Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: limma

https://packages.ecosyste.ms/registries/bioconductor.org/packages/limma

Linear Models for Microarray Data
3 versions
Latest release: about 1 year ago
314 dependent packages
4,663,292 downloads total

Papers Mentioning limma 7,776

10.1371/journal.pcbi.1008491
Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness
Cited by: 14
Author(s): Iván Cárcamo-Orive, Marc Henrion, Kuixi Zhu, Noam D. Beckmann, Paige Cundiff, Sara Moein, Zenan Zhang, Melissa Alamprese, Sunita L. D’Souza, Martin Wabitsch, Eric E. Schadt, Thomas Quertermous, Joshua W. Knowles, Rui Chang
Software Mentions: 6
Published: almost 4 years ago
10.18632/aging.103807
Identification of long-term survival-associated gene in breast cancer
Cited by: 12
Author(s): Shipeng Ning, Hui Li, Kun Qiao, Qin Wang, Meiying Shen, Yujuan Kang, Yanling Yin, Jiena Liu, Lei Liu, Siyu Hou, Yunlong Wang, Shouping Xu, Da Pang
Software Mentions: 6
Published: about 4 years ago
10.3390/nu13041340
Ileal Lactase Expression Associates with Lactase Persistence Genotypes
Cited by: 1
Author(s): Jan Krzysztof Nowak, Emilia Dybska, Marzena Dworacka, Natallia Tsikhan, Victoria Kononets, Saule Bermagambetova, Jarosław Walkowiak
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pgen.1009506
Comparative analysis reveals distinctive epigenetic features of the human cerebellum
Cited by: 11
Author(s): Elaine E. Guevara, William D. Hopkins, Patrick R. Hof, John J. Ely, Brenda J. Bradley, Chet C. Sherwood
Software Mentions: 6
Published: over 3 years ago
10.1155/2021/5552623
Integrative Functional Genomic Analysis of Molecular Signatures and Mechanistic Pathways in the Cell Cycle Underlying Alzheimer’s Disease
Cited by: 5
Author(s): Zhike Zhou, Jun Bai, Shanshan Zhong, Rongwei Zhang, Kexin Kang, Xiaoqian Zhang, Ying Xu, Chuansheng Zhao, Mei Zhao
Software Mentions: 6
Published: over 3 years ago
10.1289/EHP595
Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children’s Environmental Health Studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group
Cited by: 212
Author(s): Carrie V. Breton, Carmen J. Marsit, Elaine M. Faustman, Kari Nadeau, Jaclyn M. Goodrich, Dana C. Dolinoy, Julie B. Herbstman, Nina Holland, Janine M. LaSalle, Rebecca Jean Schmidt, Paul Yousefi, Frederica P. Perera, Bonnie R. Joubert, Joseph L. Wiemels, Miles G. Taylor, Ivana V. Yang, Rui Chen, Kinjal Hew, Deborah M. Hussey Freeland, Rachel L. Miller, Susan K. Murphy
Software Mentions: 6
Published: over 7 years ago
10.1186/1471-2164-10-270
Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events
Cited by: 110
Author(s): Sônia Sousa Melo Cavalcanti de Albuquerque, Céline Carret, Ana Rita Grosso, Alice S. Tarun, Xinxia Peng, Stefan H. I. Kappe, Miguel Prudêncio, Maria M. Mota
Software Mentions: 6
Published: over 15 years ago
10.1371/journal.pcbi.1007162
Cross-species functional modules link proteostasis to human normal aging
Cited by: 10
Author(s): Andrea Komljenović, Hao Li, Vincenzo Sorrentino, Zoltán Kutalik, Johan Auwerx, Marc Robinson‐Rechavi
Software Mentions: 6
Published: over 5 years ago
10.1186/1471-2105-9-86
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Cited by: 75
Author(s): Frédéric Chalmel, Michael Primig
Software Mentions: 6
Published: almost 17 years ago
10.1080/22221751.2020.1799723
Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells
Cited by: 203
Author(s): Sofia Appelberg, Soham Gupta, Sara Svensson Akusjärvi, Anoop T. Ambikan, Flora Mikaeloff, Elisa Saccon, Ákos Végvári, Rui Benfeitas, Maike Sperk, Marie Ståhlberg, Shuba Krishnan, Kamal Singh, Josef Penninger, Alì Mirazimi, Ujjwal Neogi
Software Mentions: 6
Published: almost 5 years ago
10.18632/aging.102683
DNAH10 mutation correlates with cisplatin sensitivity and tumor mutation burden in small-cell lung cancer
Cited by: 19
Author(s): Man Li, Anqi Lin, Peng Luo, Weitao Shen, Dan Xiao, Lan-ying Gou, Jian Zhang, Linlang Guo
Software Mentions: 6
Published: almost 5 years ago
10.1186/s12967-020-02689-y
Three hematologic/immune system-specific expressed genes are considered as the potential biomarkers for the diagnosis of early rheumatoid arthritis through bioinformatics analysis
