cran: pheatmap | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2017.02559

Patterns and Drivers of Vertical Distribution of the Ciliate Community from the Surface to the Abyssopelagic Zone in the Western Pacific Ocean
Cited by: 32
Author(s): Feng Zhao, Sabine Filker, Kuidong Xu, Pingping Huang, Shan Zheng
Software Mentions: 4
Published: over 8 years ago

10.7717/peerj.8061

Identification of genes and functional coexpression modules closely related to ulcerative colitis by gene datasets analysis
Cited by: 7
Author(s): Jie Zhu, Zheng Wang, Fengzhe Chen, Changhong Liu
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms22020736

Omics Analysis of Blood-Responsive Regulon in Bordetella pertussis Identifies a Novel Essential T3SS Substrate
Cited by: 2
Author(s): Jakub Držmíšek, Daniel Štipl, Denisa Petráčková, Branislav Večerek, Ana Dienstbier
Software Mentions: 4
Published: over 5 years ago

10.1126/scisignal.abf8483

Kynurenic acid may underlie sex-specific immune responses to COVID-19
Cited by: 55
Author(s): Yuping Cai, Daniel Kim, Takehiro Takahashi, David Broadhurst, Yan Hong, Shuanagge Ma, Nicholas J. W. Rattray, Arnau Casanovas‐Massana, Benjamin Israelow, Jonathan Klein, Carolina Lucas, Tianyang Mao, Adam J. Moore, M. Catherine Muenker, Ji Eun Oh, Julio Silva, Patrick Wong, Albert Icksang Ko, Sajid Khan, Akiko Iwasaki, Caroline H. Johnson
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-5910-z

Identification and differential expression analysis of anthocyanin biosynthetic genes in leaf color variants of ornamental kale
Cited by: 24
Author(s): Na Guo, Shuo Han, Ming Zong, Guixiang Wang, Shuning Zheng, Fan Liu
Software Mentions: 4
Published: about 7 years ago

10.1128/AAC.01207-19

Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling
Cited by: 50
Author(s): Aubrie O’Rourke, Sinem Beyhan, Yongwook Choi, Pavel Morales, Agnes P. Chan, Josh L. Espinoza, Chris L. Dupont, Kirsten J. Meyer, Amy L. Spoering, Kim Lewis, William C. Nierman, Karen E. Nelson
Software Mentions: 4
Published: over 6 years ago

10.1016/j.celrep.2020.107857

GM-CSF Calibrates Macrophage Defense and Wound Healing Programs during Intestinal Infection and Inflammation
Cited by: 65
Author(s): Tomas Castro‐Dopico, Aaron Fleming, Thomas W. Dennison, John R. Ferdinand, Katherine Harcourt, Benjamin J Stewart, M Zaeem Cader, Zewen Kelvin Tuong, Chenzhi Jing, Laurence S.C. Lok, Rebeccah J. Mathews, Anaïs Portet, Arthur Kaser, Simon Clare, Menna R. Clatworthy
Software Mentions: 4
Published: about 6 years ago

10.1186/s13395-016-0115-5

Skeletal muscle characteristics are preserved in hTERT/cdk4 human myogenic cell lines
Cited by: 53
Author(s): Matthew Thorley, Stéphanie Duguez, Emilia Maria Cristina Mazza, Sara Valsoni, Anne Bigot, Kamel Mamchaoui, Brennan Harmon, Thomas Voït, Vincent Mouly, William Duddy
Software Mentions: 4
Published: almost 10 years ago

10.3390/cancers12092466

Expression Profiling of Extracellular Matrix Genes Reveals Global and Entity-Specific Characteristics in Adenoid Cystic, Mucoepidermoid and Salivary Duct Carcinomas
Cited by: 16
Author(s): Christoph Arolt, Moritz Meyer, Franziska Hoffmann, Svenja Wagener‐Ryczek, David Schwarz, Lisa Nachtsheim, Dirk Beutner, Margarete Odenthal, Orlando Guntinas‐Lichius, Reinhard Buettner, Ferdinand von Eggeling, Jens Peter Klußmann, Alexander Quaas
Software Mentions: 4
Published: about 6 years ago

10.1007/s12015-020-10103-9

ActivinA Induced SMAD1/5 Signaling in an iPSC Derived EC Model of Fibrodysplasia Ossificans Progressiva (FOP) Can Be Rescued by the Drug Candidate Saracatinib
Cited by: 9
Author(s): Susanne Hildebrandt, Branka Kampfrath, Kristin Fischer, Laura de Campos Hildebrand, Julia Haupt, Harald Stachelscheid, Petra Knaus
Software Mentions: 4
Published: over 5 years ago

10.3390/toxins13010025

Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant?
Cited by: 16
Author(s): Farhad Jalili, Hana Trigui, Juan Maldonado, Sarah Dorner, Arash Zamyadi, Ben Shapiro, Yves Terrat, Nathalie Fortin, Sébastien Sauvé, Michèle Prévost
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-5213-9

