bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.7150/jca.48245

Identification of Seven Cell Cycle-Related Genes with Unfavorable Prognosis and Construction of their TF-miRNA-mRNA regulatory network in Breast Cancer
Cited by: 14
Author(s): Zhipeng Hong, Qinglan Wang, Chengye Hong, Meimei Liu, Pengqin Qiu, Ronggui Lin, Xiaolan Lin, Fangfang Chen, Qiuhuang Li, Lingling Liu, Chuan Wang, Debo Chen
Software Mentions: 2
Published: almost 6 years ago

10.7150/jca.51264

Multiple microarray analyses identify key genes associated with the development of Non-Small Cell Lung Cancer from Chronic Obstructive Pulmonary Disease
Cited by: 13
Author(s): Lemeng Zhang, Jianhua Chen, Hua Yang, Changqie Pan, Haitao Li, Yuanming Luo, Tianli Cheng
Software Mentions: 2
Published: almost 6 years ago

10.7150/jca.48045

Comprehensive investigation of the clinical significance of long non-coding RNA HOXA-AS2 in acute myeloid leukemia using genome-wide RNA sequencing dataset
Cited by: 3
Author(s): Rui Huang, Xiwen Liao, Xiangkun Wang, Qiaochuan Li
Software Mentions: 2
Published: almost 6 years ago

10.7150/jca.55113

Identification and validation of the clinical roles of the VHL-related LncRNAs in clear cell renal cell carcinoma
Cited by: 19
Author(s): Wuping Yang, Jingcheng Zhou, Kenan Zhang, Lei Li, Yawei Xu, Kaifang Ma, Haibiao Xie, Lin Cai, Yanqing Gong, Kan Gong
Software Mentions: 2
Published: almost 6 years ago

10.1111/jcmm.13789

Circular RNAs: Methodological challenges and perspectives in cardiovascular diseases
Cited by: 49
Author(s): Matteo Carrara, Paola Fuschi, Cristina Ivan, Fabio Martelli
Software Mentions: 2
Published: about 8 years ago

10.1111/jcmm.14242

Therapeutic efficacy of anti‐MMP9 antibody in combination with nab‐paclitaxel‐based chemotherapy in pre‐clinical models of pancreatic cancer
Cited by: 20
Author(s): Niranjan Awasthi, Amanda Mikels‐Vigdal, Erin Stefanutti, Margaret A. Schwarz, Sheena Monahan, Victoria Smith, Roderich E. Schwarz
Software Mentions: 2
Published: over 7 years ago

10.1111/jcmm.14859

Silencing of LINC00461 enhances radiosensitivity of lung adenocarcinoma cells by down‐regulating HOXA10 via microRNA‐195
Cited by: 18
Author(s): Jiqiu Hou, Yanjun Wang, Hongmei Zhang, Yuxin Hu, Xiuqin Xin, Xiaodan Li
Software Mentions: 2
Published: almost 7 years ago

10.1111/jcmm.15960

Identification of a prognostic gene signature based on an immunogenomic landscape analysis of bladder cancer
Cited by: 22
Author(s): Yongwen Luo, Liang Chen, Qiang Zhou, Yaoyi Xiong, Gang Wang, Xuefeng Li, Yu Xiao, Lingao Ju, Xinghuan Wang
Software Mentions: 2
Published: about 6 years ago

10.1111/jcmm.16021

Single‐cell multi‐omics analysis presents the landscape of peripheral blood T‐cell subsets in human chronic prostatitis/chronic pelvic pain syndrome
Cited by: 15
Author(s): Meng Zhang, Yi Liu, Junyi Chen, Lei Chen, Jialin Meng, Cheng Yang, Shuiping Yin, Xiansheng Zhang, Li Zhang, Zongyao Hao, Xianguo Chen, Chaozhao Liang
Software Mentions: 2
Published: about 6 years ago

10.1111/jcmm.15525

Effect of emodin on long non‐coding RNA‐mRNA networks in rats with severe acute pancreatitis‐induced acute lung injury
Cited by: 13
Author(s): Caiming Xu, Yalan Luo, Michael Ntim, Weili Quan, Zhaoxia Li, Qiushi Xu, Jiang Liu, Jingwen Zhang, Dong Shang, Lei Li, Guixin Zhang, Hailong Chen
Software Mentions: 2
Published: almost 6 years ago

