cran: UpSetR | Projects | Ecosyste.ms: Papers

10.3390/biom10121595

Identifying Genes Involved in Alkaloid Biosynthesis in Vinca minor through Transcriptomics and Gene Co-Expression Analysis
Cited by: 11
Author(s): Emily Amor Stander, Liuda Johana Sepúlveda, Thomas Dugé de Bernonville, Inês Carqueijeiro, Κωνσταντίνος Κουδούνας, Pamela Lemos Cruz, Sébastien Besseau, Arnaud Lanoue, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Ron P. Dirks, Sarah E. O’Connor, Lucía Atehortúa, Audrey Oudin, Vincent Courdavault
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1007721

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries
Cited by: 24
Author(s): Cedoljub Bundalovic-Torma, Gregory B. Whitfield, Lindsey S. Marmont, P. Lynne Howell, John Parkinson
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms21030965

The Cannabis Proteome Draft Map Project
Cited by: 13
Author(s): Conor Jenkins, Benjamin C. Orsburn
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pcbi.1006933

An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis
Cited by: 12
Author(s): Niki Karagianni, Ksanthi Kranidioti, Nikolaos Fikas, Maria Tsochatzidou, Panagiotis Chouvardas, Maria C Denis, George Kollias, Christoforos Nikolaou
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.00726

Prognostic Value and Potential Role of Alternative mRNA Splicing Events in Cervical Cancer
Cited by: 6
Author(s): Xiangyang Shao, Jin Tang Dong, Han Zhang, Yanni Wu, Lei Zheng
Software Mentions: 3
Published: over 4 years ago

10.3389/fonc.2021.645912

Identification of Tumor Microenvironment-Related Alternative Splicing Events to Predict the Prognosis of Endometrial Cancer
Cited by: 4
Author(s): Xuan Li, Chuan Liu, Jie Liu, Ying Song, Shanshan Wang, Miaoqing Wu, Shanshan Yu, Luya Cai
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-021-02051-y

Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation
Cited by: 6
Author(s): Haroon Butt, Jérémie Bazin, Sahar Alshareef, Ayman Eid, Moussa Benhamed, Anireddy S. N. Reddy, Martín Crespi, Magdy M. Mahfouz
Software Mentions: 3
Published: over 3 years ago

10.7150/thno.36585

Comprehensive characterization of the alternative splicing landscape in head and neck squamous cell carcinoma reveals novel events associated with tumorigenesis and the immune microenvironment
Cited by: 66
Author(s): Zhixuan Li, Zi-Qi Zheng, Zhuo-Hui Wei, Lulu Zhang, Li Feng, Lin Li, Ruiqi Liu, Xiao-Dan Huang, Jiawei Lv, Fo-Ping Chen, Xiaoxi He, Jia-Li Guan, Jia Kou, Jingfei Ma, Guan-Qun Zhou
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms21113746

Differential Secretome Profiling of Human Osteoarthritic Synoviocytes Treated with Biotechnological Unsulfated and Marine Sulfated Chondroitins
Cited by: 15
Author(s): Rosita Russo, Valentina Vassallo, Antonietta Stellavato, Mariangela Valletta, Donatella Cimini, Paolo V. Pedone, Chiara Schiraldi, Angela Chambery
Software Mentions: 3
Published: over 4 years ago

10.1038/s42003-021-02331-7

Insights into rumen microbial biosynthetic gene cluster diversity through genome-resolved metagenomics
Cited by: 13
Author(s): Christopher L. Anderson, Samodha C. Fernando
Software Mentions: 3
Published: over 3 years ago

10.1093/gbe/evaa132

Bumblebee Workers Show Differences in Allele-Specific DNA Methylation and Allele-Specific Expression
Cited by: 11
Author(s): Hollie Marshall, Alun R. C. Jones, Zoë N. Lonsdale, Eamonn B. Mallon
Software Mentions: 3
Published: over 4 years ago

10.1155/2021/4664955

Systematic Profiling of mRNA Splicing Reveals the Prognostic Predictor and Potential Therapeutic Target for Glioblastoma Multiforme
Cited by: 5
Author(s): Botao Zhang, Quanyou Wu, Shujun Cheng, Wenbin Li
Software Mentions: 3
Published: over 3 years ago

