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: analysis
https://packages.ecosyste.ms/registries/pypi.org/packages/analysis
Source code analysis of Python programs
8 versions
Latest release: over 18 years ago
348 downloads last month
Papers Mentioning analysis 2,036
10.1371/journal.pgen.1006294
The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel TranscriptsCited by: 44
Author(s): Maléne E. Lindholm, Stefania Giacomello, Beata Werne Solnestam, Håkan Fischer, Mikael Huss, Sanela Kjellqvist, Carl Johan Sundberg
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pcbi.1000920
Latent Factor Analysis to Discover Pathway-Associated Putative Segmental Aneuploidies in Human CancersCited by: 48
Author(s): Joseph E. Lucas, Hsiu‐Ni Kung, Jen‐Tsan Chi
Software Mentions: 3
Published: about 14 years ago
10.1371/journal.pgen.1007822
De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disordersCited by: 74
Author(s): Hongjian Qi, Lan Yu, Xueya Zhou, Julia Wynn, Haoquan Zhao, Yicheng Guo, Na Zhu, Alexander Kitaygorodsky, Rebecca Hernan, Guðrún Aspelund, Foong‐Yen Lim, Timothy M. Crombleholme, Robert A. Cusick, Kenneth S. Azarow, Melissa E. Danko, Dai H. Chung, Brad W. Warner, George B. Mychaliska, Douglas A. Potoka, Amy J. Wagner, Mahmoud Elfiky, Jay M. Wilson, Debbie Nickerson, Michael J. Bamshad, Frances A. High, Mauro Longoni, Patricia K. Donahoe, Wendy K. Chung, Yufeng Shen
Software Mentions: 3
Published: almost 6 years ago
10.15252/emmm.201708304
A <scp>HIF</scp> – <scp>LIMD</scp> 1 negative feedback mechanism mitigates the pro‐tumorigenic effects of hypoxiaCited by: 17
Author(s): Daniel E. Foxler, Katherine S. Bridge, John G. Foster, Paul Grevitt, Sean Curry, Kunal M. Shah, Kathryn M. Davidson, A. Nagano, Emanuela Gadaleta, Hefin Rhys, Paul Kennedy, Miguel A. Hermida, Ting‐Yu Chang, Peter E. Shaw, Louise E. Reynolds, Tristan R. McKay, Hsei Wei Wang, Paulo S. Ribeiro, Michael J. Plevin, Dimitrios Lagos, Nick R. Lemoine, Prabhakar Rajan, Trevor A. Graham, Claude Chelala, Kairbaan Hodivala‐Dilke, Ian Spendlove, Tyson V. Sharp
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pcbi.1005335
Representing high throughput expression profiles via perturbation barcodes reveals compound targetsCited by: 22
Author(s): Tracey Filzen, Peter S. Kutchukian, Jeffrey D. Hermes, Jing Li, Matthew Tudor
Software Mentions: 3
Published: almost 8 years ago
10.1371/journal.pgen.1006706
Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular diseaseCited by: 174
Author(s): Lasse Folkersen, Eric B. Fauman, Maria Sabater‐Lleal, Rona J. Strawbridge, Mattias Frånberg, Bengt Sennblad, Damiano Baldassarre, Fabrizio Veglia, Steve E. Humphries, Rainer Rauramaa, Ulf dé Fairé, Andries J. Smit, Philippe Giral, Sudhir Kurl, Elmo Mannarino, Stefan Enroth, Åsa Johansson, Sofia Bosdotter Enroth, Stefan Gustafsson, Lars Lind, Cecilia M. Lindgren, Andrew P. Morris, Vilmantas Giedraitis, Angela Silveira, Anders Franco‐Cereceda, Elena Tremoli, Ulf Gyllensten, Erik Ingelsson, Søren Brunak, Per Eriksson, Daniel Ziemek, Anders Hamsten, Anders Mälarstig
Software Mentions: 3
Published: over 7 years ago
10.1186/1471-2105-11-257
Detecting microRNA activity from gene expression dataCited by: 33
Author(s): Stephen F. Madden, Susan Carpenter, Ian B. Jeffery, Harry Björkbacka, Katherine A. Fitzgerald, Luke A. J. O’Neill, Desmond G. Higgins
Software Mentions: 3
Published: over 14 years ago
10.1002/ejp.1270
A machine-learned analysis of human gene polymorphisms modulating persisting pain points to major roles of neuroimmune processesCited by: 11
Author(s): Dario Kringel, Catharina Lippmann, Michael J. Parnham, Eija Kalso, Alfred Ultsch, Jörn Lötsch
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pcbi.1007308
Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansionsCited by: 14
Author(s): Joel A. Paulson, Marc Martin-Casas, Ali Mesbah
Software Mentions: 3
Published: about 5 years ago
10.3389/fcell.2020.620164
Analysis of Cyclin-Dependent Kinase 1 as an Independent Prognostic Factor for Gastric Cancer Based on Statistical MethodsCited by: 7
