bioconductor: clusterProfiler | Projects

10.1038/s41598-020-75688-0

Analysis of open chromatin regions in bladder cancer links β-catenin mutations and Wnt signaling with neuronal subtype of bladder cancer
Cited by: 3
Author(s): Aleyna Eray, Perihan Yağmur Güneri, Gülden Özden Yılmaz, Gökhan Karakülah, Serap Erkek
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-86048-x

A ceRNA-associated risk model predicts the poor prognosis for head and neck squamous cell carcinoma patients
Cited by: 9
Author(s): Yuzi Xu, Fengqin Xu, Yiming Lv, Siyuan Wang, Jia Li, Chuan Zhou, Jimin Jiang, Binbin Xie, Fuming He
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-019-50119-x

Tissue-specific mouse mRNA isoform networks
Cited by: 12
Author(s): Gaurav Kandoi, Julie A. Dickerson
Software Mentions: 6
Published: over 6 years ago

10.21203/rs.3.rs-362886/v1

Maternal-Fetal Immune Responses in Pregnant Women Infected with SARS-CoV-2
Cited by: 6
Author(s): Valeria Garcia‐Flores, Roberto Romero, Yi Xu, Kevin R. Theis, Marcia Arenas-Hernández, Derek Miller, Azam Peyvandipour, José Galaz, Dustyn Levenson, Gaurav Bhatti, Meyer Gershater, Errile Pusod, David Kracht, Violetta Florova, Yaozhu Leng, Tao Li, Megan Faucett, Robert Para, Chaur‐Dong Hsu, Gary Zhang, Adi L. Tarca, Roger Piqué-Regi, Nardhy Gomez-López
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-019-47343-w

A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line
Cited by: 9
Author(s): Nikolaï Genov, Alireza Basti, Marconi Abreu, Rosario Astaburuaga, Angela Relógio
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-019-48435-3

Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction
Cited by: 22
Author(s): Junbo Zou, Herzl Chai, Xiaofei Zhang, Deliang Guo, Jia Tai, Yu Wang, Yulin Liang, Fang Wang, Jiangxue Cheng, Jing Wang, Yajun Shi
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-020-60638-7

Aberrant expression of PAR bZIP transcription factors is associated with epileptogenesis, focus on hepatic leukemia factor
Cited by: 7
Author(s): Lukáš Rambousek, Tilo Gschwind, Carlos Lafourcade, Jean-Charles Paterna, Linda Dib, Jean‐Marc Fritschy, Adriano Fontana
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1008057

Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape
Cited by: 65
Author(s): Abimbola O. Kolawole, Carmen Mirabelli, David R. Hill, Sophia A. Svoboda, Andrew B. Janowski, Karla D. Passalacqua, Benancio N. Rodriguez, Michael K. Dame, Pamela Freiden, Ryan P. Berger, Diem Vu, Myra Hosmillo, Mary X. O’Riordan, Stacey Schultz‐Cherry, Susana Guix, Jason R. Spence, David Wang, Christiane E. Wobus
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1009256

A murine model of Lyme disease demonstrates that Borrelia burgdorferi colonizes the dura mater and induces inflammation in the central nervous system
Cited by: 23
Author(s): Timothy Casselli, Ali Divan, Emilie E. Vomhof-DeKrey, Yvonne Tourand, Heidi L. Pecoraro, Catherine A. Brissette
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-86919-3

Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis
Cited by: 3
Author(s): Tongqiang Fan, Yajiang Huang
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-86294-z

Development of a novel transcription factors-related prognostic signature for serous ovarian cancer
Cited by: 5
Author(s): Lei He, Nayiyuan Wu, Zhaoyi Liu, Yongchang Chen, Quan Cheng, Jing Wang
Software Mentions: 5
Published: about 5 years ago

10.1073/pnas.2100920118

Single-cell sequencing reveals suppressive transcriptional programs regulated by MIS/AMH in neonatal ovaries
Cited by: 23
Author(s): Marie-Charlotte Meinsohn, Hatice D. Saatcioglu, Lina Wei, Yang Li, Heiko Horn, Maëva Chauvin, Mariko Kano, Ngoc Minh Nguyen, Nicholas Nagykery, A Kashiwagi, Wesley Samore, Dan Wang, Esther Oliva, Guangping Gao, Mary E. Morris, Patricia K. Donahoe, David Pépin
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-84190-0

Development of a poor-prognostic-mutations derived immune prognostic model for acute myeloid leukemia
Cited by: 7
Author(s): Feng‐Ting Dao, Jun Wang, Lu Yang, Ya‐Zhen Qin
Software Mentions: 5
Published: over 5 years ago

10.1038/s41597-020-0352-7

Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.
Cited by: 69
Author(s): Won-Hee Kang, Young Mi Sim, Namjin Koo, Jae Do Nam, Junesung Lee, Nayoung Kim, Hakgi Jang, Yongmin Kim, Seon-In Yeom
Software Mentions: 5
Published: over 6 years ago

10.1038/srep21911

Transcriptional profiling of human smooth muscle cells infected with gingipain and fimbriae mutants of Porphyromonas gingivalis
Cited by: 6
Author(s): Boxi Zhang, Allan Sirsjö, Hazem Khalaf, Torbjörn Bengtsson
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-021-81447-6

Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway
Cited by: 16
Author(s): Inca A. Dieterich, Yusi Cui, Megan M. Braun, Alexis J. Lawton, Nicklaus H. Robinson, Jennifer L. Peotter, Qing Yu, Jason C. Casler, Benjamin S. Glick, Anjon Audhya, John M. Denu, Lingjun Li, Luigi Puglielli
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-23366-7

