Ecosyste.ms: Papers

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

Projects: pypi: db

https://packages.ecosyste.ms/registries/pypi.org/packages/db

Databases for Humans
15 versions
Latest release: almost 10 years ago
1 dependent package
136,126 downloads last month

Papers Mentioning db 108

10.1016/j.xcrm.2020.100096
Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV Infection
Cited by: 11
Author(s): Sean M. Hughes, Claire Levy, Fernanda Calienes, Joanne D. Stekler, Urvashi Pandey, Lucia Vojtech, Alicia R. Berard, Kenzie Birse, Laura Noël‐Romas, Brian Richardson, Jackelyn B. Golden, Michael Cartwright, Ann C. Collier, Claire E. Stevens, Marcel E. Curlin, Timothy H. Holtz, Nelly Mugo, Elizabeth Irungu, Elly Katabira, Timothy Muwonge, Javier R. Lama, Jared M. Baeten, Adam Burgener, Jairam R. Lingappa, M. Juliana McElrath, Romel D. Mackelprang, Ian McGowan, Ross D. Cranston, Mark J. Cameron, Florian Hladik
Software Mentions: 21
Published: about 4 years ago
10.1016/j.molcel.2021.05.023
Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection
Cited by: 87
Author(s): Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I Järvelin, Mohamed Kammoun, Young Seok Lee, Shuai Ni, Manuel García-Moreno, Anna Andrejeva, Michael J. Deery, Natasha Johnson, Christopher J Neufeldt, Mirko Cortese, Michael Knight, Kathryn S. Lilley, Javier Martı̂nez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 18
Published: over 3 years ago
10.1186/s12859-015-0453-z
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
Cited by: 41
Author(s): Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido
Software Mentions: 13
Published: almost 10 years ago
10.1038/s41421-021-00321-x
Dynamics of TCR repertoire and T cell function in COVID-19 convalescent individuals
Cited by: 23
Author(s): Lingjie Luo, Wenhua Liang, Jianfeng Pang, Gang Xu, Yingying Chen, Xinrong Guo, Xin Wang, Yi Zhao, Yang-dian Lai, Yang Liu, Bin Li, Bing Su, Shuye Zhang, Michal Baniyash, Lei Shen, Lei Chen, Yun Ling, Ying Wang, Qiming Liang, Hongzhou Lu, Zheng Zhang, Feng Wang
Software Mentions: 12
Published: about 3 years ago
10.26508/lsa.201900461
Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion
Cited by: 5
Author(s): Antonio Vitobello, Juliane Perner, Johanna Beil, Jiang Zhu, Alberto Del Río-Espínola, Laurent Morawiec, Magdalena Westphal, Valérie Dubost, Marc Altorfer, Ulrike Naumann, Arne Mueller, Karen Kapur, Mark Borowsky, Colin J. Henderson, Charles Wolf, Michael Schwarz, Jonathan G. Moggs, Rémi Terranova
Software Mentions: 12
Published: about 5 years ago
10.1186/1756-0500-3-81
Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays
Cited by: 17
Author(s): Colin S. Gillespie, Guiyuan Lei, Richard J. Boys, Amanda Greenall, Darren J. Wilkinson
Software Mentions: 11
Published: over 14 years ago
10.1155/2016/7972351
Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments
Cited by: 11
Author(s): Francesco Russo, Dario Righelli, Claudia Angelini
Software Mentions: 11
Published: almost 9 years ago
10.3389/pore.2021.594649
Bcl-2 Associated Athanogene 2 (BAG2) is Associated With Progression and Prognosis of Hepatocellular Carcinoma: A Bioinformatics-Based Analysis
Cited by: 7
Author(s): Xi Zhang, Junjun Zhang, Yang Liu, Jie Li, Juan Tan, Zewen Song
Software Mentions: 10
Published: over 3 years ago
10.1111/eva.13143
Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( <i>Sebastes mentella </i> and <i>Sebastes fasciatus</i> )
Cited by: 20
Author(s): Laura Benestan, Quentin Rougemont, Caroline Senay, Éric Normandeau, Éric Parent, Rick M. Rideout, Louis Bernatchez, Yvan Lambert, Céline Audet, Gérard Parent
Software Mentions: 10
Published: almost 4 years ago
10.1111/jcmm.15848
m6A RNA methylation regulators could contribute to the occurrence of chronic obstructive pulmonary disease
Cited by: 43
