cran: pheatmap | Projects | Ecosyste.ms: Papers

10.1186/s13059-021-02413-z

Integration of metabolomics, genomics, and immune phenotypes reveals the causal roles of metabolites in disease
Cited by: 24
Author(s): Xiaojing Chu, Martin Jaeger, Joep Beumer, Olivier B. Bakker, Raúl Aguirre-Gamboa, Marije Oosting, Sanne P. Smeekens, Simone J.C.F.M. Moorlag, Vera P. Mourits, Valerie A C M Koeken, Charlotte de Bree, Trees Jansen, Ian T. Mathews, Khoi Dao, Mahan Najhawan, Jeramie D. Watrous, Irma Joosten, Sonia Sharma, Hans J. P. M. Koenen, Sebo Withoff, Iris Jonkers, Romana T. Netea‐Maier, Ramnik J. Xavier, Lude Franke, Cheng‐Jian Xu, Leo A. B. Joosten, Serena Sanna, Mohit Jain, Vinod Kumar, Hans Clevers, Cisca Wijmenga, Mihai G. Netea, Yang Li
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2020.00520

Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum
Cited by: 20
Author(s): Chengxi Li, Shuai Zhao, Xi Luo, Jia‐Xun Feng
Software Mentions: 2
Published: over 6 years ago

10.3390/genes11050489

Transcriptome Analysis of circRNA and mRNA in Theca Cells during Follicular Development in Chickens
Cited by: 15
Author(s): Manman Shen, Ping Wu, Tingting Li, Pengfei Wu, Fuxiang Chen, Lan Chen, Kaizhou Xie, Jinyu Wang, Genxi Zhang
Software Mentions: 2
Published: over 6 years ago

10.1093/gbe/evu211

Phylogenomics and Evolutionary Dynamics of the Family Actinomycetaceae
Cited by: 22
Author(s): Kelei Zhao, Wujiao Li, Chunlan Kang, Lianming Du, Ting Huang, Xiuyue Zhang, Min Wu, Bisong Yue
Software Mentions: 2
Published: about 12 years ago

10.1093/gbe/evab051

Evolutionary Contribution of Duplicated Genes to Genome Evolution in the Ginseng Species Complex
Cited by: 3
Author(s): Ming-Rui Li, Ning Ding, Tianyuan Lu, Jing Zhao, Zhenhui Wang, Peng Jiang, Sitong Liu, Xinfeng Wang, Bao Liu, Linfeng Li
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-89713-3

Heme cytotoxicity is the consequence of endoplasmic reticulum stress in atherosclerotic plaque progression
Cited by: 2
Author(s): Dávid Pethő, Zoltán Hendrik, Annamária Nagy, Lívia Beke, Andreas Patsalos, László Nagy, Szilárd Póliska, Gábor Méhes, Csaba Tóth, László Potor, John W. Eaton, Harry S. Jacob, György Balla, József Balla, Tamás Gáll
Software Mentions: 2
Published: over 5 years ago

10.1186/s13073-016-0330-z

The early infant gut microbiome varies in association with a maternal high-fat diet
Cited by: 256
Author(s): Derrick M. Chu, Kathleen M. Antony, Jun Ma, Amanda Prince, Lori Showalter, Michelle Moller, Kjersti M. Aagaard
Software Mentions: 2
Published: about 10 years ago

10.1186/s13073-016-0375-z

Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
Cited by: 36
Author(s): Tanjina Kader, David Goode, Stephen Q. Wong, Jacquie Connaughton, Simone M. Rowley, Lisa Devereux, David Byrne, Stephen B. Fox, Gisela Mir Arnau, Richard W. Tothill, Ian Campbell, Kylie L. Gorringe
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13073-017-0409-1

Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients
Cited by: 75
Author(s): Jessica Galloway-Peña, Daniel P. Smith, Pranoti Sahasrabhojane, W. Duncan Wadsworth, Bryan Fellman, Nadim J. Ajami, Elizabeth J. Shpall, Naval Daver, Michele Guindani, Joseph F. Petrosino, Dimitrios P. Kontoyiannis, Samuel A. Shelburne
Software Mentions: 2
Published: over 9 years ago

10.3390/genes11050515

Genomic Identification, Evolution, and Expression Analysis of Collagen Genes Family in Water Buffalo during Lactation
Cited by: 11
Author(s): Xingrong Lu, Anqin Duan, Shasha Liang, Xiaoya Ma, Tingxian Deng
Software Mentions: 2
Published: over 6 years ago

10.3390/genes11020219

Clinical Ketosis-Associated Alteration of Gene Expression in Holstein Cows
Cited by: 10
Author(s): Zhoulin Wu, Shiyi Chen, Chao Qin, Xianbo Jia, Feilong Deng, Jie Wang, Songjia Lai
Software Mentions: 2
Published: over 6 years ago

10.1128/mBio.02940-20

SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike
Cited by: 75
Author(s): Jenna J. Guthmiller, Olivia Stovicek, Jiaolong Wang, Siriruk Changrob, Lei Li, Peter Halfmann, Nai Ying Zheng, Henry A. Utset, Christopher T. Stamper, Haley L. Dugan, William Miller, Min Huang, Ya-Nan Dai, Christopher A. Nelson, Paige D. Hall, Maud O. Jansen, Kumaran Shanmugarajah, Jessica S. Donington, Florian Krammer, Daved H. Fremont, A. Joachimiak, Yoshihiro Kawaoka, Vera Tešić, Maria Lucia Madariaga, Patrick C. Wilson
Software Mentions: 2
Published: over 5 years ago