10.1186/s12920-018-0467-2

Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells
Cited by: 29
Author(s): Mahmoud Mostafa, Christopher F. Rider, Suharsh Shah, Suzanne L. Traves, Paul M. Gordon, Anna Miller‐Larsson, Richard Leigh, Robert Newton
Software Mentions: 3
Published: almost 6 years ago

10.3390/proteomes9020029

Mining Proteome Research Reports: A Bird’s Eye View
Cited by: 1
Author(s): Jagajjit Sahu
Software Mentions: 3
Published: over 3 years ago

10.1186/s12870-020-02809-2

Tight association of genome rearrangements with gene expression in conifer plastomes
Cited by: 5
Author(s): Ching‐Yi Wu, Edi Sudianto, Shu‐Miaw Chaw
Software Mentions: 3
Published: almost 4 years ago

10.3390/pathogens9110899

Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species
Cited by: 23
Author(s): Martin Hölzer, Lisa-Marie Barf, Kevin Lamkiewicz, Fabien Vorimore, Marie Lataretu, Alison Favaroni, Christiane Schnee, Karine Laroucau, Konrad Sachse
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-021-07690-3

Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection
Cited by: 0
Author(s): Bahiyah Azli, Sharanya Ravi, M. Hair-Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa
Software Mentions: 3
Published: over 3 years ago

10.3390/foods10020362

Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage
Cited by: 16
Author(s): Aurélien Maillet, Pauline Denojean, Agnès Bouju-Albert, Erwan Scaon, Sébastien Leuillet, Xavier Dousset, Emmanuel Jaffrès, Jérôme Combrisson, Hervé Prévost
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-017-4385-z

Transcriptional effects of a positive feedback circuit in Drosophila melanogaster
Cited by: 5
Author(s): Jarosław Bryk, R. Guy Reeves, Floyd A. Reed, Jai A. Denton
Software Mentions: 3
Published: almost 7 years ago

10.3390/pathogens10020242

An Integrated Sequencing Approach for Updating the Pseudorabies Virus Transcriptome
Cited by: 8
Author(s): Gábor Torma, Dóra Tombácz, Zsolt Csabai, Dániel Göbhardter, Zoltán Deim, M Snyder, Zsolt Boldogkői
Software Mentions: 3
Published: almost 4 years ago

10.1128/AEM.01319-20

Editing of the Proteolytic System of Lactococcus lactis Increases Its Bioactive Potential
Cited by: 6
Author(s): Chenxi Huang, Jan Kok
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-62424-x

Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture
Cited by: 17
Author(s): Lisa A. Cummings, Daniel R. Hoogestraat, Sara L. Rassoulian-Barrett, Christopher Rosenthal, Stephen J. Salipante, Brad T. Cookson, Noah G. Hoffman
Software Mentions: 3
Published: over 4 years ago

10.1186/s12885-021-08681-z

Genome-wide profiling of alternative splicing in glioblastoma and their clinical value
Cited by: 3
Author(s): Youwei Li, Dongsheng Guo
Software Mentions: 3
Published: about 3 years ago

10.1186/s12864-021-07944-0

Altered synthesis of genes associated with short-chain fatty acids in the gut of patients with atrial fibrillation
Cited by: 18
Author(s): Jing Zhang, Kun Zuo, Fang Chen, Xiandong Yin, Xiaoqing Liu, Jiu-Chang Zhong, Kuibao Li, Jing Li, Lisha Xu, Xinchun Yang
Software Mentions: 3
Published: about 3 years ago

10.1016/j.dib.2020.106337

Standardized data to support conservation prioritization for sharks and batoids (Elasmobranchii)
Cited by: 2
Author(s): Rikke Oegelund Nielsen, Rita da Silva, Jacqueline Juergens, Johanna Staerk, Line L. Sørensen, John A Jackson, Simeon Q. Smeele, Dalia Amor Conde
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-019-57367-x

Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics
Cited by: 28
Author(s): Reilly O. Cooper, Clayton E. Cressler
Software Mentions: 3
Published: almost 5 years ago