Cited by: 60
Author(s): Qi Cheng, Xin Chen, Huaxiang Wu, Yan Du
Software Mentions: 6
Published: almost 4 years ago
10.18632/aging.202474
Clinical and genomic characteristics of metabolic syndrome in colorectal cancer
Cited by: 2
Author(s): Yanyan Li, Jungang Zhao, Xiaoli Wu, Yini Zhang, Jia Yin, Weiyang Cai
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12876-021-01734-4
Identification of the angiogenesis related genes for predicting prognosis of patients with gastric cancer
Cited by: 9
Author(s): Shu Zheng, Zizhen Zhang, Ning Ding, Jiawei Sun, Yaowang Lin, Jingyu Chen, Jing Zhong, Liming Shao, Zhenghua Lin, Min Xue
Software Mentions: 6
Published: over 3 years ago
10.1186/s12967-020-02260-9
Identification of key genes controlling breast cancer stem cell characteristics via stemness indices analysis
Cited by: 42
Author(s): Jianying Pei, Yanxia Wang, Yan Li
Software Mentions: 6
Published: almost 5 years ago
10.3390/nu13030807
Transient Effect of Infant Formula Supplementation on the Intestinal Microbiota
Cited by: 6
Author(s): Ning Chin, Gema Méndez-Lagares, Diana H. Taft, Victoria Laleau, Hung T. Kieu, Narayan Nicole, Susan B. Roberts, David A. Mills, Dennis J. Hartigan-O’Connor, Valerie J. Flaherman
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12967-021-03012-z
Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression
Cited by: 18
Author(s): Xu Liu, Li Yao, Jingkun Qu, Lin Liu, Ning Lü, Jiansheng Wang, Zhang Jia
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pgen.1008531
ELF5 modulates the estrogen receptor cistrome in breast cancer
Cited by: 16
Author(s): Catherine Piggin, Daniel Roden, Andrew M. K. Law, Mark P. Molloy, Christoph Krisp, Alexander Swarbrick, Matthew J. Naylor, Maria Kalyuga, Warren Kaplan, Samantha Oakes, David Gallego‐Ortega, Susan J. Clark, Jason S. Carroll, Nenad Bartoniček, Christopher J. Ormandy
Software Mentions: 6
Published: almost 5 years ago
10.1186/s12967-020-02545-z
Development and validation of a robust immune-related prognostic signature in early-stage lung adenocarcinoma
Cited by: 13
Author(s): Pancheng Wu, Yi Zheng, Yanyu Wang, Yadong Wang, Ning Liang
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pone.0153355
Immune Profiles to Predict Response to Desensitization Therapy in Highly HLA-Sensitized Kidney Transplant Candidates
Cited by: 20
Author(s): Julie M. Yabu, Janet Siebert, Holden T. Maecker
Software Mentions: 6
Published: over 8 years ago
10.18632/aging.203190
Immune infiltration and a ferroptosis-associated gene signature for predicting the prognosis of patients with endometrial cancer
Cited by: 32
Author(s): Wenwu Yin, Liao Fuchun, Mengjie Chen, Xiaoqing Qin, Hao Lai, Yuan Lin, Desheng Yao
Software Mentions: 6
Published: over 3 years ago
10.15252/embj.2018100882
Life‐long impairment of glucose homeostasis upon prenatal exposure to psychostimulants
Cited by: 11
Author(s): Solomiia Korchynska, Maria Krassnitzer, Katarzyna Maleńczyk, Rashmi B. Prasad, Evgenii Tretiakov, Sabah Rehman, Valentina Cinquina, Victoria Gernedl, Matthias Farlik, Julian Petersen, S Hannes, Julia Schachenhofer, Sonali N. Reisinger, Alice Zambon, Olof Asplund, Isabella Artner, Erik Keimpema, Gert Lübec, Jan Mulder, Christoph Bock, Daniela D. Pollak, Roman A. Romanov, Christian Pifl, Leif Groop, Tomas Hökfelt, Tibor Harkany
Software Mentions: 6
Published: about 5 years ago
10.3390/ijms22179337
Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients
Cited by: 3
Author(s): Alicja Pacholewska, Christina Grimm, Carmen D. Herling, Matthias Lienhard, Anja Königs, Bernd Timmermann, Janine Altmüller, Oliver Mücke, Hans Christian Reinhardt, Christoph Plass, Ralf Herwig, Michael Hallek, Michal R. Schweiger
Software Mentions: 6
Published: over 3 years ago
10.18632/aging.103350
A novel molecular-clinicopathologic nomogram to improve prognosis prediction of hepatocellular carcinoma
Cited by: 3
Author(s): Zhongjing Zhang, Wanqing Weng, Weiguo Huang, Boda Wu, Yi Zhou, Jie Zhang, Tuo Deng, Yan Wen, Jiecheng Zhang, Jian‐Yang Ao, Qiyu Zhang, Ke‐Qing Shi
