bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1128/IAI.00686-19

Cutaneous Immunoprofiles of Three Spotted Fever Group Rickettsia Cases
Cited by: 5
Author(s): Na Jia, Hongbo Liu, Yuan-Chun Zheng, Wenqiang Shi, Ran Wei, Yan-Li Chu, Nianzhi Ning, Bao-Gui Jiang, Rui-Ruo Jiang, Tao Li, Qiu-Bo Huo, Cai Bian, Xiong Liu, Yi Sun, Lian-Feng Li, Qian Wang, Wei Wei, Yawei Wang, Frans Jongejan, Jia-Fu Jiang, Jie Song, Hui Wang, Wu‐Chun Cao
Software Mentions: 2
Published: over 6 years ago

10.1128/IAI.00270-21

A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response, and Host-Pathogen Interactions
Cited by: 2
Author(s): Adam Blanchard, Ceri Staley, Laurence Shaw, Sean Wattegedera, Christina‐Marie Baumbach, Jule Kristin Michler, Catrin S. Rutland, Charlotte Back, Nerissa Newbold, Gary Entrican, Sabine Tötemeyer
Software Mentions: 2
Published: about 5 years ago

10.1155/2015/731938

Similarities in Gene Expression Profiles duringIn VitroAging of Primary Human Embryonic Lung and Foreskin Fibroblasts
Cited by: 33
Author(s): Shiva Marthandan, Stefan Priebe, Mario Baumgart, Marco Groth, Alessandro Cellerino, Reinhard Guthke, Peter Hemmerich, Stephan Diekmann
Software Mentions: 2
Published: almost 12 years ago

10.3390/insects12020152

Sublethal Exposure Effects of the Neonicotinoid Clothianidin Strongly Modify the Brain Transcriptome and Proteome in the Male Moth Agrotis ipsilon
Cited by: 4
Author(s): Camille Meslin, Françoise Bozzolan, Virginie Braman, Solenne Chardonnet, Cédric Pionneau, Marie-Christine François, Dany Séverac, Christophe Gadenne, Sylvia Anton, Martine Maı̈bèche, Emmanuelle Jacquin‐Joly, David Siaussat
Software Mentions: 2
Published: over 5 years ago

10.1186/s13071-014-0622-3

Functional analysis of Girardia tigrina transcriptome seeds pipeline for anthelmintic target discovery
Cited by: 11
Author(s): Nicholas J. Wheeler, Prince N Agbedanu, Michael J. Kimber, Paula Ribeiro, Tim A. Day, Mostafa Zamanian
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13071-019-3506-8

Anopheles aquasalis transcriptome reveals autophagic responses to Plasmodium vivax midgut invasion
Cited by: 7
Author(s): Rosa Amélia Gonçalves Santana, Maurício Oliveira, Iria Cabral, Rubens Celso Andrade Silva, Débora Raysa Teixeira de Sousa, L. S. Ferreira, Marcus Vinícius Guimarães Lacerda, Wuelton Marcelo Monteiro, Patrícia Abrantes, Maria das Graças Vale Barbosa Guerra, Henrique Silveira
Software Mentions: 2
Published: over 7 years ago

10.1172/jci.insight.139628

PFKFB3-mediated glycolysis rescues myopathic outcomes in the ischemic limb
Cited by: 20
Author(s): Terence E. Ryan, Cameron A. Schmidt, Michael D. Tarpey, Adam J. Amorese, Dean T. Yamaguchi, Emma J. Goldberg, Melissa Mae R. Inigo, Reema Karnekar, Allison R. O’Rourke, James M. Ervasti, Patricia Brophy, Thomas D. Green, P. Darrell Neufer, Kelsey H. Fisher‐Wellman, Espen E. Spangenburg, Joseph M. McClung
Software Mentions: 2
Published: about 6 years ago

10.1172/jci.insight.139032

Pathogenic, glycolytic PD-1+ B cells accumulate in the hypoxic RA joint
Cited by: 36
Author(s): Achilleas Floudas, Nuno Neto, Viviana Marzaioli, Kieran Murray, Barry Moran, Michael G. Monaghan, Candice Low, Ronan Mullan, Navin Rao, Vinod Krishna, Sunil Nagpal, Douglas J. Veale, Ursula Fearon
Software Mentions: 2
Published: almost 6 years ago

