cran: pheatmap | Projects | Ecosyste.ms: Papers

10.15252/msb.20209539

Predictive features of gene expression variation reveal mechanistic link with differential expression
Cited by: 36
Author(s): Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E. M. Furlong, Judith B. Zaugg
Software Mentions: 30
Published: over 4 years ago

10.3389/fcell.2020.577125

Development of a Metastasis-Related Immune Prognostic Model of Metastatic Colorectal Cancer and Its Usefulness to Immunotherapy
Cited by: 11
Author(s): Zhiwen Luo, Xiao Chen, Yefan Zhang, Zhen Huang, Hong Zhao, Jianjun Zhao, Zhiyu Li, Jianguo Zhou, Jianmei Liu, Jianqiang Cai, Xinyu Bi
Software Mentions: 26
Published: almost 4 years ago

10.3389/fmolb.2020.570702

Prognostic Prediction Using a Stemness Index-Related Signature in a Cohort of Gastric Cancer
Cited by: 27
Author(s): Xiaowei Chen, Dawei Zhang, Fei Jiang, Yan Shen, Xin Li, Xin Hu, Pingmin Wei, Xiaobing Shen
Software Mentions: 24
Published: over 4 years ago

10.3389/fimmu.2021.616967

A Multi-Omics Analysis of Mucosal-Associated-Invariant T Cells Reveals Key Drivers of Distinct Modes of Activation
Cited by: 12
Author(s): Kristin Schubert, Isabel Karkossa, Jana Schor, Beatrice Engelmann, Lisa Maria Steinheuer, Tony Bruns, Ulrike Rolle-Kampczyk, Jörg Hackermüller, Martin von Bergen
Software Mentions: 24
Published: over 3 years ago

10.3389/fimmu.2021.701085

A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients
Cited by: 29
Author(s): Florian Bieberich, Rodrigo Vazquez-Lombardi, Alexander Yermanos, Roy Ehling, Derek M Mason, Bastian Wagner, Edo Kapetanovic, Raphaël Brisset Di Roberto, Cédric R. Weber, Miodrag Savic, Fabian Rudolf, Sai T. Reddy
Software Mentions: 23
Published: over 3 years ago

10.3389/fgene.2019.00594

BioNetStat: A Tool for Biological Networks Differential Analysis
Cited by: 21
Author(s): Vinícius Carvalho Jardim, Suzana de Siqueira Santos, André Fujita, Marcos Silveira Buckeridge
Software Mentions: 22
Published: over 5 years ago

10.3389/fmicb.2020.550420

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
Cited by: 91
Author(s): Daniel Straub, Nia Blackwell, Adrian Langarica‐Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
Software Mentions: 22
Published: about 4 years ago

10.1080/19490976.2021.1940792

Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections
Cited by: 13
Author(s): Robert Thänert, Anna Thänert, Jocelyn Ou, Adam Bajinting, Carey Ann D. Burnham, Holly J. Engelstad, Maria E. Tecos, I. Malick Ndao, Carla Hall-Moore, Colleen Rouggly-Nickless, Mike A. Carl, Deborah C. Rubin, Nicholas O. Davidson, Phillip I. Tarr, Barbara B. Warner, Gautam Dantas, Brad W. Warner
Software Mentions: 22
Published: almost 4 years ago

10.3389/fimmu.2021.632333

Immunological Feature and Transcriptional Signaling of Ly6C Monocyte Subsets From Transcriptome Analysis in Control and Hyperhomocysteinemic Mice
Cited by: 7
Author(s): Panpan Yang, Lu Liu, Lili Sun, Fang Pu, Nathaniel W. Snyder, Jason Saredy, Yong Ji, Wen Shen, Xuebin Qin, Qinghua Wu, Xiaofeng Yang, Hong Wang
Software Mentions: 21
Published: almost 4 years ago

10.3390/cells8091045

Systematic Assessment of Blood-Borne MicroRNAs Highlights Molecular Profiles of Endurance Sport and Carbohydrate Uptake
Cited by: 12
Author(s): Fabian Kern, Nicole Ludwig, Christina Backes, Esther Maldener, Tobias Fehlmann, Artur Suleymanov, Eckart Meese, Anne Hecksteden, Andreas Keller, Tim Meyer
Software Mentions: 21
Published: over 5 years ago

10.1186/s12864-017-4353-7

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism
Cited by: 72
Author(s): Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J. Araúzo-Bravo
Software Mentions: 21
Published: about 7 years ago

10.3390/genes11030257

mRNAsi Index: Machine Learning in Mining Lung Adenocarcinoma Stem Cell Biomarkers
Cited by: 61
Author(s): Yitong Zhang, Joseph T. Tseng, I-Chia Lien, Fenglan Li, Wei Wu, Hui Li
Software Mentions: 20
Published: almost 5 years ago