Transcriptome analysis of human heart failure reveals dysregulated cell adhesion in dilated cardiomyopathy and activated immune pathways in ischemic heart failure
Cited by: 136
Author(s): Mary E. Sweet, Andrea Cocciolo, Dobromir Slavov, Kenneth L. Jones, Joseph R. Sweet, Sharon Graw, T. Brett Reece, Amrut V. Ambardekar, Michael R. Bristow, Luisa Mestroni, Matthew R.G. Taylor
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-018-4457-8

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon
Cited by: 10
Author(s): Li Liu, Shuchao Ren, Junqiang Guo, Qingyi Wang, Xiaotuo Zhang, Peiran Liao, Shipeng Li, Ramanjulu Sunkar, Yun Zheng
Software Mentions: 4
Published: over 8 years ago

10.1016/j.celrep.2021.109583

Dynamic bi-directional phosphorylation events associated with the reciprocal regulation of synapses during homeostatic up- and down-scaling
Cited by: 19
Author(s): Kristina Desch, Julian D. Langer, Erin M. Schuman
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-017-3755-x

Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults
Cited by: 3
Author(s): Haiwang Yang, Denis Basquin, Daniel Pauli, Brian Oliver
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-021-07881-y

Comprehensive analysis of lncRNAs involved in skeletal muscle development in ZBED6-knockout Bama pigs
Cited by: 5
Author(s): Dandan Wang, Pu Yun, Yefang Li, Dengke Pan, Shengnan Wang, Wenjie Tian, Yuehui Ma, Lin Jiang
Software Mentions: 4
Published: about 5 years ago

10.1111/cpr.13096

Base editing‐mediated perturbation of endogenous PKM1/2 splicing facilitates isoform‐specific functional analysis in vitro and in vivo
Cited by: 6
Author(s): Jianxiang Lin, Susu Wu, Qingmei Shen, Jie Liu, Shisheng Huang, Guangdun Peng, Yong Qiao
Software Mentions: 4
Published: about 5 years ago

10.1007/s12975-020-00863-4

Disruptions of Anaerobic Gut Bacteria Are Associated with Stroke and Post-stroke Infection: a Prospective Case–Control Study
Cited by: 60
Author(s): Bastiaan W. Haak, Willeke F. Westendorp, Tjitske S. R. van Engelen, Xanthe Brands, Matthijs C. Brouwer, Jan-Dirk Vermeij, Floor Hugenholtz, Aswin Verhoeven, Rico Derks, Martin Giera, Paul J. Nederkoorn, Willem M. de Vos, Diederik van de Beek, W. Joost Wiersinga
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.9452

Integrative analysis of competitive endogenous RNA network reveals the regulatory role of non-coding RNAs in high-glucose-induced human retinal endothelial cells
Cited by: 6
Author(s): Nanjue Cao, Henan Liu, Feng Dong, Wei Wang, Wei Sun, Gang Wang
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-021-07713-z

Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (2): impacts of post-partum negative energy balance on stromal, glandular and luminal epithelial cells
Cited by: 6
Author(s): Wiruntita Chankeaw, Sandra Lignier, Christophe Richard, Theodoros Ntallaris, Mariam Raliou, Yongkang Guo, Damien Plassard, Claudia Bevilacqua, Olivier Sandra, Gerhard Andersson, P. Humblot, Gilles Charpigny
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-6018-1

Transcriptome profile of Corynebacterium pseudotuberculosis in response to iron limitation
Cited by: 19
Author(s): Izabela Coimbra Ibraim, Mariana Teixeira Dornelles Parise, Doglas Parise, Michelle Zibetti Tadra Sfeir, Thiago Luiz de Paula Castro, Alice R. Wattam, Preetam Ghosh, Debmalya Barh, Emannuel Maltempi Souza, Aristóteles Goés-Neto, Anne Cybelle Pinto Gomide, Vasco Azevedo
Software Mentions: 4
Published: about 7 years ago

10.3389/fimmu.2020.01982

Human Regulatory Dendritic Cells Develop From Monocytes in Response to Signals From Regulatory and Helper T Cells
Cited by: 10
Author(s): Xiangyue Zhang, Pingping Zheng, Tyler R. Prestwood, Hong Zhang, Yaron Carmi, Lorna Tolentino, Nancy Wu, Okmi Choi, Daniel A. Winer, Samuel Strober, Eun‐Suk Kang, Michael N. Alonso, Edgar G. Engleman
Software Mentions: 4
Published: about 6 years ago

10.18632/oncotarget.26322

Differential gene expression in human tissue resident regulatory T cells from lung, colon, and blood
Cited by: 13
Author(s): Magdalena Niedzielska, Elisabeth Israelsson, B. Angermann, Ben S. Sidders, Maryam Clausen, Matthew C. Catley, Rajneesh Malhotra, Céline Dumont
Software Mentions: 4
Published: almost 8 years ago