10.3389/fphar.2020.559618

Metabolomics Deciphers Potential Targets of Xuefu Zhuyu Decoction Against Traumatic Brain Injury in Rat
Cited by: 9
Author(s): Teng Li, En Hu, Pengfei Li, Zhaoyu Yang, Yi-Ming Wu, Ruoqi Ding, Xiaofei Zhu, Tao Tang, Yang Wang
Software Mentions: 3
Published: about 4 years ago

10.1186/s12920-018-0452-9

Comparison of different functional prediction scores using a gene-based permutation model for identifying cancer driver genes
Cited by: 6
Author(s): Alice Djotsa Nono, Ken Chen, Xiaoming Liu
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-020-02511-3

Identification of small RNAs during cold acclimation in Arabidopsis thaliana
Cited by: 21
Author(s): Bhavika Tiwari, Kristin Habermann, Muhammad Arif, Heinrich Lukas Weil, Antoni García-Molina, Tatjana Kleine, Timo Mühlhaus, Wolfgang Frank
Software Mentions: 3
Published: over 4 years ago

10.1186/s13100-018-0143-2

Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
Cited by: 17
Author(s): Fritjof Lammers, Moritz Blumer, Cornelia Rücklé, Maria A. Nilsson
Software Mentions: 3
Published: almost 6 years ago

10.3390/microorganisms9010021

Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions
Cited by: 8
Author(s): Abdul Ghafar, Anson V. Koehler, Ross S. Hall, Charles G. Gauci, Robin B. Gasser, Abdul Jabbar
Software Mentions: 3
Published: almost 4 years ago

10.1038/s42003-020-01274-9

The genetic framework of shoot regeneration in Arabidopsis comprises master regulators and conditional fine-tuning factors
Cited by: 28
Author(s): Robin Lardon, Erik Wijnker, Joost J. B. Keurentjes, Danny Geelen
Software Mentions: 2
Published: about 4 years ago

10.18632/aging.101753

A novel alternative splicing-based prediction model for uteri corpus endometrial carcinoma
Cited by: 12
Author(s): Gao Li, Gang Chen, Jin‐Shu Pang, Tiantian Li
Software Mentions: 2
Published: almost 6 years ago

10.3390/ani10101792

Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds
Cited by: 4
Author(s): Hongyang Wang, Yang Fu, Peng Gu, Yingying Zhang, Weilong Tu, Zhe Chao, Huali Wu, Jian Cao, Xiang Zhou, Bang Liu, Jennifer J. Michal, Chun Chieh Fan, Yongsong Tan
Software Mentions: 2
Published: about 4 years ago

10.3390/ani11051469

Characterization of Alternative Splicing (AS) Events during Chicken (Gallus gallus) Male Germ-Line Stem Cell Differentiation with Single-Cell RNA-seq
Cited by: 4
Author(s): Chen Sun, Kai Jin, Hongyan Sun, Jiuzhou Song, Yani Zhang, Guohong Chen
Software Mentions: 2
Published: over 3 years ago

10.1186/s12862-019-1388-1

A large close relative of C. elegans is slow-developing but not long-lived
Cited by: 12
Author(s): Gavin C. Woodruff, Erik Johnson, Patrick C. Phillips
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-020-6579-z

Phytochemical and comparative transcriptome analyses reveal different regulatory mechanisms in the terpenoid biosynthesis pathways between Matricaria recutita L. and Chamaemelum nobile L.
Cited by: 11
Author(s): Yuling Tai, Xiaojuan Hou, Chun Liu, Jun Sun, Chunxiao Guo, Ling Su, Wei Jiang, Chengcheng Ling, Cheng-Xiang Wang, Huanhuan Wang, Guifang Pan, Xiongyuan Si, Yuan Yang
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12920-021-01015-9

Screening the genome for HCC-specific CpG methylation signatures as biomarkers for diagnosis and prognosis evaluation
Cited by: 2
Author(s): Rui-Kun Zhang, Jialin Liu
Software Mentions: 2
Published: over 3 years ago