10.1186/s13059-020-02100-5

Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data
Cited by: 56
Author(s): Nikolaus Fortelny, Christoph Bock
Software Mentions: 20
Published: over 4 years ago

10.1186/s12866-021-02282-3

Associations between the gut microbiome and metabolome in early life
Cited by: 14
Author(s): Quang P. Nguyen, Margaret R. Karagas, Juliette C. Madan, Erika Dade, Thomas J. Palys, Hilary G. Morrison, Wimal Pathmasiri, Susan McRitche, Susan Sumner, H. Robert Frost, Anne G. Hoen
Software Mentions: 19
Published: over 3 years ago

10.1155/2021/6613151

Genomic and Transcriptome Analysis to Identify the Role of the mTOR Pathway in Kidney Renal Clear Cell Carcinoma and Its Potential Therapeutic Significance
Cited by: 6
Author(s): Xiangyu Che, Xiaochen Qi, Yingkun Xu, Qifei Wang, Guangzhen Wu
Software Mentions: 19
Published: over 3 years ago

10.18632/aging.103499

Multi-omics network analysis reveals distinct stages in the human aging progression in epidermal tissue
Cited by: 16
Author(s): Nicholas Holzscheck, Jörn Söhle, Boris Kristof, Elke Grönniger, Stefan Gallinat, Horst Wenck, Marc Winnefeld, Cassandra Falckenhayn, Lars Kaderali
Software Mentions: 18
Published: over 4 years ago

10.3389/fonc.2020.607727

Gene Panel of Persister Cells as a Prognostic Indicator for Tumor Repopulation After Radiation
Cited by: 3
Author(s): Yucui Zhao, Yanwei Song, Ruyi Zhao, Minghui Zhao, Qian Huang
Software Mentions: 18
Published: about 4 years ago

10.3389/fonc.2021.605810

A Novel Risk Factor Model Based on Glycolysis-Associated Genes for Predicting the Prognosis of Patients With Prostate Cancer
Cited by: 6
Author(s): Kaixuan Guo, Cong Lai, Juan Shi, Zhuang Tang, Cheng Liu, Kuiqing Li, Kailin Xu
Software Mentions: 18
Published: over 3 years ago

10.1093/gigascience/giz028

Rice Galaxy: an open resource for plant science
Cited by: 13
Author(s): Venice Margarette Juanillas, Alexis Dereeper, Nicolas Beaume, Gaëtan Droc, Joshua Gregor A. Dizon, J. Mendoza, Jon Peter Perdon, Locedie Mansueto, Lindsay R. Triplett, Jillian M. Lang, Gabriel Zhou, Kunalan Ratharanjan, Beth Plale, Jason Haga, Jan E. Leach, Manuel Ruiz, Michael J. Thomson, Nickolai Alexandrov, Pierre Larmande, Tobias Kretzschmar, Ramil Mauleon
Software Mentions: 18
Published: over 5 years ago

10.15252/emmm.202012640

Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor
Cited by: 7
Author(s): Maggie H. Chassé, Benjamin K. Johnson, Elissa A. Boguslawski, Katie M. Sorensen, Jessica E Rosien, Min H. Kang, C. Patrick Reynolds, Lyong Heo, Zachary Madaj, Ian Beddows, Gabrielle E. Foxa, Susan M. Kitchen-Goosen, Bart O. Williams, Timothy J. Triche, Patrick J. Grohar
Software Mentions: 18
Published: about 4 years ago

10.1016/j.cell.2020.12.016

Spatiotemporal analysis of human intestinal development at single-cell resolution
Cited by: 215
Author(s): David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren J. Fowler, Edward Morrissey, Christine M. Cunningham, Johnson Prv., Hashem Koohy, Alison Simmons
Software Mentions: 18
Published: almost 4 years ago

10.3390/ijms21228837

Machine Learning Identifies Robust Matrisome Markers and Regulatory Mechanisms in Cancer
Cited by: 6
Author(s): Anni Kääriäinen, Vilma Pesola, Annalena Dittmann, Juho A. J. Kontio, Jarkko Koivunen, Taina Pihlajaniemi, Valerio Izzi
Software Mentions: 18
Published: about 4 years ago

10.1371/journal.pone.0135831

CoGA: An R Package to Identify Differentially Co-Expressed Gene Sets by Analyzing the Graph Spectra
Cited by: 18
Author(s): Suzana de Siqueira Santos, Thais Fernanda de Almeida Galatro, Rodrigo Akira Watanabe, Sueli Mieko Oba-Shinjo, Suely Kazue Nagahashi Marie, André Fujita
Software Mentions: 17
Published: over 9 years ago