Author(s): Xu Zhang, Hua Ma, Quan Zou, Jin Wu
Software Mentions: 3
Published: almost 4 years ago
10.1186/1471-2105-15-162
A multivariate approach to the integration of multi-omics datasetsCited by: 214
Author(s): Chen Meng, Bernhard Küster, Aedín C. Culhane, Amin Moghaddas Gholami
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pone.0248429
Hypomethylation mediates genetic association with the major histocompatibility complex genes in Sjögren’s syndromeCited by: 4
Author(s): Calvin Chi, Kimberly E. Taylor, Hong Quach, Diana Quach, Lindsey A. Criswell, Lisa F. Barcellos
Software Mentions: 3
Published: over 3 years ago
10.3389/fimmu.2019.00869
Immunomodulatory Effects and Induction of Apoptosis by Different Molecular Weight Chitosan Oligosaccharides in Head Kidney Macrophages From Blunt Snout Bream (Megalobrama amblycephala)Cited by: 17
Author(s): Changcai Wu, Yishan Dai, Gailing Yuan, Jian Su, Xiaoling Liu
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pbio.3001364
The Δ40p53 isoform inhibits p53-dependent eRNA transcription and enables regulation by signal-specific transcription factors during p53 activationCited by: 14
Author(s): Cecilia B. Levandowski, Taylor Jones, Margaret Gruca, Sivapriya Ramamoorthy, Robin D. Dowell, Dylan J. Taatjes
Software Mentions: 3
Published: over 3 years ago
10.1186/s13000-014-0210-z
Unveiling transcription factor regulation and differential co-expression genes in Duchenne muscular dystrophyCited by: 7
Author(s): Lijun Tian, Junhua Cao, Xingqiang Deng, Chuanling Zhang, Tong Qian, Xianxiang Song, Baoshan Huang
Software Mentions: 3
Published: about 10 years ago
10.1093/database/baw099
SorghumFDB: sorghum functional genomics database with multidimensional network analysisCited by: 40
Author(s): Tian Tian, Qi You, Liwei Zhang, Xin Yi, Hengyu Yan, Wenying Xu, Zhen Su
Software Mentions: 3
Published: almost 9 years ago
10.1016/j.dib.2017.10.014
Waste management CDM projects barriers NVivo 10® qualitative datasetCited by: 5
Author(s): André Luiz Bufoni, Aracéli Cristina de Sousa Ferreira, Luciano Basto Oliveira
Software Mentions: 3
Published: almost 7 years ago
10.3389/fcvm.2021.713983
Pan-Cancer Analysis of Atrial-Fibrillation-Related Innate Immunity Gene ANXA4Cited by: 6
Author(s): Tao Yan, Shijie Zhu, Yu Shi, Changming Xie, Miao Zhu, Yangyang Zhang, Chunsheng Wang, Changfa Guo
Software Mentions: 3
Published: about 3 years ago
10.1155/2017/8347085
Identification of Transcriptional Modules and Key Genes in Chickens Infected with Salmonella enterica Serovar Pullorum Using Integrated Coexpression AnalysesCited by: 7
Author(s): Baohong Liu, Jianping Cai
Software Mentions: 3
Published: almost 8 years ago
10.3390/plants10040798
Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive IronCited by: 2
Author(s): Reunreudee Kaewcheenchai, Phanchita Vejchasarn, Kousuke Hanada, Kazumasa Shirai, Chatchawan Jantasuriyarat, Piyada Juntawong
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pmed.1003100
Metabolic risk factors and incident advanced liver disease in non-alcoholic fatty liver disease (NAFLD): A systematic review and meta-analysis of population-based observational studiesCited by: 177
Author(s): Helen Jarvis, Dawn Craig, Robert Barker, Gemma Spiers, Daniel Stow, Quentin M. Anstee, Barbara Hanratty
Software Mentions: 3
Published: over 4 years ago
10.3390/ijms18040747
Metabolic Effect of an Oriental Herbal Medicine on Obesity and Its Comorbidities with Transcriptional Responses in Diet-Induced Obese MiceCited by: 4
Author(s): Jiyoung Choi, Ye Jin Kim, Su-Jung Cho, Eun‐Young Kwon, Ri Ryu, Myung‐Sook Choi
Software Mentions: 3
Published: over 7 years ago
10.3390/plants9070919
Effects of Two Invasive Weeds on Arthropod Community Structure on the Central Plateau of New ZealandCited by: 6
Author(s): Evans Effah, D. Paul Barrett, Paul G. Peterson, Murray A. Potter, Jarmo K. Holopainen, Andrea Clavijo McCormick
Software Mentions: 3
Published: over 4 years ago
10.1186/s12859-020-03921-8