Author(s): Xinwei Huang, Dongjin Lv, Yao Xiao, Min Li, Hong Zhang
Software Mentions: 10
Published: about 4 years ago
10.3389/fphar.2021.621359
Compound Dihuang Granule Inhibits Nigrostriatal Pathway Apoptosis in Parkinson’s Disease by Suppressing the JNK/AP-1 Pathway
Cited by: 8
Author(s): Li Wang, Yufang Yang, Long Chen, Zhu-qing He, Dian-yong Bi, Lei Zhang, Yuanfu Xu, Jiancheng He
Software Mentions: 9
Published: over 3 years ago
10.1186/1471-2105-13-136
Down-weighting overlapping genes improves gene set analysis
Cited by: 120
Author(s): Adi L. Tarca, Sorin Drăghici, Gaurav Bhatti, Roberto Romero
Software Mentions: 9
Published: over 12 years ago
10.1371/journal.pone.0158259
Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers
Cited by: 15
Author(s): Inna Tishchenko, Heloisa Helena Milioli, Carlos Riveros, Pablo Moscato
Software Mentions: 9
Published: over 8 years ago
10.7150/ijms.50704
Integral Analysis of the RNA Binding Protein-associated Prognostic Model for Renal Cell Carcinoma
Cited by: 11
Author(s): Qin Xin, Zhengfang Liu, Yan Kou, Zhiqing Fang, Yi‐Ming Fan
Software Mentions: 9
Published: almost 4 years ago
10.1002/cam4.2774
Identification of prognostic genes in adrenocortical carcinoma microenvironment based on bioinformatic methods
Cited by: 39
Author(s): Xiao Li, Yang Gao, Zicheng Xu, Zheng Zhang, Yuxiao Zheng, Feng Qi
Software Mentions: 9
Published: almost 5 years ago
10.1186/s12935-020-01560-w
Identification of an immune gene signature for predicting the prognosis of patients with uterine corpus endometrial carcinoma
Cited by: 19
Author(s): Cankun Zhou, Chaomei Li, Fangli Yan, Yuhua Zheng
Software Mentions: 8
Published: about 4 years ago
10.1186/s12974-020-01931-0
Effects of long-term and brain-wide colonization of peripheral bone marrow-derived myeloid cells in the CNS
Cited by: 28
Author(s): Lindsay A. Hohsfield, Allison R. Najafi, Yasamine Ghorbanian, Neelakshi Soni, Edna E. Hingco, Sung Jin Kim, Ayer Darling Jue, Vivek Swarup, Mathew A. Inlay, Kim N. Green
Software Mentions: 8
Published: about 4 years ago
10.1038/s41416-019-0571-x
Prognosis and modulation mechanisms of COMMD6 in human tumours based on expression profiling and comprehensive bioinformatics analysis
Cited by: 24
Author(s): Mi Yang, Weiqiang Huang, Yaling Sun, Huazhen Liang, Min Chen, Xixi Wu, Xiaoqing Wang, Longshan Zhang, Xiaobin Cheng, Yu Fan, Hua Pan, Longhua Chen, Jian Guan
Software Mentions: 7
Published: about 5 years ago
10.1186/s12859-016-1180-9
Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model
Cited by: 21
Author(s): Xiaoxiao Sun, David Dalpiaz, Di Wu, Jun S. Liu, Wenxuan Zhong, Ping Ma
Software Mentions: 7
Published: about 8 years ago
10.1038/srep29042
Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana
Cited by: 35
Author(s): Frédéric Bouché, Maria D’Aloia, Pierre Tocquin, Guillaume Lobet, Nathalie Detry, Claire Périlleux
Software Mentions: 7
Published: over 8 years ago
10.3390/ijms22116034
mTOR Driven Gene Transcription Is Required for Cholesterol Production in Neurons of the Developing Cerebral Cortex
Cited by: 9
Author(s): Martin Schüle, Tamer Butto, Sri Dewi, Laura Schlichtholz, Susanne Strand, Susanne Gerber, Kristina Endres, Susann Schweiger, Jennifer Winter
Software Mentions: 6
Published: over 3 years ago
10.7150/ijms.49126
Construction and validation of a three-microRNA signature as prognostic biomarker in patients with hepatocellular carcinoma
Cited by: 9
Author(s): Xi Zhang, Li Ma, Li Zhai, Dong Chen, Yong Li, Zhongjun Shang, Zongmei Zhang, Yu Gao, Wei Yang, Yixun Li, Yu‐Qing Pan
Software Mentions: 6
Published: almost 4 years ago
10.3390/life11020115
A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression
Cited by: 6
Author(s): Theodora-Dafni Michalettou, Ioannis Michalopoulos, Sylvain V. Costes, Christine E. Hellweg, Megumi Hada, Alexandros G. Georgakilas
Software Mentions: 6