10.1016/j.stem.2019.07.008

Defining the Identity and Dynamics of Adult Gastric Isthmus Stem Cells
Cited by: 85
Author(s): Seungmin Han, J. Lynn Fink, David J. Jörg, Eunmin Lee, Min Kyu Yum, Lemonia Chatzeli, Sebastian R. Merker, Manon Josserand, Teodora Trendafilova, Amanda Andersson-Rolf, Catherine Dabrowska, Hyunki Kim, Ronald Naumann, Ji–Hyun Lee, Nobuo Sasaki, Richard L. Mort, Onur Basak, Hans Clevers, Daniel E. Stange, Anna Philpott, Jong Kim, Benjamin D. Simons, Bon‐Kyoung Koo
Software Mentions: 17
Published: over 5 years ago

10.3389/fonc.2021.658165

Using Tumor-Infiltrating Immune Cells and a ceRNA Network Model to Construct a Prognostic Analysis Model of Thyroid Carcinoma
Cited by: 11
Author(s): Fan Zhang, Xiao‐Juan Yu, Zheyu Lin, Xichang Wang, Tengteng Gao, Di Teng, Weiping Teng
Software Mentions: 17
Published: over 3 years ago

10.3389/fimmu.2020.565730

Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
Cited by: 22
Author(s): Marco Antônio M. Pretti, Rômulo Gonçalves Galvani, Gustavo Fioravanti Vieira, Adriana Bonomo, Martín Bonamino, Mariana Boroni
Software Mentions: 17
Published: about 4 years ago

10.3389/fvets.2021.620327

Detection of Mycobacterium avium ssp. paratuberculosis in Cultures From Fecal and Tissue Samples Using VOC Analysis and Machine Learning Tools
Cited by: 6
Author(s): Philipp Vitense, Elisa Kasbohm, Anne Klassen, Peter Gierschner, Phillip Trefz, M. Weber, Wolfram Miekisch, Jochen K. Schubert, Petra Möbius, Petra Reinhold, Volkmar Liebscher, Heike Köhler
Software Mentions: 17
Published: almost 4 years ago

10.1093/gigascience/giz061

LION/web: a web-based ontology enrichment tool for lipidomic data analysis
Cited by: 110
Author(s): Martijn R. Molenaar, Aike Jeucken, Tsjerk A. Wassenaar, Chris H.A. van de Lest, Jos F. Brouwers, J. Bernd Helms
Software Mentions: 16
Published: over 5 years ago

10.1186/s12935-020-01571-7

RETRACTED ARTICLE: Aging-related tumor associated fibroblasts changes could worsen the prognosis of GBM patients
Cited by: 7
Author(s): Hongwang Song, Xiaojun Fu, Chenxing Wu, Shouwei Li
Software Mentions: 16
Published: about 4 years ago

10.3389/fcell.2020.596679

Development and Validation of a Combined Ferroptosis and Immune Prognostic Classifier for Hepatocellular Carcinoma
Cited by: 77
Author(s): Yang Liu, Xi Zhang, Junjun Zhang, Juan Tan, Jie Li, Zewen Song
Software Mentions: 16
Published: almost 4 years ago

10.1126/sciimmunol.abd6832

Natural killer cell immunotypes related to COVID-19 disease severity
Cited by: 315
Author(s): Christopher Maucourant, Iva Filipovic, Andrea Ponzetta, Soo Aleman, Martin Cornillet, Laura Hertwig, Benedikt Strunz, Antonio Lentini, Björn Reinius, Demi Brownlie, Angélica Cuapio, Eivind Heggernes Ask, Ryan M. Hull, Alvaro Haroun-Izquierdo, Marie Schaffer, Jonas Klingström, Elin Folkesson, Marcus Buggert, Johan K. Sandberg, Lars Eriksson, Olav Rooyackers, Hans‐Gustaf Ljunggren, Karl‐Johan Malmberg, Jakob Michaëlsson, Nicole Marquardt, Quirin Hammer, Kristoffer Strålin, Niklas K. Björkström
Software Mentions: 16
Published: over 4 years ago

10.1038/s41598-020-69683-8

Concomitant DNA methylation and transcriptome signatures define epidermal responses to acute solar UV radiation
Cited by: 5
Author(s): Nicholas Holzscheck, Jörn Söhle, T. Schläger, Cassandra Falckenhayn, Elke Grönniger, Ludger Kolbe, Horst Wenck, Lara Terstegen, Lars Kaderali, Marc Winnefeld, Katharina Gorges
Software Mentions: 16
Published: over 4 years ago

10.7150/ijms.53531

Identification novel prognostic signatures for Head and Neck Squamous Cell Carcinoma based on ceRNA network construction and immune infiltration analysis
Cited by: 18
Author(s): Haiting Zhou, Yi He, Lingling Li, Cheng Wu, Guoqing Hu
Software Mentions: 16
Published: almost 4 years ago

10.3390/cancers12040957

Pan-Cancer Analysis of Radiotherapy Benefits and Immune Infiltration in Multiple Human Cancers
Cited by: 10
Author(s): Pengbo Wen, Yang Gao, Bin Chen, Xiaojing Qi, Guanshuo Hu, An Xu, Junfeng Xia, Lijun Wu, Lu Han, Guoping Zhao
Software Mentions: 16
Published: over 4 years ago