Software Mentions: 6
Published: over 4 years ago
10.1186/s12872-021-02166-4
Identification of biomarkers associated with metabolic cardiovascular disease using mRNA-SNP-miRNA regulatory network analysis
Cited by: 4
Author(s): Zhiyuan Fan, Wei Peng, Zhiwen Wang, Ling Zhang, Kuo Li
Software Mentions: 6
Published: over 3 years ago
10.3390/ijms22105322
The Detection and Bioinformatic Analysis of Alternative 3′ UTR Isoforms as Potential Cancer Biomarkers
Cited by: 4
Author(s): Nitika Kandhari, Calvin A. Kraupner-Taylor, Paul F. Harrison, David Powell, Traude H. Beilharz
Software Mentions: 6
Published: over 3 years ago
10.3390/ijms22126307
Transcriptional Profiling Identifies Upregulation of Neuroprotective Pathways in Retinitis Pigmentosa
Cited by: 4
Author(s): Christina B. Bielmeier, Saskia Roth, Sabrina I. Schmitt, Stefaniya Boneva, Anja Schlecht, Mario Vallon, Ernst R. Tamm, Süleyman Ergün, Andreas Neueder, Barbara M. Braunger
Software Mentions: 6
Published: over 3 years ago
10.3390/ijms22094598
Combined Transcriptomic and Proteomic Analysis of Perk Toxicity Pathways
Cited by: 6
Author(s): Rebeka Popovic, Ivana Celardo, Yao Yu, Ana Carolina Oliveira Costa, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 6
Published: over 3 years ago
10.1186/1471-2164-15-1053
Cross-species transcriptomic analysis elucidates constitutive aryl hydrocarbon receptor activity
Cited by: 10
Author(s): Ren Sun, Lauren C. Chong, Trent T. Simmons, Kathleen E. Houlahan, Stephenie D. Prokopec, John D. Watson, Ivy D. Moffat, Sanna Lensu, Jere Lindén, Christine P’ng, Allan B. Okey, Raimo Pohjanvirta, Paul C. Boutros
Software Mentions: 6
Published: about 10 years ago
10.1155/2020/1686480
miRNA-Based Feature Classifier Is Associated with Tumor Mutational Burden in Head and Neck Squamous Cell Carcinoma
Cited by: 7
Author(s): Yu Xia, Qi Wang, Xiaolin Huang, Xinhai Yin, Jukun Song, Ke Zhao, Xiaofeng Duan
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pcbi.1006701
New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Cited by: 271
Author(s): Mohamed Mounir, Marta Lucchetta, Tiago Henrique Da T.C. Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo
Software Mentions: 6
Published: over 5 years ago
10.1016/j.ebiom.2021.103383
Clinically relevant aberrant Filip1l DNA methylation detected in a murine model of cutaneous squamous cell carcinoma
Cited by: 4
Author(s): Kevin A. Roth, Louis Coussement, Elena V. Knatko, Maureen Higgins, Sandra Steyaert, Charlotte M. Proby, Tim De Meyer, Albena T. Dinkova‐Kostova
Software Mentions: 6
Published: over 3 years ago
10.3389/fcell.2021.723676
Integrative Epigenome Map of the Normal Human Prostate Provides Insights Into Prostate Cancer Predisposition
Cited by: 5
Author(s): Tao Wang, Juan Song, Min Qu, Xu Gao, Wenhui Zhang, Ziwei Wang, Lin Zhao, Yan Wang, Bing Li, Jing Li, Jinjian Yang
Software Mentions: 6
Published: over 3 years ago
10.1186/s13148-019-0755-5
Alzheimer’s disease-associated (hydroxy)methylomic changes in the brain and blood
Cited by: 79
Author(s): Roy Lardenoije, Janou A. Y. Roubroeks, Ehsan Pishva, Markus Leber, Holger Wagner, Artemis Iatrou, Adam R. Smith, Rebecca G. Smith, Lars Eijssen, Luca Kleineidam, Amit Kawalia, Per Hoffmann, Tobias Luck, Steffi G. Riedel‐Heller, Frank Jessen, Wolfgang Maier, Michael Wagner, René Hurlemann, Günter Kenis, Muhammad Ali, Antonio del Sol, Diego Mastroeni, Elaine Delvaux, Paul D. Coleman, Jonathan Mill, Bart P. F. Rutten, Katie Lunnon, Alfredo Ramı́rez, Daniël L.A. van den Hove
Software Mentions: 6
Published: about 5 years ago
10.1186/s12885-021-08341-2
Identification of the prognostic value of ferroptosis-related gene signature in breast cancer patients
Cited by: 55
Author(s): Ding Wang, Guodong Wei, Jiangwei Ma, Shuai Cheng, Longyuan Jia, Xinyue Song, Ming Zhang, Mingyi Ju, Lin Wang, Lin Zhao, Shijie Xin
Software Mentions: 6
Published: over 3 years ago
10.1002/pld3.279
Gene expression changes occurring at bolting time are associated with leaf senescence in Arabidopsis
Cited by: 12
Author(s): Will E. Hinckley, Judy A. Brusslan
Software Mentions: 6
Published: about 4 years ago