Published: almost 4 years ago
10.3389/fcell.2021.622021
Identification of Potential ceRNA Network and Patterns of Immune Cell Infiltration in Systemic Sclerosis-Associated Interstitial Lung Disease
Cited by: 6
Author(s): Qiuhong Wu, Yang Liu, Yan Xie, Shixiong Wei, Yi Liu
Software Mentions: 6
Published: over 3 years ago
10.1111/mec.15743
The strength and form of natural selection on transcript abundance in the wild
Cited by: 9
Author(s): Freed Ahmad, Paul V. Debes, Ilkka Nousiainen, Siim Kahar, Lilian Pukk, Riho Gross, Mikhail Ozerov, Anti Vasemägi
Software Mentions: 6
Published: almost 4 years ago
10.1155/2020/8468303
Investigation of the Potential Mechanism Governing the Effect of the Shen Zhu San on COVID-19 by Network Pharmacology
Cited by: 5
Author(s): Yuxuan Wang, Yuhua Ru, Guowei Zhuo, Maozheng Sheng, Shuangqiu Wang, Jiarui Ma, Guowei Zhou, Xiaohe Sun, Yanqi Zeng, Ya Zhang, Hui Li, Zhigang Lu, Depei Wu, Minghua Wu
Software Mentions: 6
Published: about 4 years ago
10.1111/1462-2920.15260
The biogeochemical variability of Arctic thermokarst ponds is reflected by stochastic and niche‐driven microbial community assembly processes
Cited by: 11
Author(s): Alizée Le Moigne, Maciej Bartosiewicz, Gabriela Schaepman‐Strub, Samuel Abiven, Jakob Pernthaler
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pgen.1009140
Drosophila Caliban preserves intestinal homeostasis and lifespan through regulating mitochondrial dynamics and redox state in enterocytes
Cited by: 12
Author(s): Zhaoxia Dai, Dong Liu, Xiao Du, Ying Ge, Deborah A. Hursh, Xiaolin Bi
Software Mentions: 5
Published: about 4 years ago
10.1111/eva.12708
The genetic legacy of 50 years of desert bighorn sheep translocations
Cited by: 27
Author(s): Joshua P. Jahner, Marjorie D. Matocq, Jason L. Malaney, Mike Cox, Peregrine L. Wolff, Mitchell A. Gritts, Thomas L. Parchman
Software Mentions: 5
Published: about 6 years ago
10.1111/eva.12638
Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale
Cited by: 31
Author(s): Alicia Dalongeville, Marco Andrello, David Mouillot, Stéphane Lobreaux, Marie‐Josée Fortin, Frida Ben Rais Lasram, Jonathan Belmaker, Delphine Rocklin, Stéphanie Manel
Software Mentions: 5
Published: over 6 years ago
10.1038/s41598-020-67690-3
Transcriptomic analysis of the mechanisms of alleviating renal interstitial fibrosis using the traditional Chinese medicine Kangxianling in a rat model
Cited by: 13
Author(s): Yufeng Jiang, Yaohan Zhu, Timing Zhen, Jie Li, Kaichen Xing, Liqun He, Sibo Zhu
Software Mentions: 5
Published: over 4 years ago
10.3390/ijms21061938
Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis
Cited by: 8
Author(s): Dimitrios S. Kanakoglou, Theodora-Dafni Michalettou, Christina Vasileiou, Evangelos Gioukakis, Δωροθέα Μανέτα, Konstantinos Kyriakidis, Alexandros G. Georgakilas, Ioannis Michalopoulos
Software Mentions: 5
Published: over 4 years ago
10.1186/s13046-020-1541-0
FKBP9 promotes the malignant behavior of glioblastoma cells and confers resistance to endoplasmic reticulum stress inducers
Cited by: 16
Author(s): Huizhe Xu, Peng Liu, Yumei Yan, Kun Fang, Dapeng Liang, Yangcheng Liu, Xiaohong Zhang, Songyan Wu, Jin Ma, Ruoyu Wang, Tao Li, Haozhe Piao, Meng Shao
Software Mentions: 4
Published: over 4 years ago
10.1186/1755-8794-7-39
Identification of Chiari Type I Malformation subtypes using whole genome expression profiles and cranial base morphometrics
Cited by: 22
Author(s): Christina A. Markunas, Eric F. Lock, Karen Soldano, Heidi Cope, Chien‐Kuang Cornelia Ding, David S. Enterline, Gerald A. Grant, Herbert E. Fuchs, Allison E. Ashley-Koch, Simon G. Gregory
Software Mentions: 4
Published: over 10 years ago
10.1186/s12891-021-04109-8
Major ceRNA regulation and key metabolic signature analysis of intervertebral disc degeneration
Cited by: 7
Author(s): Shuai Cao, Jie Li, Kai Yang, Haopeng Li