10.3389/fonc.2021.644416

An Inflammatory Response-Related Gene Signature Can Impact the Immune Status and Predict the Prognosis of Hepatocellular Carcinoma
Cited by: 62
Author(s): Zhuo Lin, Xu Qian, Dan Miao, Fang Yu
Software Mentions: 16
Published: almost 4 years ago

10.3389/fgene.2021.719204

RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization
Cited by: 2
Author(s): Zhaoyuan Wei, Jiahe Sun, Qinhui Li, Ting Yao, Haiyue Zeng, Yi Wang
Software Mentions: 16
Published: over 3 years ago

10.1186/s12866-019-1598-0

Characterization of Salmonella Dublin isolated from bovine and human hosts
Cited by: 35
Author(s): Narayan Paudyal, Hang Pan, Mohammed Elbediwi, Xiao Hua Zhou, Xianqi Peng, Xiaoliang Li, Weihuan Fang, Min Yue
Software Mentions: 15
Published: about 5 years ago

10.3389/fcell.2021.671736

Identification of a Novel Immune Landscape Signature for Predicting Prognosis and Response of Endometrial Carcinoma to Immunotherapy and Chemotherapy
Cited by: 6
Author(s): Jinhui Liu, Yichun Wang, Jie Mei, Song Nie, Yan Zhang
Software Mentions: 15
Published: over 3 years ago

10.1093/gigascience/giy123

PiGx: reproducible genomics analysis pipelines with GNU Guix
Cited by: 51
Author(s): Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Software Mentions: 15
Published: about 6 years ago

10.1186/s12967-021-02773-x

Multi-omics characterization and validation of invasiveness-related molecular features across multiple cancer types
Cited by: 5
Author(s): Guoshu Bi, Jiaqi Liang, Yuansheng Zheng, Runmei Li, Mengnan Zhao, Yiwei Huang, Cheng Zhan, Songtao Xu, Hong Fan
Software Mentions: 15
Published: over 3 years ago

10.1038/s42003-021-01796-w

Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults
Cited by: 73
Author(s): Rong Xu, Renfei Lu, Tao Zhang, Qian Wu, Wei Cai, Xudong Han, Zhenzhou Wan, Xia Jin, Zhigang Zhang, Chiyu Zhang
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12885-021-08559-0

A novel ferroptosis-related 12-gene signature predicts clinical prognosis and reveals immune relevancy in clear cell renal cell carcinoma
Cited by: 42
Author(s): Ying‐Kai Hong, Mingen Lin, Dehua Ou, Zhuangkai Huang, Peilin Shen
Software Mentions: 15
Published: over 3 years ago

10.3389/fcell.2021.657667

Identification of the Prognostic Significance of Somatic Mutation-Derived LncRNA Signatures of Genomic Instability in Lung Adenocarcinoma
Cited by: 31
Author(s): Geng Wang, Zhi Lv, Jinshuo Fan, Jing Xu, Kaimin Mao, Zhengrong Yin, Wanlu Qing, Yang Jin
Software Mentions: 14
Published: over 3 years ago

10.3389/fgene.2021.689406

Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing
Cited by: 26
Author(s): Júber Herrera-Uribe, Jayne E Wiarda, Sathesh K Sivasankaran, Lance Daharsh, Haibo Li, Kristen A Byrne, Timothy P. L. Smith, Joan K. Lunney, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 14
Published: over 3 years ago

10.1186/s12967-021-02894-3

Identification of immune subtypes of cervical squamous cell carcinoma predicting prognosis and immunotherapy responses
Cited by: 8
Author(s): Yimin Li, Shun Lü, Shubin Wang, Xinhao Peng, Jinyi Lang
Software Mentions: 14
Published: over 3 years ago

10.1093/gigascience/giab039

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
Cited by: 8
Author(s): Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Mengmeng Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Software Mentions: 14
Published: over 3 years ago

10.3389/fmicb.2021.709611

Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System
Cited by: 2
Author(s): Yousri Abdelhafiz, Jorge M. O. Fernandes, Simone Larger, Davide Albanese, Claudio Donati, Omid Jafari, Artem Nedoluzhko, Viswanath Kiron
Software Mentions: 14
Published: over 3 years ago

10.7150/jca.55970

Characteristics of Infiltrating Immune Cells and a Predictive Immune Model for Cervical Cancer
Cited by: 11
Author(s): Ruanmin Zou, Ruihong Gu, Xinbing Yu, Yingying Hu, Ji Hee Yu, Xiangyang Xue, Xueqiong Zhu
Software Mentions: 14
Published: almost 4 years ago

10.3389/fimmu.2020.572924

Differential Skewing of Circulating MR1-Restricted and γδ T Cells in Human Psoriasis Vulgaris
Cited by: 7
Author(s): Vera Plužarić, Mario Štefanić, Martina Mihalj, Maja Tolušić Levak, Ivanka Muršić, Ljubica Glavaš‐Obrovac, Martin Petřek, Péter Balogh, Stana Tokić
Software Mentions: 14
Published: about 4 years ago