Glucose Levels Alter the Mga Virulence Regulon in the Group A Streptococcus
Cited by: 25
Author(s): Kayla M. Valdes, Ganesh S. Sundar, Ashton T. Belew, Emrul Islam, Najib M. El-Sayed, Yoann Le Breton, Kevin S. McIver
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-021-81472-5

Drosophila Hox genes induce melanized pseudo-tumors when misexpressed in hemocytes
Cited by: 6
Author(s): Titus Ponrathnam, Ravina Saini, Sofia Banu, Rakesh Mishra
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-34160-w

Transcriptomic and functional network features of lung squamous cell carcinoma through integrative analysis of GEO and TCGA data
Cited by: 72
Author(s): Yin Li, Jie Gu, Fan Xu, Qinqing Zhu, Di Ge
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-020-66721-3

Cardiac transcriptional and metabolic changes following thoracotomy
Cited by: 0
Author(s): Markus Heckmann, Ashraf Yusuf Rangrez, Daniel Finke, Andreas Jungmann, Julia S. Kreußer, Alexandra Rosskopf, Nesrin Schmiedel, Hugo A. Katus, Norbert Frey, Oliver Müller
Software Mentions: 5
Published: almost 6 years ago

10.1186/s40170-020-00216-7

Fine-tuning the metabolic rewiring and adaptation of translational machinery during an epithelial-mesenchymal transition in breast cancer cells
Cited by: 3
Author(s): Tamara Fernández-Calero, Marcos Davyt, Karen Perelmuter, Cora Chalar, Giovana Bavia Bampi, Helena Persson, Juan Pablo Tosar, Völundur Hafstað, Hugo Naya, Carlos Rovira, Mariela Bollati-Fogolín, Ricardo Ehrlich, Gilles Flouriot, Zoya Ignatova, Mónica Marı́n
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12866-020-01938-w

A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer
Cited by: 15
Author(s): Qian Zhang, Huan Zhao, Dedong Wu, D Y Cao, Wei Ma
Software Mentions: 5
Published: over 5 years ago

10.1038/s41398-019-0384-y

Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism
Cited by: 63
Author(s): Manav Kapoor, Jen Chyong Wang, Sean P. Farris, Yunlong Liu, Jeanette N. McClintick, Ishaan Gupta, Jacquelyn L. Meyers, Sarah Bertelsen, Michael J. Chao, John I. Nürnberger, Jay A. Tischfield, Oscar Harari, Zeran Li, Victor Hesselbrock, Lance O. Bauer, Towfique Raj, Bernice Porjesz, Arpana Agrawal, Tatiana Foroud, Howard J. Edenberg, R. Dayne Mayfield, Alison Goate
Software Mentions: 5
Published: over 7 years ago

10.3389/fmolb.2021.633299

Identification of Lymph Node Metastasis–Related Key Genes and Prognostic Risk Model in Bladder Cancer by Co-Expression Analysis
Cited by: 8
Author(s): Cheng Luo, Bin Huang, Yukun Wu, Yadong Xu, Wei Ou, Junxing Chen, Lingwu Chen
Software Mentions: 5
Published: almost 5 years ago

10.1002/cam4.3289

Predicting biomarkers from classifier for liver metastasis of colorectal adenocarcinomas using machine learning models
Cited by: 12
Author(s): Shuwen Han, Yang Xi, Qing Zhou, Zhuang Jing, Wei Wu
Software Mentions: 5
Published: almost 6 years ago

10.7150/thno.63416

Mapping the landscape of synthetic lethal interactions in liver cancer
Cited by: 7
Author(s): Chen Yang, Yuchen Guo, Ruolan Qian, Yi‐Wen Huang, Linmeng Zhang, Jun Wang, Xiaowen Huang, Zhicheng Liu, Wenxin Qin, Cun Wang, Huimin Chen, Xuhui Ma, Dayong Zhang
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2021.648806

Construction of a Prognostic Immune-Related LncRNA Risk Model for Lung Adenocarcinoma
Cited by: 16
Author(s): Yue Li, Ruoyi Shen, Anqi Wang, Jian Zhao, Jieqi Zhou, Weijie Zhang, Ruochen Zhang, Jianjie Zhu, Zeyi Liu, Jian-An Huang
Software Mentions: 5
Published: about 5 years ago

10.1111/1759-7714.14002

Significance of tumor mutation burden and immune infiltration in thymic epithelial tumors
Cited by: 8
Author(s): Zi-Ming Wang, Qiang Xu, David Kaul, Mahmoud Ismail, Harun Badakhshi
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-019-3008-x

An equivalence approach to the integrative analysis of feature lists
Cited by: 1
Author(s): Álex Sánchez-Pla, Miquel Salicrú, Jordi Ocaña
Software Mentions: 5
Published: almost 7 years ago

10.1002/cam4.4109

A prognostic nomogram based on competing endogenous RNA network for clear‐cell renal cell carcinoma
Cited by: 2
Author(s): Yun Peng, Sanlan Wu, Zihan Xu, Dingkun Hou, Nan Li, Zheyu Zhang, Lili Wang, Haitao Wang
Software Mentions: 5
Published: almost 5 years ago

10.1002/cam4.4206

Key sunitinib‐related biomarkers for renal cell carcinoma
Cited by: 9
Author(s): Yun Peng, Shiqiang Dong, Yuxuan Song, Dingkun Hou, Lili Wang, Bowen Li, Haitao Wang
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12920-021-00928-9

Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of esophageal squamous cell carcinoma
Cited by: 8
Author(s): Mingdi Liu, Faping Li, Bin Liu, Yong‐Ping Jian, Dan Zhang, Honglan Zhou, Yishu Wang, Zhixiang Xu
Software Mentions: 5
Published: about 5 years ago

10.1002/cam4.3526

Construction of a disease‐specific lncRNA‐miRNA‐mRNA regulatory network reveals potential regulatory axes and prognostic biomarkers for hepatocellular carcinoma
Cited by: 12
Author(s): Qi Zhang, Lin Sun, Qiuju Zhang, Wei Zhang, Wei Tian, Meina Liu, Yupeng Wang
Software Mentions: 5
Published: over 5 years ago

10.1038/s41392-020-00457-4

Longitudinal transcriptome analyses show robust T cell immunity during recovery from COVID-19
Cited by: 55
Author(s): Hong Zheng, Min Xu, Cui Xian Yang, Ren Rong Tian, Mi Zhang, Jian Jian Li, Xi Cheng Wang, Zhao Ding, Gui Mei Li, Xiaolu Li, Yu He, Xing-qi Dong, Yong Yao, Yong Zheng
Software Mentions: 5
Published: over 5 years ago

10.18632/aging.203081

Pan-cancer analysis of the prognostic value of C12orf75 based on data mining
Cited by: 3
Author(s): Guangzhen Cai, Guan-Nan Jin, Jintai Liang, Ganxun Li, Xiaoping Chen, Huifang Liang, Zhao Ding
Software Mentions: 5
Published: about 5 years ago

10.1186/s13287-021-02508-1

Transcriptome-wide m6A methylome during osteogenic differentiation of human adipose-derived stem cells
Cited by: 4
Author(s): Weihao Sun, Yidan Song, Kai Xia, Liyuan Yu, Xinqi Huang, Zhihe Zhao, Jun Liu
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12916-020-01806-4

ADAM22/LGI1 complex as a new actionable target for breast cancer brain metastasis
Cited by: 7
Author(s): Sara Charmsaz, Ben Doherty, Sinéad Cocchiglia, Damir Varešlija, Attilio Marino, Nicola Cosgrove, Ricardo Marques, Nolan Priedigkeit, Siobhan Purcell, Fiona T. Bane, Jarlath Bolger, Christopher Byrne, Philip J. O’Halloran, Francesca Brett, Katherine M. Sheehan, Kieran Brennan, Ann M. Hopkins, Stephen Keelan, Petra Jagušt, Stephen F. Madden, Chiara Martinelli, Matteo Battaglini, Steffi Oesterreich, Adrian V. Lee, Gianni Ciofani, Arnold D. Hill, Leonie S. Young
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2020.01943

Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials
Cited by: 4
Author(s): Felix Laguna-Teno, María Suárez-Diez, Juan Antonio Tamayo-Ramos
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-021-96966-5

Molecular characterization and cell type composition deconvolution of fibrosis in NAFLD
Cited by: 26
Author(s): Lorena Pantano, George Agyapong, Yang Shen, Zhuo Zhu, Francesc Fernández-Albert, Werner Rust, Dagmar Knebel, Jon Hill, Carine M. Boustany-Kari, Julia F. Doerner, Jörg F. Rippmann, Raymond T. Chung, Shannan Ho Sui, Eric J. Simon, Kathleen E. Corey
Software Mentions: 5
Published: over 4 years ago

10.3389/fcell.2021.633607

Development and Validation of a Hypoxia-Associated Prognostic Signature Related to Osteosarcoma Metastasis and Immune Infiltration
Cited by: 35
Author(s): Yucheng Fu, Qiyuan Bao, Zhuochao Liu, Guoyu He, Junxiang Wen, Qi Liu, Yanguang Xu, Zhijian Jin, Weibin Zhang
Software Mentions: 5
Published: about 5 years ago

10.1038/s41419-021-03740-6

Single-cell analysis reveals urothelial cell heterogeneity and regenerative cues following cyclophosphamide-induced bladder injury
Cited by: 12
Author(s): Xiaomu Cheng, Huadong Lai, Wenqin Luo, Man Zhang, Juju Miao, Weichen Song, Shunpeng Xing, Jia Wang, Wei‐Qiang Gao
Software Mentions: 5
Published: about 5 years ago

10.1111/jcmm.16366

ARL4C might serve as a prognostic factor and a novel therapeutic target for gastric cancer: bioinformatics analyses and biological experiments
Cited by: 7
Author(s): Ning Xie, Yongping Bai, Qiao Liao, Yuxiang Bai, Jian Wu, Yan Li, Mingzuo Jiang, Bing Xu, Ni Zhen, Ting Yuan, Yongquan Shi, Kaijie Wu, Feng Xu, Jinhai Wang, Dong Liu, Na Liu
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-020-07002-1

Analysis of the brain transcriptome in lines of laying hens divergently selected for feather pecking
Cited by: 13
Author(s): Clemens Falker‐Gieske, Andrea Mott, Siegfried Preuß, Sören Franzenburg, W. Bessei, Jörn Bennewitz, Jens Tetens
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcell.2021.641960

Immune-Related Long Non-coding RNA Signature and Clinical Nomogram to Evaluate Survival of Patients Suffering Esophageal Squamous Cell Carcinoma
Cited by: 14
Author(s): Tong Zhu, Zhifeng Ma, Haiyong Wang, Desheng Wei, Bin Wang, Chu Zhang, Linhai Fu, Zhupeng Li, Guangmao Yu
Software Mentions: 5
Published: over 5 years ago