10.1111/jcmm.16563

Integrated microenvironment‐associated genomic profiles identify LRRC15 mediating recurrent glioblastoma‐associated macrophages infiltration
Cited by: 6
Author(s): Haoneng Tang, Wensi Liu, Zhao‐Xu Xu, Jinwen Zhao, Weitao Wang, Zhaojin Yu, Minjie Wei
Software Mentions: 2
Published: over 5 years ago

10.1111/jcmm.16850

Knockdown of CENPK inhibits cell growth and facilitates apoptosis via PTEN‐PI3K‐AKT signalling pathway in gastric cancer
Cited by: 8
Author(s): Shusheng Wu, Lulu Cao, Lihong Ke, Ying Yan, Huiqin Luo, Xiucai Hu, Jingping Niu, Huimin Li, Huijun Xu, Wenju Chen, Yueyin Pan, Yong He
Software Mentions: 2
Published: about 5 years ago

10.1242/jcs.167148

<i>Dgcr8</i> and <i>Dicer</i> are essential for sex chromosome integrity during meiosis in males
Cited by: 39
Author(s): A Modzelewski, Stephanie Hilz, Elizabeth A. Crate, Caterina T. H. Schweidenback, Elizabeth A. Fogarty, Jennifer K. Grenier, Raimundo Freire, Paula E. Cohen, Andrew Grimson
Software Mentions: 2
Published: over 11 years ago

10.1172/JCI144195

A therapeutic cancer vaccine delivers antigens and adjuvants to lymphoid tissues using genetically modified T cells
Cited by: 11
Author(s): Joshua R. Veatch, Naina Singhi, Shivani Srivastava, Julia Szeto, Brenda L. Jesernig, Sylvia M. Stull, Matthew Fitzgibbon, Megha Sarvothama, Sushma Yechan-Gunja, Scott James, Stanley R. Riddell
Software Mentions: 2
Published: about 5 years ago

10.3390/jcm8111772

A CTC-Cluster-Specific Signature Derived from OMICS Analysis of Patient-Derived Xenograft Tumors Predicts Outcomes in Basal-Like Breast Cancer
Cited by: 35
Author(s): Hariprasad Thangavel, Carmine De Angelis, Suhas Vasaikar, Raksha Bhat, Mohit Kumar Jolly, Chandandeep Nagi, Chad J. Creighton, Ken Chen, Lacey E. Dobrolecki, Jason T. George, Tanya Kumar, Noor Mazin Abdulkareem, Sufeng Mao, Agostina Nardone, Mothaffar F. Rimawi, C. Kent Osborne, Michael T. Lewis, Herbert Levine, Bing Zhang, Rachel Schiff, Mario Giuliano, Meghana V. Trivedi
Software Mentions: 2
Published: about 7 years ago

10.3390/jcm10184095

Biological Mechanism(s) Underpinning the Association between Antipsychotic Drugs and Weight Gain
Cited by: 8
Author(s): Bruna Panizzutti, Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Mark F. Richardson, Trang T. T. Truong, Zoe Liu, Laura J. Gray, Jee Hyun Kim, Olivia Dean, Michael Berk, Ken Walder
Software Mentions: 2
Published: about 5 years ago