10.3390/genes11010020

Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition
Cited by: 11
Author(s): Fernando Manuel Matias Hurtado, Maísa de Siqueira Pinto, Perla Novais de Oliveira, Diego Mauricio Riaño-Pachón, Laura Beatriz Inocente, Helaine Carrer
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13073-021-00880-4

Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer
Cited by: 24
Author(s): Miriam Ragle Aure, Osbreac, Thomas Fleischer, Sunniva Bjørklund, Jørgen Ankill, Jaime A Castro-Mondragón, Anne‐Lise Børresen‐Dale, Jörg Tost, Kristine Kleivi Sahlberg, Anthony Mathelier, Xavier Tekpli, Vessela N. Kristensen
Software Mentions: 2
Published: over 5 years ago

10.3390/cells10061410

Regulatory miRNA–mRNA Networks in Parkinson’s Disease
Cited by: 10
Author(s): Bruno Lopes Santos‐Lobato, Amanda Ferreira Vidal, Ândrea Ribeiro-dos-Santos
Software Mentions: 2
Published: over 5 years ago

10.1016/j.gpb.2020.06.012

Screening of Potential Biomarkers for Gastric Cancer with Diagnostic Value Using Label-free Global Proteome Analysis
Cited by: 12
Author(s): Yongxi Song, Jun Wang, Jingwei Sun, Xiaowan Chen, Jinxin Shi, Zhonghua Wu, Dehao Yu, Fei Zhang, Zhenning Wang
Software Mentions: 2
Published: almost 6 years ago

10.1128/IAI.00311-19

Identification of Potential Cerebrospinal Fluid Biomarkers To Discriminate between Infection and Sterile Inflammation in a Rat Model of Staphylococcus epidermidis Catheter Infection
Cited by: 5
Author(s): Gwenn Skar, Matthew Beaver, Amy Aldrich, Dragana Lagundžin, Ishwor Thapa, Nicholas T. Woods, Hesham Ali, Jessica Snowden, Tammy Kielian
Software Mentions: 2
Published: about 7 years ago

10.3390/cells9051078

Characterization of Endoplasmic Reticulum (ER) in Human Pluripotent Stem Cells Revealed Increased Susceptibility to Cell Death upon ER Stress
Cited by: 9
Author(s): Tae Won Ha, Ji Hun Jeong, HyeonSeok Shin, Hyun Kyu Kim, Jeong Suk Im, Byung Hoo Song, Jacob Hanna, Jae Sang Oh, Dong Hun Woo, Jaeseok Han, Man Ryul Lee
Software Mentions: 2
Published: over 6 years ago

10.3390/genes10100730

Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis
Cited by: 14
Author(s): Ruibin Sun, Shaohui Wang, Dan Ma, Yilin Li, Chuanliang Liu
Software Mentions: 2
Published: about 7 years ago

10.1128/mBio.03328-20

Balancing Positive and Negative Selection: In Vivo Evolution of Candida lusitaniae MRR1
Cited by: 7
Author(s): Elora G. Demers, Jason E. Stajich, Alix Ashare, Patricia Occhipinti, Deborah A. Hogan
Software Mentions: 2
Published: over 5 years ago

10.3390/genes10100804

Transcriptional Analysis of Masson Pine (Pinus massoniana) under High CO2 Stress
Cited by: 17
Author(s): Fan Wu, Xiaobo Sun, Bingzhang Zou, Peihuang Zhu, Nengqing Lin, Jingquan Lin, Kongshu Ji
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes10100827

Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca)
Cited by: 54
Author(s): Wei Guo, Saurabh Mishra, Chengdong Wang, Hemin Zhang, Ruihong Ning, Fanli Kong, Bo Zeng, Jiangchao Zhao, Ying Liu
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2021.610196

The Transcriptomic and Bioinformatic Characterizations of Iron Acquisition and Heme Utilization in Avibacterium paragallinarum in Response to Iron-Starvation
Cited by: 2
Author(s): Caiyun Huo, Xianying Zeng, Fanxing Xu, Fangbing Li, Donghai Li, Guiping Li, Zhenguo Hu, Yanxin Hu, Jun Lin, Hsin‐Yun Sun
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2021.621336

Transcriptomic Analysis of Wheat Seedling Responses to the Systemic Acquired Resistance Inducer N-Hydroxypipecolic Acid
Cited by: 6
Author(s): Eric T Zhang, Hao Zhang, Weihua Tang
Software Mentions: 2
Published: over 5 years ago

10.1128/mSphere.00762-20

Staphylococcus aureus Tolerance and Genomic Response to Photodynamic Inactivation
Cited by: 10
Author(s): Sara B. Snell, Ann Lindley Gill, Constantine G. Haidaris, Thomas H. Foster, Timothy M. Baran, Steven R. Gill
Software Mentions: 2
Published: over 5 years ago

10.3390/genes10020155

Identification of Differentially Expressed Genes and Pathways for Abdominal Fat Deposition in Ovariectomized and Sham-Operated Chickens
Cited by: 5
Author(s): Xiaopeng Mu, Xiaoyan Cui, Ranran Liu, Qinghe Li, Maiqing Zheng, Guiping Zhao, Chao Ge, Jie Wen, Yaodong Hu, Huanxian Cui
Software Mentions: 2
Published: over 7 years ago

