: 5
Author(s): Hee‐Sun Yang, Hyo Jung Sim, Hanna Cho, Woo Young Bang, Ha Eun Kim, Taeg Kyu Kwon, Taejoon Kwon, Tae Joo Park
Software Mentions: 2
Published: over 6 years ago

10.1002/cam4.3375

Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan‐cancer
Cited by: 8
Author(s): Zhanghan Chen, Jie Huang, Yinchang Feng, Zehuan Li, Ying Jiang
Software Mentions: 2
Published: about 6 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

10.1038/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

10.1002/cam4.2642

A network‐based predictive gene expression signature for recurrence risks in stage II colorectal cancer
Cited by: 14
Author(s): Wenjing Yang, Haibo Wang, Wen-da Wang, P Y Bai, Lu Hongxia, Chang‐He Sun, Zishen Liu, Ding‐Kun Guan, Guowang Yang, Gan‐Lin Zhang
Software Mentions: 2
Published: almost 7 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: over 5 years ago

10.1186/s12935-019-0928-5

A nomogram based on 9-lncRNAs signature for improving prognostic prediction of clear cell renal cell carcinoma
Cited by: 24
Author(s): Wen Jiang, Qing Guo, Chenghe Wang, Yu Zhu
Software Mentions: 2
Published: about 7 years ago

10.1080/20002297.2019.1653124

Sex-specific differences in the salivary microbiome of caries-active children
Cited by: 24
Author(s): Stephanie Ortiz, Elisa Herrman, Claudia Lyashenko, Anne Purcell, Kareem Raslan, Brandon Khor, Michael Snow, Anna Forsyth, Dong‐Hee Choi, Tom Maier, Curtis A. Machida
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12935-019-0934-7

Long non-coding RNA LINC00485 acts as a microRNA-195 sponge to regulate the chemotherapy sensitivity of lung adenocarcinoma cells to cisplatin by regulating CHEK1
Cited by: 21
Author(s): Wei Zuo, Wei Zhang, Fei Xu, Jing Zhou, Wei Bai
Software Mentions: 2
Published: about 7 years ago

10.1080/20002297.2019.1599670

Metatranscriptomic analysis of an <i>in vitro</i> biofilm model reveals strain-specific interactions among multiple bacterial species
Cited by: 15
Author(s): Yifei Zhang, Wenyu Shi, Yeqing Song, Jinfeng Wang
Software Mentions: 2
Published: almost 8 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: over 5 years ago

10.1186/s12935-020-1140-3

Identification of molecular markers associated with the progression and prognosis of endometrial cancer: a bioinformatic study
Cited by: 12
Author(s): Jinhui Liu, Mingming Feng, Siyue Li, Song Nie, Hui Wang, Shan Wu, Jiangnan Qiu, Jie Zhang, Wenjun Cheng
Software Mentions: 2
Published: over 6 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: over 5 years ago

10.1186/s12935-020-01274-z

Random-forest algorithm based biomarkers in predicting prognosis in the patients with hepatocellular carcinoma
Cited by: 21
Author(s): Ling‐Yun Guo, Zhenjiang Wang, Yuanyuan Du, Jie Mao, Junqiang Zhang, Zeyuan Yu, Jiwu Guo, Jun Zhao, Huinian Zhou, Haitao Wang, Yanmei Gu, Yumin Li
Software Mentions: 2
Published: over 6 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: over 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: over 5 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: about 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: about 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: about 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: over 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

10.1186/s12935-020-1134-1

Construction of a circRNA-miRNA-mRNA network based on competitive endogenous RNA reveals the function of circRNAs in osteosarcoma
Cited by: 32
Author(s): Yu Qiu, Pu Chen, Yanchao Li, Baochuang Qi
Software Mentions: 2
Published: over 6 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: almost 6 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: over 5 years ago