10.1038/sdata.2017.112

FANTOM5 CAGE profiles of human and mouse samples
Cited by: 169
Author(s): Shuhei Noguchi, Takahiro Arakawa, Shiro Fukuda, Masaaki Furuno, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Kaoru Kaida, Ai Kaiho, Mutsumi Kanamori-Katayama, Tsugumi Kawashima, Miki Kojima, Atsutaka Kubosaki, Ri Ichiroh Manabe, Mitsuyoshi Murata, Sayaka Nagao-Sato, Kenichi Nakazato, Noriko Ninomiya, Hiromi Nishiyori-Sueki, Shohei Noma, Eri Saijyo, Akiko Saka, Mizuho Sakai, Christophe Simon, Naoki Suzuki, Michihira Tagami, Shoko Watanabe, Shigehiro Yoshida, Peter Arner, Richard Axton, Magda Babina, J Kenneth Baillie, Timothy C. Barnett, Anthony G Beckhouse, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, Ailsa J Carlisle, Hans Clevers, Carrie A. Davis, Michael Detmar, Taeko Dohi, B. Albert S. Edge, Matthias Edinger, Anna Ehrlund, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Afsaneh Eslami, Michela Fagiolini, Lynsey Fairbairn, Mary C. Farach-Carson, Geoffrey J. Faulkner, Carmelo Ferrai, Malcolm E Fisher, Lesley M. Forrester, Rie Fujita, Jun Furusawa, Teunis B. H. Geijtenbeek, T Gingeras, Daniel Goldowitz, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas Ha, Masahide Hamaguchi, Mitsuko Hara, Yuki Hasegawa, Meenhard Herlyn, Peter Heutink, Kelly J Hitchens, David Hume, Tomokatsu Ikawa, Yuri Ishizu, Chieko Kai, Hiroshi Kawamoto, Yuki I. Kawamura, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, Sarah Klein, S. Peter Klinken, Alan J. Knox, Soichi Kojima, Haruhiko Koseki, Shigeo Koyasu, Weon-Ju Lee, Andreas Lennartsson, Alan Mackay‐Sim, Niklas Mejhert, Yosuke Mizuno, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Kelly J. Morris, Hozumi Motohashi, Christine L. Mummery, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Tomohiro Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada‐Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Robert Passier, Margaret Patrikakis, Ana Pombo, Swati Pradhan-Bhatt, Xian Qin, Michael Rehli, Patrizia Rizzu, Sugata Roy, Antti Sajantila, Shimon Sakaguchi, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Christian Schmidl, Claudio Schneider, Gundula Schulze‐Tanzil, Anita Schwegmann, Guojun Sheng, Jay W. Shin, Daisuke Sugiyama, Takaaki Sugiyama, Kim M. Summers, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Andru Tomoiu, Hiroo Toyoda, Marcvande Wetering, Linda Berg, Roberto Verardo, Dipti Vijayan, Christine A. Wells, Louise N. Winteringham, Ernst J. Wolvetang, Yoko Yamaguchi, Masayuki Yamamoto, Chiyo Yanagi-Mizuochi, Misako Yoneda, Yohei Yonekura, Peter G. Zhang, S. Zucchelli, Imad Abugessaisa, Peter Arner, Jayson Harshbarger, Atsushi Kondo, Timo Lassmann, Marina Lizio, Serkan Sahin, Thierry Sengstag, Jessica Severin, Hisashi Shimoji, Masanori Suzuki, Harukazu Suzuki, Jun Kawai, Naoto Kondo, Masayoshi Itoh, Carsten O. Daub, Takeya Kasukawa, Hideya Kawaji, Piero Carninci, Alistair R.R. Forrest, Yoshihide Hayashizaki
Software Mentions: 2
Published: about 9 years ago

10.1038/sdata.2018.61

Unifying cancer and normal RNA sequencing data from different sources
Cited by: 123
Author(s): Qingguo Wang, Joshua Armenia, Chao Zhang, A. Penson, Ed Reznik, Liguo Zhang, Thais Minet, Angelica Ochoa, Benjamin Groß, Christine A. Iacobuzio‐Donahue, Doron Betel, Barry S. Taylor, Jianjiong Gao, Nikolaus Schultz
Software Mentions: 2
Published: over 8 years ago

10.1038/sdata.2018.287

Polysome profiling followed by RNA-seq of cardiac differentiation stages in hESCs
Cited by: 11
Author(s): Isabela Tiemy Pereira, Lucía Spangenberg, Anny Waloski Robert, Rocío Amorín, Marco Augusto Stimamiglio, Hugo Naya, Bruno Dallagiovanna
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41597-019-0256-6

Transcriptomic profile of cystic fibrosis airway epithelial cells undergoing repair
Cited by: 17
Author(s): Alice Zoso, Aderonke Sofoluwe, Marc Bacchetta, Marc Chanson
Software Mentions: 2
Published: about 7 years ago

10.1038/s41597-019-0216-1

Multiomics analysis of tolerant interaction of potato with potato virus Y
Cited by: 11
Author(s): Tjaša Stare, Živa Ramšak, Maja Križnik, Kristina Gruden
Software Mentions: 2
Published: about 7 years ago

10.1038/s41597-020-0541-4

RNA sequencing analysis of the human retina and associated ocular tissues
Cited by: 8
Author(s): Scott Schumacker, Krista R Coppage, Ray A. Enke
Software Mentions: 2
Published: over 6 years ago

10.1038/s41597-020-00636-6

Cross-sectional study of human coding- and non-coding RNAs in progressive stages of Helicobacter pylori infection
Cited by: 1
Author(s): Sergio Lario, María José Ramírez‐Lázaro, Aintzane González-Lahera, José L. Lavín, María Vila-Casadesús, María Elisa Quílez, Anna Brunet-Vega, Juan José Lozano, Ana M. Aransay, Xavier Calvet
Software Mentions: 2
Published: about 6 years ago