10.3389/fmed.2021.716869

An Immune Signature Robustly Predicts Clinical Deterioration for Hepatitis C Virus-Related Early-Stage Cirrhosis Patients
Cited by: 1
Author(s): Cheng Guo, Chunyan Dong, Junjie Zhang, Rui Wang, Zhe Wang, Jie Zhou, Wei Wang, Bing Ji, Ben Ma, Yanli Ge, Zhirong Wang
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41419-020-02948-2

Acyl-CoA thioesterase 1 prevents cardiomyocytes from Doxorubicin-induced ferroptosis via shaping the lipid composition
Cited by: 55
Author(s): Yunchang Liu, Liping Zeng, Yong Yang, Chen Chen, Daowen Wang, Hong Wang
Software Mentions: 5
Published: over 5 years ago

10.18632/aging.102399

DNA methylation profile is a quantitative measure of biological aging in children
Cited by: 23
Author(s): Xiaohui Wu, Weidan Chen, Fangqin Lin, Qingsheng Huang, Jiayong Zhong, Huan Gao, Yanyan Song, Huiying Liang
Software Mentions: 5
Published: over 6 years ago

10.1111/jcmm.16714

Single‐cell RNA sequencing identify SDCBP in ACE2‐positive bronchial epithelial cells negatively correlates with COVID‐19 severity
Cited by: 16
Author(s): Ding Ma, Shuwen Liu, Lili Hu, Qinyu He, Weiwei Shi, Dongming Yan, Chunyue Yin, Guang Zhang, Zhong‐Xia Wang, Junhua Wu, Chunping Jiang
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41419-020-2520-2

NF-kappa B interacting long noncoding RNA enhances the Warburg effect and angiogenesis and is associated with decreased survival of patients with gliomas
Cited by: 16
Author(s): Chen Zheng, Shiting Li, Lin Shen, Xiangyu Wei, Hanshuo Zhu, Xueyi Wang, Min Yang, Xiaohang Zheng
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-015-1787-7

Identification and functional analysis of early gene expression induced by circadian light-resetting in Drosophila
Cited by: 20
Author(s): Adeolu B. Adewoye, Charalambos P. Kyriacou, Eran Tauber
Software Mentions: 5
Published: almost 11 years ago

10.3389/fcell.2021.723721

Identification of the Immune-Related Genes in Tumor Microenvironment That Associated With the Recurrence of Head and Neck Squamous Cell Carcinoma
Cited by: 6
Author(s): Chengcheng Liu, Wenwen Qi, Nianqiao Gong, Fenlu Zhu, Ran Xu, Zhaogang Teng, Fanxing Xu, Ya‐Zhen Qin, Mingqiu Zhao, Xiaoming Li, Ming Xia
Software Mentions: 5
Published: almost 5 years ago

10.3389/fcell.2021.648331

Fibrillarin-GFP Facilitates the Identification of Meiotic Competent Oocytes
Cited by: 6
Author(s): Ting Wang, Jie Na
Software Mentions: 5
Published: about 5 years ago

10.1186/s12935-021-01933-9

Low expression of CHRDL1 and SPARCL1 predicts poor prognosis of lung adenocarcinoma based on comprehensive analysis and immunohistochemical validation
Cited by: 13
Author(s): Huan Deng, Hang Qin, Deyan Shen, Yibi Zhang, Ming Chen
Software Mentions: 5
Published: about 5 years ago

10.1186/s12935-021-02038-z

Identification of methylation-driven genes prognosis signature and immune microenvironment in uterus corpus endometrial cancer
Cited by: 10
Author(s): Jinhui Liu, Chengjian Ji, Yichun Wang, Cheng Zhang, Hongjun Zhu
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12935-019-0866-2

LncRNA H19 regulates PI3K–Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network
Cited by: 45
Author(s): Min-Er Zhong, Yanyu Chen, Guannan Zhang, Lai Xu, Wei Ge, Bin Wu
Software Mentions: 5
Published: about 7 years ago

10.3389/fmed.2021.674338

Role of Immune Cell-Specific Hypermethylation Signatures in Classification and Risk Stratification of Breast Cancer
Cited by: 0
Author(s): Yong Chen, Fada Xia, Bo Jiang, Wenlong Wang, Xinying Li
Software Mentions: 5
Published: almost 5 years ago