Software Mentions: 4
Published: over 3 years ago
10.3390/microorganisms8111663
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut
Cited by: 11
Author(s): Hiroki Nishiyama, Hisashi Endo, Romain Blanc-Mathieu, Hiroyuki Ogata
Software Mentions: 4
Published: about 4 years ago
10.7717/peerj.9627
Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment
Cited by: 5
Author(s): Jiong Ma, Pu Cheng, Xuejun Chen, Chunxia Zhou, Zheng Wei
Software Mentions: 4
Published: over 4 years ago
10.1002/ece3.4305
Lake regionalization and diatom metacommunity structuring in tropical South America
Cited by: 46
Author(s): Xavier Benito, Sherilyn C. Fritz, Miriam Steinitz‐Kannan, María Isabel Álvarez Vélez, Michael M. McGlue
Software Mentions: 4
Published: over 6 years ago
10.1111/eva.12660
Impact of supplementation on deleterious mutation distribution in an exploited salmonid
Cited by: 26
Author(s): Anne‐Laure Ferchaud, Martin Laporte, Charles Perrier, Louis Bernatchez
Software Mentions: 4
Published: over 6 years ago
10.3389/fgene.2020.609117
Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in Arabidopsis thaliana
Cited by: 4
Author(s): Muhammad Farooq, Aalt D. J. van Dijk, Harm Nijveen, M.N.C. Aarts, Willem Kruijer, Thu Phuong Nguyen, Shahid Mansoor, Dick de Ridder
Software Mentions: 4
Published: almost 4 years ago
10.3389/fgene.2020.584624
Development and Validation of an RNA-Binding Protein-Based Prognostic Model for Ovarian Serous Cystadenocarcinoma
Cited by: 1
Author(s): Yunan He, Sen Zeng, Shunjie Hu, Fengqian Zhang, Nianchun Shan
Software Mentions: 4
Published: about 4 years ago
10.3389/fmolb.2021.696072
Decreased Expression of PACSIN1 in Brain Glioma Samples Predicts Poor Prognosis
Cited by: 6
Author(s): Zimu Zhou, Zhiyuan Jia, Xi-an Fu, Rui Ma, Ren Yuting, Yuan Wang, Tao Wen, Ming Ma, Yinlong Liu, Enfang Shan
Software Mentions: 4
Published: over 3 years ago
10.7150/jca.52105
Identification of the hub genes and prognostic indicators of gastric cancer and correlation of indicators with tumor-infiltrating immune cell levels
Cited by: 4
Author(s): Yun Ji, Lu Gao, Can Zhang, Xu Sun, Liping Dai, Zhenyu Ji, Jianying Zhang, Zhida Zhang, Weimin Cao, Yang Zhao, Liguo Zhang
Software Mentions: 4
Published: almost 4 years ago
10.7554/eLife.57603
Endothelial TGF-β signaling instructs smooth muscle cell development in the cardiac outflow tract
Cited by: 16
Author(s): Giulia L. M. Boezio, Anabela Bensimon-Brito, Janett Piesker, Stefan Guenther, Christian S. M. Helker, Didier Y.R. Stainier
Software Mentions: 4
Published: about 4 years ago
10.1186/1752-0509-6-38
Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma
Cited by: 23
Author(s): Ricardo de Matos Simoes, Shailesh Tripathi, Frank Emmert‐Streib
Software Mentions: 3
Published: over 12 years ago
10.1186/s12935-020-01398-2
Identification of a three-miRNA signature as a novel prognostic model for papillary renal cell carcinoma
Cited by: 2
Author(s): Ge Li, Hongbo Yang, Yong Cheng, Xin Zhao, Xu Li, Rui Jiang
Software Mentions: 3
Published: over 4 years ago
10.1038/s41419-020-2381-8
MOB2 suppresses GBM cell migration and invasion via regulation of FAK/Akt and cAMP/PKA signaling
Cited by: 41
Author(s): Ke Jiang, Gang Yao, Lulu Hu, Yumei Yan, Jia Liu, Jingwei Shi, Youwei Chang, Ye Zhang, Dapeng Liang, Dachuan Shen, Guirong Zhang, Meng Shao, Haozhe Piao
Software Mentions: 3
Published: over 4 years ago
10.15252/msb.156240
Extensive allele‐specific translational regulation in hybrid mice
Cited by: 30
Author(s): Jingyi Hou, Xi Wang, Erik McShane, Henrik Zauber, Wei Sun, Matthias Selbach, Wei Chen
Software Mentions: 3
Published: over 9 years ago
10.3390/md10081765
The Transcriptome of Bathymodiolus azoricus Gill Reveals Expression of Genes from Endosymbionts and Free-Living Deep-Sea Bacteria
Cited by: 22
Author(s): Conceição Egas, Miguel Pinheiro, Paula Fernanda Gomes, Cristina Barroso, Raúl Bettencourt