MiBiOmics: an interactive web application for multi-omics data exploration and integrationCited by: 39
Author(s): Johanna Zoppi, Jean-François Guillaume, Michel Neunlist, Samuel Chaffron
Software Mentions: 3
Published: almost 4 years ago
10.1111/pbi.13132
Genome sequencing and <scp>CRISPR</scp>/Cas9 gene editing of an early flowering Mini‐Citrus (<i>Fortunella hindsii</i>)Cited by: 76
Author(s): Chenqiao Zhu, Xiongjie Zheng, Yue Huang, Junli Ye, Peng Chen, Chenglei Zhang, Fei Zhao, Zongzhou Xie, Siqi Zhang, Nan Wang, Hang Li, Lun Wang, Xiaomei Tang, Lijun Chai, Qiang Xu, Xiuxin Deng
Software Mentions: 3
Published: over 5 years ago
10.1155/2020/6725753
Comprehensive Characterization of Prognostic Long Noncoding RNAs in OsteosarcomaCited by: 4
Author(s): Hua Gao, Yuanyuan Guo, Miaomiao Zhang, Zuqiang Yi
Software Mentions: 3
Published: about 4 years ago
10.1016/j.csbj.2021.05.055
Genetic mapping of developmental trajectories for complex traits and diseasesCited by: 1
Author(s): Eldad D. Shulman, Ran Elkon
Software Mentions: 3
Published: almost 4 years ago
10.3390/ijms20071587
Transcriptomic Sequencing and Co-Expression Network Analysis on Key Genes and Pathways Regulating Nitrogen Use Efficiency in Myriophyllum aquaticumCited by: 9
Author(s): Rui Wang, Shengjun Xu, Cancan Jiang, Hanjun Sun, Shugeng Feng, Sining Zhou, Guoqiang Zhuang, Zhihui Bai
Software Mentions: 3
Published: over 5 years ago
10.1155/2021/9971353
P3H4 Overexpression Serves as a Prognostic Factor in Lung AdenocarcinomaCited by: 5
Author(s): Xiangfeng Jin, Haiqing Zhou, Jianfang Song, Hong Cui, Yiren Luo, Haiping Jiang
Software Mentions: 3
Published: over 3 years ago
10.1186/s12883-020-01709-0
The prevalence of Restless Legs Syndrome/Willis-ekbom disease (RLS/WED) in the third trimester of pregnancy: a systematic reviewCited by: 18
Author(s): Niloofar Darvishi, Alireza Daneshkhah, Behnam Khaledi-Paveh, Asad Vaisi-Raygani, Masoud Mohammadi, Nader Salari, Fateme Darvishi, Alireza Abdi, Rostam Jalali
Software Mentions: 3
Published: over 4 years ago
10.3390/ph14040351
Absence of Association between Methylene Blue Reduced Susceptibility and Polymorphisms in 12 Genes Involved in Antimalarial Drug Resistance in African Plasmodium falciparumCited by: 2
Author(s): Mathieu Gendrot, Océane Delandre, M Robert, Francis Tsombeng Foguim, B. Nicolas, Rémy Amalvict, Isabelle Fonta, Joël Mosnier, Marylin Madamet, Bruno Pradines
Software Mentions: 3
Published: over 3 years ago
10.1016/j.csbj.2020.04.011
Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smokeCited by: 21
Author(s): Bjoern Titz, Justyna Szostak, Alain Sewer, Blaine Phillips, Catherine Nury, Thomas Schneider, Sophie Dijon, Oksana Lavrynenko, Ashraf Elamin, Emmanuel Guedj, Ee Tsin Wong, Stefan Lebrun, Grégory Vuillaume, Athanasios Kondylis, Sylvain Gubian, Stéphane Cano, Patrice Leroy, Brian Keppler, Nikolai V. Ivanov, Patrick Vanscheeuwijck, Florian Martin, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 3
Published: almost 5 years ago
10.7554/eLife.36330
TFAP2 transcription factors are regulators of lipid droplet biogenesisCited by: 31
Author(s): Cameron C. Scott, Stefania Vossio, Jacques Rougemont, Jean Grüenberg
Software Mentions: 3
Published: about 6 years ago
10.7717/peerj.8456
Key genes and co-expression modules involved in asthma pathogenesisCited by: 12
Author(s): Yuyi Huang, Hui Liu, Li Zuo, Ailin Tao
Software Mentions: 3
Published: almost 5 years ago
10.1186/1471-2164-10-405
Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patientsCited by: 151
Author(s): Christiaan G J Saris, Steve Horvath, Paul W.J. van Vught, Michael A. van Es, Hylke M. Blauw, Tova Fuller, Peter Langfelder, Joseph DeYoung, John H. J. Wokke, Jan H. Veldink, Leonard H van den Berg, Roel A. Ophoff
Software Mentions: 3
Published: about 15 years ago
10.1093/infdis/jix519
Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus InfectionCited by: 28