10.1186/s12935-021-01789-z

Construction of a competitive endogenous RNA network and analysis of potential regulatory axis targets in glioblastoma
Cited by: 5
Author(s): Kai Yu, Huan Yang, Qiao‐Li Lv, Li-chong Wang, Zilong Tan, Zhe Zhang, Yulong Ji, Qian-xia Lin, Junjun Chen, Wei He, Zhe Chen, Xiaoli Shen
Software Mentions: 2
Published: over 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

10.1038/s41418-020-0541-0

Targeting triple-negative breast cancers with the Smac-mimetic birinapant
Cited by: 27
Author(s): Najoua Lalaoui, Delphine Mérino, Göknur Giner, François Vaillant, Diep Chau, Lin Liu, Tobias Kratina, Bhupinder Pal, James R. Whittle, Nima Etemadi, Jean Berthelet, Julius Gräsel, Cathrine Hall, Matthew E. Ritchie, Matthias Ernst, Gordon K. Smyth, David Vaux, Jane E. Visvader, Geoffrey J. Lindeman, John Silke
Software Mentions: 2
Published: over 6 years ago

10.1038/s41418-020-00653-3

HDAC inhibition ameliorates cone survival in retinitis pigmentosa mice
Cited by: 21
Author(s): Marijana Samardzija, Andrea Corna, Raquel Gómez‐Sintes, Mohamed Ali Jarboui, Angela Armento, Jérôme E. Roger, Eleni Petridou, Wadood Haq, François Paquet-Durand, Eberhart Zrenner, Pedro de la Villa, Günther Zeck, Christian Grimm, Patricia Boya, Marius Ueffing, Dragana Trifunović
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41419-020-2435-y

CCL5 derived from tumor-associated macrophages promotes prostate cancer stem cells and metastasis via activating β-catenin/STAT3 signaling
Cited by: 131
Author(s): Renlun Huang, Shengqi Wang, Neng Wang, Yifeng Zheng, Jianfu Zhou, Bowen Yang, Xuan Wang, Juping Zhang, Lang Guo, Shusheng Wang, Zhiqiang Chen, Zhiyu Wang, Shulin Xiang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41419-021-04005-y

ETV7 regulates breast cancer stem-like cell features by repressing IFN-response genes
Cited by: 11
Author(s): Laura Pezzè, Erna Marija Meškytė, Mattia Forcato, Stefano Pontalti, Kalina Aleksandra Badowska, Dario Rizzotto, Ira Skvortsova, Silvio Bicciato, Yari Ciribilli
Software Mentions: 2
Published: over 5 years ago

10.1038/s41419-021-04076-x

Toll-like receptor 4 is a master regulator for colorectal cancer growth under high-fat diet by programming cancer metabolism
Cited by: 6
Author(s): Xianjing Hu, Sarwat Fatima, Minting Chen, Keyang Xu, Chunhua Huang, Rui Gong, Tao Su, Hoi Leong Xavier Wong, Zhaoxiang Bian, Hiu Yee Kwan
Software Mentions: 2
Published: about 5 years ago

10.1038/s41419-019-1938-x

TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP
Cited by: 22
Author(s): Janin Knop, Lisanne M. Spilgies, Stefanie Rufli, Ramona Reinhart, Lazaros Vasilikos, Monica Yabal, Erika Owsley, Philipp J. Jost, Rebecca Marsh, Harald Wajant, Mark D. Robinson, Thomas Kaufmann, Wendy Wei-Lynn Wong
Software Mentions: 2
Published: about 7 years ago

10.1007/s10565-020-09516-6

Estrogen receptor alpha (ERα)–mediated coregulator binding and gene expression discriminates the toxic ERα agonist diethylstilbestrol (DES) from the endogenous ERα agonist 17β-estradiol (E2)
Cited by: 10
Author(s): Aziza Hussein Bakheit Adam, L.H.J. de Haan, Ignacio Miro Estruch, Guido Hooiveld, Jochem Louisse, Ivonne M.C.M. Rietjens
Software Mentions: 2
Published: over 6 years ago