10.1126/science.abe9403

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms
Cited by: 461
Author(s): David E. Gordon, Joseph Hiatt, Mehdi Bouhaddou, Veronica V. Rezelj, Svenja Ulferts, Hannes Braberg, Alexander S. Jureka, Kirsten Obernier, Jeffrey Z. Guo, Jyoti Batra, Robyn M. Kaake, Andrew Weckstein, Tristan W. Owens, Meghna Gupta, Sergei Pourmal, Erron W. Titus, Merve Çakır, Margaret Soucheray, Michael McGregor, Zeynep Çakır, Gwendolyn Μ. Jang, Matthew J. O’Meara, Tia A. Tummino, Ziyang Zhang, Helene Foussard, Ajda Rojc, Yuan Zhou, Dmitry Kuchenov, Ruth Hüttenhain, Jiewei Xu, Manon Eckhardt, Danielle L. Swaney, Jacqueline M. Fabius, Manisha R. Ummadi, Beril Tutuncuoglu, Ujjwal Rathore, Maya Modak, Paige Haas, Kelsey M. Haas, Zun Zar Chi Naing, Ernst H. Pulido, Ying Shi, Iñigo Barrio-Hernandez, Danish Memon, Eirini Petsalaki, Alistair S. Dunham, Miguel Marrero, David F. Burke, Cassandra Koh, Thomas Vallet, Jesus A. Silvas, Caleigh M. Azumaya, Christian Billesboelle, Axel F. Brilot, Melody G. Campbell, Amy Diallo, Miles Sasha Dickinson, Devan Diwanji, Nadia Herrera, Nick Hoppe, Huong T. Kratochvil, Yanxin Liu, Gregory E. Merz, Michelle Moritz, Henry C. Nguyen, Carlos Nowotny, Cristina Puchades, Alexandrea N. Rizo, Ursula Schulze‐Gahmen, Amber M. Smith, Ming Sun, I.D. Young, Jianhua Zhao, Daniel Asarnow, J.T. Biel, Alisa Bowen, Julian R. Braxton, Jen Chen, Cynthia M. Chio, Un Seng Chio, Ishan Deshpande, Loan Doan, Bryan Faust, Sebastián Flores, Mingliang Jin, Sun Kyung Kim, Victor Lam, Fei Li, J Li, Yen-Li Li, Yang Li, Xi Liu, Megan Lo, Kyle E. Lopez, Arthur A. Melo, Frank R. Moss, Phuong T. Nguyen, Joana Paulino, Komal Ishwar Pawar, Jessica K. Peters, Thomas H. Pospiech, Maliheh Safari, Smriti Sangwan, Kaitlin Schaefer, Paul Thomas, Aye C. Thwin, Raphael Trenker, Eric Tse, Tsz Kin Martin Tsui, Feng Wang, Natalie Whitis, Zanlin Yu, Kaihua Zhang, Sunny Zhang, Fengbo Zhou, Daniel J. Saltzberg, Anthony J. Hodder, Amber S Shun-Shion, Daniel M. Williams, Kris M. White, Romel Rosales, Thomas Kehrer, Lisa Miorin, Elena Moreno, Arvind H. Patel, Suzannah J. Rihn, Mir M. Khalid, Albert Vallejo-Gracia, Parinaz Fozouni, Camille R. Simoneau, Theodore L. Roth, David Wu, Mohd Anisul Karim, Maya Ghoussaini, Ian Dunham, Francesco Berardi, Sebastian Weigang, Maxime Chazal, Jisoo Park, James Logue, Marisa E. McGrath, Stuart Weston, Robert Haupt, C. James Hastie, Matthew Elliott, Fiona Brown, Kerry Burness, Elaine Reid, Mark Dorward, Clare Johnson, Stuart G. Wilkinson, Anna Geyer, Daniel M. Giesel, Carla Baillie, Samantha L. Raggett, Hannah Leech, Rachel Toth, Nicola Goodman, Kathleen C. Keough, Abigail Lind, Reyna Klesh, Kafi Hemphill, Jared Carlson-Stevermer, Jennifer Oki, Kevin Holden, Travis J. Maures, Katherine S. Pollard, Andrej S̆ali, David A. Agard, Yifan Cheng, James S. Fraser, Adam Frost, Natalia Jura, Tanja Kortemme, Aashish Manglik, Daniel R. Southworth, Robert M. Stroud, Dario R. Alessi, Paul Davies, Matthew B. Frieman, Trey Ideker, Carmen Abate, Nolwenn Jouvenet, Georg Kochs, Brian K Shoichet, Melanie Ott, Massimo Palmarini, Kevan M. Shokat, Adolfo Garcı́a-Sastre, Jeremy A. Rassen, Robert Grosse, Oren S. Rosenberg, Kliment A. Verba, Christopher F. Basler, Marco Vignuzzi, Andrew A. Peden, Pedro Beltrão, Nevan J. Krogan, Tristan W. Owens, Meghna Gupta, Sergei Pourmal, Erron W. Titus, Caleigh M. Azumaya, Christian B. Billesbølle, Axel F. Brilot, Melody G. Campbell, Amy Diallo, Miles Sasha Dickinson, Devan Diwanji, Nadia Herrera, Nick Hoppe, Huong T. Kratochvil, Yanxin Liu, Gregory E. Merz, Michelle Moritz, Henry C. Nguyen, Carlos Nowotny, Cristina Puchades, Alexandrea N. Rizo, Ursula Schulze‐Gahmen, Amber M. Smith, Ming Sun, I.D. Young, Jianhua Zhao, Daniel Asarnow, J.T. Biel, Alisa Bowen, Julian R. Braxton, Jen Chen, Cynthia M. Chio, Un Seng Chio, Ishan Deshpande, Loan Doan, Bryan Faust, Sebastián Flores, Mingliang Jin, Kate Kim, Victor Lam, Fēi Li, Junrui Li, Yen-Li Li, Yang Li, Xi Liu, Megan Lo, Kyle E. Lopez, Arthur A. Melo, Frank R. Moss, Phuong T. Nguyen, Joana Paulino, Komal Ishwar Pawar, Jessica K. Peters, Thomas H. Pospiech, Maliheh Safari, Smriti Sangwan, Kaitlin Schaefer, Paul Thomas, Aye C. Thwin, Raphael Trenker, Eric Tse, Tsz Kin Martin Tsui, Feng Wang, Natalie Whitis, Zanlin Yu, Kaihua Zhang, Zifeng Yang, Fengbo Zhou, Donovan Trinidad, David A. Agard, Yifan Cheng, James S. Fraser, Adam Frost, Natalia Jura, Tanja Kortemme, Aashish Manglik, Daniel R. Southworth, Robert M. Stroud, Oren S. Rosenberg, Kliment A. Verba, Joana Damas, Graham M. Hughes, Kathleen C. Keough, Corrie Painter, Nicole S. Persky, Marco Corbo, Bodgan Kirilenko, Michael Hiller, Klaus‐Peter Koepfli, Irene M. Kaplow, Morgan Wirthlin, Andreas R. Pfenning, Huabin Zhao, Diane P. Genereux, Ross Swofford, Abigail Lind, Katherine S. Pollard, Oliver A. Ryderq, Martin Nweeia, Jennifer R. S. Meadows, Michael X. Dong, Ola Wallerman, Vikki Marinescu, Kerstin Lindblad‐Toh, David A. Ray, Sarahjane Power, Emma C. Teeling, Gaurav Chauhan, Shirley Xue Li, Elinor K. Karlsson, Harris A. Lewin
Software Mentions: 5
Published: over 5 years ago