10.1038/srep10624

Lipidome and Transcriptome Profiling of Pneumolysin Intoxication Identifies Networks Involved in Statin-Conferred Protection of Airway Epithelial Cells
Cited by: 4
Author(s): Sarah Statt, Jhen-Wei Ruan, Chih Ting Huang, Reen Wu, Cheng–Yuan Kao
Software Mentions: 2
Published: over 11 years ago

10.1038/srep11087

Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense
Cited by: 55
Author(s): Yingjie Zhu, Jiang Xu, Chao Sun, Shiguo Zhou, Haibin Xu, David R. Nelson, Jun Qian, Jingyuan Song, Hongmei Luo, Xiang Li, Ying Liu, Zhichao Xu, Aijia Ji, Lizhi Wang, Shanfa Lu, Alice Hayward, Wei Sun, Xiwen Li, David C. Schwartz, Yitao Wang, Shilin Chen
Software Mentions: 2
Published: over 11 years ago

10.1038/srep13541

Antennal RNA-sequencing analysis reveals evolutionary aspects of chemosensory proteins in the carpenter ant, Camponotus japonicus
Cited by: 24
Author(s): Masaru Hojo, Kenichi Ishii, Midori Sakura, Katsushi Yamaguchi, Shuji Shigenobu, Mamiko Ozaki
Software Mentions: 2
Published: about 11 years ago

10.1038/srep14015

Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis
Cited by: 84
Author(s): Shu Huang, Chenghui Wang, Wucheng Yue, Jiao Chen, Sarah Gaughan, Wei Lu, Guoqing Lu, Chenghui Wang
Software Mentions: 2
Published: about 11 years ago

10.1038/srep14476

Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon
Cited by: 39
Author(s): Yusuke Kakei, Keiichi Mochida, Tetsuya Sakurai, Takuhiro Yoshida, Kazuo Shinozaki, Yukihisa Shimada
Software Mentions: 2
Published: about 11 years ago

10.1038/srep15435

DNA methylation signatures of long intergenic noncoding RNAs in porcine adipose and muscle tissues
Cited by: 21
Author(s): Zhongyin Zhou, Aimin Li, Ligang Wang, David M. Irwin, Liu Yan-hu, Dan Xu, Xu-Man Han, Lu Wang, Shi-Fang Wu, Lixian Wang, Hailian Xie, Yaping Zhang
Software Mentions: 2
Published: about 11 years ago

10.1038/srep16224

Forager bees (Apis mellifera) highly express immune and detoxification genes in tissues associated with nectar processing
Cited by: 52
Author(s): Rachel L. Vannette, Abbas Sheikh Mohamed, Brian R. Johnson
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep13629

RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli
Cited by: 37
Author(s): Nicolas C. Nalpas, David A. Magee, Kevin M. Conlon, John A. Browne, Claire Healy, Kirsten E. McLoughlin, Kévin Rue-Albrecht, Paul A. McGettigan, Kate E. Killick, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 2
Published: about 11 years ago

10.1038/srep22583

Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress
Cited by: 27
Author(s): Yasmín Zorrilla-Fontanesi, Mathieu Rouard, Alberto Cenci, Ewaut Kissel, Hien Do, Emeric Dubois, Sabine Nidelet, Nicolás Roux, Rony Swennen, Sébastien Carpentier
Software Mentions: 2
Published: over 10 years ago

10.1038/srep24501

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts
Cited by: 84
Author(s): Chao Bian, Yinchang Hu, Vydianathan Ravi, Irina M. Kuznetsova, Xueyan Shen, Xuemei Mu, Yu Sun, Xinxin You, Jia Li, Xiaofeng Li, Ying Qiu, Boon-Hui Tay, Natascha May Thevasagayam, Aleksey Komissarov, Vladimir A. Trifonov, Мarsel R. Kabilov, Alexey E. Tupikin, Jingjing Luo, Yi Liu, Hongmei Song, Chao Liu, Xuejie Wang, Donghong Gu, Yexin Yang, Wujiao Li, Gianluca Polgar, Guangyi Fan, Peng Zeng, He Zhang, Zijun Xiong, Zhujing Tang, Chao Peng, Zhiqiang Ruan, Hui Yu, Jieming Chen, Mingjun Fan, Yu Huang, Min Wang, Xiaomeng Zhao, Guojie Hu, Huanming Yang, Jian Wang, Jun Wang, Xun Xu, Linsheng Song, Gaosi Xu, Pao Xu, Junmin Xu, Stephen J. O’Brien, László Orbán, Byrappa Venkatesh, Qiong Shi
Software Mentions: 2
Published: over 10 years ago