10.1111/jcmm.15705

Collagen Type III Alpha 1 chain regulated by GATA‐Binding Protein 6 affects Type II IFN response and propanoate metabolism in the recurrence of lower grade glioma
Cited by: 18
Author(s): Runzhi Huang, Zhenyu Li, Xiaolong Zhu, Penghui Yan, Dianwen Song, Huabin Yin, Peng Hu, Ruoyi Lin, Shengyu Wu, Tong Meng, Jie Zhang, Zongqiang Huang
Software Mentions: 14
Published: over 4 years ago

10.1093/bioinformatics/btx657

heatmaply: an R package for creating interactive cluster heatmaps for online publishing
Cited by: 334
Author(s): Tal Galili, Alan O’Callaghan, Jonathan Savage, Carson Sievert
Software Mentions: 14
Published: about 7 years ago

10.1186/s40478-020-0880-6

Single-nucleus RNA-seq identifies Huntington disease astrocyte states
Cited by: 147
Author(s): Osama Al‐Dalahmah, Alexander A. Sosunov, Ayesha Shaik, Kenneth Ofori, Yang Liu, Jean Paul Vonsattel, István Adorján, Vilas Menon, James E. Goldman
Software Mentions: 14
Published: almost 5 years ago

10.1371/journal.ppat.1008653

Genome-wide transcriptomics identifies an early preclinical signature of prion infection
Cited by: 39
Author(s): Silvia Sorce, Mario Nuvolone, Giancarlo Russo, Andra Chincisan, Daniel Heinzer, Merve Avar, Manuela Pfammatter, Petra Schwarz, Mirzet Delic, Mattia Müller, Simone Hornemann, Despina Sanoudou, Claudia Scheckel, Adriano Aguzzi
Software Mentions: 14
Published: over 4 years ago

10.3389/fonc.2021.643104

TRIM68, PIKFYVE, and DYNLL2: The Possible Novel Autophagy- and Immunity-Associated Gene Biomarkers for Osteosarcoma Prognosis
Cited by: 10
Author(s): Jie Jiang, Dachang Liu, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Liyi Chen, Shengsheng Huang, Xuhua Sun, Ming Yi, Zide Zhang, Zhaojun Lu, Zequn Wang, Jiarui Chen, Tianyou Chen, Hao Li, Yuanlin Yao, Wu‐Hua Chen, Hao Guo, Chong Liu, Xinli Zhan
Software Mentions: 13
Published: over 3 years ago

10.3389/fonc.2021.639013

Single-Cell Transcriptome Analysis Identifies Ligand–Receptor Pairs Associated With BCP-ALL Prognosis
Cited by: 3
Author(s): Liang Wu, Mingming Jiang, Ping Yu, Jianfeng Li, Wen Ouyang, Chong Feng, Wei Zhao, Yuting Dai, Jinyan Huang
Software Mentions: 13
Published: almost 4 years ago

10.7554/eLife.50087

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle
Cited by: 58
Author(s): Elias T Friman, Cédric Deluz, Antonio C. A. Meireles-Filho, Subashika Govindan, Vincent Gardeux, Bart Deplancke, David M. Suter
Software Mentions: 13
Published: about 5 years ago

10.1371/journal.pcbi.1007859

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease
Cited by: 10
Author(s): Christine Tataru, Maude M. David
Software Mentions: 13
Published: over 4 years ago

10.1186/s13073-020-00823-5

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients
Cited by: 169
Author(s): Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger, Miriam Herbert, Lisa Holsten, Arik Horne, Ioanna Gemünd, Nikoletta Rovina, Shobhit Agrawal, K. Dahm, Martina van Uelft, Anna Drews, Lena Lenkeit, Niklas Bruse, Jelle Gerretsen, Jannik Gierlich, Matthias Becker, Kristian Händler, Michael Kraut, Heidi Theis, Simachew Abebe Mengiste, Elena De Domenico, Jonas Schulte-Schrepping, Lea Seep, Jan Raabe, Christoph Hoffmeister, Michael ToVinh, Verena Keitel, Gereon J Rieke, Valentina Talevi, Dirk Skowasch, N. Ahmad Aziz, Peter Pickkers, Frank L. van de Veerdonk, Mihai G. Netea, Joachim L. Schultze, Matthijs Kox, Monique M.B. Breteler, Jacob Nattermann, Antonia Koutsoukou, Evangelos J. Giamarellos‐Bourboulis, Thomas Ulas
Software Mentions: 13
Published: almost 4 years ago

10.7554/eLife.61980

Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues
Cited by: 43
Author(s): Andrew W. DeVilbiss, Zhiyu Zhao, Misty S. Martin-Sandoval, Jessalyn M. Ubellacker, Alpaslan Tasdogan, Michalis Agathocleous, Thomas P. Mathews, Sean J. Morrison
Software Mentions: 13
Published: almost 4 years ago