10.3390/genes9120592

Genome-Wide Analysis of LRR-RLK Gene Family in Four Gossypium Species and Expression Analysis during Cotton Development and Stress Responses
Cited by: 11
Author(s): Ruibin Sun, Shaohui Wang, Dan Ma, Chuanliang Liu
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.celrep.2019.12.078

Probiotic Bacillus subtilis Protects against α-Synuclein Aggregation in C. elegans
Cited by: 98
Author(s): María Eugenia Goya, Feng Xue, Cristina Sampedro-Torres-Quevedo, Sofia Arnaouteli, Lourdes Riquelme-Dominguez, Andrés Romanowski, Jack Brydon, Kathryn L. Ball, Nicola R. Stanley‐Wall, Maria Doitsidou
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes9110547

Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes
Cited by: 32
Author(s): Shuaibin Wang, Qingwei Song, Shanshan Li, Zhigang Hu, Dong Gao, Chi Song, Hongwen Huang, Yifei Liu
Software Mentions: 2
Published: almost 8 years ago

10.3390/genes9010032

Genome-Wide Methylation Patterns in Androgen-Independent Prostate Cancer Cells: A Comprehensive Analysis Combining MeDIP-Bisulfite, RNA, and microRNA Sequencing Data
Cited by: 5
Author(s): Yumin Wang, Tingting Qin, Wangqiang Hu, Binghua Chen, Mei-jie Dai, Gang Xu
Software Mentions: 2
Published: over 8 years ago

10.1074/jbc.RA120.015755

Genomic determinants implicated in the glucocorticoid-mediated induction of KLF9 in pulmonary epithelial cells
Cited by: 9
Author(s): Mahmoud Mostafa, Akanksha Bansal, Aubrey N. Michi, Sarah K. Sasse, David Proud, Anthony N. Gerber, Robert Newton
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.celrep.2021.109230

Integrin intra-heterodimer affinity inversely correlates with integrin activatability
Cited by: 11
Author(s): Guangyu Sun, Emilie Guillon, Scott A. Holley
Software Mentions: 2
Published: over 5 years ago

10.1128/mBio.00863-21

Functional Genomic and Biochemical Analysis Reveals Pleiotropic Effect of Congo Red on Aspergillus fumigatus
Cited by: 18
Author(s): Liu Z, Shriya Raj, Norman van Rhijn, Marcin G. Fraczek, Jean‐Philippe Michel, Odile Sismeiro, Rachel Legendre, Hugo Varet, Thierry Fontaine, Michael Bromley, Jean‐Paul Latgé
Software Mentions: 2
Published: over 5 years ago

10.1186/s41065-020-00166-6

Immunological analysis and differential genes screening of venous thromboembolism
Cited by: 2
Author(s): Lina Gao, Qiang Li, Jianqin Xie, Wan-Xia Yang, Chongge You
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40709-020-00116-3

A potential prognostic model based on miRNA expression profile in The Cancer Genome Atlas for bladder cancer patients
Cited by: 3
Author(s): Yan Liu, Dong Zhu, Hong Xing, Yi Hou, Yan Sun
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2016.00889

Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups
Cited by: 12
Author(s): Huong T. Le, Cuong Tu Ho, Quan Hong Trinh, Anh Duc Trinh, Minh Thi Nguyet Luu, Hai S. Tran, Didier Orange, Jean‐Louis Janeau, A. Merroune, Emma Rochelle-Newall, Thomas Pommier
Software Mentions: 2
Published: over 10 years ago

10.1186/s12967-021-02814-5

Gut microbiota accelerates cisplatin-induced acute liver injury associated with robust inflammation and oxidative stress in mice
Cited by: 31
Author(s): Shenhai Gong, Ying Feng, Yunong Zeng, Huanrui Zhang, Meiping Pan, Fangjie He, Rong Wu, Jingrui Chen, Jiuling Lu, Siyou Zhang, Songhua Yuan, Xia Chen
Software Mentions: 2
Published: over 5 years ago

10.1038/s41419-021-03800-x

MFG-E8 regulated by miR-99b-5p protects against osteoarthritis by targeting chondrocyte senescence and macrophage reprogramming via the NF-κB pathway
Cited by: 26
Author(s): Yuheng Lu, Liangliang Liu, Jinhe Pan, Bingsheng Luo, Hua Zeng, Yan Shao, Hongbo Zhang, Hong Guan, Dong Guo, Chun Zeng, Rongkai Zhang, Xiaochun Bai, Haiyan Zhang, Daozhang Cai
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2021.636284

Antimicrobial Resistance and Genomic Characterization of Two mcr-1-Harboring Foodborne Salmonella Isolates Recovered in China, 2016
Cited by: 4
Author(s): Yujie Hu, Scott V. Nguyen, Wei Wang, Xin Gan, Yinping Dong, Chang Liu, Xiquan Cui, Jin Xu, Fengqin Li, Séamus Fanning
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-91934-5

Differential methylation of G-protein coupled receptor signaling genes in gastrointestinal neuroendocrine tumors
Cited by: 5
Author(s): Seyoun Byun, Kajsa E. Affolter, Angela K. Snow, Karen Curtin, Austin R. Cannon, Lisa Cannon-Albright, Ramya Thota, Deborah W. Neklason
Software Mentions: 2
Published: over 5 years ago