10.1186/s13148-019-0787-x
Methylomic profiling in trisomy 21 identifies cognition- and Alzheimer’s disease-related dysregulation
Cited by: 12
Author(s): Larissa Haertle, Tobias Müller, Roy Lardenoije, Anna Maierhofer, Marcus Dittrich, Renzo J. M. Riemens, Samantha Stora, M Roche, Markus Leber, Steffi G. Riedel‐Heller, Michael Wagner, Martin Scherer, Aimé Ravel, Clotilde Mircher, Cécile Cieuta‐Walti, Sophie Durand, Daniel L. A. van de Hove, Per Hoffmann, Alfredo Ramı́rez, Thomas Haaf, Nady El Hajj, André Mégarbané
Software Mentions: 6
Published: about 5 years ago
10.3389/fgene.2021.709133
Identification of Transcription Factor-Related Gene Signature and Risk Score Model for Colon Adenocarcinoma
Cited by: 4
Author(s): Jia Wei Lin, Zichao Cao, Du Yu, Wei Cai
Software Mentions: 6
Published: about 3 years ago
10.1186/s13007-020-00611-7
DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models
Cited by: 22
Author(s): Ilana Lambert, Christine Paysant‐Le Roux, Stefano Colella, Marie-Laure Martin
Software Mentions: 6
Published: over 4 years ago
10.7554/eLife.57345
Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes
Cited by: 37
Author(s): Michelle C. Ward, Nicholas E. Banovich, Abhishek Sarkar, Matthew Stephens, Yoav Gilad
Software Mentions: 6
Published: almost 4 years ago
10.7554/eLife.37925
Multiple tumor suppressors regulate a HIF-dependent negative feedback loop via ISGF3 in human clear cell renal cancer
Cited by: 22
Author(s): Lili Liao, Zongzhi Z. Liu, Lauren Langbein, Weijia Cai, Eunah Cho, Jie Na, Xiaohua Niu, Wei Jiang, Zhijiu Zhong, Wesley L. Cai, Geetha Jagannathan, Essel Dulaimi, Joseph R. Testa, Robert G. Uzzo, Yuxin Wang, George R. Stark, Jianxin Sun, Stephen C. Peiper, Yaomin Xu, Qin Yan, Haifeng Yang
Software Mentions: 6
Published: about 6 years ago
10.3390/ijms20164037
Consistent Biomarkers and Related Pathogenesis Underlying Asthma Revealed by Systems Biology Approach
Cited by: 18
Author(s): Xiner Nie, Jinyi Wei, Youjin Hao, Jingxin Tao, Yinghong Li, Mingwei Liu, Bo-Ying Xu, Bo Li
Software Mentions: 6
Published: over 5 years ago
10.7717/peerj.9697
Phytotoxin synthesis genes and type III effector genes of <i>Pseudomonas syringae</i> pv. <i>actinidiae</i> biovar 6 are regulated by culture conditions
Cited by: 2
Author(s): Karin Hirose, Yasuhiro Ishiga, Takashi Fujikawa
Software Mentions: 6
Published: over 4 years ago
10.1186/s13148-020-00944-z
Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions
Cited by: 38
Author(s): Qingqin Li, Yu Sun, Tania Wang
Software Mentions: 6
Published: about 4 years ago
10.1186/s12885-019-6101-7
A large cohort study identifying a novel prognosis prediction model for lung adenocarcinoma through machine learning strategies
Cited by: 43
Author(s): Yin Li, Di Ge, Jie Gu, Fan Xu, Qinqing Zhu
Software Mentions: 6
Published: about 5 years ago
10.1186/s12885-021-08431-1
Five metastasis-related mRNAs signature predicting the survival of patients with liver hepatocellular carcinoma
Cited by: 7
Author(s): Chao Chen, Yan Qun Liu, Shi Qiu, Ya Li, Ning Jun Yu, Kang Liu, Li Ming Zhong
Software Mentions: 6
Published: over 3 years ago
10.12688/f1000research.28608.2
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
Cited by: 6
Author(s): Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø. Arntzen, Benoît J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 6
Published: over 3 years ago
10.7717/peerj.9975
Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer
Cited by: 11
Author(s): Xiuming Zhai, Zhaowei Yang, Xiji Liu, Z P Dong, Dandan Zhou
Software Mentions: 6
Published: about 4 years ago
10.1007/s00109-020-01908-9
Immune landscape and a novel immunotherapy-related gene signature associated with clinical outcome in early-stage lung adenocarcinoma
Cited by: 17
Author(s): Xuanwen Bao, Run Shi, Tianyu Zhao, Yanfang Wang
Software Mentions: 6
Published: over 4 years ago
10.1002/JLB.5MA0120-209R
Distinct and shared gene expression for human innate versus adaptive helper lymphoid cells
Cited by: 28
Author(s): Giuseppe Ercolano, Tania Wyss, Bérengère Salomé, Pedro Romero, Sara Trabanelli, Camilla Jandus