10.3389/fimmu.2021.730346

Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens
Cited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: over 3 years ago

10.1038/s42003-021-02335-3

A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues
Cited by: 9
Author(s): José M. Ranz, Pablo M. González, Bryan D. Clifton, Nestor O. Nazario-Yepiz, Pablo Luis Hernández-Cervantes, María J. Palma-Martínez, Dulce I. Valdivia, Andrés Jiménez-Kaufman, Megan Lu, Therese A. Markow, Cei Abreu‐Goodger
Software Mentions: 13
Published: over 3 years ago

10.1038/srep42130

Dissecting the brown adipogenic regulatory network using integrative genomics
Cited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: almost 8 years ago

10.3389/fonc.2021.583547

Alternative Splicing Events in Tumor Immune Infiltration in Colorectal Cancer
Cited by: 5
Author(s): Shi Jian-yu, Yan-yan Bi, Bo Yu, Qingfeng Wang, Teng Dan, WU Dong-ning
Software Mentions: 13
Published: over 3 years ago

10.1126/sciadv.abg6070

Enhancing the heat tolerance of reef-building corals to future warming
Cited by: 36
Author(s): Emily J. Howells, David Abrego, Yi Jin Liew, John A. Burt, Eli Meyer, Manuel Aranda
Software Mentions: 13
Published: over 3 years ago

10.3389/fonc.2021.623170

Clinical and Prognostic Pan-Cancer Analysis of N6-Methyladenosine Regulators in Two Types of Hematological Malignancies: A Retrospective Study Based on TCGA and GTEx Databases
Cited by: 21
Author(s): Xiangsheng Zhang, Li-Ye Zhong, Zhilin Zou, Guosheng Liang, Zhenye Tang, Kai Li, Shuhua Tan, Yongmei Huang, Xiao Zhu
Software Mentions: 13
Published: almost 4 years ago

10.1038/s41398-021-01596-0

Autoantibody profiles associated with clinical features in psychotic disorders
Cited by: 6
Author(s): August Jernbom Falk, Cherrie Galletly, David R. Just, Catherine Toben, Bernhard T. Baune, Scott Clark, Dennis Liu, Peter Nilsson, Anna Månberg, Klaus Oliver Schubert
Software Mentions: 13
Published: over 3 years ago

10.3389/fgene.2021.690530

Predicting the Survival and Immune Landscape of Colorectal Cancer Patients Using an Immune-Related lncRNA Pair Model
Cited by: 3
Author(s): Chi Ma, Xin Zhang, Xudong Zhao, Nan Zhang, Sixin Zhou, Yonghui Zhang, Peiyu Li
Software Mentions: 13
Published: over 3 years ago

10.3390/cancers11010091

The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis
Cited by: 5
Author(s): Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu, Liping Qu
Software Mentions: 13
Published: almost 6 years ago

10.1186/s12859-021-04142-3

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Cited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: over 3 years ago

10.1186/s12864-020-07204-7

Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout
Cited by: 5
Author(s): Pratima Chapagain, Donald M. Walker, Timothy D. Leeds, Beth M. Cleveland, Mohamed Salem
Software Mentions: 13
Published: about 4 years ago

10.1016/j.mbplus.2019.04.001

Pan-Cancer analysis of the expression and regulation of matrisome genes across 32 tumor types
Cited by: 37
Author(s): Valerio Izzi, Juho Lakkala, Raman Devarajan, Anni Kääriäinen, Jarkko Koivunen, Ritva Heljasvaara, Taina Pihlajaniemi
Software Mentions: 13
Published: almost 6 years ago

10.1186/s12935-020-01362-0

Immune-related long non-coding RNA signature identified prognosis and immunotherapeutic efficiency in bladder cancer (BLCA)
Cited by: 40
Author(s): Rui Cao, Lushun Yuan, Bo Ma, Gang Wang, Ye Tian
Software Mentions: 13
Published: over 4 years ago

10.3390/ijms22031075

A Novel Epigenetic Machine Learning Model to Define Risk of Progression for Hepatocellular Carcinoma Patients
Cited by: 7
Author(s): Luca Bedon, Michele Dal Bo, Monica Mossenta, Davide Busato, Giuseppe Toffoli, Maurizio Polano
Software Mentions: 13
Published: almost 4 years ago

10.1186/s12974-021-02235-7

Sex differences and similarities in the neuroimmune response to central administration of poly I:C
Cited by: 14
Author(s): Caitlin K. Posillico, Rosa E. Garcia-Hernandez, Natalie C. Tronson
Software Mentions: 12
Published: over 3 years ago