10.7150/ijbs.45050

A Novel Ferroptosis-related Gene Signature for Overall Survival Prediction in Patients with Hepatocellular Carcinoma
Cited by: 342
Author(s): Jie Liang, De-Shen Wang, Haocheng Lin, Xiuxing Chen, Hui Yang, Yun Zheng, Yuhong Li
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2019.01716

Enhanced Immunomodulation in Inflammatory Environments Favors Human Cardiac Mesenchymal Stromal-Like Cells for Allogeneic Cell Therapies
Cited by: 3
Author(s): Falk Diedrichs, Meaghan Stolk, Karsten Jürchott, Marion Haag, Michael Sittinger, Martina Seifert
Software Mentions: 5
Published: almost 7 years ago

10.3389/fimmu.2021.666137

Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer
Cited by: 9
Author(s): Yang Peng, Haochen Yu, Yudi Jin, Fanli Qu, Haoyu Ren, Zhenrong Tang, Yingzi Zhang, Chi Qu, Beige Zong, Shengchun Liu
Software Mentions: 5
Published: about 5 years ago

10.1186/s12935-021-01826-x

Systematic identification of key functional modules and genes in esophageal cancer
Cited by: 4
Author(s): Rui Wu, Hao Zhuang, Yukun Mei, Jin‐Yu Sun, Tao Dong, Lili Zhao, Zhining Fan, Li Liu
Software Mentions: 5
Published: over 5 years ago

10.7150/jca.50868

Data mining analysis of the prognostic impact of N<sup>6</sup>-methyladenosine regulators in patients with endometrial adenocarcinoma
Cited by: 7
Author(s): Junyu Zhai, Shang Li, Yu Liu, Yanzhi Du
Software Mentions: 5
Published: over 5 years ago

10.1186/s12935-021-02117-1

Plastin-3 is a diagnostic and prognostic marker for pancreatic adenocarcinoma and distinguishes from diffuse large B-cell lymphoma
Cited by: 6
Author(s): Fei Xiong, Guanhua Wu, Bing Wang, Yongjun Chen
Software Mentions: 5
Published: almost 5 years ago

10.3389/fcell.2021.684643

Development of an Individualized Ubiquitin Prognostic Signature for Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Yue Wu, Xi Zhang, Wa Xian, Huan Feng, Bintao Hu, Zhiyao Deng, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Jihong Liu, Tao Wang
Software Mentions: 5
Published: almost 5 years ago

10.7150/jca.55719

MRPS17 promotes invasion and metastasis through PI3K/AKT signal pathway and could be potential prognostic marker for gastric cancer
Cited by: 5
Author(s): Wenjie Zhou, Jun Ouyang, Junqing Li, Fangjie Liu, Tailai An, Lv-Jia Cheng, Zi Chong Kuo, Changhua Zhang, Yulong He
Software Mentions: 5
Published: over 5 years ago

10.1186/s13195-021-00862-z

Prediction of differentially expressed microRNAs in blood as potential biomarkers for Alzheimer’s disease by meta-analysis and adaptive boosting ensemble learning
Cited by: 26
Author(s): Sze Chung Yuen, Xueya Liang, Hongmei Zhu, Yongliang Jia, Siu-wai Leung
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-020-06911-5

Wild mice with different social network sizes vary in brain gene expression
Cited by: 2
Author(s): Patrícia C. Lopes, Barbara König
Software Mentions: 5
Published: almost 6 years ago

10.18632/aging.103721

Gene expression-based clinical predictions in lung adenocarcinoma
Cited by: 3
Author(s): Yanlu Xiong, Jie Lei, Jinbo Zhao, Yangbo Feng, Tianyun Qiao, Yongsheng Zhou, Tao Jiang, Han Ye
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcell.2021.736540

Characterization of Molecular Heterogeneity Associated With Tumor Microenvironment in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy
Cited by: 9
Author(s): Weimin Zhong, Yinan Li, Yazhou Yuan, Hongbin Zhong, Chaoqun Huang, Jiwei Huang, Yao Lin, Jian Huang
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2020.575488

Integrated Analysis of Transcriptome and Secretome From Umbilical Cord Mesenchymal Stromal Cells Reveal New Mechanisms for the Modulation of Inflammation and Immune Activation
Cited by: 18
Author(s): Mónica Cruz-Barrera, Nathalia Flórez-Zapata, Nicolás Lemus-Diaz, Carlos O. Medina, Cristian Camilo Galindo, Lorena-Xiomara González-Acero, Luz Correa, Bernardo Camacho, Jens Gruber, Gustavo Salguero
Software Mentions: 5
Published: over 5 years ago