10.1038/s41419-020-2666-y

ΔNp63α-induced DUSP4/GSK3β/SNAI1 pathway in epithelial cells drives endometrial fibrosis
Cited by: 24
Author(s): Guangfeng Zhao, Ruotian Li, Yun Cao, Minmin Song, Pengju Jiang, Qianwen Wu, Zhenhua Zhou, Hui Zhu, Huiyan Wang, Chenyan Dai, Dan Liú, Simin Yao, Haining Lv, Limin Wang, Jianwu Dai, Yan Zhou, Yali Hu
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-021-91742-x

Gender specific airway gene expression in COPD sub-phenotypes supports a role of mitochondria and of different types of leukocytes
Cited by: 7
Author(s): Anna Esteve‐Codina, Thomas P. Hofer, Dorothe Burggraf, Marion Heiß-Neumann, Wolfgang Gesierich, Anne Boland, Robert Olaso, Marie-Thérèse Bihoreau, Jean‐François Deleuze, Winfried Moeller, Otmar Schmid, María Soler Artigas, Kathrin Renner, Jens M. Hohlfeld, Tobias Welte, Thomas Fuehner, Lukas Jerrentrup, Andreas Rembert Koczulla, Timm Greulich, Antje Prasse, Joachim Müller–Quernheim, Sumit Gupta, Christopher Brightling, Deepak Subramanian, David Parr, Umme Kolsum, Vandana Gupta, Imre Barta, Balázs Döme, J. Strausz, Mariarita Stendardo, Marco Piattella, Pierà Boschetto, Damian Korzybski, Dorota Górecka, Adam Nowiński, Marc Dabad, Marcos Fernández-Callejo, David Endesfelder, Wolfgang zu Castell, Pieter S. Hiemstra, Per Venge, Elfriede Noeßner, Thasso Griebel, Simon Heath, Dave Singh, Marta Gut, Loems Ziegler-Heitbrock
Software Mentions: 2
Published: over 5 years ago

10.1155/2020/8951907

Baicalin Represses C/EBPβ via Its Antioxidative Effect in Parkinson’s Disease
Cited by: 24
Author(s): Kecheng Lei, Yijue Shen, Yijing He, Liwen Zhang, Jingxing Zhang, Weifang Tong, Yawei Xu, Lingjing Jin
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.119.400743

Evaluation ofSaccharomyces cerevisiaeWine Yeast Competitive Fitness in Enologically Relevant Environments by Barcode Sequencing
Cited by: 9
Author(s): Simon A. Schmidt, Radka Kolouchova, Angus H. Forgan, Anthony R. Borneman
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-021-92701-2

Integrated network analysis identifying potential novel drug candidates and targets for Parkinson's disease
Cited by: 8
Author(s): Pusheng Quan, Kai Wang, Yan Shi, Shirong Wen, Chengqun Wei, Xinyu Zhang, Jingwei Cao, Lifen Yao
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-80264-7

Integrated mRNA and miRNA expression profile analysis of female and male gonads in Hyriopsis cumingii
Cited by: 10
Author(s): Yayu Wang, Shenghua Duan, Guiling Wang, Jiale Li
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2018.00399

Unique Microbial Diversity and Metabolic Pathway Features of Fermented Vegetables From Hainan, China
Cited by: 36
Author(s): Qingyun Peng, Shuaiming Jiang, Jieling Chen, Chenchen Ma, Dongxue Huo, Yiming Shao, Jiachao Zhang
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2021.653998

Characterization and Comparison of Bacterial Communities of an Invasive and Two Native Caribbean Seagrass Species Sheds Light on the Possible Influence of the Microbiome on Invasive Mechanisms
Cited by: 7
Author(s): Tânia Aires, Tamara M. Stuij, Gerard Muyzer, Ester A. Serrão, Aschwin H. Engelen
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2019.03012

Combined Application of High-Throughput Sequencing and Metabolomics Reveals Metabolically Active Microorganisms During Panxian Ham Processing
Cited by: 32
Author(s): Yu Mu, Wei Su, Yingchun Mu, Li Jiang
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2021.653283

Illumina Sequencing and Metabolomics Analysis Reveal Thiamine Modulation of Ruminal Microbiota and Metabolome Characteristics in Goats Fed a High-Concentrate Diet
Cited by: 15
Author(s): Yuxiang Ma, Chao Wang, Hao Zhang, Lihuai Yu, Dong Li, Daoqing Gong, Junhu Yao, Hongrong Wang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41419-018-0896-z

Somatic loss of WWOX is associated with TP53 perturbation in basal-like breast cancer
Cited by: 20
Author(s): Suhaib K. Abdeen, Uri Ben‐David, Aya Shweiki, Bella Maly, Rami I. Aqeilan
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2017.02630

The Expressed MicroRNA—mRNA Interactions of Toxoplasma gondii
Cited by: 9
Author(s): İlhan E. Acar, Müşerref Duygu Saçar Demirci, Uwe Groß, Jens Allmer
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-021-94287-1

Silicon mitigates nutritional stress in quinoa (Chenopodium quinoa Willd.)
Cited by: 19
Author(s): Ana Paula de Assis Sales, Cid Naudi Silva Campos, Jonás Pereira de Souza, Dalila Lopes da Silva, Kamilla Silva Oliveira, Larissa Pereira Ribeiro Teodoro, Paulo Eduardo Teodoro
Software Mentions: 2
Published: about 5 years ago