Software Mentions: 6
Published: almost 5 years ago
10.1186/s13148-018-0463-6
Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia
Cited by: 60
Author(s): Katherine Leavey, Samantha L. Wilson, Shannon Bainbridge, Wendy P. Robinson, Brian Cox
Software Mentions: 6
Published: almost 7 years ago
10.1186/1471-2105-7-467
Goulphar: rapid access and expertise for standard two-color microarray normalization methods
Cited by: 55
Author(s): Sophie Lemoine, Florence Combes, Nicolas Servant, Stéphane Le Crom
Software Mentions: 6
Published: about 18 years ago
10.1186/s13148-018-0593-x
Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals
Cited by: 19
Author(s): Ilze Elbere, Ivars Silamiķelis, Monta Ustinova, Ineta Kalniņa, Linda Zaharenko, Raitis Pečulis, Ilze Konrāde, Diana M. Ciuculete, Christina Zhukovsky, Dita Gudrā, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Valdis Pīrāgs, Helgi B. Schiöth, Jānis Kloviņš
Software Mentions: 6
Published: about 6 years ago
10.1186/s12885-021-08083-1
Gene expression and immune infiltration in melanoma patients with different mutation burden
Cited by: 8
Author(s): Liwei Wang, Chuanxi Fu, Rui Li, Lei Shi, Guosheng Zhao, Yan Zhang
Software Mentions: 6
Published: over 3 years ago
10.18632/aging.102714
ISG20 serves as a potential biomarker and drives tumor progression in clear cell renal cell carcinoma
Cited by: 22
Author(s): Tianbo Xu, Hailong Ruan, Su Gao, Jingchong Liu, Yuenan Liu, Zhengshuai Song, Qi Cao, Keshan Wang, Lin Bao, Di Liu, Junwei Tong, Jian Shi, Huageng Liang, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 6
Published: almost 5 years ago
10.1186/s13045-021-01131-0
High-resolution Hi-C maps highlight multiscale 3D epigenome reprogramming during pancreatic cancer metastasis
Cited by: 16
Author(s): Bo Ren, Jinshou Yang, Yuming Wang, Gang Ye, Huanyu Wang, Chen Yuan, Ruiyuan Xu, Xu-Ning Fan, Lei You, Taiping Zhang, Yupei Zhao
Software Mentions: 6
Published: over 3 years ago
10.1016/j.cels.2018.08.001
Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts
Cited by: 77
Author(s): Aleksej Zelezniak, Jakob Vowinckel, Floriana Capuano, Christoph B. Messner, Vadim Demichev, Nicole Polowsky, Michael Mülleder, Stephan Kamrad, Bernd Klaus, Markus A. Keller, Markus Ralser
Software Mentions: 6
Published: over 6 years ago
10.1155/2013/203681
Time Series Expression Analyses Using RNA-seq: A Statistical Approach
Cited by: 23
Author(s): Sangwon Oh, Seongho Song, Gregory A. Grabowski, Hongyu Zhao, James P. Noonan
Software Mentions: 6
Published: almost 12 years ago
10.18632/aging.103695
Glioblastoma cell differentiation trajectory predicts the immunotherapy response and overall survival of patients
Cited by: 26
Author(s): Zihao Wang, Xiaopeng Guo, Lu Gao, Yu Wang, Wenbin Ma, Bing Xing
Software Mentions: 6
Published: about 4 years ago
10.1155/2020/8537381
Autophagy Regulatory Genes MET and RIPK2 Play a Prognostic Role in Pancreatic Ductal Adenocarcinoma: A Bioinformatic Analysis Based on GEO and TCGA
Cited by: 10
Author(s): Xingyu Li, Zhiqiang Li, Hongwei Zhu, Xiao Yu
Software Mentions: 6
Published: about 4 years ago
10.7150/ijms.51918
Exploration of the relationship between tumor mutation burden and immune infiltrates in colon adenocarcinoma
Cited by: 3
Author(s): Rong Ouyang, Zhongzhuan Li, Peng Peng, Jinxiu Zhang, Jun Li, Mengbin Qin, Jiean Huang
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12885-021-08052-8
Comprehensive analysis of immune-related prognostic genes in the tumour microenvironment of hepatocellular carcinoma
Cited by: 2
Author(s): Weike Gao, Luan Li, Xinyin Han, Siyao Liu, Chengzhen Li, Guanying Yu, Lei Zhang, Dongsheng Zhang, Caiyun Liu, Erhong Meng, Shuai Hong, Dongliang Wang, Peiming Guo, Guangjun Shi
Software Mentions: 6
Published: over 3 years ago
10.1186/s13045-018-0679-0
Whole-exon sequencing of human myeloma cell lines shows mutations related to myeloma patients at relapse with major hits in the DNA regulation and repair pathways
Cited by: 31
Author(s): Benoît Tessoulin, Agnès Moreau-Aubry, Géraldine Descamps, Patricia Gomez‐Bougie, Sophie Maïga, Alban Gaignard, David Chiron, Emmanuelle Ménoret, Steven Le Gouill, Philippe Moreau, Martine Amiot, Catherine Pellat‐Deceunynck