10.17305/bjbms.2020.5096

Bionformatics analysis reveals TSPAN1 as a candidate biomarker of progression and prognosis in pancreatic cancer
Cited by: 5
Author(s): Chenhui Ma, Zelong Cui, YiChao Wang, Lei Zhang, Jiaxin Wen, Huaibin Guo, Na Li, Wanxing Zhang
Software Mentions: 5
Published: over 5 years ago

10.18632/aging.203422

Hedgehog dysregulation contributes to tissue-specific inflammaging of resident macrophages
Cited by: 8
Author(s): Mahamat Babagana, Kyu-Seon Oh, Sayantan Chakraborty, Alicja Pacholewska, Mohammad Aqdas, Myong-Hee Sung
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13068-018-1215-8

The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973
Cited by: 42
Author(s): Xiaoming Tan, Songjun Hou, Kuo Song, Jens Georg, Stephan Klähn, Xuefeng Lü, Wolfgang R. Hess
Software Mentions: 5
Published: almost 8 years ago

10.3389/fimmu.2021.711980

Characterization of Organ-Specific Regulatory B Cells Using Single-Cell RNA Sequencing
Cited by: 7
Author(s): Si Yu Yang, Jie Long, Meng Huang, Pan Luo, Zhen Bian, Ya Xu, Chengbo Wang, Shu Yang, Li Liang, Carlo Selmi, M. Eric Gershwin, Zhi Bin Zhao, Zhe Xiong Lian
Software Mentions: 5
Published: over 4 years ago

10.1186/s13578-020-00517-w

Identification of predictors based on drug targets highlights accurate treatment of goserelin in breast and prostate cancer
Cited by: 6
Author(s): Yue Zhao, Huimin Sun, Jianzhong Zheng, Chen Shao, Dongwei Zhang
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2021.641987

Timing Does Matter: Nerve-Mediated HDAC1 Paces the Temporal Expression of Morphogenic Genes During Axolotl Limb Regeneration
Cited by: 3
Author(s): Mu-Hui Wang, Chih‐Cheng Hsu, Cheng‐Hsun Wu, Ling-Ling Chiou, Yi-Tzang Tsai, Hsuan-Shu Lee, Shau-Ping Lin
Software Mentions: 5
Published: about 5 years ago

10.7150/jca.29958

TGFBI Promotes Tumor Growth and is Associated with Poor Prognosis in Oral Squamous Cell Carcinoma
Cited by: 16
Author(s): Bingjie Wang, Kun-Ping Chi, Ruling Shen, Saiwei Zheng, Yang Guo, Jianfeng Li, Jian Fei, Yuan He
Software Mentions: 5
Published: over 7 years ago

10.1111/jcmm.14886

Expression signature of six‐snoRNA serves as novel non‐invasive biomarker for diagnosis and prognosis prediction of renal clear cell carcinoma
Cited by: 28
Author(s): Yimeng Zhao, Yuanyuan Yan, Rong Ma, Xuemei Lv, Liwen Zhang, Jinlong Wang, Wenjing Zhu, Liang Zhao, Longyang Jiang, Lin Zhao, Lijie Wen, Bo Yang, Yu Zong Chen, Miao He, Mingyan Liu, Minjie Wei
Software Mentions: 5
Published: over 6 years ago

10.1186/s41065-021-00181-1

Prognostic biomarkers and therapeutic targets in oral squamous cell carcinoma: a study based on cross-database analysis
Cited by: 10
Author(s): Wanli Yang, Wei Zhou, Xinhui Zhao, Xiaoqian Wang, Lili Duan, Yiding Li, Liaoran Niu, Junfeng Chen, Yujie Zhang, Yu Han, Daiming Fan, Liu Hong
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-020-07313-3

The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation
Cited by: 7
Author(s): Longsheng Xing, Yu X, Xi Qiao, Cong Huang, Qiang Wu, Yang Ni, Jiao Guo, Wan‐Xue Liu, Wei Fan, Fang‐Hao Wan, Wanqiang Qian
Software Mentions: 5
Published: over 5 years ago

10.1038/s41438-021-00529-8

Chromatin accessibility and translational landscapes of tea plants under chilling stress
Cited by: 21
Author(s): Pengjie Wang, Shan Jin, Xuejin Chen, Lihua Wu, Yuanrun Zheng, Chuan Yue, Yan Guo, Xingtan Zhang, Jing Yang, Naixing Ye
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2021.637832

Dynamic Intracellular Metabolic Cell Signaling Profiles During Ag-Dependent B-Cell Differentiation
Cited by: 3
Author(s): Paula Díez, Martín Pérez‐Andrés, Martin Bøgsted, Mikel Azkargorta, Rodrigo García-Valiente, Rosa Ma Dégano, E Blanco, Sheila Mateos-Gomez, Paloma Bárcena, Santiago Cruz, Rafael Góngora, Félix Elortza, Alicia Landeira-Viñuela, Pablo Juanes-Velasco, Víctor Segura, Raúl Manzano-Román, Júlia Almeida, Karen Dybkær, Alberto Órfão, Manuel Fuentes
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-021-07451-2

Multi-species transcriptome meta-analysis of the response to retinoic acid in vertebrates and comparative analysis of the effects of retinol and retinoic acid on gene expression in LMH cells
Cited by: 5
Author(s): Clemens Falker‐Gieske, Andrea Mott, Sören Franzenburg, Jens Tetens
Software Mentions: 5
Published: over 5 years ago