10.7717/peerj.8763

Identification of key genes and pathways affected in epicardial adipose tissue from patients with coronary artery disease by integrated bioinformatics analysis
Cited by: 6
Author(s): Liao Tan, Qian Xu, Qianchen Wang, Ruizheng Shi, Guogang Zhang
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-020-07171-z

A comprehensive analysis of cotton VQ gene superfamily reveals their potential and extensive roles in regulating cotton abiotic stress
Cited by: 14
Author(s): Pengyun Chen, Fei Wei, Shuaishuai Cheng, Liang Ma, Hantao Wang, Meng Zhang, Guangzhi Mao, Jianhua Lü, Pengbo Hao, Adeel Ahmad, Lijiao Gu, Qiang Ma, Aimin Wu, Hengling Wei, Shuang Yu
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-020-6766-y

Decoupling behavioral and transcriptional responses to color in an eyeless cnidarian
Cited by: 9
Author(s): Whitney B. Leach, Adam M. Reitzel
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.10572

Genomic diversity of Escherichia coli from healthy children in rural Gambia
Cited by: 7
Author(s): Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Usman N. Ikumapayi, Golam Sarwar, Catherine Okoi, Peggy-Estelle Tientcheu, Marianne Defernez, Justin O’Grady, Martín Antonio, Mark J. Pallen
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers13153680

PlasmiR: A Manual Collection of Circulating microRNAs of Prognostic and Diagnostic Value
Cited by: 5
Author(s): Spyros Tastsoglou, Marios Miliotis, Ioannis Kavakiotis, Αθανάσιος Αλεξίου, Eleni C. Gkotsi, Anastasia Lambropoulou, Vasileios Lygnos, Vasiliki Kotsira, Vasileios Maroulis, Dimitrios Zisis, Giorgos Skoufos, Artemis G. Hatzigeorgiou
Software Mentions: 4
Published: about 5 years ago

10.1186/s13018-021-02658-1

Potential genes and pathways associated with heterotopic ossification derived from analyses of gene expression profiles
Cited by: 5
Author(s): Zhanyu Yang, Delong Liu, Rui Guan, Li X, Yiwei Wang, Bin Sheng
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.56554

Cytotoxic T cells swarm by homotypic chemokine signalling
Cited by: 32
Author(s): Jorge Luis Galeano Niño, Sophie V. Pageon, Szun S. Tay, Feyza Colakoglu, Daryan Kempe, Jack D. Hywood, Jessica K Mazalo, James Cremasco, Matt Govendir, Laura F. Dagley, Ku‐Lung Hsu, Simone Rizzetto, Jerzy Zieba, Gregory Rice, Victoria Prior, Geraldine M. O’Neill, Richard J. Williams, David R. Nisbet, Belinda Kramer, Andrew I. Webb, Fabio Luciani, Mark Read, Maté Biro
Software Mentions: 4
Published: almost 6 years ago

10.1111/cmi.12397

The co‐transcriptome of uropathogenic<scp>E</scp>scherichia coli‐infected mouse macrophages reveals new insights into host–pathogen interactions
Cited by: 62
Author(s): Charalampos Harris Mavromatis, Nilesh J. Bokil, Makrina Totsika, Asha Kakkanat, Kolja Schaale, Carlo Vittorio Cannistraci, Tae Woo Ryu, Scott A. Beatson, Glen C. Ulett, Mark A. Schembri, Matthew J. Sweet, Timothy Ravasi
Software Mentions: 4
Published: over 11 years ago

10.3389/fcell.2021.709498

The Dynamic Changes of Transcription Factors During the Development Processes of Human Biparental and Uniparental Embryos
Cited by: 3
Author(s): Chenxi Zhang, Conghui Li, Ling Yang, Lizhi Leng, Dragomirka Jovic, Jun Wang, Fang Fang, Guibo Li, Depeng Zhao, Xuemei Li, Lin Lin, Yonglun Luo, Lars Bolund, Jinrong Huang, Ge Lin, Fengping Xu
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.35786

Human axial progenitors generate trunk neural crest cells in vitro
Cited by: 70
Author(s): Thomas J.R. Frith, Ilaria Granata, Matthew Wind, Erin Stout, Oliver Thompson, Katrin Neumann, Dylan Stavish, Paul R. Heath, Daniel Ortmann, James Hackland, Konstantinos Anastassiadis, Mina Gouti, James Briscoe, Valerie Wilson, Stuart L. Johnson, Marysia Placzek, Mario Rosario Guarracino, Peter W. Andrews, Anestis Tsakiridis
Software Mentions: 4
Published: about 8 years ago