10.1038/s41438-020-00381-2

Coexpression network analysis reveals an MYB transcriptional activator involved in capsaicinoid biosynthesis in hot peppers
Cited by: 43
Author(s): Binmei Sun, Xin Zhou, Changming Chen, Chengjie Chen, Kunhao Chen, Muxi Chen, Shaoqun Liu, Guoju Chen, Bihao Cao, Fanrong Cao, Jing Liu, Zhiwen Zhu
Software Mentions: 2
Published: about 6 years ago

10.1016/j.cmet.2016.04.001

Mapping the Human Platelet Lipidome Reveals Cytosolic Phospholipase A2 as a Regulator of Mitochondrial Bioenergetics during Activation
Cited by: 149
Author(s): David A. Slatter, Maceler Aldrovandi, Anne E O’Connor, Stuart M. Allen, Christopher J. Brasher, Robert C. Murphy, Sven Mecklemann, Saranya Ravi, Victor Darley‐Usmar, Valerie Bridget O'Donnell
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2018.00749

Overview of Virus Metagenomic Classification Methods and Their Biological Applications
Cited by: 95
Author(s): Sam Nooij, Dennis Schmitz, Harry Vennema, Annelies Kroneman, Marion Koopmans
Software Mentions: 2
Published: over 8 years ago

10.3389/fmed.2021.713312

Topical Application of the PI3Kβ-Selective Small Molecule Inhibitor TGX-221 Is an Effective Treatment Option for Experimental Epidermolysis Bullosa Acquisita
Cited by: 4
Author(s): Hannah Zillikens, Anika Kasprick, Colin Osterloh, Natalie Gross, Michael Radziewitz, Cindy Hass, Veronika Hartmann, Martina Behnen-Härer, Nancy Ernst, Katharina Boch, Gestur Vidarsson, Remco Visser, Tamás Laskay, Xinhua Yu, Frank Petersen, Ralf J. Ludwig, Katja Bieber
Software Mentions: 2
Published: about 5 years ago

10.1016/j.immuni.2020.07.004

Flexible Usage and Interconnectivity of Diverse Cell Death Pathways Protect against Intracellular Infection
Cited by: 83
Author(s): Marcel Doerflinger, Yexuan Deng, Paul G. Whitney, Ranja Salvamoser, Sven Engel, Andrew J. Kueh, Lin Tai, Annabell Bachem, Elise Gressier, Niall Geoghegan, Stephen Wilcox, Kelly L. Rogers, Alexandra L. Garnham, Michael A. Dengler, Stefanie Bader, Gregor Ebert, Jaclyn S. Pearson, Dominic De Nardo, Nancy Wang, Chenying Yang, Milton Pereira, Clare E. Bryant, Richard A. Strugnell, James E. Vince, Marc Pellegrini, Andreas Strasser, Sammy Bedoui, Marco J. Herold
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-021-82709-z

Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis
Cited by: 7
Author(s): Qian Wang, Xuelan Chen, Huan Hu, Xiaoyuan Wei, Xiaofan Wang, Zhiqing Peng, Rui Ma, Qian Zhao, Jiangchao Zhao, Jianguo Liu, Feilong Deng
Software Mentions: 2
Published: over 5 years ago

10.1038/s41438-020-0261-0

Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander
Cited by: 31
Author(s): Xiaoming Song, Fulei Nie, Wei Chen, Xiao Ma, Ke Gong, Qing Yang, Jinpeng Wang, Nan Li, Pengchuan Sun, Qiaoying Pei, Tong Yu, Jingjing Hu, Xinyu Li, Tong Wu, Shuyan Feng, Xiuqing Li, Xiyin Wang
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2021.625244

Neutrophils Encompass a Regulatory Subset Suppressing T Cells in Apparently Healthy Cattle and Mice
Cited by: 10
Author(s): Marion Rambault, Émilie Doz-Deblauwe, Yves Le Vern, Florence Carreras, Patricia Cunha, Pierre Germon, Pascal Rainard, Nathalie Winter, Aude Rémot
Software Mentions: 2
Published: over 5 years ago

10.1038/s41419-021-03863-w

Multilevel regulation of Wnt signaling by Zic2 in colon cancer due to mutation of β-catenin
Cited by: 5
Author(s): Zhengshui Xu, Jianbao Zheng, Zilu Chen, Jing Guo, Xiaopeng Li, Xingjie Wang, Chao Qu, Liyue Yuan, Cheng Chen, Xuejun Sun, Ji Hee Yu
Software Mentions: 2
Published: over 5 years ago

10.1038/cddis.2017.398

Three-dimensional tumor cell growth stimulates autophagic flux and recapitulates chemotherapy resistance
Cited by: 40
Author(s): Corinna Bingel, E Koeneke, Johannes Ridinger, Annika Bittmann, Martin Sill, Heike Peterziel, Jagoda K. Wrobel, Inga Edeltraud Rettig, Till Milde, Uta Fernekorn, Frank Weise, Andreas Schober, Olaf Witt, Ina Oehme
Software Mentions: 2
Published: about 9 years ago

10.3389/fimmu.2020.600012

IL4I1 Accelerates the Expansion of Effector CD8+ T Cells at the Expense of Memory Precursors by Increasing the Threshold of T-Cell Activation
Cited by: 10
Author(s): Marie-Line Puiffe, Aurélie Dupont, Nouhoum Sako, Jérôme Gatineau, José L. Cohen, Denis Mestivier, Agnès Lebon, Armelle Prévost-Blondel, Flavia Castellano, Valérie Molinier‐Frenkel
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-98184-5