10.1038/s41419-019-1696-9

FGF1ΔHBS ameliorates chronic kidney disease via PI3K/AKT mediated suppression of oxidative stress and inflammation
Cited by: 48
Author(s): Dezhong Wang, Mengyun Jin, Xinyu Zhao, Tianyang Zhao, Wei Lin, Zhengle He, Miaojuan Fan, Wei Jin, Jie Zhou, Lingwei Jin, Chao Zheng, Hui Jin, Yushuo Zhao, Xiaokun Li, Ying Lei, Yang Wang, Guo‐Qing Zhu, Zhifeng Huang
Software Mentions: 2
Published: over 7 years ago

10.1038/s41419-020-2589-7

BCL-xL/BCL2L1 is a critical anti-apoptotic protein that promotes the survival of differentiating pancreatic cells from human pluripotent stem cells
Cited by: 19
Author(s): Larry Sai Weng Loo, Andreas Alvin Purnomo Soetedjo, Hwee Hui Lau, Natasha Hui Jin Ng, Soumita Ghosh, Linh Nguyen, Vidhya G. Krishnan, Hyungwon Choi, Xavier Roca, Shawn Hoon, Adrian Kee Keong Teo
Software Mentions: 2
Published: over 6 years ago

10.1038/s41419-020-2704-9

Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe
Cited by: 4
Author(s): Bastian Gastl, Kathleen Klotz-Noack, Bertram Klinger, Sylvia Ispasanie, Krenoula Hani Fouad Salib, Johannes Zuber, Soulafa Mamlouk, Natalie Bublitz, Nils Blüthgen, David Horst, Markus Morkel, Reinhold Schäfer, Christine Sers
Software Mentions: 2
Published: over 6 years ago

10.1038/s41419-018-1296-0

Transcriptome profiling of caspase-2 deficient EμMyc and Th-MYCN mouse tumors identifies distinct putative roles for caspase-2 in neuronal differentiation and immune signaling
Cited by: 4
Author(s): Loretta Dorstyn, Emily Hackett-Jones, Andrej Nikolic, Murray D. Norris, Yoon Pin Lim, John Toubia, Michelle Haber, Sharad Kumar
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41419-018-0869-2

LncRNA MIR100HG promotes cell proliferation in triple-negative breast cancer through triplex formation with p27 loci
Cited by: 105
Author(s): Shaowei Wang, Ke Hao, Honglei Zhang, Yujie Ma, Lei Ao, Li Zou, Qin Yang, Huiping Zhu, Jianyun Nie, Chen Wu, Baowei Jiao
Software Mentions: 2
Published: over 8 years ago

10.1038/s41419-020-2372-9

Myofibroblast induces hepatocyte-to-ductal metaplasia via laminin–ɑvβ6 integrin in liver fibrosis
Cited by: 15
Author(s): Ting Xu, Zhijie Lu, Zhuanglong Xiao, Fang Liu, Yuhua Chen, Zhijun Wang, Shenghua Zhu, Yufang Song
Software Mentions: 2
Published: over 6 years ago

10.1016/j.cell.2017.11.042

Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner
Cited by: 497
Author(s): Morgane Sonia Thion, Donovan Low, Aymeric Silvin, Jinmiao Chen, Pauline Grisel, Jonas Schulte-Schrepping, Ronnie Blecher‐Gonen, Thomas Ulas, Paola Squarzoni, Guillaume Hoeffel, Fanny Coulpier, Eleni Siopi, Friederike S. David, Claus‐Jürgen Scholz, Shihui Foo, Josephine Lum, Arlaine Anne Amoyo, Anis Larbi, Michael Poidinger, Anne Buttgereit, Pierre-Marie Lledo, Melanie Greter, Jerry Kok Yen Chan, Ido Amit, Marc Beyer, Joachim L. Schultze, Andreas Schlitzer, Sven Pettersson, Florent Ginhoux, Sonia Garel
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41420-020-00295-x