10.1186/s12860-020-00268-z

PGRMC1 effects on metabolism, genomic mutation and CpG methylation imply crucial roles in animal biology and disease
Cited by: 14
Author(s): Bashar M. Thejer, Partho P. Adhikary, Sarah L. Teakel, Johnny Fang, Paul A. Weston, Saliya Gurusinghe, Ayad G. Anwer, Martin E. Gosnell, Jalal Jazayeri, Marina Ludescher, Lesley-Ann Gray, Michael Pawlak, Robyn H. Wallace, Sameer D. Pant, Marie Wong, Tamás Fischer, Elizabeth J. New, Tanja Fehm, Hans Neubauer, Ewa M. Goldys, Jane C. Quinn, Leslie A. Weston, Michael A. Cahill
Software Mentions: 2
Published: over 4 years ago

10.1093/bioinformatics/bty541

Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees
Cited by: 3
Author(s): Christian X. Weichenberger, Johannes Michael Rainer, Cristian Pattaro, Peter P. Pramstaller, Francisco S. Domingues
Software Mentions: 2
Published: over 6 years ago

10.1155/2019/2686875

Whole Genome Analysis and Prognostic Model Construction Based on Alternative Splicing Events in Endometrial Cancer
Cited by: 12
Author(s): Caixia Wang, Mingjun Zheng, Shuang Wang, Xin Nie, Qin Guo, Lingling Gao, Xiao Li, Yue Qi, Juanjuan Liu, Bei Lin
Software Mentions: 2
Published: over 5 years ago

10.1186/s12935-020-01507-1

Comprehensive analysis of key genes associated with ceRNA networks in nasopharyngeal carcinoma based on bioinformatics analysis
Cited by: 9
Author(s): Yujin Xu, Xinyi Huang, Wangzhong Ye, Yangfan Zhang, Changkun Li, Peide Bai, Zhongqiu Lin, Chuanben Chen
Software Mentions: 2
Published: about 4 years ago

10.1186/s12935-020-01368-8

Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance
Cited by: 7
Author(s): Chuan Liu, Chuan Hu, Zhi Li, Jing Feng, Jiale Huang, Bowen Yang, Ti Wen
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms8121947

Comparative Genomics of Xanthomonas citri pv. citri A* Pathotype Reveals Three Distinct Clades with Varying Plasmid Distribution
Cited by: 3
Author(s): J Webster, Daniel R. Bogema, Toni A. Chapman
Software Mentions: 2
Published: almost 4 years ago

10.7717/peerj.7995

Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt
Cited by: 11
Author(s): Zhanji Liu, Mingchuan Fu, Hao Li, Yizhen Chen, Liguo Wang, Renzhong Liu
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pntd.0007362

In-depth proteomic characterization of Schistosoma haematobium: Towards the development of new tools for elimination
Cited by: 30
Author(s): Javier Sotillo, Mark S. Pearson, Luke Becker, Gebeyaw G Mekonnen, Abena S. Amoah, Govert J. van Dam, Paul L. A. M. Corstjens, Joanne F. Murray, Takafira Mduluza, Francisca Mutapi, Alex Loukas
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0006438

Profiling extracellular vesicle release by the filarial nematode Brugia malayi reveals sex-specific differences in cargo and a sensitivity to ivermectin
Cited by: 85
Author(s): Hiruni Harischandra, Yuan Wang, Hannah J. Loghry, Mostafa Zamanian, Michael J. Kimber
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0190836

Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds
Cited by: 7
Author(s): Clifford G. Clark, Chih-Yu Chen, Chrystal Berry, Matthew Walker, Stuart McCorrister, Patrick Chong, Garrett Westmacott
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0254049

Use and experiences of galactagogues while breastfeeding among Australian women
Cited by: 14
Author(s): Grace M. McBride, Robyn Stevenson, Gabriella Zizzo, Alice Rumbold, Lisa H Amir, Amy Keir, Luke E. Grzeskowiak
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0245131

Prevalence and factors associated with multimorbidity among primary care patients with decreased renal function
Cited by: 8
Author(s): Jennifer Hirst, José M. Ordóñez‐Mena, Chris O’Callaghan, Emma Ogburn, Clare Taylor, Yaling Yang, F D Richard Hobbs
Software Mentions: 2
Published: almost 4 years ago

10.1002/fsn3.2366

Effects of thermal and nonthermal processing technology on the quality of red sour soup after storage
Cited by: 6
Author(s): Yangbo He, Yongfu Li, Luo Xingbang, Guolin Li, Duan Zhaoyan, Chao-Jun Chen
Software Mentions: 2
Published: over 3 years ago