10.1172/jci.insight.138312

Short-term Western-style diet negatively impacts reproductive outcomes in primates
Cited by: 9
Author(s): Sweta Ravisankar, Alison Y. Ting, Mark K. Murphy, Nash Redmayne, Dorothy Wang, Carrie McArthur, Diana Takahashi, Paul Kievit, Shawn L. Chavez, Jon D. Hennebold
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.143283

A global live cell barcoding approach for multiplexed mass cytometry profiling of mouse tumors
Cited by: 8
Author(s): Soren Charmsaz, Nicole Groß, Elizabeth M. Jaffee, Won Jin Ho
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.151005

NR4A family members regulate T cell tolerance to preserve immune homeostasis and suppress autoimmunity
Cited by: 13
Author(s): Ryosuke Hiwa, Hailyn V. Nielsen, James L. Mueller, Ravi Mandla, Julie Zikherman
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.27192

Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions
Cited by: 56
Author(s): Amy E. Brinegar, Zheng Xia, James A. Loehr, Wei Li, George G. Rodney, Thomas A. Cooper
Software Mentions: 2
Published: about 9 years ago

10.1186/s40104-021-00560-8

Feeding a Saccharomyces cerevisiae fermentation product improves udder health and immune response to a Streptococcus uberis mastitis challenge in mid-lactation dairy cows
Cited by: 13
Author(s): Mario Vailati-Riboni, Dennis D. Coleman, Vincenzo Lopreiato, Abdulrahman S. Alharthi, Ryan Bucktrout, Emad Abdel-Hamied, Ismael Martínez-Cortés, Yu Liang, Erminio Trevisi, I. Yoon, JuanJuan Loor
Software Mentions: 2
Published: over 5 years ago

10.1007/s10815-021-02191-4

Single-center thorough evaluation and targeted treatment of globozoospermic men
Cited by: 9
Author(s): Stephanie Cheung, Alessandra Parrella, Danielle Rebecca Tavares, Derek Keating, Philip Xie, Zev Rosenwaks, Gianpiero D. Palermo
Software Mentions: 2
Published: over 5 years ago

10.1074/jbc.M117.807487

A protein interaction network centered on leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) regulates growth factor receptors
Cited by: 24
Author(s): Mahmood Faraz, Carl Herdenberg, Camilla Holmlund, Roger Henriksson, Håkan Hedman
Software Mentions: 2
Published: over 8 years ago

10.1074/jbc.RA120.013017

A novel stress-inducible CmtR-ESX3-Zn2+ regulatory pathway essential for survival of Mycobacterium bovis under oxidative stress
Cited by: 9
Author(s): Xiaohui Li, Liu Chen, Jingjing Liao, Jiechen Hui, Weihui Li, Zheng‐Guo He
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.jbc.2021.100283

Acquired deficiency of peroxisomal dicarboxylic acid catabolism is a metabolic vulnerability in hepatoblastoma
Cited by: 6
Author(s): Huabo Wang, Jie Lu, Xiaoguang Chen, Marie Schwalbe, Joanna E. Gorka, Jordan A. Mandel, Jinglin Wang, Eric S. Goetzman, Sarangarajan Ranganathan, Steven F. Dobrowolski, Edward V. Prochownik
Software Mentions: 2
Published: almost 6 years ago

10.1074/jbc.RA120.014682

ABHD5 suppresses cancer cell anabolism through lipolysis-dependent activation of the AMPK/mTORC1 pathway
Cited by: 11
Author(s): Guohua Chen, Guoli Zhou, Aaron Lotvola, James G. Granneman, Jian Wang
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12929-021-00751-5

AUY922 induces retinal toxicity through attenuating TRPM1
Cited by: 6
Author(s): Che-Hung Shen, Chi-Hsun Hsieh, Kuan-Ying Jiang, Chih‐Yu Lin, Nai‐Jung Chiang, Tingwei Li, Chen‐Tung Yen, Wan-Ju Chen, Daw-Yang Hwang, Li-Tzong Chen
Software Mentions: 2
Published: over 5 years ago