Software Mentions: 3
Published: over 12 years ago
10.3389/fgene.2020.567262
A Recently Formed Triploid Cardamine insueta Inherits Leaf Vivipary and Submergence Tolerance Traits of Parents
Cited by: 5
Author(s): Jianqiang Sun, Rie Shimizu‐Inatsugi, Hugo Hofhuis, Kentaro Shimizu, Angela Hay, Kentaro Shimizu, Jun Sese
Software Mentions: 3
Published: about 4 years ago
10.3390/ijms22168574
Comparison of Histone H3K4me3 between IVF and ICSI Technologies and between Boy and Girl Offspring
Cited by: 6
Author(s): Huixia Yang, Zhi Ma, Peng Lin, Christina Kühn, Martina Rahmeh, Sven Mahner, Udo Jeschke, Viktoria von Schönfeldt
Software Mentions: 3
Published: over 3 years ago
10.3389/fgene.2019.00903
SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes
Cited by: 12
Author(s): Zishuai Wang, Xikang Feng, Shuai Cheng Li
Software Mentions: 3
Published: about 5 years ago
10.1186/s12864-019-6134-y
Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing
Cited by: 13
Author(s): Jennifer M. Bouso, Paul J. Planet
Software Mentions: 3
Published: about 5 years ago
10.3389/fimmu.2021.662465
Comprehensive Profiling of Inflammatory Factors Revealed That Growth Differentiation Factor-15 Is an Indicator of Disease Severity in COVID-19 Patients
Cited by: 18
Author(s): Xiangyun Teng, Jiaqi Zhang, Yawei Shi, Yuntao Liu, Yanqing Yang, Jinyong He, Shuhong Luo, Youhua Huang, Yanxia Liu, Dongdong Liu, Yizhe Li, Shuangzhe Zhang, Ruo‐Pan Huang, Dawei Wang, Jianhua Xu
Software Mentions: 3
Published: over 3 years ago
10.1007/s00018-016-2401-0
Multi-OMIC profiling of survival and metabolic signaling networks in cells subjected to photodynamic therapy
Cited by: 24
Author(s): Ruud Weijer, Séverine Clavier, Esther A. Zaal, Maud M. E. Pijls, Robert T. van Kooten, Klaas Vermaas, René Leen, Aldo Jongejan, Perry D. Moerland, Antoine H. C. van Kampen, André B. P. Kuilenburg, Celia R. Berkers, Simone Lemeer, Michal Heger
Software Mentions: 3
Published: about 8 years ago
10.1186/s13007-017-0159-5
Medical Subject Heading (MeSH) annotations illuminate maize genetics and evolution
Cited by: 7
Author(s): Timothy Beissinger, Gota Morota
Software Mentions: 3
Published: over 7 years ago
10.1038/s41598-019-44305-0
Variable protein homeostasis in housekeeping and non-housekeeping pathways under mycotoxins stress
Cited by: 6
Author(s): Yu Sun, Jikai Wen, Ruohong Chen, Yiqun Deng
Software Mentions: 3
Published: over 5 years ago
10.3390/cancers12061654
Prognostic Effect of Comorbid Disease and Immune Gene Expression on Mortality in Kidney Cancer—A Population Based Study
Cited by: 2
Author(s): Chu‐Kwan Wong, Tzu Ting Chen, Wei Pin Chang, Henry Sung Ching Wong, Mei‐Yi Wu, Wirawan Adikusuma, Yuh Feng Lin, Wei Chiao Chang
Software Mentions: 3
Published: over 4 years ago
10.1186/s13040-020-00227-6
Examining the effector mechanisms of Xuebijing injection on COVID-19 based on network pharmacology
Cited by: 30
Author(s): Wenjiang Zheng, Qian Yan, Yongshi Ni, Shaofeng Zhan, Liuliu Yang, Hongfa Zhuang, Xiaohong Liu, Yong Jiang
Software Mentions: 3
Published: about 4 years ago
10.3390/cancers9120160
Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE)
Cited by: 4
Author(s): Constantinos Yeles, Efstathios–Iason Vlachavas, Olga Papadodima, Eleftherios Pilalis, Constantinos E. Vorgias, Alexandros G. Georgakilas, Aristotelis Chatziioannou
Software Mentions: 2
Published: almost 7 years ago
10.3389/fcell.2021.680947
Single-Cell Transcriptome Profiling Reveals the Suppressive Role of Retinal Neurons in Microglia Activation Under Diabetes Mellitus
Cited by: 5
Author(s): Yao Xiao, Xiaoyi Hu, Shuangshuang Fan, Jiawei Zhong, Xinzhi Mo, Xialin Liu, Youjin Hu
Software Mentions: 2
Published: over 3 years ago
10.1002/ece3.4622
Birds in the Himalayas: What drives beta diversity patterns along an elevational gradient?