The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids
Cited by: 5
Author(s): Tue Kjærgaard Nielsen, Benjamin Horemans, Cédric Lood, Jeroen T’Syen, Vera van Noort, Rob Lavigne, Lea Ellegaard-Jensen, Ole Hylling, Jens Aamand, Dirk Springael, Lars Hestbjerg Hansen
Software Mentions: 2
Published: about 5 years ago

10.1038/s41419-019-1402-y

Subverted regulation of Nox1 NADPH oxidase-dependent oxidant generation by protein disulfide isomerase A1 in colon carcinoma cells with overactivated KRas
Cited by: 17
Author(s): Tiphany De Bessa, Alessandra Pagano, Ana Iochabel Soares Moretti, Percíllia Oliveira, Samir Andrade Mendonça, Hervé Kovacic, Francisco Rafael Martins Laurindo
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-021-82252-x

Inhibition of androgen/AR signaling inhibits diethylnitrosamine (DEN) induced tumour initiation and remodels liver immune cell networks
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Author(s): Timothy H. Helms, Riley Mullins, Jennifer M. Thomas‐Ahner, Samuel K. Kulp, Moray J. Campbell, Fabienne Lucas, Nathan W. Schmidt, D. Lemoine, Surafel Getaneh, Zhiliang Xie, Mitch A. Phelps, Steven K. Clinton, Christopher C. Coss
Software Mentions: 2
Published: over 5 years ago

10.1126/scitranslmed.abf8654

High titers and low fucosylation of early human anti–SARS-CoV-2 IgG promote inflammation by alveolar macrophages
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Author(s): Willianne Hoepel, Hung Jen Chen, Chiara E. Geyer, Sona Allahverdiyeva, Xue D. Manz, Steven W. de Taeye, Jurjan Aman, Lynn Mes, Maurice Steenhuis, Guillermo R. Griffith, Peter I. Bonta, Philip J.M. Brouwer, Tom G. Caniels, Karlijn van der Straten, Korneliusz Golebski, René E. Jonkers, Mads Delbo Larsen, Federica Linty, Jan Nouta, Cindy P. A. A. van Roomen, Frank E.H.P. van Baarle, Cornelis M. van Drunen, Gertjan Wolbink, Alexander P.J. Vlaar, Godelieve J. de Bree, Rogier W. Sanders, Lisa Willemsen, Annette E. Neele, Diederik van de Beek, Theo Rispens, Manfred Wuhrer, Harm Jan Bogaard, Marit J. van Gils, Gestur Vidarsson, Menno P.J. de Winther, Jeroen den Dunnen
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83752-6

Allelopathic effect of Artemisia argyi on the germination and growth of various weeds
Cited by: 29
Author(s): Jinxin Li, Le Chen, Qiaohuan Chen, Yuhuan Miao, Peng Zheng, Bisheng Huang, Lan-Ping Guo, Dahui Liu, Hongzhi Du
Software Mentions: 2
Published: over 5 years ago

10.1016/j.immuni.2020.10.020

Antagonistic Inflammatory Phenotypes Dictate Tumor Fate and Response to Immune Checkpoint Blockade
Cited by: 113
Author(s): Eduardo Bonavita, Christian P. Bromley, Gustav Jonsson, Victoria S. Pelly, Sudhakar Sahoo, Katherine Walwyn-Brown, Sofia Mensurado, Agrin Moeini, Eimear Flanagan, Charlotte R. Bell, Shih‐Chieh Chiang, C.P. Chikkanna-Gowda, Neil C. Rogers, Bruno Silva‐Santos, Sébastien Jaillon, Alberto Mantovani, Caetano Reis e Sousa, Nadia Guerra, Daniel M. Davis, Santiago Zelenay
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2021.637659

Activation of Toll-Like Receptor 7 Signaling Pathway in Primary Sjögren's Syndrome-Associated Thrombocytopenia
Cited by: 10
Author(s): Shuo Zhang, Jingge Qu, Li Wang, Mengtao Li, Dong Xu, Yan Zhao, Fengchun Zhang, Xiaofeng Zeng
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2021.700009

Comparative Proteomic Analysis of Polarized Human THP-1 and Mouse RAW264.7 Macrophages
Cited by: 39
Author(s): Pengfei Li, Hao Zou, Jingyu Wu, Chen Ma, Yintai Xu, Jun Li, Rongxia Lan, Bojing Zhu, Pengyu Ren, Daidi Fan, Shisheng Sun
Software Mentions: 2
Published: over 5 years ago

10.1038/s41392-021-00690-5

The zinc finger transcription factor, KLF2, protects against COVID-19 associated endothelial dysfunction
Cited by: 27
Author(s): Suowen Xu, Yujie Liu, Yu Ding, Sihui Luo, Xueying Zheng, Xiumei Wu, Zhenghong Liu, Iqra Ilyas, Su-Yu Chen, Shuxin Han, Peter J. Little, Mukesh K. Jain, Jianping Weng
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.639572

3D Bioprinting Allows the Establishment of Long-Term 3D Culture Model for Chronic Lymphocytic Leukemia Cells
Cited by: 19
Author(s): Francesca Sbrana, Riccardo Pinos, Federica Barbaglio, Davide Ribezzi, Fiorella Scagnoli, Lydia Scarfò, Itedale Namro Redwan, Héctor Martínez, Silvia Farè, Paolo Ghia, Cristina Scielzo
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2018.01040