10.7150/jca.32768

Aldo-Keto Reductase Family 1 Member B10 (AKR1B10) overexpression in tumors predicts worse overall survival in hepatocellular carcinoma
Cited by: 15
Author(s): Jia Shi, Lixiang Chen, Yi Chen, Yao Lu, Xiaorong Chen, Zongguo Yang
Software Mentions: 2
Published: almost 8 years ago

10.7150/jca.40726

Transcriptomic analysis reveals the oncogenic role of S6K1 in hepatocellular carcinoma
Cited by: 8
Author(s): Keng Po Lai, Angela Cheung, Cheuk Hin Ho, Nathan Tam, Jing Woei Li, Xiao Lin, Ting‐Fung Chan, Nikki P. Lee, Rong Li
Software Mentions: 2
Published: almost 7 years ago

10.7150/jca.40010

Prognostic Value of ANXA8 in Gastric Carcinoma
Cited by: 8
Author(s): Li X, Fang Hou, Young-Woo Jin, Qing‐Yuan Sun
Software Mentions: 2
Published: almost 7 years ago

10.7150/jca.46156

Application of cAMP-dependent catalytic subunit β (PRKACB) Low Expression in Predicting Worse Overall Survival: A Potential Therapeutic Target for Colorectal Carcinoma
Cited by: 10
Author(s): Xiaoya Yao, Weixian Hu, Jie Zhang, Chengzhi Huang, Haibi Zhao, Xueqing Yao
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12957-020-01909-5

Combining texture features of whole slide images improves prognostic prediction of recurrence-free survival for cutaneous melanoma patients
Cited by: 7
Author(s): Yanbin Peng, Yunfeng Chu, Zhong Chen, Wen Zhou, Shengxiang Wan, Yingfeng Xiao, Youlong Zhang, Jialu Li
Software Mentions: 2
Published: over 6 years ago

10.7150/jca.45296

Identification of a Glucose Metabolism-related Signature for prediction of Clinical Prognosis in Clear Cell Renal Cell Carcinoma
Cited by: 13
Author(s): Sheng Wang, Ling Zhang, Zhihong Yu, Kequn Chai, Jiabin Chen
Software Mentions: 2
Published: almost 7 years ago

10.7150/jca.39888

Genome-wide RNA-sequencing dataset reveals the prognostic value and potential molecular mechanisms of lncRNA in non-homologous end joining pathway 1 in early stage Pancreatic Ductal Adenocarcinoma
Cited by: 4
Author(s): Liming Shang, Xiwen Liao, Guangzhi Zhu, Ketuan Huang, Chuangye Han, Chengkun Yang, Xiangkun Wang, Xin Zhou, Hao Su, Xinping Ye, Tao Peng
Software Mentions: 2
Published: almost 7 years ago

10.12688/wellcomeopenres.15059.1

Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313
Cited by: 8
Author(s): Edna Ondari, Elizabeth J. Klemm, Chisomo Msefula, Moataz Abd El Ghany, Jennifer N. Heath, Derek Pickard, Lars Barquist, Gordon Dougan, Robert A. Kingsley, Calman A. MacLennan
Software Mentions: 2
Published: over 7 years ago

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

10.12688/wellcomeopenres.14797.2

Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern
Cited by: 10
Author(s): Jing-wen Lin, Adam J. Reid, Deirdre Cunningham, Ulrike Böhme, Irene Tumwine, Sara Keller-Mclaughlin, Mandy Sanders, Matthew Berriman, Jean Langhorne
Software Mentions: 2
Published: almost 8 years ago

10.1155/2020/1836542

Development and Validation of a Seven-Gene Signature for Predicting the Prognosis of Lung Adenocarcinoma
Cited by: 5
Author(s): Yingqing Zhang, Xiaoping Zhang, Xiaodong Liu, Ming Zhang, Xixi Gao, Jialiang Li, Yufen Xu, Zhixian Fang, Wenyu Chen
Software Mentions: 2
Published: about 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

10.12688/wellcomeopenres.14645.4

Probing Plasmodium falciparum sexual commitment at the single-cell level
Cited by: 44
Author(s): Nicolas M. B. Brancucci, Mariana De Niz, Timothy J. Straub, Deepali Ravel, Lauriane Sollelis, Bruce W. Birren, Till S. Voss, Daniel E. Neafsey, Matthias Marti
Software Mentions: 2
Published: about 8 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