Software Mentions: 6
Published: about 6 years ago
10.1016/j.xcrm.2021.100267
Cabozantinib and dasatinib synergize to induce tumor regression in non-clear cell renal cell carcinoma
Cited by: 2
Author(s): Hui Wen Lue, Daniel S. Derrick, Soumya Rao, Ahna Van Gaest, Larry C. Cheng, Jennifer Podolak, Samantha Lawson, Changhui Xue, Devin Garg, Ralph E. White, Christopher W. Ryan, Justin M. Drake, Anna Ritz, Laura M. Heiser, George V. Thomas
Software Mentions: 6
Published: over 3 years ago
10.3389/fgene.2021.701065
Identification of Tumor Antigens and Immune Landscape in Glioblastoma for mRNA Vaccine Development
Cited by: 12
Author(s): Liguo Ye, Long Wang, Jian Yang, Ping Hu, Chunyu Zhang, Shiao Tong, Zhennan Liu, Daofeng Tian
Software Mentions: 6
Published: over 3 years ago
10.1016/j.celrep.2019.03.104
Notch Signaling Mediates Secondary Senescence
Cited by: 72
Author(s): Yee Voan Teo, Nattaphong Rattanavirotkul, Nelly Olova, Angela Salzano, Andrea Quintanilla, Núria Tarrats, Christos Kiourtis, Miryam Müller, Anthony Green, Peter D. Adams, Juan Carlos Acosta, Tom Bird, Kristina Kirschner, Nicola Neretti, Tamir Chandra
Software Mentions: 6
Published: over 5 years ago
10.7150/ijms.46456
Lipid Metabolism is the common pathologic mechanism between Type 2 Diabetes Mellitus and Parkinson's disease
Cited by: 6
Author(s): Xi Zhang, Yu Fan, Yuan Luo, Lingjing Jin, Siguang Li
Software Mentions: 6
Published: almost 5 years ago
10.7150/ijms.61309
Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis
Cited by: 6
Author(s): Ke Zhu, Aiqun Xu, Wanli Xia, Pulin Li, Rui Han, Enze Wang, Sijing Zhou, Ran Wang
Software Mentions: 6
Published: almost 4 years ago
10.1016/j.celrep.2020.108629
VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide
Cited by: 10
Author(s): Kathrin Leppek, Gun Woo Byeon, Kotaro Fujii, Maria Barna
Software Mentions: 6
Published: almost 4 years ago
10.1038/s41598-021-90538-3
Identification of prognostic biomarkers related to the tumor microenvironment in thyroid carcinoma
Cited by: 6
Author(s): Junwei Du, Guoquan Li, Yang-sen Li, Xinguang Qiu
Software Mentions: 6
Published: over 3 years ago
10.1038/s41421-020-00200-x
Single-cell transcriptome atlas of lung adenocarcinoma featured with ground glass nodules
Cited by: 45
Author(s): Tao Lu, Xiaodong Yang, Yu Shi, Mengnan Zhao, Guoshu Bi, Jiaqi Liang, Zhencong Chen, Yiwei Huang, Wei Jiang, Lin Zhang, Junjie Xi, Shuai Wang, Yong Yang, Cheng Zhan, Qun Wang, Liang Tan
Software Mentions: 6
Published: about 4 years ago
10.1007/s00018-020-03485-z
Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue
Cited by: 17
Author(s): Tiziana Caputo, Van Du T. Tran, Nasim Bararpour, Carine Winkler, Gabriela Aguileta, Bao Khanh Trang, Greta Maria Paola Giordano Attianese, Anne Wilson, Aurélien Thomas, Marco Pagni, Nicolas Guex, Béatrice Desvergne, Federica Gilardi
Software Mentions: 6
Published: over 4 years ago
10.1186/s12885-020-06741-4
A novel risk score model based on eight genes and a nomogram for predicting overall survival of patients with osteosarcoma
Cited by: 30
Author(s): Guangzhi Wu, Minglei Zhang
Software Mentions: 6
Published: over 4 years ago
10.1038/s41598-021-92439-x
The amniotic fluid cell-free transcriptome in spontaneous preterm labor
Cited by: 11
Author(s): Gaurav Bhatti, Roberto Romero, Nardhy Gómez-López, Roger Piqué-Regi, Percy Pacora, Eun-Jung Jung, Lami Yeo, Chaur‐Dong Hsu, Mahendra Kavdia, Adi L. Tarca
Software Mentions: 6
Published: over 3 years ago
10.1038/s41598-019-41315-w
Novel Data Transformations for RNA-seq Differential Expression Analysis
Cited by: 23
Author(s): Zeyu Zhang, Danyang Yu, Minseok Seo, Craig P. Hersh, Scott T. Weiss, Weiliang Qiu
Software Mentions: 6
Published: over 5 years ago
10.18632/aging.103923
Two machine learning methods identify a metastasis-related prognostic model that predicts overall survival in medulloblastoma patients
Cited by: 3
Author(s): Kui Chen, Bingqing Huang, Shan Yan, Siyi Xu, Keqin Li, Kuiming Zhang, Qi Wang, Zhongwei Zhuang, Liang Wei, Yanfei Zhang, Min Liu, Hao Lian, Chunlong Zhong