10.1038/s41438-021-00487-1

Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development
Cited by: 34
Author(s): Anzhen Fu, Qing Wang, Jianlou Mu, Lili Ma, Changlong Wen, Xiaoyan Zhao, Lipu Gao, Jian Li, Kai Shi, Yunxiang Wang, Xuechuan Zhang, Xuewen Zhang, Fengling Wang, Donald Grierson, Jinhua Zuo
Software Mentions: 5
Published: over 5 years ago

10.1186/s13073-021-00876-0

In vivo genome editing in mouse restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers
Cited by: 9
Author(s): Menglong Chen, Hui Shi, Shixue Gou, Xiaomin Wang, Lei Li, Jin Qiu, Han Wu, Huili Zhang, Yaqin Li, Liang Wang, Huan Li, Jixian Lin, Wenjing Guo, Zhiwu Jiang, Xiaoyu Yang, Anding Xu, Yunping Zhu, Cheng Zhang, Liangxue Lai, Xiaoping Li
Software Mentions: 5
Published: about 5 years ago

10.3389/fcvm.2021.631650

Integrated DNA Methylation and Gene Expression Analysis Identified S100A8 and S100A9 in the Pathogenesis of Obesity
Cited by: 7
Author(s): Ningyuan Chen, Miao Liu, Wei Lin, Donghua Zou, Ling Huang, Jian Huang, Wei Shi, Li-Lin Li, Yu-Xing Luo, Hao Liang, Shang‐Ling Pan, Junhua Peng
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-016-3228-7

RNA-seq based transcriptomic map reveals new insights into mouse salivary gland development and maturation
Cited by: 30
Author(s): Christian Gluck, Sang‐Won Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha, Rose‐Anne Romano
Software Mentions: 5
Published: over 9 years ago

10.1042/BSR20194324

Identification of metastasis and prognosis-associated genes for serous ovarian cancer
Cited by: 12
Author(s): Yijun Yang, Suwan Qi, Chun Shi, Xiao Han, Juanpeng Yu, Lei Zhang, Shanshan Qin, Yingming Gao
Software Mentions: 5
Published: about 6 years ago

10.1186/s12863-020-00852-4

Transcriptome analysis identifies genes and co-expression networks underlying heat tolerance in pigs
Cited by: 9
Author(s): Yuqing He, Christian Maltecca, Francesco Tiezzi, Emmanuel Lozada Soto, W. L. Flowers
Software Mentions: 5
Published: about 6 years ago

10.3389/fimmu.2018.01868

Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development
Cited by: 11
Author(s): Friederike Ebner, Mathias Kuhring, Aleksandar Radonić, Ankur Midha, Bernhard Y. Renard, Susanne Hartmann
Software Mentions: 5
Published: almost 8 years ago

10.3390/biom9100586

Allogenic Faecal Microbiota Transfer Induces Immune-Related Gene Sets in the Colon Mucosa of Patients with Irritable Bowel Syndrome
Cited by: 5
Author(s): Savanne Holster, Guido Hooiveld, Dirk Repsilber, Willem M. de Vos, Robert Jan Brummer, Julia König
Software Mentions: 5
Published: over 6 years ago

10.1186/s12862-021-01753-5

Rapid evolution and molecular convergence in cryptorchidism-related genes associated with inherently undescended testes in mammals
Cited by: 4
Author(s): Simin Chai, Ran Tian, Juanjuan Bi, Shixia Xu, Wenhua Ren
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2021.695865

Prognosis and Characterization of Immune Microenvironment in Acute Myeloid Leukemia Through Identification of an Autophagy-Related Signature
Cited by: 19
Author(s): Denggang Fu, Biyu Zhang, Shiyong Wu, Yinghua Zhang, Jingwu Xie, Wangbin Ning, Hua Jiang
Software Mentions: 5
Published: about 5 years ago

10.1093/gigascience/giz057

Map and model—moving from observation to prediction in toxicogenomics
Cited by: 15
Author(s): Andreas Schüttler, Rolf Altenburger, Madeleine Ammar, Marcella Bader-Blukott, Gianina Jakobs, Johanna Knapp, Janet Krüger, Kristin Reiche, Gi‐Mick Wu, Wibke Busch
Software Mentions: 5
Published: about 7 years ago

10.1186/s12979-020-00182-0

Effect of aging on the transcriptomic changes associated with the expression of the HERV-K (HML-2) provirus at 1q22
Cited by: 11
Author(s): Arttu Autio, Tapio Nevalainen, Binisha H. Mishra, Marja Jylhä, Heini Flinck, Mikko Hurme
Software Mentions: 5
Published: about 6 years ago

10.1186/s12263-021-00688-2

An 8-week freeze-dried blueberry supplement impacts immune-related pathways: a randomized, double-blind placebo-controlled trial
Cited by: 7
Author(s): Michèle Rousseau, Justine Horne, Frédéric Guénard, Juan de Toro‐Martín, Véronique Garneau, Valérie Guay, Michèle Kearney, Geneviève Pilon, Denis Roy, Patrick Couture, Charles Couillard, André Marette
Software Mentions: 5
Published: about 5 years ago

10.3390/genes11080868

Identification of circRNA-lncRNA-miRNA-mRNA Competitive Endogenous RNA Network as Novel Prognostic Markers for Acute Myeloid Leukemia
Cited by: 52
Author(s): Yuanrong Cheng, Yangfeng Su, Shoubi Wang, Yurun Liu, Lin Jin, Qi Wan, Ying Liu, Chaoyang Li, Xuan Sang, Yang Liu, Chang Liu, Zhichong Wang
Software Mentions: 5
Published: almost 6 years ago

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Papers Mentioning clusterProfiler 2,223