Author(s): Lien Anh Ha, Johann Pellet, H. Rogier van Doorn, Anh Tuấn Trần, Bach Hue Nguyen, Thi Thu Loan Tran, Quynh Huong Tran, Quoc Bao Vo, Nguyen Anh Tran Dac, Hong Nhien Trinh, Thi Thanh Hai Nguyen, Bao Tinh Le Binh, Huu Mai Khanh Nguyen, Minh Tien Nguyen, Quang Tung Thai, Thanh Vu Vo, Ngoc Quang Minh Ngo, Thi Kim Huyen Dang, Ngoc Huong Cao, Thu Van Tran, Lu Viet Ho, Bertrand De Meulder, Charles Auffray, Jorrit–Jan H. Hofstra, Jeremy Farrar, Juliet E. Bryant, Menno D. de Jong, Martin L. Hibberd
Software Mentions: 3
Published: about 7 years ago
10.1038/s42003-021-01946-0
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepodCited by: 14
Author(s): Petra H. Lenz, Vittoria Roncalli, Matthew Cieslak, Ann M. Tarrant, Ann M. Castelfranco, Daniel K. Hartline
Software Mentions: 3
Published: over 3 years ago
10.1186/s10194-017-0817-z
11th European Headache Federation Congress jointly with 31st Congress of the Italian Society for the Study of HeadachesCited by: 6
Author(s): Brigida Fierro, Giuseppe Cosentino, Salvatore Cillino, Filippo Brighina, Viviana Firpo
Software Mentions: 3
Published: about 7 years ago
10.7717/peerj.4384
Phylogenetic surveys on the newt genus <i>Tylototriton sensu lato</i> (Salamandridae, Caudata) reveal cryptic diversity and novel diversification promoted by historical climatic shiftsCited by: 15
Author(s): Bin Wang, Kanto Nishikawa, Masafumi Matsui, Truong Q. Nguyen, Feng Xie, Cheng Li, Janak Raj Khatiwada, Baowei Zhang, Gong Dajie, Yunming Mo, Gang Wei, Xiaohong Chen, Youhui Shen, Daode Yang, Rongchuan Xiong, Jianping Jiang
Software Mentions: 3
Published: over 6 years ago
10.1002/cnm.2602
Novel wave intensity analysis of arterial pulse wave propagation accounting for peripheral reflectionsCited by: 40
Author(s): Jordi Alastruey, Anthony A. E. Hunt, Peter D. Weinberg
Software Mentions: 3
Published: about 11 years ago
10.1155/2020/3126592
Identification of Heat-Responsive Genes in Guar [<i>Cyamopsis tetragonoloba</i> (L.) Taub]Cited by: 8
Author(s): Aref Alshameri, Fahad Al‐Qurainy, Abdel-Rhman Z. Gaafar, Salim Khan, Mohammad Nadeem, Saleh Alansi
Software Mentions: 3
Published: over 4 years ago
10.1186/s13045-020-00854-w
Identification of cross-talk between m6A and 5mC regulators associated with onco-immunogenic features and prognosis across 33 cancer typesCited by: 44
Author(s): Yutong Chen, Jiayi Shen, Dongping Chen, Chengdong Wu, Rui Guo, Panpan Zhang, Jiawei Lv, Wenfei Li, Zi‐Xian Wang, Yu-Pei Chen
Software Mentions: 3
Published: over 4 years ago
10.3390/biology9090260
Computational and Transcriptome Analyses Revealed Preferential Induction of Chemotaxis and Lipid Synthesis by SARS-CoV-2Cited by: 7
Author(s): Hibah Shaath, Nehad M. Alajez
Software Mentions: 3
Published: about 4 years ago
10.5402/2012/546721
Computerized Decision Support System for Intraoperative Analysis of Margin Status in Breast Conservation TherapyCited by: 3
Author(s): Manuel E. Ruidíaz, Sarah L. Blair, Andrew C. Kummel, Jessica Wang‐Rodriguez
Software Mentions: 3
Published: about 12 years ago
10.1098/rsbl.2018.0064
Non-uniform evolutionary response of gecko eye size to changes in diel activity patternsCited by: 12
Author(s): Lars Schmitz, Timothy E. Higham
Software Mentions: 3
Published: over 6 years ago
10.1038/s41598-018-24978-9
Relationships between digestive efficiency and metabolomic profiles of serum and intestinal contents in chickensCited by: 20
Author(s): Stéphane Beauclercq, Lydie Nadal-Desbarats, Christelle Hennequet-Antier, Irène Gabriel, Sophie Tesseraud, Fanny Calenge, Elisabeth Le Bihan‐Duval, Sandrine Mignon-Grasteau
Software Mentions: 3
Published: over 6 years ago
10.7150/ijbs.56152
MLKL inhibits intestinal tumorigenesis by suppressing STAT3 signaling pathwayCited by: 11
Author(s): Qun Zhao, Xinran Cheng, Jian Guo, Yunbo Bi, Li Qing Kuang, Jianhua Ren, Jing Zhong, Longrui Pan, Xudong Zhang, Yang Guo, Yongqiang Liu, S. Jin, Yan Tan, Yu Lei
Software Mentions: 3
Published: almost 4 years ago
10.7717/peerj.11319
Identification of P2RY13 as an immune-related prognostic biomarker in lung adenocarcinoma: A public database-based retrospective studyCited by: 6