10.3390/ijms18030627

Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens
Cited by: 14
Author(s): Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert T. Greenlee, Deborah Multerer, Stacey Honda, Yihe G. Daida, Heather Spencer Feigelson, Andrew G. Glass, Fergus J. Couch, Thomas E. Rohan, Iddo Z. Ben‐Dov
Software Mentions: 4
Published: over 9 years ago

10.7717/peerj.7696

The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers
Cited by: 4
Author(s): Shuaibin Lian, Liansheng Li, Yongjie Zhou, Zixiao Liu, Lei Wang
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmed.2020.615981

DNA Repair-Based Gene Expression Signature and Distinct Molecular Subtypes for Prediction of Clinical Outcomes in Lung Adenocarcinoma
Cited by: 8
Author(s): Bin Hu, Di Liu, Yinqiang Liu, Zhixi Li
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12876-020-01512-8

Changes in plasma bile acids are associated with gallbladder stones and polyps
Cited by: 11
Author(s): Linshi Wu, Wang Yin-ping, Sibo Zhu, Xiao Bao, Fu Zhuo, Timing Zhen, Zhiqing Yuan, Qiwei Li, Zheng Deng, J. Z. Sun, Tao Chen
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.103253

Systematic metabolic analysis of potential target, therapeutic drug, diagnostic method and animal model applicability in three neurodegenerative diseases
Cited by: 10
Author(s): Wen‐Xing Li, Gong‐Hua Li, Xin Tong, Pengpeng Yang, Jing‐Fei Huang, Lin Xu, Shao‐Xing Dai
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.4017

5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro.
Cited by: 7
Author(s): Eline Vanlancker, Barbara Vanhoecke, Andrea M. Stringer, Tom Van de Wiele
Software Mentions: 4
Published: over 9 years ago

10.1186/s12862-021-01762-4

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume
Cited by: 10
Author(s): Man Zhang, Ping Li, Xiao-lan Yan, Jia Wang, Tangren Cheng, Qixiang Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12872-020-01653-4

Identification of key genes in atrial fibrillation using bioinformatics analysis
Cited by: 4
Author(s): Yueheng Liu, Rui Tang, Ye Zhao, Xuan Jiang, Yuchao Wang, Tingting Gu
Software Mentions: 4
Published: about 6 years ago

10.1186/s12885-020-07513-w

Ovarian cancer cells direct monocyte differentiation through a non-canonical pathway
Cited by: 5
Author(s): Kaitlin C. Fogg, Andrew Miller, Ying Liu, Will Flanigan, Alyssa Walker, Amy O'Shea, Christina Kendziorski, Pamela K. Kreeger
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41419-020-02884-1

NLRP7 plays a functional role in regulating BMP4 signaling during differentiation of patient-derived trophoblasts
Cited by: 18
Author(s): Aybuke Alici-Garipcan, Burcu Özçimen, Ilke Süder, Volkan Ülker, Tamer T. Önder, Nesrin Özören
Software Mentions: 4
Published: about 6 years ago

10.1186/s12885-020-07702-7

The effect of a novel glycolysis-related gene signature on progression, prognosis and immune microenvironment of renal cell carcinoma
Cited by: 35
Author(s): Fangshi Xu, Yawen Guan, Li Xue, Sheng‐Li Huang, Ke Gao, Zhen Yang, Tie Chong
Software Mentions: 4
Published: almost 6 years ago

10.1002/2211-5463.12982

Metabolomic analysis of fibrotic mice combined with public RNA‐Seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis
Cited by: 8
Author(s): Yosui Nojima, Yoshito Takeda, Yohei Maeda, Takeshi Bamba, Eiichiro Fukusaki, Mari Itoh, Kenji Mizuguchi, Atsushi Kumanogoh
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-019-2734-4

Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data
Cited by: 73
Author(s): Hao Yang, Daixi Li, Yong Xu, Jian Ouyang, Yongkun Wang, Yuqi Zhang, Baoguo Li, Lu Xie, Guangrong Qin
Software Mentions: 4
Published: over 7 years ago

10.3389/fcell.2021.649168

Pan-Cancer Genome-Wide DNA Methylation Analyses Revealed That Hypermethylation Influences 3D Architecture and Gene Expression Dysregulation in HOXA Locus During Carcinogenesis of Cancers
Cited by: 3
Author(s): Gang Liu, Zhenhao Liu, Xiaomeng Sun, Xiaoqiong Xia, Yunhe Liu, Lei Liu
Software Mentions: 4
Published: over 5 years ago

10.3389/fnbeh.2020.618180

PsyCoP – A Platform for Systematic Semi-Automated Behavioral and Cognitive Profiling Reveals Gene and Environment Dependent Impairments of Tcf4 Transgenic Mice Subjected to Social Defeat
Cited by: 8
Author(s): Paul Volkmann, Marius Stephan, Sven Krackow, Niels Rosendal Jensen, Moritz J. Rossner
Software Mentions: 4
Published: over 5 years ago