Bacteroides fragilis Protects Against Antibiotic-Associated Diarrhea in Rats by Modulating Intestinal Defenses
Cited by: 65
Author(s): Wendi Zhang, Bo Zhu, Jiahui Xu, Yangyang Liu, Enqi Qiu, Zhijun Li, Zhengchao Li, Yan He, Hongwei Zhou, Yang Bai, Fachao Zhi
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2018.02458

Absence of Regulatory T Cells Causes Phenotypic and Functional Switch in Murine Peritoneal Macrophages
Cited by: 15
Author(s): Jelena Škuljec, Adan Chari Jirmo, Anika Habener, Steven R. Talbot, Refik Pul, Ruth Grychtol, Malik Aydin, Christoph Kleinschnitz, Christine Happle, Gesine Hansen
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13287-020-01908-z

microRNA-375 released from extracellular vesicles of bone marrow mesenchymal stem cells exerts anti-oncogenic effects against cervical cancer
Cited by: 15
Author(s): Feng Ding, Jinhua Liu, Xiaofei Zhang
Software Mentions: 1
Published: almost 6 years ago

10.1534/g3.120.401880

High-Throughput Identification of Nuclear Envelope Protein Interactions inSchizosaccharomyces pombeUsing an Arrayed Membrane Yeast-Two Hybrid Library
Cited by: 7
Author(s): Joseph M. Varberg, Jennifer M. Gardner, Scott McCroskey, Snehabala Saravanan, W. David Bradford, Sue L. Jaspersen
Software Mentions: 1
Published: almost 6 years ago

10.1186/s41065-021-00174-0

Development and analysis of long non-coding RNA-associated competing endogenous RNA network for osteosarcoma metastasis
Cited by: 2
Author(s): Yucheng Fu, Qi Liu, Qiyuan Bao, Junxiang Wen, Zhuochao Liu, Yuehao Hu, Guoyu He, Cheng Peng, Yanguang Xu, Weibin Zhang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41438-018-0027-0

The grapevine kinome: annotation, classification and expression patterns in developmental processes and stress responses
Cited by: 29
Author(s): Kaikai Zhu, Xiaolong Wang, Jinyi Liu, Jun Tang, Qunkang Cheng, Jay Chen, Zong‐Ming Cheng
Software Mentions: 1
Published: over 8 years ago

10.1038/s41438-019-0205-8

Auxin regulation involved in gynoecium morphogenesis of papaya flowers
Cited by: 10
Author(s): Ping Zhou, Mahpara Fatima, Xinyi Ma, Juan Liu, Ray Ming
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41438-020-0331-3

Genome-wide identification of microRNAs involved in the regulation of fruit ripening and climacteric stages in melon (Cucumis melo)
Cited by: 19
Author(s): Selinge Bai, Yunyun Tian, Chao Tan, Shunbuer Bai, Jinfeng Hao, Agula Hasi
Software Mentions: 1
Published: over 6 years ago

10.1038/s41438-020-00447-1

Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight
Cited by: 14
Author(s): Stefano Pavan, Chiara Delvento, Rosa Mazzeo, Francesca Ricciardi, Pasquale Losciale, Liliana Gaeta, Nunzio D’Agostino, Francesca Taranto, Raquel Sánchez‐Pérez, Luigi M. Ricciardi, Concetta Lotti
Software Mentions: 1
Published: over 5 years ago

10.1038/s41419-020-03111-7

Targeting tumor cell-derived CCL2 as a strategy to overcome Bevacizumab resistance in ETV5+ colorectal cancer
Cited by: 24
Author(s): Haoran Feng, Kun Liu, Xiaonan Shen, Juyong Liang, Changgang Wang, Weihua Qiu, Xi Cheng, Ren Zhao
Software Mentions: 1
Published: almost 6 years ago

10.1002/iid3.454

Cyclin‐dependent kinase 1 shows to be a potential genetic target for chemical cystitis
Cited by: 1
Author(s): Kun Wang, Huaping Du, Qianfeng Zhuang, Hao Lü, Ran Xu, Dong Xue
Software Mentions: 1
Published: over 5 years ago

10.1534/g3.117.1129

Differential Expression of miRNAs in the Respiratory Tree of the Sea Cucumber Apostichopus japonicus Under Hypoxia Stress
Cited by: 20
Author(s): Da Huo, Lina Sun, Xiaoni Li, Xiaoshang Ru, Shilin Liu, Libin Zhang, Lili Xing, Hongsheng Yang
Software Mentions: 1
Published: almost 9 years ago

10.1534/g3.117.043331

Functional Profiling of Transcription Factor Genes inNeurospora crassa
Cited by: 46
Author(s): Alexander J. Carrillo, Patrick Schacht, Ilva E. Cabrera, Johnathon Blahut, Loren Prudhomme, Sarah Dietrich, Thomas Bekman, Jennifer Mei, Cristian Carrera, Vivian Chen, Isaiah Clark, Gerardo Fierro, Logan Ganzen, Jose Orellana, Shelby Wise, Kyeongcheol Yang, Hui Zhong, Katherine A. Borkovich
Software Mentions: 1
Published: about 9 years ago