Author(s): Jiang Lin, Chunlei Wu, Dehua Mao, Quanteng Hu
Software Mentions: 3
Published: over 3 years ago
10.7717/peerj.4174
Is there a link between aging and microbiome diversity in exceptional mammalian longevity?Cited by: 26
Author(s): Graham M. Hughes, John Leech, Sébastien J. Puechmaille, Jose V. Lopez, Emma C. Teeling
Software Mentions: 3
Published: almost 7 years ago
10.1038/s41598-018-20232-4
Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancersCited by: 25
Author(s): Chao Ren, Gaole An, Chenghui Zhao, Zhangyi Ouyang, Xiaochen Bo, Wenjie Shu
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pone.0231771
Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current systemCited by: 3
Author(s): Irina N. Shilova, Jonathan D. Magasin, Matthew M. Mills, Julie Robidart, Kendra A. Turk‐Kubo, Jonathan P. Zehr
Software Mentions: 3
Published: over 4 years ago
10.7554/eLife.33070
Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient miceCited by: 67
Author(s): Roman M. Stilling, Gerard M. Moloney, Feargal J. Ryan, Alan E. Hoban, Thomaz F.S. Bastiaanssen, Fergus Shanahan, Gerard Clarke, Marcus J. Claesson, Timothy G. Dinan, John F. Cryan
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0257254
Knocking out TMEM38B in human foetal osteoblasts hFOB 1.19 by CRISPR/Cas9: A model for recessive OI type XIVCited by: 4
Author(s): Laura Leoni, Francesca Tonelli, Roberta Besio, Roberta Gioia, Francesco Moccia, Antonio Rossi, Antonella Forlino
Software Mentions: 3
Published: about 3 years ago
10.1038/s41598-017-07015-z
Biochemical profiling of diabetes disease progression by multivariate vibrational microspectroscopy of the pancreasCited by: 9
Author(s): Christoffer Nord, Maria Eriksson, Andrea Dicker, Anna Eriksson, Eivind Grong, Erwin Ilegems, Ronald Mårvik, Bård Kulseng, Per Olof Berggren, András Gorzsás, Ulf Ahlgren
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0219486
Caenorhabditis elegans hub genes that respond to amyloid beta are homologs of genes involved in human Alzheimer’s diseaseCited by: 14
Author(s): Rasoul Godini, Roger Pocock, Hossein Fallahi
Software Mentions: 3
Published: over 5 years ago
10.1186/s12957-018-1381-y
Identification of key gene modules for human osteosarcoma by co-expression analysisCited by: 19
Author(s): Jing Zhang, Qing Lan, Jiasheng Lin
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0022295
Randomizing Genome-Scale Metabolic NetworksCited by: 16
Author(s): Areejit Samal, O. C. Martin
Software Mentions: 3
Published: over 13 years ago
10.1038/s41598-017-07297-3
Desiccation tolerance in bryophytes: The dehydration and rehydration transcriptomes in the desiccation-tolerant bryophyte Bryum argenteumCited by: 37
Author(s): Bei Gao, Xiaoshuang Li, Daoyuan Zhang, Yuqing Liang, Yang Hong-yuan, Moxian Chen, Yuanming Zhang, Jianhua Zhang, Andrew J. Wood
Software Mentions: 3
Published: over 7 years ago
10.1038/srep44849
Huntington’s disease blood and brain show a common gene expression pattern and share an immune signature with Alzheimer’s diseaseCited by: 39
Author(s): Davina J. Hensman Moss, Michael Flower, Kitty Lo, James R. C. Miller, G.J.B. van Ommen, Peter A.C. ’t Hoen, Timothy Stone, Amelia Guinee, Douglas R. Langbehn, Lesley Jones, Vincent Plagnol, Willeke M. C. van Roon‐Mom, Peter Holmans, Sarah J. Tabrizi
Software Mentions: 3
Published: over 7 years ago
10.1038/srep24964
Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infectionCited by: 34
Author(s): Guanxiang Liang, Nilusha Malmuthuge, Yongjuan Guan, Yan Ren, Philip Griebel, Le Luo Guan
Software Mentions: 3
Published: over 8 years ago
10.1038/s41598-017-01468-y
Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skinCited by: 15
Author(s): Richard Ahn, Keyon Taravati, Kevin Lai, Kristina M. Lee, Joanne Nititham, Rashmi Gupta, David S. Chang, Sarah T. Arron, Michael D. Rosenblum, Wilson Liao
Software Mentions: 3
Published: over 7 years ago
10.1186/s12985-014-0236-6