Software Mentions: 6
Published: about 4 years ago
10.1038/s41419-018-0600-3
Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes
Cited by: 5
Author(s): Zhen Li, Shuiping Li, Ruoyan Li, Haitao Zhu, Xia Liu, Xingxing Guo, Lili Mu, Jie-Jing Cai, Fan Bai, Guoqiang Chen, Dengli Hong
Software Mentions: 6
Published: over 6 years ago
10.1038/s41598-019-39220-3
The miRNA-targeted transcriptome of porcine alveolar macrophages upon infection with Porcine Reproductive and Respiratory Syndrome Virus
Cited by: 9
Author(s): Sophie Dhorne–Pollet, Elisa Crisci, Núria Mach, Patricia Renson, Florence Jaffrézic, Guillemette Marot, Tatiana Maroilley, Marco Moroldo, Jérôme Lecardonnel, Fany Blanc, Nicolas Bertho, Olivier Bourry, Elisabetta Giuffra
Software Mentions: 6
Published: almost 6 years ago
10.1186/s13229-020-00402-w
Evidence for the placenta-brain axis: multi-omic kernel aggregation predicts intellectual and social impairment in children born extremely preterm
Cited by: 23
Author(s): Hudson P. Santos, Arjun Bhattacharya, Robert M. Joseph, Lisa Smeester, Karl Kuban, Carmen J. Marsit, T. Michael O’Shea, Rebecca C. Fry
Software Mentions: 6
Published: about 4 years ago
10.1038/s41598-018-28233-z
Moth oviposition shapes the species-specific transcriptional and phytohormonal response of Nicotiana attenuata to larval feeding
Cited by: 11
Author(s): Sylvia Drok, Michele Bandoly, Sandra Stelzer, Tobias Lortzing, Anke Steppuhn
Software Mentions: 6
Published: over 6 years ago
10.1371/journal.pbio.2006687
Quantitative assessment of cell population diversity in single-cell landscapes
Cited by: 40
Author(s): Qi Liu, Charles A. Herring, Quanhu Sheng, Jie Ping, Alan J. Simmons, Bob Chen, Amrita Banerjee, Wei Li, Guoqiang Gu, Robert J. Coffey, Yu Shyr, Ken S. Lau
Software Mentions: 6
Published: about 6 years ago
10.1038/s41598-017-14788-w
Smoking induces DNA methylation changes in Multiple Sclerosis patients with exposure-response relationship
Cited by: 50
Author(s): Francesco Marabita, Malin Almgren, Louise K. Sjöholm, Lara Kular, Yun Liu, Tojo James, Nimrod Kiss, Andrew P. Feinberg, Tomas Olsson, Ingrid Kockum, Lars Alfredsson, Tomas J. Ekström, Maja Jagodic
Software Mentions: 6
Published: about 7 years ago
10.1016/j.cell.2018.09.040
Nervous System Regionalization Entails Axial Allocation before Neural Differentiation
Cited by: 116
Author(s): Vicki Metzis, Sebastian Steinhauser, Edvinas Pakanavicius, Mina Gouti, Despina Stamataki, Kenzo Ivanovitch, Thomas Watson, Teresa Rayón, S. Neda Mousavy Gharavy, Robin Lovell-Badge, Nicholas M. Luscombe, James Briscoe
Software Mentions: 6
Published: about 6 years ago
10.1186/s12920-021-00989-w
Identification of key genes in calcific aortic valve disease via weighted gene co-expression network analysis
Cited by: 7
Author(s): Jin-Yu Sun, Hua Yang, Hui Shen, Qiang Qu, Junyan Kan, Xiangqing Kong, Wei Sun, Yue-Yun Shen
Software Mentions: 6
Published: over 3 years ago
10.3390/cancers11101610
The Epithelial to Mesenchymal Transition Promotes Glutamine Independence by Suppressing GLS2 Expression
Cited by: 27
Author(s): Esmeralda Ramirez-Peña, James M. Arnold, Vinita Shivakumar, Robiya Joseph, Geraldine V. Vijay, Petra den Hollander, Neeraja Bhangre, Paul Allegakoen, Rishika Prasad, Zachary Conley, José M. Matés, Javier Márquez, Jeffrey T. Chang, Suhas Vasaikar, Rama Soundararajan, Arun Sreekumar, Sendurai A. Mani
Software Mentions: 6
Published: about 5 years ago
10.3390/cancers12113088
DNA Methylation and Breast Cancer Risk: An Epigenome-Wide Study of Normal Breast Tissue and Blood
Cited by: 15
Author(s): Kaoutar Ennour‐Idrissi, Dzevka Dragic, Elissar Issa, Annick Michaud, Sue-Ling Chang, Louise Provencher, Francine Durocher, Caroline Diorio
Software Mentions: 6
Published: about 4 years ago
10.1155/2021/8842105
Comparison of the Fatty Acid Metabolism Pathway in Pan-Renal Cell Carcinoma: Evidence from Bioinformatics
Cited by: 1
Author(s): Ping Wu, Yingkun Xu, Jiayi Li, Xiaowei Li, Peizhi Zhang, Ningke Ruan, Cong Zhang, Panpan Sun, Qifei Wang, Guangzhen Wu
Software Mentions: 6
Published: almost 4 years ago