10.7554/eLife.39381

Zygotic gene activation in the chicken occurs in two waves, the first involving only maternally derived genes
Cited by: 12
Author(s): Young Sun Hwang, Minseok Seo, Sang Kyung Kim, Sohyun Bang, Heebal Kim, Jae Yong Han
Software Mentions: 2
Published: about 8 years ago

10.1111/bph.15142

Regulation of gene expression by MF63, a selective inhibitor of microsomal PGE synthase 1 (mPGES1) in human osteoarthritic chondrocytes
Cited by: 5
Author(s): Lauri Tuure, Antti Pemmari, Mari Hämäläinen, Teemu Moilanen, Eeva Moilanen
Software Mentions: 2
Published: about 6 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

Dgcr8 and Dicer 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

10.1038/s41416-018-0196-5

MiR-532-5p suppresses renal cancer cell proliferation by disrupting the ETS1-mediated positive feedback loop with the KRAS-NAP1L1/P-ERK axis
Cited by: 58
Author(s): Wei Zhai, Junjie Ma, Ronggang Zhu, Chun‐Fang Xu, Jin Zhang, Yonghui Chen, Zhiguo Chen, Dongkui Gong, Jiayi Zheng, Chen Chen, Saiyang Li, Butang Li, Yiran Huang, Wei Xue, Junhua Zheng
Software Mentions: 2
Published: over 8 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

10.1038/s41416-020-0923-6

ASCL1-regulated DARPP-32 and t-DARPP stimulate small cell lung cancer growth and neuroendocrine tumour cell proliferation
Cited by: 15
Author(s): Sk Kayum Alam, Li Wang, Yanan Ren, Christina E. Hernandez, Farhad Kosari, Anja C. Roden, Rendong Yang, Luke H. Hoeppner
Software Mentions: 2
Published: over 6 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

10.1186/s40529-017-0185-7

Transcriptomic analyses reveal clathrin-mediated endocytosis involved in symbiotic seed germination of Gastrodia elata
Cited by: 20
Author(s): Zhiai Xu, Yuanyuan Li, Hong Ling, Sisi Liu, Mengmeng Liu, Juan Chen, Shun‐Xing Guo
Software Mentions: 2
Published: over 9 years ago

10.1038/s41413-020-00120-2

MEF2C regulates osteoclastogenesis and pathologic bone resorption via c-FOS
Cited by: 25
Author(s): Takayuki Fujii, Koichi Murata, Se-Hwan Mun, Seyeon Bae, Ye Ji Lee, Tannia Pannellini, Ki‐Woon Kang, David J. Oliver, Kyung‐Hyun Park‐Min, Lionel B. Ivashkiv
Software Mentions: 2
Published: almost 6 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/s41408-020-00404-0

Gene expression profiling-based risk prediction and profiles of immune infiltration in diffuse large B-cell lymphoma
Cited by: 22
Author(s): Selin Merdan, Kritika Subramanian, Turgay Ayer, Johan Van Weyenbergh, Andrés Chang, Jean L. Koff, Christopher R. Flowers
Software Mentions: 2
Published: almost 6 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/s41408-019-0173-0

Identification of lenalidomide resistance pathways in myeloma and targeted resensitization using cereblon replacement, inhibition of STAT3 or targeting of IRF4
Cited by: 57
Author(s): Yuan Xiao Zhu, Chao Shi, Laura A. Bruins, Xuewei Wang, Daniel L. Riggs, Brooke Porter, Jonathan M. Ahmann, Cecília Bonolo de Campos, Esteban Braggio, P. Leif Bergsagel, A. Keith Stewart
Software Mentions: 2
Published: over 7 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

10.1186/s13068-019-1393-z

Kluyveromyces marxianus developing ethanol tolerance during adaptive evolution with significant improvements of multiple pathways
Cited by: 59
Author(s): Wenjuan Mo, Mengzhu Wang, Rongrong Zhan, Yao Yu, Yungang He, Hong Lü
Software Mentions: 2
Published: over 7 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