Differential regulation of cytotoxicity pathway discriminating between HIV, HCV mono- and co-infection identified by transcriptome profiling of PBMCsCited by: 4
Author(s): Jing Qin Wu, Monica Miranda Saksena, Vincent Soriano, Eugenia Vispo, Nitin K. Saksena
Software Mentions: 3
Published: almost 10 years ago
10.1038/srep12872
Geochemical influences and mercury methylation of a dental wastewater microbiomeCited by: 17
Author(s): Asha Rani, Karl J. Rockne, James L. Drummond, Muntasar Al-Hinai, Ravi Ranjan
Software Mentions: 3
Published: over 9 years ago
10.1038/s41598-017-03121-0
Echo-Planar J-resolved Spectroscopic Imaging using Dual Read-outs: Implementation and Quantitation of Human Brain MetabolitesCited by: 4
Author(s): Manoj K. Sarma, Rajakumar Nagarajan, Zohaib Iqbal, Paul M. Macey, M. Albert Thomas
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0067922
Roles for Treg Expansion and HMGB1 Signaling through the TLR1-2-6 Axis in Determining the Magnitude of the Antigen-Specific Immune Response to MVA85ACited by: 26
Author(s): Magali Matsumiya, Elena Stylianou, Kristin Griffiths, Zoe Lang, Joel N. Meyer, Stephanie A. Harris, Rosalind Rowland, Angela M. Minassian, Ansar A. Pathan, Helen A. Fletcher, Helen McShane
Software Mentions: 3
Published: over 11 years ago
10.3762/bjnano.6.252
Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterialsCited by: 49
Author(s): Andrew Williams, Sabina Halappanavar
Software Mentions: 3
Published: almost 9 years ago
10.1186/1742-4690-8-18
Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV diseaseCited by: 53
Author(s): Jing Qin Wu, Dominic E. Dwyer, Wayne B. Dyer, Jean Yee Hwa Yang, Binbin Wang, Nitin K. Saksena
Software Mentions: 3
Published: over 13 years ago
10.1371/journal.pone.0094031
Disruption of the Homogentisate Solanesyltransferase Gene Results in Albino and Dwarf Phenotypes and Root, Trichome and Stomata Defects in Arabidopsis thalianaCited by: 12
Author(s): Yuehui Chao, Junmei Kang, Tiejun Zhang, Qingchuan Yang, Margaret Y. Gruber, Yan Sun
Software Mentions: 3
Published: over 10 years ago
10.15252/msb.20188462
Enzyme promiscuity shapes adaptation to novel growth substratesCited by: 47
Author(s): Gabriela I. Guzmán, Troy E. Sandberg, Ryan A. LaCroix, Ákos Nyerges, Henrietta Papp, Markus de Raad, Zachary A. King, Ying Hefner, Trent Northen, Richard A. Notebaart, Csaba Pál, Bernhard Palsson, Balázs Papp, Adam M. Feist
Software Mentions: 3
Published: over 5 years ago
10.1186/1471-2164-9-561
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groupsCited by: 250
Author(s): Wen Chi Chang, Tzong-Yi Lee, Hsien Da Huang, His Yuan Huang, Rong Pan
Software Mentions: 3
Published: almost 16 years ago
10.1186/s12977-016-0248-y
TLR8 regulation of LILRA3 in monocytes is abrogated in human immunodeficiency virus infection and correlates to CD4 counts and virus loadsCited by: 8
Author(s): Hui Zhi Low, Gerrit Ahrenstorf, Claudia Pommerenke, Nadine Habermann, Klaus Schughart, David Ordóñez, Renata Stripecke, Esther Wilk, Torsten Witte
Software Mentions: 3
Published: over 8 years ago
10.1186/s12917-019-1815-y
A spatial assessment of Nipah virus transmission in Thailand pig farms using multi-criteria decision analysisCited by: 7
Author(s): Weerapong Thanapongtharm, Mathilde Paul, Anuwat Wiratsudakul, Vilaiporn Wongphruksasoong, Wantanee Kalpravidh, Kachen Wongsathapornchai, Sudarat Damrongwatanapokin, Daniel Schar, Marius Gilbert
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0137829
Indirect Energy Flows in Niche Model Food Webs: Effects of Size and ConnectanceCited by: 4
Author(s): Jane Shevtsov, Rosalyn Rael
Software Mentions: 3
Published: about 9 years ago
10.1371/journal.pone.0164353
Induced Human Decidual NK-Like Cells Improve Utero-Placental Perfusion in MiceCited by: 20
Author(s): Ricardo de Carvalho Cavalli, Ana Sofia Cerdeira, Elizabeth Pernicone, Henri Augusto Korkes, Suzanne D. Burke, Augustine Rajakumar, Ravi Thadhani, Drucilla J. Roberts, Manoj Bhasin, S. Ananth Karumanchi, Hernan D. Kopcow
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pone.0157426