10.1186/s13229-019-0287-z
A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood
Cited by: 12
Author(s): Charles E. Mordaunt, Bo Y. Park, Kelly M. Bakulski, Jason I. Feinberg, Lisa Croen, Christine Ladd‐Acosta, Craig J. Newschaffer, Heather E. Volk, Sally J Ozonoff, Irva Hertz‐Picciotto, Janine M. LaSalle, Rebecca Jean Schmidt, M. Daniele Fallin
Software Mentions: 6
Published: about 5 years ago
10.3390/cancers13133330
Differential Regulation of Lacto-/Neolacto- Glycosphingolipid Biosynthesis Pathway Reveals Transcription Factors as Potential Candidates in Triple-Negative Breast Cancer
Cited by: 1
Author(s): Rui-chao Zeng, Ahmed Mohamed, Kum Kum Khanna, Michelle M. Hill
Software Mentions: 6
Published: over 3 years ago
10.1038/s41598-018-33498-5
Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer
Cited by: 28
Author(s): Raquel L. Costa, Mariana Boroni, Marcelo A. Soares
Software Mentions: 6
Published: about 6 years ago
10.1038/sdata.2017.185
An RNA-Seq atlas of gene expression in mouse and rat normal tissues
Cited by: 95
Author(s): Julia F. Söllner, Germán Leparc, Tobias Hildebrandt, H. Klein, Leo Thomas, Elia Stupka, Eric J. Simon
Software Mentions: 6
Published: almost 7 years ago
10.1186/s12920-019-0571-y
Stoichioproteomics reveal oxygen usage bias, key proteins and pathways in glioma
Cited by: 4
Author(s): Yuan Yin, Bo Li, Ke‐Jie Mou, Muhammad Tahir Khan, Aman Chandra Kaushik, Dong‐Qing Wei, Yujuan Zhang
Software Mentions: 6
Published: over 5 years ago
10.1186/s40168-018-0526-0
Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems
Cited by: 299
Author(s): Shuo Jiao, Weimin Chen, Jieli Wang, Nini Du, Qiaoping Li, Gehong Wei
Software Mentions: 6
Published: over 6 years ago
10.3390/cancers12113380
Cancer-Associated Angiogenesis: The Endothelial Cell as a Checkpoint for Immunological Patrolling
Cited by: 69
Author(s): Antonio Giovanni Solimando, Simona De Summa, Angelo Vacca, Doménico Ribatti
Software Mentions: 6
Published: about 4 years ago
10.3390/cancers12061461
PDX1 DNA Methylation Distinguishes Two Subtypes of Pancreatic Neuroendocrine Neoplasms with a Different Prognosis
Cited by: 19
Author(s): Gitta Boons, Timon Vandamme, Joe Ibrahim, Geert Roeyen, Ann Driessen, Dieter Peeters, Ben Lawrence, Cristin G. Print, Maria C. W. Peeters, Guy Van Camp, Ken Op de Beeck
Software Mentions: 6
Published: over 4 years ago
10.1186/s12931-016-0459-8
Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations
Cited by: 47
Author(s): Robert S. Busch, Weiliang Qiu, Jessica Lasky‐Su, Jarrett Morrow, Gerard J. Criner, Dawn L. DeMeo
Software Mentions: 6
Published: about 8 years ago
10.1155/2020/5816763
Screening of T Cell-Related Long Noncoding RNA-MicroRNA-mRNA Regulatory Networks in Non-Small-Cell Lung Cancer
Cited by: 6
Author(s): Jinping Duan, Yuefen Pan, Yang Xi, Liping Zhong, Jia Yin, Jingying Xu, Zhuang Jing, Shuwen Han
Software Mentions: 6
Published: about 4 years ago
10.1038/s41419-021-03680-1
Tumor-derived exosomal circPSMA1 facilitates the tumorigenesis, metastasis, and migration in triple-negative breast cancer (TNBC) through miR-637/Akt1/β-catenin (cyclin D1) axis
Cited by: 56
Author(s): Su-Jin Yang, Dandan Wang, Shanliang Zhong, Wenquan Chen, Wang Fengliang, Jian Zhang, Wen‐Xiu Xu, Di Xu, Qian Zhang, Jian Li, Heda Zhang, Jianglong Hou, Ling Mao, Jinhai Tang
Software Mentions: 6
Published: over 3 years ago
10.1002/cam4.3133
Charactering tumor microenvironment reveals stromal‐related transcription factors promote tumor carcinogenesis in gastric cancer
Cited by: 14
Author(s): Haining Liu, Shujuan Ni, Hanbo Wang, Qiongyan Zhang, Wei-Hung Weng
Software Mentions: 6
Published: over 4 years ago
10.1186/s12915-018-0547-y
Species comparison of liver proteomes reveals links to naked mole-rat longevity and human aging
Cited by: 52
Author(s): Ivonne Heinze, Martin Bens, Enrico Calzia, Susanne Holtze, Oleksandr Dakhovnik, Arne Sahm, Joanna Kirkpatrick, Karol Szafranski, Natalie Romanov, Sai Nagender Sama, Kerstin Hölzer, Stephan Singer, Maria A. Ermolaeva, Matthias Platzer, Thomas B. Hildebrandt, Alessandro Ori
Software Mentions: 6
Published: over 6 years ago