10.1111/1751-7915.13871

Strain diversity of plant‐associated Lactiplantibacillus plantarum
Cited by: 15
Author(s): Alice Yu, Elissa A. Goldman, Jason T. Brooks, Benjamin L. Golomb, Irene S. Yim, Velitchka Gotcheva, Angel Angelov, Eun Bae Kim, Maria L. Marco
Software Mentions: 4
Published: about 5 years ago

10.1186/s12934-021-01658-4

Transcriptomics reveal different metabolic strategies for acid resistance and gamma-aminobutyric acid (GABA) production in select Levilactobacillus brevis strains
Cited by: 7
Author(s): Sagarika Banerjee, M. H. Poore, Svetlana Gerdes, Derek Nedveck, Lene Lauridsen, Heidi Thomsen Kristensen, Henrik Max Jensen, Phillip M. Byrd, Arthur C. Ouwehand, Elaine Patterson, Wesley Morovic
Software Mentions: 4
Published: about 5 years ago

10.3390/metabo8030041

Unbiased Lipidomic Profiling of Triple-Negative Breast Cancer Tissues Reveals the Association of Sphingomyelin Levels with Patient Disease-Free Survival
Cited by: 27
Author(s): Preeti Purwaha, Franklin Gu, Danthasinghe Waduge Badrajee Piyarathna, Theckelnaycke Rajendiran, Anindita Ravindran, Angela R. Omilian, Sao Jiralerspong, Gokul M. Das, Carl Morrison, Christine B. Ambrosone, Cristian Coarfa, Nagireddy Putluri, Arun Sreekumar
Software Mentions: 4
Published: about 8 years ago

10.1111/acel.13178

The inherited methylome landscape is directly altered with paternal aging and associated with offspring neurodevelopmental disorders
Cited by: 27
Author(s): Michelle M. Denomme, Mary E. Haywood, Jason C. Parks, William B. Schoolcraft, Mandy G. Katz‐Jaffe
Software Mentions: 4
Published: about 6 years ago

10.3389/fphar.2021.678256

Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells
Cited by: 5
Author(s): Yanwei Cheng, Xue Cao, Jiange Zhang, Dong Chen, Juan Zhu, Lijun Xu, Lijie Qin
Software Mentions: 4
Published: about 5 years ago

10.3389/fphys.2018.00825

Transcriptomics and Fitness Data Reveal Adaptive Plasticity of Thermal Tolerance in Oysters Inhabiting Different Tidal Zones
Cited by: 28
Author(s): Ao Li, Wei Wang, Kai Song, Guofan Zhang
Software Mentions: 4
Published: about 8 years ago

10.1099/mgen.0.000582

Achromobacter spp. genetic adaptation in cystic fibrosis
Cited by: 4
Author(s): Miglė Gabrielaitė, Finn C. Nielsen, Helle Krogh Johansen, Rasmus Lykke Marvig
Software Mentions: 4
Published: about 5 years ago

10.3389/fpls.2021.727302

Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses
Cited by: 4
Author(s): Minsu Park, Wookap Choi, Sang Yoon Shin, Hongman Moon, Dowhan Lee, Yun Shil Gho, Ki Hong Jung, Jong Seong Jeon, Chanseok Shin
Software Mentions: 4
Published: about 5 years ago

10.3389/fpls.2020.580136

Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields
Cited by: 7
Author(s): Philomin Juliana, Ravi P. Singh, Hans‐Joachim Braun, Julio Huerta‐Espino, Leonardo Crespo‐Herrera, Thomas Payne, Jesse Poland, Sandesh Shrestha, Uttam Kumar, Arun Kumar Joshi, Muhammad Imtiaz, Mohammad Zillur Rahman, Fernando H. Toledo
Software Mentions: 4
Published: about 6 years ago

10.1155/2020/6420425

Protein Kinase A Is Involved in Neuropathic Pain by Activating the p38MAPK Pathway to Mediate Spinal Cord Cell Apoptosis
Cited by: 9
Author(s): Yajun Deng, Liang Yang, Qiqi Xie, Fengbiao Yang, Guoqiang Li, Guang-Zhi Zhang, Shaoping Li, Zhi-Xi Wu, Jing Wang, Xuewen Kang
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.202917

Development of a prognostic index and screening of prognosis related genes based on an immunogenomic landscape analysis of bladder cancer
Cited by: 14
Author(s): Genyi Qu, Zhengsheng Liu, Guang Yang, Yong Xu, Maolin Xiang, Chaowei Tang
Software Mentions: 4
Published: over 5 years ago

10.26508/lsa.201900535

The molecular clock protein Bmal1 regulates cell differentiation in mouse embryonic stem cells
Cited by: 12
Author(s): Amador Gallardo, Ana Rodríguez Molina, Helena G Asenjo, Jordi Martorell-Marugán, Rosa Montes, Verónica Ramos-Mejía, Antonio Sánchez–Pozo, Pedro Carmona-Sáez, Lourdes López-Onieva, David Landeira
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2016.01744

Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals
Cited by: 17
Author(s): Erich M. Schwarz, Adrienne Roeder
Software Mentions: 4
Published: almost 10 years ago

10.15252/embj.2018101430

Cyclin F‐dependent degradation of E2F7 is critical for <scp>DNA</scp> repair and G2‐phase progression
Cited by: 33
Author(s): Ruixue Yuan, Qingwu Liu, Hendrika A. Segeren, Laurensia Yuniati, Daniele Guardavaccaro, Robert Jan Lebbink, Bart Westendorp, Alain de Bruin
Software Mentions: 4
Published: about 7 years ago

10.3389/fpls.2018.00272

Ethylene-Related Gene Expression Networks in Wood Formation
Cited by: 34
Author(s): Carolin Seyfferth, Bernard A. Wessels, Soile Jokipii-Lukkari, Björn Sundberg, Nicolas Delhomme, Judith Felten, Hannele Tuominen
Software Mentions: 4
Published: over 8 years ago

10.3390/life11060578

Comparative Analysis of Flavonoid Metabolites in Foxtail Millet (Setaria italica) with Different Eating Quality
Cited by: 8
Author(s): Yakun Zhang, Jianhua Gao, Qianru Qie, Yulu Yang, Siyu Hou, Xingchun Wang, Xukai Li, Yuanhuai Han
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2018.01693

Immunophenotype and Transcriptome Profile of Patients With Multiple Sclerosis Treated With Fingolimod: Setting Up a Model for Prediction of Response in a 2-Year Translational Study
Cited by: 28
Author(s): Ivo Torres, C. Garcı́a, Marco Marconi, Aránzazu García-Grande, Luis Rodríguez‐Esparragoza, Vı́ctor Elvira, Elvira Ramil, Lucía Campos-Ruíz, Ruth García-Hernández, Fátima Al‐Shahrour, Coral Fustero-Torre, Alicia Sánchez-Sanz, Antonio Garcı́a-Merino, A.J. Sánchez López
Software Mentions: 4
Published: about 8 years ago

10.3390/life11050442

An Unsupervised Algorithm for Host Identification in Flaviviruses
Cited by: 1
Author(s): Phuoc Truong Nguyen, Santiago Garcı́a-Vallvé, Pere Puigbò
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.576615

Integrated Analysis of Distant Metastasis-Associated Genes and Potential Drugs in Colon Adenocarcinoma
Cited by: 6
Author(s): Min Wu, Weiyang Lou, Meng Lou, Peifen Fu, Xiaofang Yu
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-021-01071-4

A synthetic probiotic engineered for colorectal cancer therapy modulates gut microbiota
Cited by: 60
Author(s): Yusook Chung, Yongku Ryu, Byung Chull An, Yeo-Sang Yoon, Oksik Choi, Tai Yeub Kim, Jae Kyung Yoon, Jun Young Ahn, Ho Jin Park, Soon-Kyeong Kwon, Jihyun F. Kim, Myung Jun Chung
Software Mentions: 4
Published: over 5 years ago

10.3390/life11070701

RiboNT: A Noise-Tolerant Predictor of Open Reading Frames from Ribosome-Protected Footprints
Cited by: 8
Author(s): Bo Song, Mengyun Jiang, Lei Gao
Software Mentions: 4
Published: about 5 years ago

10.1186/s40168-019-0671-0

Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem
Cited by: 118
Author(s): Hui Yao, Xiang Sun, Chunguang He, Pulak Maitra, Xingchun Li, Liang Guo
Software Mentions: 4
Published: over 7 years ago

10.3390/life11020113

Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor
Cited by: 12
Author(s): Xueqiang Cui, Deng Jieling, Chongxing Huang, Xuan Tang, Xianmin Li, Xiuling Li, Lu JiaShi, Zibin Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2020.00852

Lnc-ITSN1-2, Derived From RNA Sequencing, Correlates With Increased Disease Risk, Activity and Promotes CD4+ T Cell Activation, Proliferation and Th1/Th17 Cell Differentiation by Serving as a ceRNA for IL-23R via Sponging miR-125a in Inflammatory Bowel Disease
Cited by: 36
Author(s): Jiayan Nie, Qiu Zhao
Software Mentions: 4
Published: over 6 years ago

10.3390/life11080814

The Role of the Songbird Trade as an Anthropogenic Vector in the Spread of Invasive Non-Native Mynas in Indonesia
Cited by: 2
Author(s): Vincent Nijman, Marco Campera, Muhammad Ali Imron, Ahmad Ardiansyah, Abdullah Langgeng, Tungga Dewi, Katherine Hedger, Rifqi Hendrik, K. A. I. Nekaris
Software Mentions: 4
Published: about 5 years ago