10.3389/fmicb.2017.01880

Nanopore Long-Read Guided Complete Genome Assembly of Hydrogenophaga intermedia, and Genomic Insights into 4-Aminobenzenesulfonate, p-Aminobenzoic Acid and Hydrogen Metabolism in the Genus Hydrogenophaga
Cited by: 20
Author(s): Han Ming Gan, Yin P. Lee, Christopher M. Austin
Software Mentions: 1
Published: almost 9 years ago

10.1128/mSphere.01002-20

Dichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis
Cited by: 5
Author(s): Mariana Galvão Ferrarini, Líndice Mitie Nisimura, Richard M. B. M. Girard, Mayke Bezerra Alencar, Mariana Sayuri Ishikawa Fragoso, Carlla Assis Araújo-Silva, Alan de Almeida Veiga, Ana Paula Ressetti Abud, Sheila Cristina Nardelli, Rossiane C. Vommaro, Ariel Mariano Silber, Marie France-Sagot, Andréa Rodrigues Ávila
Software Mentions: 1
Published: over 5 years ago

10.3390/insects12080745

Genome-Wide Identification of Neuropeptides and Their Receptors in an Aphid Endoparasitoid Wasp, Aphidius gifuensi
Cited by: 5
Author(s): Ke Xue, Zhenxiang Li, Yuqing Gao, Fang-Hua Liu, Zhenzhen Chen, He Tian, Tong‐Xian Liu, Yaobo Xu, Zhiwei Kang
Software Mentions: 1
Published: about 5 years ago

10.1038/s41419-021-03856-9

TRPM2 promotes pancreatic cancer by PKC/MAPK pathway
Cited by: 25
Author(s): Rui Lin, Xiao Bao, Hui Wang, Sibo Zhu, Zhongyan Liu, Quanning Chen, Kaixing Ai, Baomin Shi
Software Mentions: 1
Published: over 5 years ago

10.1001/jamanetworkopen.2020.14622

Prediction of Overall Survival Among Female Patients With Breast Cancer Using a Prognostic Signature Based on 8 DNA Repair–Related Genes
Cited by: 16
Author(s): Dai Zhang, Shuanying Yang, Yiche Li, Jia Yao, Jian Ruan, Yi Zheng, Yao Deng, Na Li, Bajin Wei, Ying Wu, Zhen Zhai, Jun Lyu, Zhijun Dai
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12967-018-1640-2

Systematic analysis of lncRNA–miRNA–mRNA competing endogenous RNA network identifies four-lncRNA signature as a prognostic biomarker for breast cancer
Cited by: 188
Author(s): Chi Fan, Lei Ma, Ning Liu
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2021.708009

A Comparative Transcriptome Between Anti-drug Sensitive and Resistant Candida auris in China
Cited by: 3
Author(s): Wenkai Zhou, Xiuzhen Li, Yiqing Lin, Wei Yan, Shuling Jiang, Xiaotian Huang, Xinglong Yang, Dan Qiao, Na Li
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2021.628838

Assessment of the Distribution and Safety of Tetragenococcus muriaticus for Potential Application in the Preparation of Chinese Grasshopper Sub Shrimp Paste
Cited by: 8
Author(s): Xue Sang, Xinxiu Ma, Yanan Zhang, Hongshun Hao, Jingran Bi, Gongliang Zhang, Hongman Hou
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2020.01774

Physiological and Ecological Responses of Photosynthetic Processes to Oceanic Properties and Phytoplankton Communities in the Oligotrophic Western Pacific Ocean
Cited by: 8
Author(s): Yuqiu Wei, Zhuo Chen, Congcong Guo, Qi Zhong, Chao Wu, Jun Sun
Software Mentions: 1
Published: about 6 years ago

10.1186/s12967-019-02145-6

Long non-coding RNA BZRAP1-AS1 silencing suppresses tumor angiogenesis in hepatocellular carcinoma by mediating THBS1 methylation
Cited by: 32
Author(s): Weiwei Wang, Guoyong Chen, Bing Wang, Zheng Yuan, Guangbo Liu, Biao Niu, Yongfeng Chen, Shaotang Zhou, Jin He, Hao Xue
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2021.628538

Comparative Genomic Analysis of the Foodborne Pathogen Burkholderia gladioli pv. cocovenenans Harboring a Bongkrekic Acid Biosynthesis Gene Cluster
Cited by: 5
Author(s): Zong–Gen Peng, Tania Dottorini, Yue Hu, Menghan Li, Shuling Yan, Séamus Fanning, Michelle Baker, Jin Xu, Fengqin Li
Software Mentions: 1
Published: over 5 years ago

10.1186/s40104-020-00502-w

Palm oil protects α-linolenic acid from rumen biohydrogenation and muscle oxidation in cashmere goat kids
Cited by: 4
Author(s): Xue Wang, Graeme Martin, Qi Wen, Shulin Liu, Yinhao Li, Binlin Shi, Xiaoyu Guo, Yanli Zhao, Y.P. Guo, Sumei Yan
Software Mentions: 1
Published: almost 6 years ago

10.1074/jbc.RA120.014948

The G4 resolvase RHAU modulates mRNA translation and stability to sustain postnatal heart function and regeneration
Cited by: 5
Author(s): Mingyang Jiang, Han Hu, Ke Zhao, Ruo‐Min Di, Xinyi Huang, Yingchao Shi, Yunyun Yue, Junwei Nie, Shan Yu, Wengong Wang, Zhongzhou Yang
Software Mentions: 1
Published: almost 6 years ago

Projects: cran: pheatmap

Science Score: 75/100

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Papers Mentioning pheatmap 2,572