The prognostic value of six survival-related genes in bladder cancer
Cited by: 7
Author(s): Songbai Cheng, Jiang Zhou, Jing Xiao, Huiling Guo, Zhengrong Wang, Yuhui Wang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41420-020-00392-x

Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae
Cited by: 5
Author(s): Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41420-021-00560-7

Identification of a seven-long non-coding RNA signature associated with Jab1/CSN5 in predicting hepatocellular carcinoma
Cited by: 7
Author(s): Weijie Ma, Ye Yao, Gang Xu, Xiaoling Wu, Jinghua Liu, Ganggang Wang, Xi Chen, Kunlei Wang, Yirang Chen, Yonghua Guo, Yongsheng Li, Deli Tan, Hui Guo, Zhisu Liu, Yufeng Yuan, François X. Claret
Software Mentions: 2
Published: over 5 years ago

10.14252/foodsafetyfscj.D-20-00032

Effect of Transgenic Rootstock Grafting on the Omics Profiles in Tomato
Cited by: 9
Author(s): Hiroaki Kodama, Taira Miyahara, Taichi Oguchi, Takashi Tsujimoto, Yoshihiro Ozeki, Toshiki Ogawa, Yube Yamaguchi, Daisaku Ohta
Software Mentions: 2
Published: almost 6 years ago

10.3390/foods10050936

Transcriptomic Analysis of Pseudomonas aeruginosa Response to Pine Honey via RNA Sequencing Indicates Multiple Mechanisms of Antibacterial Activity
Cited by: 16
Author(s): Ioannis Kafantaris, Christina Tsadila, Marios Nikolaidis, Eleni Tsavea, Tilemachos G. Dimitriou, Ioannis Iliopoulos, Grigoris D. Amoutzias, Dimitris Mossialos
Software Mentions: 2
Published: over 5 years ago

10.3389/fnagi.2021.645649

Transcriptome Analysis of Microglia Reveals That the TLR2/IRF7 Signaling Axis Mediates Neuroinflammation After Subarachnoid Hemorrhage
Cited by: 5
Author(s): Shenbin Xu, Shuhao Mei, Jianing Lu, Haijian Wu, Xiao Dong, Ligen Shi, Jingyi Zhou, Jianmin Zhang
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers11081179

Papillary Thyroid Carcinoma Variants are Characterized by Co-dysregulation of Immune and Cancer Associated Genes
Cited by: 14
Author(s): Jaideep Chakladar, Wei Tse Li, Michael Bouvet, Eric Y. Chang, Jessica Wang‐Rodriguez, Weg M. Ongkeko
Software Mentions: 2
Published: about 7 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

10.3389/fbioe.2018.00019

Phosphoproteome of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395, under Nitrogen-Replete and -Deplete Conditions
Cited by: 1
Author(s): Michael T. Guarnieri, Alida T. Gerritsen, Calvin A. Henard, Eric P. Knoshaug
Software Mentions: 2
Published: over 8 years ago

10.3389/fbioe.2021.701039

Identification of Key mRNAs as Prediction Models for Early Metastasis of Pancreatic Cancer Based on LASSO
Cited by: 7
Author(s): Ke Xue, Huilin Zheng, Xiaowen Qian, Zheng Chen, Yangjun Gu, Zhenhua Hu, Lei Zhang, Jian Wan
Software Mentions: 2
Published: about 5 years ago

10.3389/fbioe.2020.00668

Identification and Analysis of p53-Regulated Enhancers in Hepatic Carcinoma
Cited by: 5
Author(s): Yin Zhang, Mingming Qian, Fei Tang, Qingqing Huang, Wenzhu Wang, Yanjing Li, Zhi Xue Li, Bei-Ping Li, Zheng-Liang Qiu, Junjie Yue, Zhiyun Guo
Software Mentions: 2
Published: over 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568