10.1155/2018/8518563

Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions
Cited by: 7
Author(s): Li Guo, Liang Zheng, Yang Zhao, Qianyun Wang
Software Mentions: 2
Published: almost 9 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

10.7554/eLife.39030

Targeting MYC dependency in ovarian cancer through inhibition of CDK7 and CDK12/13
Cited by: 101
Author(s): Mei Zeng, Nicholas Kwiatkowski, Tinghu Zhang, Behnam Nabet, Mousheng Xu, Yanke Liang, Chunshan Quan, Jinhua Wang, Mingfeng Hao, Sangeetha Palakurthi, Shan Zhou, Qing Zeng, Paul Kirschmeier, Khyati Meghani, Alan L. Leggett, Jun Qi, Geoffrey I. Shapiro, Joyce F. Liu, Ursula A. Matulonis, Charles Y. Lin, Panagiotis A. Konstantinopoulos, Nathanael S. Gray
Software Mentions: 2
Published: almost 8 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

10.1186/s13068-015-0357-1

A photorespiratory bypass increases plant growth and seed yield in biofuel crop Camelina sativa
Cited by: 87
Author(s): Jyoti Dalal, Harry O. Lopez, Naresh Vasani, Zhaohui Hu, Jennifer Swift, Roopa Yalamanchili, Mia Dvora, Xiuli Lin, De‐Yu Xie, Rongda Qu, Heike Sederoff
Software Mentions: 2
Published: about 11 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

10.1186/s13068-018-1331-5

Comparative transcriptome analyses of oleaginous Botryococcus braunii race A reveal significant differences in gene expression upon cobalt enrichment
Cited by: 9
Author(s): Pengfei Cheng, Chengxu Zhou, Yan Wu, Zhihui Xu, Jilin Xu, Dongqing Zhou, Yinghui Zhang, Haizhen Wu, Xuezhi Zhang, Tianzhong Liu, Ming Tang, Yang Qiyong, Xiaojun Yan, Jianhua Fan
Software Mentions: 2
Published: almost 8 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

10.1186/s13068-020-01825-6

Evolutionary engineering of E. coli MG1655 for tolerance against isoprenol
Cited by: 12
Author(s): Heiko Babel, Jens O. Krömer
Software Mentions: 2
Published: almost 6 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

10.1155/2020/7434737

Nomogram Based on microRNA Signature Contributes to Improve Survival Prediction of Clear Cell Renal Cell Carcinoma
Cited by: 7
Author(s): Enfa Zhao, Xiaofang Bai
Software Mentions: 2
Published: over 6 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

10.7554/eLife.70557

3′HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression
Cited by: 5
Author(s): Pamela Himadewi, Xue Qing David Wang, Fan Feng, Haley Gore, Yushuai Liu, Li Yu, Ryo Kurita, Yukio Nakamura, Gerd P. Pfeifer, Jie Liu, Xiaotian Zhang
Software Mentions: 2
Published: about 5 years ago

10.1186/s13068-015-0227-x

Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses
Cited by: 131
Author(s): Noppon Lertwattanasakul, Tomoyuki Kosaka, Akira Hosoyama, Yutaka Suzuki, Nadchanok Rodrussamee, Minenosuke Matsutani, Masayuki Murata, Naoko Fujimoto, Suprayogi Suprayogi, Keiko Tsuchikane, Savitree Limtong, Nobuyuki Fujita, Mamoru Yamada
Software Mentions: 2
Published: over 11 years ago

10.1186/s13068-016-0471-8

Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq
Cited by: 31
Author(s): Yuan Fu, Michele Poli, Gaurav Sablok, Bo Wang, Yanchun Liang, Nicola La Porta, Violeta Velikova, Francesco Loreto, Mingai Li, Claudio Varotto
Software Mentions: 2
Published: over 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

10.1042/BSR20210021

Construction and analysis of the abnormal lncRNA–miRNA–mRNA network in hypoxic pulmonary hypertension
Cited by: 5
Author(s): Jie Liu, Yuhua Deng, Zeqin Fan, Shuanglan Xu, Wei Li, Xiaoxian Huang, Xin Xing, Jiao Yang
Software Mentions: 2
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568