An Integrative Transcriptomic Analysis for Identifying Novel Target Genes Corresponding to Severity Spectrum in Spinal Muscular AtrophyCited by: 6
Author(s): Chunrong Yang, Chien‐Lin Chen, Wei-Chun Chou, Ho-Chen Lin, Yuh Jyh Jong, Li-Kai Tsai, Chun‐Yu Chuang
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0245501
Balancing time use for children’s fitness and adiposity: Evidence to inform 24-hour guidelines for sleep, sedentary time and physical activityCited by: 16
Author(s): Dorothea Dumuid, Melissa Wake, David Burgner, Mark S. Tremblay, Anthony D. Okely, Ben Edwards, Terence Dwyer, Tim Olds
Software Mentions: 3
Published: almost 4 years ago
10.1186/s12931-019-0995-0
Identification of differentially expressed proteins in the injured lung from zinc chloride smoke inhalation based on proteomics analysisCited by: 13
Author(s): Xiaowei Xie, Jiemin Zhao, Lei Xie, Haiyan Wang, Yan Xiao, Yingjia She, Lingyun Ma
Software Mentions: 3
Published: almost 6 years ago
10.1038/s41598-017-11237-6
Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancerCited by: 162
Author(s): Rachel Purcell, Tina Visnovska, Patrick J. Biggs, Sebastian Schmeier, Frank Frizelle
Software Mentions: 3
Published: about 7 years ago
10.1186/s12918-015-0155-1
Spatially-resolved metabolic cooperativity within dense bacterial coloniesCited by: 69
Author(s): John A. Cole, Lars Köhler, Jamila Hedhli, Zaida Luthey‐Schulten
Software Mentions: 3
Published: over 9 years ago
10.1186/1752-0509-2-95
Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue SyndromeCited by: 152
Author(s): Angela P. Presson, Eric M. Sobel, Jeanette C. Papp, Charlyn Suarez, Toni Whistler, Mangalathu S. Rajeevan, Suzanne D. Vernon, Steve Horvath
Software Mentions: 3
Published: about 16 years ago
10.1371/journal.pone.0229334
Age-related modulations of alpha and gamma brain activities underlying anticipation and distractionCited by: 20
Author(s): Hesham A. ElShafei, Lesly Fornoni, Rémy Masson, Olivier Bertrand, Aurélie Bidet-Caulet
Software Mentions: 3
Published: over 4 years ago
10.1074/mcp.RA120.002345
Mutation-independent Proteomic Signatures of Pathological Progression in Murine Models of Duchenne Muscular DystrophyCited by: 20
Author(s): van Westering Tle., Henrik J. Johansson, Britt Hanson, Anna M.L. Coenen-Stass, Yulia Lomonosova, Jun Tanihata, Norio Matsuki, Toshifumi Yokota, Shin’ichi Takeda, Janne Lehtiö, Matthew J. Wood, Samir El Andaloussi, Yosuke Aoki, Thomas C. Roberts
Software Mentions: 3
Published: almost 4 years ago
10.1074/mcp.RA119.001737
The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer DiseaseCited by: 19
Author(s): Hazal Haytural, Georgios Mermelekas, Ceren Emre, Saket Milind Nigam, Steven L. Carroll, Bengt Winblad, Nenad Bogdanović, Gaël Barthet, Ann‐Charlotte Granholm, Lukas M. Orre, Lars O. Tjernberg, Susanne Frykman
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.ppat.1004869
Host Transcriptional Response to Influenza and Other Acute Respiratory Viral Infections – A Prospective Cohort StudyCited by: 108
Author(s): Yijie Zhai, Luis M. Franco, Robert L. Atmar, John Quarles, Nancy H. Arden, Kristine L. Bucasas, Janet Wells, Diane Niño, Xueqing Wang, Gladys Zapata, Chad A. Shaw, John W. Belmont, Robert B. Couch
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.ppat.1007950
Equine arteritis virus long-term persistence is orchestrated by CD8+ T lymphocyte transcription factors, inhibitory receptors, and the CXCL16/CXCR6 axisCited by: 19
Author(s): Mariano Carossino, Pouya Dini, Theodore S. Kalbfleisch, Alan T. Loynachan, Igor F. Canisso, R. Frank Cook, Peter J. Timoney, Udeni B. R. Balasuriya
Software Mentions: 3
Published: over 5 years ago
10.1186/s41065-021-00183-z
RTP4 is a novel prognosis-related hub gene in cutaneous melanomaCited by: 7
Author(s): Yiqi Li, Jue Qi, Jiankang Yang
Software Mentions: 3
Published: over 3 years ago
10.1111/1755-0998.12674
Graphics for relatedness researchCited by: 6
Author(s): Iván Galván-Femenía, Jan Graffelman, Carles Barceló-i-Vidal