Cited by: 25
Author(s): Yiming Hu, Zhifeng Ding, Zhigang Jiang, Quan Qing, Keji Guo, Liqiao Tian, Huijian Hu, Luke Gibson
Software Mentions: 2
Published: about 6 years ago
10.3389/fimmu.2021.573266
Pneumolysin Is Responsible for Differential Gene Expression and Modifications in the Epigenetic Landscape of Primary Monocyte Derived Macrophages
Cited by: 5
Author(s): Joby Cole, Adrienn Angyal, Richard D. Emes, Tim Mitchell, Mark J. Dickman, David H. Dockrell
Software Mentions: 2
Published: over 3 years ago
10.3389/fmed.2021.619978
iOntoBioethics: A Framework for the Agile Development of Bioethics Ontologies in Pandemics, Applied to COVID-19
Cited by: 4
Author(s): Mohammed Odeh, Faten F. Kharbat, Rana Yousef, Yousra Odeh, Dina Tbaishat, Nancy Hakooz, Rana Dajani, Asem Mansour
Software Mentions: 2
Published: over 3 years ago
10.1186/s12859-020-03700-5
scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
Cited by: 15
Author(s): Ji-Hye Choi, Hye In Kim, Hyun Goo Woo
Software Mentions: 2
Published: over 4 years ago
10.1002/ece3.7427
Processes that drive the population structuring of <i>Jenynsia lineata</i> (Cyprinidontiformes, Anablepidae) in the La Plata Basin
Cited by: 6
Author(s): Yanina F. Briñoccoli, Luiz Jardim de Queiroz, Sergio Bogan, Ariel Hernán Paracampo, Paula Posadas, Gustavo M. Somoza, Juan I. Montoya‐Burgos, Yamila Paula Cardoso
Software Mentions: 2
Published: over 3 years ago
10.1093/gbe/evaa011
Origin Recognition Complex (ORC) Evolution Is Influenced by Global Gene Duplication/Loss Patterns in Eukaryotic Genomes
Cited by: 9
Author(s): Eduard Ocaña‐Pallarès, Zaida Vergara, Bénédicte Desvoyes, Manuel Tejada‐Jiménez, Ainoa Romero-Jurado, Aurora Galván, Emilio Fernández, Iñaki Ruiz‐Trillo, Crisanto Gutiérrez
Software Mentions: 2
Published: almost 5 years ago
10.3389/fpls.2021.701969
Transcriptome Alterations of an in vitro-Selected, Moderately Resistant, Two-Row Malting Barley in Response to 3ADON, 15ADON, and NIV Chemotypes of Fusarium graminearum
Cited by: 5
Author(s): James R. Tucker, W. G. Legge, Sujit Maiti, Colin W. Hiebert, Şenay Şimşek, Zhen Yao, Wayne Xu, Ana Badea, W. G. Dilantha Fernando
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2164-7-130
A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model
Cited by: 93
Author(s): Patrícia Beldade, Stephen Rudd, Jonathan D. Gruber, Anthony D. Long
Software Mentions: 2
Published: over 18 years ago
10.1002/ece3.4901
Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality
Cited by: 21
Author(s): V. Alex Sotola, David S. Ruppel, Timothy H. Bonner, Chris C. Nice, Noland H. Martin
Software Mentions: 2
Published: almost 6 years ago
10.1186/s13321-017-0219-x
Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy
Cited by: 75
Author(s): Ivana Blaženović, Tobias Kind, Hrvoje Torbašinović, Slobodan Obrenović, Sajjan S. Mehta, Hiroshi Tsugawa, Tobias Wermuth, Nicolas Schauer, Martina Jahn, Rebekka Biedendieck, Dieter Jahn, Oliver Fiehn
Software Mentions: 2
Published: over 7 years ago
10.1089/cmb.2018.0199
INDEX-db: The Indian Exome Reference Database (Phase I)
Cited by: 11
Author(s): Parvez Ahmed, More Rp, Biju Viswanath, Sanjeev Jain, Rao Ms, Odity Mukherjee
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-021-86879-8
Transcriptomic signals in blood prior to lung cancer focusing on time to diagnosis and metastasis
Cited by: 4
Author(s): Therese Haugdahl Nøst, Matthew T. G. Holden, Tom Dønnem, Hege Bøvelstad, Charlotta Rylander, Eiliv Lund, Torkjel M. Sandanger
Software Mentions: 2
Published: over 3 years ago
10.15252/msb.20166941
Pervasive isoform‐specific translational regulation via alternative transcription start sites in mammals
Cited by: 78
Author(s): Xi Wang, Jingyi Hou, Claudia Quedenau, Wei Chen
Software Mentions: 2
Published: over 8 years ago
10.1111/acel.13099
Intrinsically altered lung‐resident γδT cells control lung melanoma by producing interleukin‐17A in the elderly
Cited by: 7
Author(s): Min Cheng, Yongyan Chen, Dake Huang, Wen Chen, Xu Wang, Chuancun Yin, Guodong Shen, Tongwen Xu, Gan Shen, Zhigang Tian, Shilian Hu
Software Mentions: 2
Published: almost 5 years ago
10.1002/jez.b.23009