10.1038/srep25211

Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions
Cited by: 54
Author(s): Monica Hongrø Solbakken, Ole K. Tørresen, Alexander J. Nederbragt, Marit Seppola, Tone F. Gregers, Kjetill S. Jakobsen, Sissel Jentoft
Software Mentions: 2
Published: over 10 years ago

10.1038/srep25486

Characterization and Small RNA Content of Extracellular Vesicles in Follicular Fluid of Developing Bovine Antral Follicles
Cited by: 91
Author(s): Raphatphorn Navakanitworakul, Wei Ting Hung, Sumedha Gunewardena, John S. Davis, Wilaiwan Chotigeat, Lane K. Christenson
Software Mentions: 2
Published: over 10 years ago

10.1038/srep25708

Transcriptomic responses of the calanoid copepod Calanus finmarchicus to the saxitoxin producing dinoflagellate Alexandrium fundyense
Cited by: 28
Author(s): Vittoria Roncalli, Matthew Cieslak, Petra H. Lenz
Software Mentions: 2
Published: over 10 years ago

10.1038/srep27310

Transcriptome profiles of metamorphosis in the ornamented pygmy frog Microhyla fissipes clarify the functions of thyroid hormone receptors in metamorphosis
Cited by: 27
Author(s): Lanying Zhao, Lusha Liu, Shouhong Wang, Hongyuan Wang, Jianping Jiang
Software Mentions: 2
Published: over 10 years ago

10.1038/srep29604

Decreased expression of Calpain-9 predicts unfavorable prognosis in patients with gastric cancer
Cited by: 24
Author(s): Peike Peng, Weicheng Wu, Junjie Zhao, Shushu Song, Xuefei Wang, Dongwei Jia, Miaomiao Shao, Mingming Zhang, Lili Li, Lan Wang, Fangfang Duan, Ran Zhao, Caiting Yang, Hao Wu, Jie Zhang, Zhongliang Shen, Yuanyuan Ruan, Jianxin Gu
Software Mentions: 2
Published: over 10 years ago

10.1038/srep31291

Transcriptomic evidence for modulation of host inflammatory responses during febrile Plasmodium falciparum malaria
Cited by: 73
Author(s): Tuan M. Tran, Marcus B. Jones, Aissata Ongoïba, Else M. Bijker, Remko Schats, Pratap Venepally, Jeff Skinner, Safiatou Doumbo, Edwin Quinten, Leo G. Visser, Elizabeth Whalen, Scott Presnell, Elise M. O’Connell, Kassoum Kayentao, Ogobara K. Doumbo, Damien Chaussabel, Hernán Lorenzi, Thomas B. Nutman, Tom H. M. Ottenhoff, Mariëlle C. Haks, Boubacar Traoré, Ewen F. Kirkness, Robert W. Sauerwein, Peter D. Crompton
Software Mentions: 2
Published: about 10 years ago

10.1038/srep32252

Intron retention-dependent gene regulation in Cryptococcus neoformans
Cited by: 47
Author(s): Sara Gonzalez-Hilarion, Damien Paulet, Kyung Tae Lee, Chung-Chau Hon, Pierre Lechat, Estelle Mogensen, Frédérique Moyrand, Caroline Proux, Rony Barboux, Giovanni Bussotti, Jungwook Hwang, Jean Yves Coppée, Yong-Sun Bahn, Guilhem Janbon
Software Mentions: 2
Published: about 10 years ago

10.1038/srep32975

Gene expression clines reveal local adaptation and associated trade-offs at a continental scale
Cited by: 18
Author(s): Damiano Porcelli, Anja M. Westram, Marta Pascual, Kevin J. Gaston, Roger K. Butlin, Rhonda R. Snook
Software Mentions: 2
Published: about 10 years ago

10.1038/srep36753

Transcriptomic analysis on the formation of the viable putative non-culturable state of beer-spoilage Lactobacillus acetotolerans
Cited by: 64
Author(s): Junyan Liu, Yang Deng, Brian M. Peters, Lin Li, Bing Li, Lequn Chen, Zhenbo Xu, Mark E. Shirtliff
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep36695