10.3390/foods10010017

Development of Antioxidant and Antihypertensive Properties during Growth of Lactobacillus helveticus, Lactobacillus rhamnosus and Lactobacillus reuteri on Cow’s Milk: Fermentation and Peptidomics Study
Cited by: 21
Author(s): A.V. Begunova, Оlga S. Savinova, Olga A. Glazunova, Konstantin V. Moiseenko, I.V. Rozhkova, Т. В. Федорова
Software Mentions: 2
Published: almost 4 years ago

10.3389/fcimb.2021.678996

Profiling Humoral Immune Response Against Pre-Erythrocytic and Erythrocytic Antigens of Malaria Parasites Among Neotropical Primates in the Brazilian Atlantic Forest
Cited by: 8
Author(s): Gabriela Maíra Pereira de Assis, Denise Anete Madureira de Alvarenga, Matheus de Oliveira Costa Pereira, Juan Camilo Sánchez‐Arcila, Anielle de Pina Costa, Júlio César de Souza, Ana Júlia Dutra Nunes, Alcides Pissinatti, Sílvia Bahadian Moreira, Letícia de Menezes Torres, Helena L. Costa, Herlandes da Penha Tinoco, Valéria do Socorro Pereira, Irene da Silva Soares, Taís Nóbrega de Sousa, Francis B. Ntumngia, John Adams, Flora Satiko Kano, Zelinda Maria Braga Hirano, Cláudio Tadeu Daniel-Ribeiro, Joseli Oliveira Ferreira, Luzia H. Carvalho, Cristiana Ferreira Alves de Brito
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2019.00889

Best Foot Forward: Nanopore Long Reads, Hybrid Meta-Assembly, and Haplotig Purging Optimizes the First Genome Assembly for the Southern Hemisphere Blacklip Abalone (Haliotis rubra)
Cited by: 17
Author(s): Han Ming Gan, Mun Hua Tan, Christopher M. Austin, Craig D. H. Sherman, Yen Ting Wong, Jan M. Strugnell, Mark Gervis, Luke McPherson, Adam D. Miller
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2020.563798

Integrated Analyses of Mouse Stem Cell Transcriptomes Provide Clues for Stem Cell Maintenance and Transdifferentiation
Cited by: 3
Author(s): Limin Wang, Xiaoxiao Li, Jie Hou, Xinhua Song, Wenhai Xie, Liang Shen
Software Mentions: 2
Published: about 4 years ago

10.3389/fmed.2020.606298

Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease
Cited by: 43
Author(s): Jagadesan Sankarasubramanian, Rizwan Ahmad, Nagavardhini Avuthu, Amar B. Singh, Chittibabu Guda
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2020.577268

Infection of Ophiocordyceps sinensis Fungus Causes Dramatic Changes in the Microbiota of Its Thitarodes Host
Cited by: 14
Author(s): Hua Wu, Zhongchen Rao, Li Cao, Patrick De Clercq, Richou Han
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2021.697553

Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach
Cited by: 14
Author(s): Amine M. Boukerb, Cyril Noël, Emmanuelle Quenot, Bernard Cadiou, Julien Chevé, Laure Quintric, Alexandre Cormier, Luc Dantan, Michèle Gourmelon
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.585428

Conversion of Rutin, a Prevalent Dietary Flavonol, by the Human Gut Microbiota
Cited by: 37
Author(s): Alessandra Riva, Ditta Kolimár, Andreas Spittler, Lukas Wisgrill, Craig W. Herbold, László Abrankó, David Berry
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2017.02394

Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici
Cited by: 25
Author(s): Chongjing Xia, Meinan Wang, Omar E. Cornejo, Derick Jiwan, Deven R. See, Xianming Chen
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2021.725776

Development, Phenotypic Characterization and Genomic Analysis of a Francisella tularensis Panel for Tularemia Vaccine Testing
Cited by: 1
Author(s): Beth A. Bachert, Joshua B. Richardson, Kevin D. Mlynek, Christopher P. Klimko, Ronald G. Toothman, David P. Fetterer, Andrea E. Luquette, Kitty Chase, Jessica L Storrs, Ashley K Rogers, Christopher K. Cote, David A. Rozak, Joel A. Bozue
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.590902