System‐level analyses of keystone genes required for mammalian tooth development
Cited by: 22
Author(s): Outi Hallikas, Rishi Das Roy, Mona M. Christensen, Élodie Renvoisé, Ana-Marija Sulic, Jukka Jernvall
Software Mentions: 2
Published: about 4 years ago
10.1002/em.20639
Pulmonary response to surface‐coated nanotitanium dioxide particles includes induction of acute phase response genes, inflammatory cascades, and changes in microRNAs: A toxicogenomic study
Cited by: 148
Author(s): Sabina Halappanavar, Petra Jackson, Andrew Williams, Keld Alstrup Jensen, Karin Sørig Hougaard, Ulla Vogel, Carole L. Yauk, Håkan Wallin
Software Mentions: 2
Published: almost 14 years ago
10.3390/v10030113
Deciphering the Human Virome with Single-Virus Genomics and Metagenomics
Cited by: 29
Author(s): Maria José de la Cruz Peña, Francisco Martínez-Hernández, Inmaculada García-Heredia, Mónica Lluesma Gómez, Òscar Fornas, Manuel Martínez‐García
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pcbi.1005496
Inferring modulators of genetic interactions with epistatic nested effects models
Cited by: 13
Author(s): Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz
Software Mentions: 2
Published: over 7 years ago
10.1002/mbo3.600
Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows
Cited by: 21
Author(s): Songlin Liu, Zhijian Jiang, Yiqin Deng, Yunchao Wu, Jingping Zhang, Changsui Zhao, Di Huang, Xiaoping Huang, Stacey M. Trevathan-Tackett
Software Mentions: 2
Published: over 6 years ago
10.1186/s13020-020-00330-0
Transcriptomics- and metabolomics-based integration analyses revealed the potential pharmacological effects and functional pattern of in vivo Radix Paeoniae Alba administration
Cited by: 4
Author(s): Sining Wang, Huihua Chen, Yufan Zheng, Zhenyu Li, Baiping Cui, Pei Zhao, Jiali Zheng, Rong Lü, Ninghui Sun
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0166852
Linking Hematopoietic Differentiation to Co-Expressed Sets of Pluripotency-Associated and Imprinted Genes and to Regulatory microRNA-Transcription Factor Motifs
Cited by: 6
Author(s): Mohamed Hamed, Johannes Trumm, Christian Spaniol, Riccha Sethi, Mohammad R. Irhimeh, Georg Fuellen, Martina Paulsen, Volkhard Helms
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0097282
HLA Diversity in the 1000 Genomes Dataset
Cited by: 150
Author(s): Pierre-Antoine Gourraud, Pouya Khankhanian, Nezih Cereb, Soo Young Yang, Michael Feolo, Martin Maiers, John D. Rioux, Stephen L. Hauser, Jorge R. Oksenberg
Software Mentions: 1
Published: over 10 years ago
10.3390/v7112919
Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome?
Cited by: 13
Author(s): Ibrahim M. Moustafa, David W. Gohara, Akira Uchida, Neela H. Yennawar, Craig Ε. Cameron
Software Mentions: 1
Published: about 9 years ago
10.3390/cells8080931
Internalization Characterization of Si Nanorod with Camouflaged Cell Membrane Proteins Reveals ATXN2 as a Negative Regulator
Cited by: 9
Author(s): Yi Lü, Jing Dai, Na Kong, Jianghuai Liu, Jinkang Gong, Yuan Yao
Software Mentions: 1
Published: over 5 years ago
10.15252/emmm.201606184
TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype
Cited by: 115
Author(s): Evelyn Fessler, Jarno Drost, Sander R. van Hooff, Janneke F. Linnekamp, Xin Wang, Marnix Jansen, Felipe de Sousa e Melo, Pramudita R. Prasetyanti, Joep E. G. IJspeert, Marek Franitza, Peter Nürnberg, Carel J. M. van Noesel, Evelien Dekker, Louis Vermeulen, Hans Clevers, Jan Paul Medema
Software Mentions: 1
Published: over 8 years ago
10.1002/ece3.5503
DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds
Cited by: 14
Author(s): Zhenhua Sun, Markus Majaneva, Ekaterina Sokolova, Sébastien Rauch, Sondre Meland, Torbjørn Ekrem
Software Mentions: 1
Published: over 5 years ago
10.1186/1756-8935-6-26
Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array
Cited by: 194
Author(s): Roderick C. Slieker, Steffan Daniël Bos, Jelle J. Goeman, Judith V.M.G. Bovée, Rudolf P. Talens, Ruud van der Breggen, H. Eka D. Suchiman, Eric Wubbo Lameijer, Hein Putter, Erik B. van den Akker, Yanju Zhang, J. Wouter Jukema, P. Eline Slagboom, Ingrid Meulenbelt, Bastiaan T. Heijmans