RNA-seq analyses of the midgut from blood- and serum-fed Ixodes ricinus ticks
Cited by: 67
Author(s): Jan Perner, Jan Provazník, Jana Schrenková, Veronika Urbanová, José M. C. Ribeiro, Petr Kopáček
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep38758

HOPX functions as a tumour suppressor in head and neck cancer
Cited by: 21
Author(s): Lee Fah Yap, Sook Ling Lai, Sathya Narayanan Patmanathan, Ravindran Caspa Gokulan, Max Robinson, Joe B. White, San Jiun Chai, Pathmanathan Rajadurai, Narayanan Prepageran, Yew Toong Liew, Victor Lopes, Wenbin Wei, Robert Hollows, Paul G. Murray, D Lambert, Keith Hunter, Ian C. Paterson
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep38889

High-resolution transcript profiling reveals shoot abscission process of spruce dwarf mistletoe Arceuthobium sichuanense in response to ethephon
Cited by: 2
Author(s): Yonglin Wang, Dan Xiong, Ning Jiang, Xuewu Li, Yang Qiqing, Chengming Tian
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep39100

The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme
Cited by: 69
Author(s): Shraddha Sharma, Santosh K. Patnaik, R. Thomas Taggart, Bora E. Baysal
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep39044

High expression of GFAT1 predicts poor prognosis in patients with pancreatic cancer
Cited by: 50
Author(s): Caiting Yang, Peike Peng, Lili Li, Miaomiao Shao, Junjie Zhao, Lan Wang, Fangfang Duan, Shushu Song, Hao Wu, Jie Zhang, Ran Zhao, Dongwei Jia, Mingming Zhang, Weicheng Wu, Can Li, Yefei Rong, Lei Zhang, Yuanyuan Ruan, Jianxin Gu
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep39709

The pan-cancer pathological regulatory landscape
Cited by: 28
Author(s): Matías M. Falco, Marta Bleda, José Carbonell-Caballero, Joaquín Dopazo
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep38556

Molecular characterization of firefly nuptial gifts: a multi-omics approach sheds light on postcopulatory sexual selection
Cited by: 12
Author(s): Nooria Al‐Wathiqui, Timothy R. Fallon, Adam South, Jing‐Ke Weng, Sara M. Lewis
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep40127

The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states
Cited by: 81
Author(s): Guy Barry, James Briggs, Do Won Hwang, Samuel Nayler, Patrick R.J. Fortuna, Nicky Jonkhout, Fabien Dachet, Jesper L.V. Mååg, Pieter Mestdagh, Erin M. Singh, Lotta Avesson, Dominik C. Kaczorowski, Ezgi Öztürk, Nigel C. Jones, Irina Vetter, Luis Arriola‐Martinez, Jianfei Hu, Glória Regina Franco, Victoria M. Warn, Andrew Gong, Marcel E. Dinger, Frank Rigo, Leonard Lipovich, Margaret J. Morris, Terence J. O’Brien, Dong Hoon Lee, Jeffrey A. Loeb, Seth Blackshaw, John S. Mattick, Ernst J. Wolvetang
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep41570

Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.HttQ111/+ model of Huntington’s disease
Cited by: 15
Author(s): Robert M. Bragg, Sydney R. Coffey, Rory M. Weston, Seth A. Ament, Jeffrey P. Cantle, Shawn Minnig, Cory C. Funk, Dominic D. Shuttleworth, Emily L. Woods, Bonnie Sullivan, Lindsey Jones, Anne Glickenhaus, John S Anderson, Michael Anderson, Stephen B. Dunnett, Vanessa C. Wheeler, Marcy E. MacDonald, Simon Philip Brooks, Nathan D. Price, Jeffrey B. Carroll
Software Mentions: 2
Published: over 9 years ago

10.1038/srep42483

The secondary resistome of multidrug-resistant Klebsiella pneumoniae
Cited by: 61
Author(s): Bimal Jana, Amy K. Cain, William T. Doerrler, Christine J. Boinett, María Fookes, Julian Parkhill, Luca Guardabassi
Software Mentions: 2
Published: over 9 years ago

10.1038/srep44383

De novo and reference transcriptome assembly of transcripts expressed during flowering provide insight into seed setting in tetraploid red clover
Cited by: 17
Author(s): Mallikarjuna Rao Kovi, Helga Amdahl, Muath Alsheikh, Odd Arne Rognli
Software Mentions: 2
Published: over 9 years ago

10.1038/srep46107

Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana)
Cited by: 6
Author(s): Hansheng Zhao, Huayu Sun, Lichao Li, Yonggen Lou, Rongsheng Li, Lin Qi, Zhimin Gao
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-018-25605-3

Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle
Cited by: 45
Author(s): Robert Mukiibi, Michael Vinsky, Kate Keogh, Carolyn Fitzsimmons, Paul Stothard, Sinéad M. Waters, Changxi Li
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-25845-3

De novo characterization of Phenacoccus solenopsis transcriptome and analysis of gene expression profiling during development and hormone biosynthesis
Cited by: 13
Author(s): Shashi Arya, Yogeshwar Vikram Dhar, Santosh Kumar Upadhyay, Mehar Hasan Asif, Praveen Chandra Verma
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-26035-x

Computational identification and validation of alternative splicing in ZSF1 rat RNA-seq data, a preclinical model for type 2 diabetic nephropathy
Cited by: 10
Author(s): Chi Zhang, Ken Dower, Baohong Zhang, Robert V. Martinez, Lih-Ling Lin, Shanrong Zhao
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-27019-7

Immunome differences between porcine ileal and jejunal Peyer’s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues
Cited by: 12
Author(s): Tatiana Maroilley, Mustapha Berri, Gaëtan Lemonnier, Diane Esquerré, Claire Chevaleyre, Sandrine Melo, François Meurens, Jean‐Luc Coville, Jean Jacques Leplat, Andrea Rau, Bertrand Bed’Hom, Silvia Vincent‐Naulleau, Marie‐José Mercat, Yvon Billon, Patricia Lepage, Claire Rogel–Gaillard, Jordi Estellé
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-27646-0

Independent regulation of Plasmodium falciparum rif gene promoters
Cited by: 5
Author(s): Rosana Beatriz Duque Araujo, Tatiane Macedo Silva, Charlotte Kaiser, Gabriela Fernandes Leite, Diego Peres Alonso, Paulo Eduardo Martins Ribolla, Gerd Wunderlich
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-28957-y

Comprehensive analysis of competitive endogenous RNAs network associated with head and neck squamous cell carcinoma
Cited by: 51
Author(s): Xiaonan Fang, Miao Yin, Hua Li, Cheng Liang, Cong Xu, Yang Gao, Huaxiang Zhang
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-29074-6

Culture of haploid blastocysts in FGF4 favors the derivation of epiblast stem cells with a primed epigenetic and transcriptional landscape
Cited by: 2
Author(s): Runsheng He, Benjamin L. Kidder
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-29374-x

Cotton rat lung transcriptome reveals host immune response to Respiratory Syncytial Virus infection
Cited by: 10
Author(s): Seesandra V. Rajagopala, Harinder Singh, Manan S. Patel, Wei Wang, Yi Tan, Meghan H. Shilts, Tina V. Hartert, Marina S. Boukhvalova, Jorge C. G. Blanco, Suman Das
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-29612-2

Periostin as a novel biomarker for postoperative recurrence of chronic rhinosinitis with nasal polyps
Cited by: 55
Author(s): Takahiro Ninomiya, Emiko Noguchi, Haruna Tamano, Masayo Hasegawa, Tsukasa Yoshida, Yukiko Yamashita, Mitsuhiro Okano, Naohiro Yoshida, Shinichi Haruna, Yasunori Sakuma, Shoichiro Ohta, Junya Ono, Kenji Izuhara, Masafumi Okada, Masanori Kidoguchi, Tohru Tokunaga, Masayuki Okamoto, Masafumi Kanno, Masafumi Sakashita, Tetsuji Takabayashi, Norihiko Narita, Shigeharu Fujieda
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-29250-8

GM-CSF driven myeloid cells in adipose tissue link weight gain and insulin resistance via formation of 2-aminoadipate
Cited by: 19
Author(s): Deanna Plubell, Alexandra M Fenton, Phillip A. Wilmarth, Paige Bergstrom, Yuqi Zhao, Jessica Minnier, Jay W. Heinecke, Xia Yang, Nathalie Pamir
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-30655-8

Integrated analysis of lncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fillet quality traits
Cited by: 36
Author(s): Ali R. Ali, Rafet Al-Tobasei, Brett Kenney, Timothy D. Leeds, Mohamed Salem
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-30649-6

Unbiased shRNA screening, using a combination of FACS and high-throughput sequencing, enables identification of novel modifiers of Polycomb silencing
Cited by: 8
Author(s): Kusuki Nishioka, Hiroyuki Miyazaki, Hidenobu Soejima
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-29848-y