Antibiotic Resistance Genes and Bacterial Communities of Farmed Rainbow Trout Fillets (Oncorhynchus mykiss)
Cited by: 13
Author(s): Nicolas Helsens, Ségolène Calvez, Hervé Prévost, Agnès Bouju-Albert, Aurélien Maillet, Albert Rossero, Dominique Hurtaud‐Pessel, Monique Zagorec, Catherine Magras
Software Mentions: 2
Published: almost 4 years ago

10.3389/fonc.2021.666847

Identification of Mutator-Derived Alternative Splicing Signatures of Genomic Instability for Improving the Clinical Outcome of Cholangiocarcinoma
Cited by: 4
Author(s): Zijing Lin, Jie Gong, Guo‐Chao Zhong, Jie‐Jun Hu, Dong Cai, Lei Zhao, Zhibo Zhang
Software Mentions: 2
Published: over 3 years ago

10.3389/fonc.2019.00511

Genome-Wide Profiling Reveals the Landscape of Prognostic Alternative Splicing Signatures in Pancreatic Ductal Adenocarcinoma
Cited by: 22
Author(s): Chengkun Yang, Qiongyuan Wu, Ketuan Huang, Xiangkun Wang, Tingdong Yu, Xiwen Liao, Jianlu Huang, Guangzhi Zhu, Yizhen Gong, Chuangye Han, Hao Su, Wei Qin, Tao Peng
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2020.547942

CircRNA_000864 Upregulates B-cell Translocation Gene 2 Expression and Represses Migration and Invasion in Pancreatic Cancer Cells by Binding to miR-361-3p
Cited by: 20
Author(s): Lei Huang, Junxiang Han, Huifan Yu, Jialing Liu, Lili Gui, Zhengkun Wu, Xinxu Zhao, Shiqi Su, Gaohang Fu, Fēi Li
Software Mentions: 2
Published: almost 4 years ago

10.3389/fpls.2021.639014

A Vernalization Response in a Winter Safflower (Carthamus tinctorius) Involves the Upregulation of Homologs of FT, FUL, and MAF
Cited by: 5
Author(s): Darren Cullerne, Siri Fjellheim, Andrew Spriggs, Andrew L. Eamens, Ben Trevaskis, Craig C. Wood
Software Mentions: 2
Published: over 3 years ago

10.3389/fpls.2021.679047

Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins
Cited by: 1
Author(s): J. Lucas Boatwright, Cheng‐Ting Yeh, Heng-Cheng Hu, Alfonso Susanna, Douglas E. Soltis, Pamela S. Soltis, Patrick S. Schnable, W. Brad Barbazuk
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-016-0985-1

The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence
Cited by: 125
Author(s): Sebastian Eves‐van den Akker, Dominik R. Laetsch, Peter Thorpe, Catherine J. Lilley, Etienne G. J. Danchin, Martine Da Rocha, Corinne Rancurel, Nancy Holroyd, James A. Cotton, Amir Szitenberg, Éric Grenier, Josselin Montarry, Benjamin Mimee, Marc‐Olivier Duceppe, Ian Boyes, Jessica Marvin, Laura M. Jones, Hazijah Yusup, Joël Lafond-Lapalme, Magali Esquibet, Michaël Sabeh, Michael Rott, H.A. Overmars, A.M. Finkers-Tomczak, G. Smant, Georgios Koutsovoulos, Vivian C. Blok, Sophie Mantelin, Peter J. A. Cock, W. M. Phillips, Bernard Henrissat, Peter E. Urwin, Mark Blaxter, John T. Jones
Software Mentions: 2
Published: over 8 years ago

10.1093/gbe/evz137

Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase
Cited by: 32
Author(s): Jessica Nelson, Duncan Hauser, José A. Gudiño, Yessenia A Guadalupe, John C. Meeks, Noris Salazar Allen, Juan Carlos Villarreal, Fay‐Wei Li
Software Mentions: 2
Published: over 5 years ago

10.1111/jcmm.16439

Fructose‐1,6‐bisphosphatase aggravates oxidative stress‐induced apoptosis in asthma by suppressing the Nrf2 pathway
Cited by: 9
Author(s): Jiapeng Hu, Jia Wang, Chunlu Li, Yunxiao Shang
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.ppat.1007531

Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds
Cited by: 12
Author(s): Henan Zhu, Batchuluun Damdinjav, Gaëlle Gonzalez, Livia Victoria Patrono, Humberto Ramírez‐Mendoza, Julien A R Amat, Joanna Crispell, Yasmin A. Parr, Toni-Ann Hammond, Enkhtuvshin Shiilegdamba, Connie Y. H. Leung, Malik Peiris, John F. Marshall, Joseph Hughes, Martin Gilbert, Pablo R. Murcia
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1009112

Bacterial persisters in long-term infection: Emergence and fitness in a complex host environment
Cited by: 49
Author(s): Jennifer A. Bartell, David R. Cameron, Biljana Mojsoska, Janus Anders Juul Haagensen, Tacjana Pressler, Lea Mette Madsen Sommer, Kim Lewis, Søren Molin, Helle Krogh Johansen
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-019-52312-4

Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly
Cited by: 23
Author(s): Alexandra B. Bentz, Gregg W.C. Thomas, Douglas B. Rusch, Kimberly A. Rosvall
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-83436-1

Low-coverage whole-genome sequencing of extracellular vesicle-associated DNA in patients with metastatic cancer
Cited by: 6
Author(s): Bella Nguyen, Nicholas C. Wong, Timothy Semple, Michael E. Clark, Stephen Q. Wong, Connull Leslie, Bob Mirzai, Michael Millward, Katie Meehan, Annette Lim
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-98201-7

Proteomic and molecular dynamic investigations of PTM-induced structural fluctuations in breast and ovarian cancer
Cited by: 6
Author(s): Д. А. Тихонов, Liudmila I. Kulikova, Arthur T. Kopylov, Vladimir R. Rudnev, Alexander A. Stepanov, Kristina A. Malsagova, Alexander Izotov, Д. А. Куликов, Aleksei Zulkarnaev, Dmitry Enikeev, Natalia V. Potoldykova, Anna L. Kaysheva
Software Mentions: 2
Published: about 3 years ago

10.1128/mSystems.00480-21

Untargeted Metabolomics Reveals Species-Specific Metabolite Production and Shared Nutrient Consumption by Pseudomonas aeruginosa and Staphylococcus aureus
Cited by: 10
Author(s): Laura J. Dunphy, Kassandra L. Grimes, Nishikant Wase, Glynis L. Kolling, Jason A. Papin
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms20215403

Meta-Analysis of Gene Expression Changes in the Blood of Patients with Mild Cognitive Impairment and Alzheimer’s Disease Dementia
Cited by: 28
Author(s): Virginie Bottero, Judith A. Potashkin
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22010289

Whole-Transcriptome RNA Sequencing Reveals the Global Molecular Responses and CeRNA Regulatory Network of mRNAs, lncRNAs, miRNAs and circRNAs in Response to Salt Stress in Sugar Beet (Beta vulgaris)
Cited by: 39
Author(s): Junliang Li, Jie Cui, Chunhua Dai, Tianjiao Liu, Dansong Cheng, Chen Luo
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms22126323

Proteome Profiling of PMJ2-R and Primary Peritoneal Macrophages
Cited by: 5
Author(s): А. Л. Русанов, П. М. Кожин, Olga V. Tikhonova, Victor G. Zgoda, Dmitry S. Loginov, Adéla Chlastáková, Martin Selinger, Ján Štěrba, Libor Grubhoffer, Н. Г. Лузгина
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.11344

Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines
Cited by: 4
Author(s): Elham Karimi, Enora Geslain, Arnaud Belcour, Clémence Frioux, Méziane Aïte, Anne Siegel, Erwan Corre, Simon M. Dittami
Software Mentions: 1
Published: over 3 years ago

10.7150/jca.47877

Prognostic alternative splicing signature reveals the landscape of immune infiltration in Pancreatic Cancer
Cited by: 8
Author(s): Lin Wang, Jia Bi, Xueping Li, Miao He, Lin Zhao
Software Mentions: 1
Published: almost 5 years ago

10.3390/insects12050408

Tephritid Fruit Fly Semiochemicals: Current Knowledge and Future Perspectives
Cited by: 32
Author(s): Francesca Scolari, Federica Valerio, Giovanni Benelli, Nikos T. Papadopoulos, Lucie Vaníčková
Software Mentions: 1
Published: over 3 years ago