Software Mentions: 1
Published: over 11 years ago
10.1002/mgg3.548
Upregulation of miR‐200a and miR‐204 in MPP<sup>+</sup>‐treated differentiated PC12 cells as a model of Parkinson’s disease
Cited by: 17
Author(s): Maryam Talepoor Ardakani, Mohsen Rostamian Delavar, Masoud Baghi, Mohammad Hossein Nasr-Esfahani, Abbas Kiani-Esfahani, Kamran Ghaedi
Software Mentions: 1
Published: almost 6 years ago
10.3390/microorganisms8040583
Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics
Cited by: 11
Author(s): Yunzeng Zhang, Jin Xu, En Tao Wang, Nian Wang
Software Mentions: 1
Published: over 4 years ago
10.3390/ijms22158018
Occurrence of Calcium Oscillations in Human Spermatozoa Is Based on Spatial Signaling Enzymes Distribution
Cited by: 1
Author(s): Julia Korobkin, Fedor A. Balabin, S.A. Yakovenko, E.Y. Simonenko, Anastasia N. Sveshnikova
Software Mentions: 1
Published: over 3 years ago
10.3390/foods10092105
Microcapsules Consisting of Whey Proteins-Coated Droplets of Lipids Embedded in Wall Matrices of Spray-Dried Microcapsules Consisting Mainly of Non-Fat Milk Solids
Cited by: 2
Author(s): Minghua Wang, Yael Rosenberg, M. Rosenberg
Software Mentions: 1
Published: about 3 years ago
10.3389/fnagi.2021.650740
Stress Granules and Neurodegenerative Disorders: A Scoping Review
Cited by: 18
Author(s): Mohammad Reza Asadi, Marziyeh Sadat Moslehian, Hani Sabaie, Abbas Jalaiei, Soudeh Ghafouri‐Fard, Mohammad Taheri, Maryam Rezazadeh
Software Mentions: 1
Published: over 3 years ago
10.3390/ijms22168606
A Time-Course Study of the Expression Level of Synaptic Plasticity-Associated Genes in Un-Lesioned Spinal Cord and Brain Areas in a Rat Model of Spinal Cord Injury: A Bioinformatic Approach
Cited by: 3
Author(s): Vito Antonio Baldassarro, Marco Sanna, Andrea Bighinati, Michele Sannia, Marco Gusciglio, Luciana Giardino, Luca Lorenzini, Laura Calzà
Software Mentions: 1
Published: over 3 years ago
10.1186/s40170-020-00231-8
The effect of statin treatment on intratumoral cholesterol levels and LDL receptor expression: a window-of-opportunity breast cancer trial
Cited by: 8
Author(s): Maria Feldt, Julien A. Menard, Ann H. Rosendahl, Barbara Lettiero, Pär‐Ola Bendahl, Mattias Belting, Signe Borgquist
Software Mentions: 1
Published: about 4 years ago
10.1186/s13099-017-0212-y
Community-acquired infection with hypervirulent Clostridium difficile isolates that carry different toxin and antibiotic resistance loci: a case report
Cited by: 4
Author(s): Marina Muñoz, Milena Camargo, Dora I. Ríos-Chaparro, Paula Gómez, Manuel A. Patarroyo, Juan David Ramírez
Software Mentions: 1
Published: about 7 years ago
10.1107/S1600577520015659
The 1-Megapixel pnCCD detector for the Small Quantum Systems Instrument at the European XFEL: system and operation aspects
Cited by: 8
Author(s): M. Kuster, Karim Ali Ahmed, Kai Erik Ballak, Cyril Danilevski, M. Ekmedzič, Bruno Fernandes, P. Geßler, R. Hartmann, Steffen Hauf, P. Holl, Michael Meyer, J. Montaño, A. Münnich, Yevheniy Ovcharenko, Nils Rennhack, Tonn Rüter, Daniela Rupp, Dieter Schlosser, Kiana Setoodehnia, Rüdiger Schmitt, L. Strüder, Rico Mayro P. Tanyag, Anatoli Ulmer, Hazem Yousef
Software Mentions: 1
Published: almost 4 years ago
10.1242/bio.201410959
mir-34b/c and mir-449a/b/c are required for spermatogenesis, but not for the first cleavage division in mice
Cited by: 128
Author(s): Shuiqiao Yuan, Chong Tang, Ying Zhang, Jingwen Wu, Jianqiang Bao, Huili Zheng, Chen Xu, Wei Yan
Software Mentions: 1
Published: almost 10 years ago
10.7150/ijbs.39769
Comprehensive understanding of B7 family in gastric cancer: expression profile, association with clinicopathological parameters and downstream targets
Cited by: 18
Author(s): Dan Li, Shixin Xiang, Jing Shen, Mingtao Xiao, Yueshui Zhao, Xu Wu, Fukuan Du, Huijiao Ji, Mingxing Li, Qijie Zhao, Parham Jabbarzadeh Kaboli, Yang Xiao-mi, Zhangang Xiao, Bo Qin, Qinglian Wen
Software Mentions: 1
Published: almost 5 years ago
10.1186/1471-2202-15-S1-P171
Model exchange with the NeuroML model database
Cited by: 4
Author(s): Sharon Crook, Suzanne W. Dietrich
Software Mentions: 1
Published: over 10 years ago