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0179065
Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesisCited by: 64
Author(s): Thomas Mohr, Verena Haudek-Prinz, Astrid Slany, Johannes Grillari, M. Micksche, Christopher Gerner
Software Mentions: 3
Published: over 7 years ago
10.1186/s10020-019-0116-z
Inhibition of phosphatidylinositol 3-kinase by PX-866 suppresses temozolomide-induced autophagy and promotes apoptosis in glioblastoma cellsCited by: 24
Author(s): Bryan Harder, Sen Peng, Chris Sereduk, Andrej M. Sodoma, Gaspar J. Kitange, Joseph C. Loftus, Jann N. Sarkaria, Nhan L. Tran
Software Mentions: 3
Published: about 5 years ago
10.1038/s41438-020-0287-3
Transcriptome analysis and metabolic profiling reveal the key role of carotenoids in the petal coloration of Liriodendron tulipiferaCited by: 39
Author(s): Zhaodong Hao, Siqin Liu, Lingfeng Hu, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: over 4 years ago
10.1186/s12918-016-0336-6
The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirusCited by: 51
Author(s): Jason McDermott, Hugh D. Mitchell, Lisa E. Gralinski, Amie J. Eisfeld, Laurence Josset, Armand Bankhead, Gabriele Neumann, Susan C. Tilton, Alexandra Schäfer, Chengjun Liu, Shufang Fan, Shannon K. McWeeney, Ralph S. Baric, Michael G. Katze, Katrina M. Waters
Software Mentions: 3
Published: about 8 years ago
10.1098/rsos.190958
Low connectivity between shallow, mesophotic and rariphotic zone benthosCited by: 18
Author(s): Paris V. Stefanoudis, Molly Rivers, Struan R. Smith, Craig W. Schneider, Daniel Wagner, Helen Ford, Alex D. Rogers, Lucy C. Woodall
Software Mentions: 3
Published: about 5 years ago
10.3390/molecules25040904
Understanding the Pyrimethamine Drug Resistance Mechanism via Combined Molecular Dynamics and Dynamic Residue Network AnalysisCited by: 26
Author(s): Arnold Amusengeri, Rolland Bantar Tata, Özlem Tastan Bishop
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.pone.0087804
Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling ApproachCited by: 33
Author(s): Nag Chetan, Karanth K. Praveen, Gururaja Kotambylu Vasudeva
Software Mentions: 3
Published: almost 11 years ago
10.1111/jcmm.15193
To construct a ceRNA regulatory network as prognostic biomarkers for bladder cancerCited by: 45
Author(s): Jiazhi Jiang, Yaqiong Bi, Xiaoping Li, Donghu Yu, Xin Yan, Jie Yao, Tongzu Liu, Li Sheng
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0192606
Maternal high-fat diet associated with altered gene expression, DNA methylation, and obesity risk in mouse offspringCited by: 86
Author(s): Madeline Rose Keleher, Syeda Nuzhat Fatima Zaidi, Shyam Shah, MaryAnn Oakley, Cassondra Pavlatos, Samir El Idrissi, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pone.0074256
Gene Regulatory Networks Elucidating Huanglongbing Disease MechanismsCited by: 90
Author(s): Federico Martinelli, Russell L. Reagan, Sandra L. Uratsu, My L. Phu, Ute Albrecht, Wenwei Zhao, Cristina E. Davis, Kim D. Bowman, Abhaya M. Dandekar
Software Mentions: 3
Published: about 11 years ago
10.7150/jca.45553
The <i>miR-370</i>/UQCRC2 axis facilitates tumorigenesis by regulating epithelial-mesenchymal transition in Gastric CancerCited by: 11
Author(s): Danwen Wang, Fei Su, Tao Zhang, Tiecheng Yang, Huaqiao Wang, Lei Yang, Fenfang Zhou, Feng Mao
Software Mentions: 3
Published: almost 5 years ago
10.1186/1471-2407-12-426
Stress associated gene expression in blood cells is related to outcome in radiotherapy treated head and neck cancer patientsCited by: 5
Author(s): Siv Kjølsrud Bøhn, Kjell Magne Russnes, Amrit Kaur Sakhi, Magne Thoresen, Matthew T. G. Holden, Jan Øivind Moskaug, Mari Myhrstad, Ole Kristoffer Olstad, Sigbjørn Smeland, Rune Blomhoff
Software Mentions: 3
Published: about 12 years ago
10.7150/jca.51591
Increased Expression of <i>KNSTRN</i> in Lung Adenocarcinoma Predicts Poor Prognosis: A Bioinformatics Analysis Based on TCGA DataCited by: 11
Author(s): Pengbo Deng, Rongrong Zhou, Jinghui Zhang, Liming Cao
Software Mentions: 3
Published: almost 4 years ago