10.3389/fpls.2021.640789

Coupling Between the Responses of Plants, Soil, and Microorganisms Following Grazing Exclusion in an Overgrazed Grassland
Cited by: 13
Author(s): Zhen Wang, Xiliang Li, Baoming Ji, P.C. Struik, Ke Jin, Shiming Tang
Software Mentions: 4
Published: about 5 years ago

10.1093/database/bau092

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease
Cited by: 18
Author(s): Qingzhou Zhang, Bo Yang, Xujiao Chen, Jing Xu, Changlin Mei, Zhiguo Mao
Software Mentions: 4
Published: almost 12 years ago

10.3389/fpls.2015.00918

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean
Cited by: 61
Author(s): Vikash Singh, Mukesh Jain
Software Mentions: 4
Published: almost 11 years ago

10.1186/s13054-020-2788-8

Dynamic LTR retrotransposon transcriptome landscape in septic shock patients
Cited by: 5
Author(s): Marine Mommert, Olivier Tabone, Audrey Guichard, Guy Oriol, Elisabeth Cerrato, Mélanie Denizot, Valérie Cheynet, Alexandre Pachot, Alain Lepape, Guillaume Monneret, Fabienne Venet, Karen Brengel‐Pesce, Julien Textoris, François Mallet
Software Mentions: 4
Published: over 6 years ago

10.1186/s40168-018-0515-3

Breast cancer in postmenopausal women is associated with an altered gut metagenome
Cited by: 157
Author(s): Jia Zhu, Ming Liao, Ziting Yao, Wenying Liang, Qibin Li, Jianlun Liu, Huawei Yang, Yinan Ji, Wei Wei, Aihua Tan, Sai Liang, Yang Chen, Haisong Lin, Xinyuan Zhu, Shengzhu Huang, Jiarong Tian, Rongjiang Tang, Qiuyan Wang, Zengnan Mo
Software Mentions: 4
Published: about 8 years ago

10.1002/cam4.3854

Identification of MEG8/miR‐378d/SOBP axis as a novel regulatory network and associated with immune infiltrates in ovarian carcinoma by integrated bioinformatics analysis
Cited by: 7
Author(s): Jiang Lei, Zhen-Yu He, Jun Wang, Min Hu, Ping Zhou, Chen-Lu Lian, Hua Li, San‐Gang Wu, Juan Zhou
Software Mentions: 4
Published: over 5 years ago

10.1002/cam4.2035

Dysregulation, functional implications, and prognostic ability of the circadian clock across cancers
Cited by: 19
Author(s): Yi Li, Kai Yu, Jian Zheng, Huan Lin, Qi Zhao, Xiaolong Zhang, Wei Feng, Li-Yu Wang, Jianjun Xu, Dawei Xie, Zhixiang Zuo, Zexian Liu, Qi Zheng
Software Mentions: 4
Published: over 7 years ago

10.1186/s12935-021-02069-6

Integrative analysis of ceRNA network reveals functional lncRNAs associated with independent recurrent prognosis in colon adenocarcinoma
Cited by: 11
Author(s): Yinling Mao, Jiachen Lv, Li Jiang, Yihui Wang
Software Mentions: 4
Published: about 5 years ago

10.1186/s40168-021-01115-9

Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis
Cited by: 181
Author(s): Zhenhua Wu, Shimeng Huang, Tiantian Li, Na Li, Dandan Han, Bing Zhang, Zhenjiang Xu, Shiyi Zhang, Jiaman Pang, Shilan Wang, Guolong Zhang, Jiangchao Zhao, Junjun Wang
Software Mentions: 4
Published: about 5 years ago

10.1186/s40168-021-01046-5

Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome
Cited by: 39
Author(s): Qixin Han, Juan Wang, Weiping Li, Zi‐Jiang Chen, Yanzhi Du
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-021-01132-8

Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter
Cited by: 12
Author(s): Lena Granehäll, Kun Huang, Adrian Tett, Paolo Manghi, Alice Paladin, Niall O’Sullivan, Omar Rota‐Stabelli, Nicola Segata, Albert Zink, Frank Maixner
Software Mentions: 4
Published: almost 5 years ago

10.3389/fcell.2021.688855

Transcriptomics Profiling Identifies Cisplatin-Inducible Death Receptor 5 Antisense Long Non-coding RNA as a Modulator of Proliferation and Metastasis in HeLa Cells
Cited by: 7
Author(s): Dilek Cansu Gürer, İpek Erdoğan, Ulvi Ahmadov, Merve Başol, Osama Sweef, Gulcin Cakan-Akdogan, Bünyamin Akgül
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms7100475

Low Temperature (15 °C) Reduces Bacterial Diversity and Prolongs the Preservation Time of Volvariella volvacea
Cited by: 6
Author(s): Xiuling Wang, Shunjie Liu, Mingjie Chen, Changxia Yu, Yan Zhao, Haiyan Yang, Zhe Li, Zhengpeng Li
Software Mentions: 4
Published: almost 7 years ago