10.18632/aging.202871

A novel focal adhesion related gene signature for prognostic prediction in hepatocellular carcinoma
Cited by: 4
Author(s): Zhuo Lin, Dan Miao, Xu Qian, Xiaodong Wang, Fang Yu
Software Mentions: 12
Published: over 3 years ago

10.3389/fmolb.2021.681526

Identification of Key Biomarkers and Immune Infiltration in Systemic Juvenile Idiopathic Arthritis by Integrated Bioinformatic Analysis
Cited by: 2
Author(s): Min Zhang, Rongxin Dai, Qianqian Zhao, Lina Zhou, Yunfei An, Xuemei Tang, Xiaodong Zhao
Software Mentions: 12
Published: over 3 years ago

10.1186/s12967-021-02800-x

Identification of 4 immune cells and a 5-lncRNA risk signature with prognosis for early-stage lung adenocarcinoma
Cited by: 25
Author(s): Liancai Mu, Ke Ding, Ranran Tu, Wei Yang
Software Mentions: 12
Published: over 3 years ago

10.7554/eLife.58993

Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns
Cited by: 23
Author(s): Kathleen Greenham, Ryan C. Sartor, Stevan Zorich, Ping Lou, Todd C. Mockler, C. Robertson McClung
Software Mentions: 12
Published: about 4 years ago

10.7554/eLife.55529

Smchd1 is a maternal effect gene required for genomic imprinting
Cited by: 22
Author(s): Iromi Wanigasuriya, Quentin Gouil, Sarah Kinkel, Andrés Tapia del Fierro, Tamara Beck, Ellise A Roper, Kelsey Breslin, Jessica M Stringer, Karla J. Hutt, Heather Lee, Andrew Keniry, Matthew E. Ritchie, Marnie E. Blewitt
Software Mentions: 12
Published: about 4 years ago

10.1093/molbev/msaa128

Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression
Cited by: 25
Author(s): Xavier Grau‐Bové, Sean Tomlinson, Andrias O. O’Reilly, Nicholas J. Harding, Alistair Miles, Dominic Kwiatkowski, Martin Donnelly, David Weetman
Software Mentions: 12
Published: over 4 years ago

10.18632/aging.202317

Identification and validation of an immune-related gene signature predictive of overall survival in colon cancer
Cited by: 33
Author(s): Xuening Zhang, Hao Zhao, Xiaoguang Shi, Xiaocan Jia, Yongli Yang
Software Mentions: 12
Published: about 4 years ago

10.1371/journal.pone.0251323

The role of multiple metabolic genes in predicting the overall survival of colorectal cancer: A study based on TCGA and GEO databases
Cited by: 2
Author(s): Weijun Shi, Xincan Li, Shuai Xu, Hexin Wen, Tianwen Chen, Huazhang Wu, Mulin Liu
Software Mentions: 12
Published: over 3 years ago

10.3389/fimmu.2021.647832

Large-Scale Gene Expression Signatures Reveal a Microbicidal Pattern of Activation in Mycobacterium leprae-Infected Monocyte-Derived Macrophages With Low Multiplicity of Infection
Cited by: 9
Author(s): Thyago Leal-Calvo, Bruna Letícia Martins, Daniele Ferreira de Faria Bertoluci, Patrícia Sammarco Rosa, Rodrigo Mendes de Camargo, G. Germano, Vânia Niéto Brito de Souza, Ana Carla Pereira Latini, Milton Ozório Moraes
Software Mentions: 12
Published: over 3 years ago

10.1186/s13059-021-02493-x

Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish
Cited by: 7
Author(s): Hyo Sik Jang, Yujie Chen, Jiaxin Ge, Alicia N Wilkening, Yiran Hou, Hyung Joo Lee, You Rim Choi, Rebecca F. Lowdon, Xiaoyun Xing, Daofeng Li, Charles Kaufman, Stephen L. Johnson, Ting Wang
Software Mentions: 12
Published: about 3 years ago

10.1186/s13073-021-00869-z

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home
Cited by: 13
Author(s): Quinten R Ducarmon, Elisabeth M. Terveer, Sam Nooij, Michelle N Bloem, Karuna E W Vendrik, Monique A. A. Caljouw, Ingrid M J G Sanders, S.M. van Dorp, M.C. Wong, Romy D. Zwittink, Ed J. Kuijper
Software Mentions: 12
Published: over 3 years ago

10.1155/2021/4743971

Exploration of the Immune-Related Signatures and Immune Infiltration Analysis in Melanoma
Cited by: 0
Author(s): Ai-lan Li, Yong‐Mei Zhu, Lai-qiang Gao, Shuyue Wei, Mingtao Wang, Qiang Ma, Yuanna Zheng, Jianhua Li, Qingfeng Wang
Software Mentions: 12
Published: almost 4 years ago

10.1038/s41598-021-86286-z

Construction and validation of a metabolic risk model predicting prognosis of colon cancer
Cited by: 5
Author(s): Didi Zuo, Chao Li, Tao Liu, Meng Yue, Jiantao Zhang, Guang Ning
Software Mentions: 12
Published: over 3 years ago