3D microfluidic in vitro model and bioinformatics integration to study the effects of Spatholobi Caulis tannin in cervical cancer
Cited by: 12
Author(s): Nijia Wang, Jiayi Wang, Xin-He Meng, Yong-Rui Bao, Shuai Wang, Tianjiao Li
Software Mentions: 2
Published: about 8 years ago

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: about 8 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: about 8 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: about 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: about 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: about 8 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: almost 8 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

10.1038/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

10.1038/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

10.1038/s41598-020-63741-x

Smooth-muscle-derived WNT5A augments allergen-induced airway remodelling and Th2 type inflammation
Cited by: 12
Author(s): Tim Koopmans, Laura Hesse, Martijn C. Nawijn, Kuldeep Kumawat, Mark H. Menzen, I. Sophie T. Bos, Ron Smits, Elvira Bakker, Maarten van den Berge, Gerard H. Koppelman, Victor Guryev, Reinoud Gosens
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-64193-z

Evaluation of the effects of cell-dispensing using an inkjet-based bioprinter on cell integrity by RNA-seq analysis
Cited by: 7
Author(s): Masayuki Yumoto, Natsuko Hemmi, Naoki Sato, Yudai Kawashima, Koji Arikawa, Keigo Ide, Masahito Hosokawa, Manabu Seo, Haruko Takeyama
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-65438-7

Nuclear Parkin Activates the ERRα Transcriptional Program and Drives Widespread Changes in Gene Expression Following Hypoxia
Cited by: 14
Author(s): Sarah E. Shires, Justin M. Quiles, Rita H. Najor, Leonardo J Leon, Melissa Q. Cortez, Mark A Lampert, Adam Mark, Åsa B. Gustafsson
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-64972-8

Comparison of two different host plant genera responding to grapevine leafroll-associated virus 3 infection
Cited by: 6
Author(s): Cecilia A. Prator, Kar Mun Chooi, Dan Jones, Marcus Davy, Robin M. MacDiarmid, Rodrigo P. P. Almeida
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-66951-5

An Integrated Genomic and Transcriptomic Analysis Reveals Candidates of Susceptibility Genes for Crohn’s Disease in Japanese Populations
Cited by: 6
Author(s): Yoichi Kakuta, Ryo Ichikawa, Yuta Fuyuno, Atsushi Hirano, Junji Umeno, Takehiro Torisu, Kazuhiro Watanabe, Akihiro Asakura, Toshihiko Nakano, Yasuhiro Izumiyama, Daisuke Okamoto, Takeo Naito, Rintaro Moroi, Masatake Kuroha, Yoshitake Kanazawa, Tsutomu Kimura, Hisashi Shiga, Toshio Naito, Motohiro Esaki, Yosuke Kawai, Katsushi Tokunaga, Minoru Nakamura, Takayuki Matsumoto, Masao Nagasaki, Yoshitaka Kinouchi, Michiaki Unno, Atsushi Masamune
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-68195-9

Long-term and transgenerational phenotypic, transcriptional and metabolic effects in rabbit males born following vitrified embryo transfer
Cited by: 15
Author(s): Ximo García‐Domínguez, Francisco Marco‐Jiménez, David S. Peñaranda, Gianfranco Diretto, Victor García‐Carpintero, Joaquı́n Cañizares, J.S. Vicente
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-68330-6

New group of transmembrane proteins associated with desiccation tolerance in the anhydrobiotic midge Polypedilum vanderplanki
Cited by: 10
Author(s): Taisiya A. Voronina, А. А. Несмелов, Sabina A. Kondratyeva, Ruslan Deviatiiarov, Yugo Miyata, Shoko Tokumoto, Richard Cornette, Oleg Gusev, Takahiro Kikawada, Elena Shagimardanova
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-69175-9

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat
Cited by: 28
Author(s): Aymé Spor, Agathe Roucou, Arnaud Mounier, David Bru, Marie-Christine Breuil, Florian Fort, Denis Vile, Pierre Roumet, Laurent Philippot, Cyrille Violle
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-70315-4

Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis
Cited by: 13
Author(s): Mónica Fass, Máximo Rivarola, Guillermo F. Ehrenbolger, Carla Maringolo, Juan Francisco Montecchia, Facundo Quiróz, Francisco García‐García, Joaquín Dopazo Blázquez, H. Esteban Hopp, Ruth Amelia Heinz, Norma Paniego, Verónica Viviana Lia
Software Mentions: 2
Published: about 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568