10.3390/microorganisms9061297

Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction
Cited by: 1
Author(s): Valentín Pérez-Hernández, Mario Hernández-Guzmán, Marco Luna‐Guido, Yendi E. Navarro‐Noya, Elda M. Romero-Tepal, Luc Dendooven
Software Mentions: 4
Published: about 5 years ago

10.7150/jca.51321

AURKA and FAM83A are prognostic biomarkers and correlated with Tumor-infiltrating Lymphocytes in smoking related Lung Adenocarcinoma
Cited by: 7
Author(s): Mengyu Zhang, Huo Chen, Yingxiao Jiang, Jianyu Liu, Yi-Can Yang, Yunhong Yin, Yi-Qing Qu
Software Mentions: 4
Published: over 5 years ago

10.7150/jca.51173

Identification of a Prognostic Signature Model with Tumor Microenvironment for predicting Disease-free Survival after Radical Prostatectomy
Cited by: 6
Author(s): Hao Zhao, Xuening Zhang, Zhan Shi, Bingxin Guo, Wenli Zhang, Kun He, Xueqi Hu, Songhe Shi
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms9020459

A Mucoralean White Collar-1 Photoreceptor Controls Virulence by Regulating an Intricate Gene Network during Host Interactions
Cited by: 6
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Carlos Lax, Marta Silva, Javier Capilla, Eusebio Navarro, Victoriano Garre
Software Mentions: 4
Published: over 5 years ago

10.1186/s12935-020-01281-0

Long noncoding RNAs as potential biomarkers in retinoblastoma: a systematic review and meta-analysis
Cited by: 8
Author(s): Jiali Wu, Dashi Qian, Xiaodong Sun
Software Mentions: 4
Published: over 6 years ago

10.1111/jcmm.13941

Deciphering molecular properties of hypermutated gastrointestinal cancer
Cited by: 8
Author(s): Wangxiong Hu, Yanmei Yang, Weiting Ge, Shu Zheng
Software Mentions: 4
Published: almost 8 years ago

10.3390/microorganisms8111679

Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
Cited by: 13
Author(s): Valentina Méndez, Matías A. Valenzuela, Francisco Salvà‐Serra, Daniel Jaén‐Luchoro, Ximena Besoaín, Edward R. B. Moore, Michael Seeger
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2020.573920

High Abundance of Intratumoral γδ T Cells Favors a Better Prognosis in Head and Neck Squamous Cell Carcinoma: A Bioinformatic Analysis
Cited by: 16
Author(s): Huanzi Lu, Daixiu Wei, Junyi Guo, Dikan Wang, Sheng Wen, Lisa Yang, Daowei Lin, Wenqiang Xie, Liling Wen, Juan Fang, Zhi Wang
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12935-020-01238-3

Identification of a m6A RNA methylation regulators-based signature for predicting the prognosis of clear cell renal carcinoma
Cited by: 34
Author(s): Jing Chen, Kun Yu, Guansheng Zhong, Wei Shen
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00211-17

Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese
Cited by: 55
Author(s): Andrea S. Bertuzzi, Aaron M. Walsh, Jeremiah J. Sheehan, Paul D. Cotter, Fiona Crispie, P.L.H. McSweeney, Kieran N. Kilcawley, Mary C. Rea
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-019-40495-9

Differential gene expression induced by Verteporfin in endometrial cancer cells
Cited by: 8
Author(s): Lisa Bang, Venkata Ramesh Dasari, Dokyoon Kim, Radhika Gogoi
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0149171

RNA-Seq Reveals the Angiogenesis Diversity between the Fetal and Adults Bone Mesenchyme Stem Cell
Cited by: 2
Author(s): Xin Zhao, Yingmin Han, Yu Liang, Chao Nie, Jian Wang
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-020-63434-5

Identification of tipifarnib sensitivity biomarkers in T-cell acute lymphoblastic leukemia and T-cell lymphoma
Cited by: 5
Author(s): Ruth Alonso‐Alonso, Rufino Mondéjar, Nerea Martínez, Nuria García-Díaz, Cristina Fernández Pérez, David Merino, Marta Rodríguez, Anna Esteve‐Codina, Berta Fusté, Marta Gut, Francis Burrows, Catherine Scholz, José P. Vaqué, Antonio Gualberto, Miguel Á. Piris
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pbio.2006249

Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver
Cited by: 35
Author(s): Adrija Kalviša, Majken Siersbæk, Stine M. Præstholm, Line Julie Lindorf Christensen, Ronni Nielsen, Oliver Stöhr, Sabine Vettorazzi, Jan Tuckermann, Morris F. White, Susanne Mandrup, Lars Grøntved
Software Mentions: 4
Published: over 7 years ago

Projects: cran: pheatmap

Science Score: 75/100

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Papers Mentioning pheatmap 2,572