10.26508/lsa.202000770

In vivo CRISPR/Cas9 knockout screen: TCEAL1 silencing enhances docetaxel efficacy in prostate cancer
Cited by: 12
Author(s): Linda Rushworth, Victoria Harle, Peter Repiščák, William Clark, Robin Shaw, Holly Hall, Martin Bushell, Hing Y. Leung, Rachana Patel
Software Mentions: 12
Published: about 4 years ago

10.7717/peerj.10255

Comprehensive genomic analysis of microenvironment phenotypes in ovarian cancer
Cited by: 4
Author(s): Jingshu Wang, Tingting Zhang, Lina Yang, Gong Yang
Software Mentions: 12
Published: about 4 years ago

10.3390/cells10051066

Integrated microRNA and mRNA Expression Profiling Identifies Novel Targets and Networks Associated with Ebstein’s Anomaly
Cited by: 5
Author(s): Masood Abu‐Halima, Viktoria Wagner, Lea Simone Becker, Basim Ayesh, Mohammed Abd El-Rahman, Ulrike Fischer, Eckart Meese, Hashim Abdul‐Khaliq
Software Mentions: 12
Published: over 3 years ago

10.3389/fgene.2019.01200

Dysregulation of MicroRNA Regulatory Network in Lower Extremities Arterial Disease
Cited by: 22
Author(s): Anna Bogucka‐Kocka, Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Łukasz Komsta, Przemysław Kołodziej, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki
Software Mentions: 12
Published: about 5 years ago

10.3389/fgene.2020.00363

Novel Immune-Related Gene Signature for Risk Stratification and Prognosis of Survival in Lower-Grade Glioma
Cited by: 114
Author(s): Mingwei Zhang, Xuezhen Wang, Xiaoping Chen, Qiuyu Zhang, Jinsheng Hong
Software Mentions: 12
Published: over 4 years ago

10.1038/s41598-020-69239-w

Neural innervation as a potential trigger of morphological color change and sexual dimorphism in cichlid fish
Cited by: 14
Author(s): Yipeng Liang, Axel Meyer, Claudius F. Kratochwil
Software Mentions: 12
Published: over 4 years ago

10.3389/fphar.2021.726529

CD3D, GZMK, and KLRB1 Are Potential Markers for Early Diagnosis of Rheumatoid Arthritis, Especially in Anti-Citrullinated Protein Antibody-Negative Patients
Cited by: 8
Author(s): Junqin Lu, Yihui Bi, Yapeng Zhu, Hanyu Shi, Wenxiu Duan, Jian Zhou
Software Mentions: 12
Published: over 3 years ago

10.1084/jem.20160553

Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation
Cited by: 46
Author(s): Tizong Miao, Alistair L. J. Symonds, Randeep Singh, Janine D. Symonds, Ane Ogbe, Becky Omodho, Bo Zhu, Suling Li, Ping Wang
Software Mentions: 12
Published: over 7 years ago

10.3389/fgene.2021.667610

The Construction and Analysis of ceRNA Network and Immune Infiltration in Kidney Renal Clear Cell Carcinoma
Cited by: 10
Author(s): Lugang Deng, Peixi Wang, Zhi Qu, Nan Liu
Software Mentions: 12
Published: over 3 years ago

10.1155/2021/5575286

Screening and Bioinformatics Analysis of Competitive Endogenous RNA Regulatory Network ––Related to Circular RNA in Breast Cancer
Cited by: 3
Author(s): Tao Wang, Yi Zhang, Yan He, Yang Liu, Qi Peng
Software Mentions: 12
Published: over 3 years ago

10.1186/s12957-021-02175-9

A prognostic model for hepatocellular carcinoma based on apoptosis-related genes
Cited by: 15
Author(s): Renjie Liu, Guifu Wang, Chi Zhang, Dou‐Sheng Bai
Software Mentions: 12
Published: almost 4 years ago

10.18632/aging.103965

Establishing and validating a pathway prognostic signature in pancreatic cancer based on miRNA and mRNA sets using GSVA
Cited by: 8
Author(s): Junfeng Zhang, Jianyou Gu, Shixiang Guo, Wenjie Huang, Yongqiang Zheng, Xianxing Wang, Tao Zhang, Weibo Zhao, Bing Ni, Yingfang Fan, Huaizhi Wang
Software Mentions: 12
Published: about 4 years ago

10.1111/jcmm.16605

Leptin receptor is a key gene involved in the immunopathogenesis of thyroid‐associated ophthalmopathy
Cited by: 3
Author(s): Ziyi Chen, Zhe Chen, Jingya Wang, Meng Zhang, Xiaofei Wang, Deji Cuomu, Bingyin Shi, Yue Wang
Software Mentions: 12
Published: over 3 years ago

Projects: cran: pheatmap

Papers Mentioning pheatmap 2,572