10.1093/gbe/evy196

Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units
Cited by: 1
Author(s): Lifei Li, Nicolai K H Barth, Eva Hirth, Leila Taher
Software Mentions: 1
Published: about 6 years ago

10.3390/genes11020200

Prognostic Value and Potential Regulatory Mechanism of Alternative Splicing in Geriatric Breast Cancer
Cited by: 4
Author(s): Xin Li, Yaxuan Wang, Bingjie Li, Wei Ma
Software Mentions: 1
Published: almost 5 years ago

10.1093/g3journal/jkab258

The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population
Cited by: 7
Author(s): L. Basten Snoek, Mark G. Sterken, Harm Nijveen, Rita J. M. Volkers, J.A.G. Riksen, Philip Rosenstiel, Hinrich Schulenburg, J.E. Kammenga
Software Mentions: 1
Published: over 3 years ago

10.1093/g3journal/jkab094

Genomes of the willow-galling sawflies Euura lappo and Eupontania aestiva (Hymenoptera: Tenthredinidae): a resource for research on ecological speciation, adaptation, and gall induction
Cited by: 3
Author(s): Craig Michell, Saskia Wutke, Manuel Aranda, Tommi Nyman
Software Mentions: 1
Published: over 3 years ago

10.1534/g3.120.401596

Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae
Cited by: 6
Author(s): Dhanushya Ramachandran, Michael R. McKain, Elizabeth A. Kellogg, Jennifer Hawkins
Software Mentions: 1
Published: almost 4 years ago

10.1534/g3.119.400563

Whole Genome Sequence of the Commercially Relevant Mushroom StrainAgaricus bisporusvar.bisporusARP23
Cited by: 11
Author(s): Eabhann O’Connor, Jamie McGowan, Charley G. P. McCarthy, Aniça Amini, Helen Grogan, David A. Fitzpatrick
Software Mentions: 1
Published: about 5 years ago

10.1128/mSphere.00787-20

Development of a Plasmid Shuttle Vector System for Genetic Manipulation of Chlamydia psittaci
Cited by: 11
Author(s): Kensuke Shima, Mary M. Weber, Christiane Schnee, Konrad Sachse, Nadja Käding, Matthias Klinger, Jan Rupp
Software Mentions: 1
Published: about 4 years ago

10.3389/fonc.2020.01257

Development of a Nomogram With Alternative Splicing Signatures for Predicting the Prognosis of Glioblastoma: A Study Based on Large-Scale Sequencing Data
Cited by: 6
Author(s): Zihao Wang, Lu Gao, Xiaopeng Guo, Cheng Feng, Wei Lian, Kan Deng, Bing Xing
Software Mentions: 1
Published: over 4 years ago

10.3389/fonc.2018.00537

Genome-Wide Profiling of Prognostic Alternative Splicing Signature in Colorectal Cancer
Cited by: 43
Author(s): Zhen Zong, Hui Li, Chenghao Yi, Hou-Qun Ying, Zhengming Zhu, He Wang
Software Mentions: 1
Published: about 6 years ago

10.3389/fnins.2020.615362

Comparative Analysis of Dorsal Root, Nodose and Sympathetic Ganglia for the Development of New Analgesics
Cited by: 14
Author(s): Matthew R. Sapio, Fernando A. Vazquez, Amelia J. Loydpierson, Dragan Maric, Jaeyeon Kim, Danielle M. LaPaglia, Henry L. Puhl, Van B. Lu, Stephen R. Ikeda, Andrew J. Mannes, Michael J. Iadarola
Software Mentions: 1
Published: almost 4 years ago

10.3389/fneur.2020.00309

Memory Impairment in Relapsing-Remitting Multiple Sclerosis Using a Challenging Semantic Interference Task
Cited by: 5
Author(s): Jordi A. Matías‐Guiu, Ana Cortés‐Martínez, Rosie E. Curiel, Alfonso Delgado‐Álvarez, Aníbal Fernández-Oliveira, Vanesa Pytel, Paloma Montero, Teresa Moreno‐Ramos, David Loewenstein
Software Mentions: 1
Published: over 4 years ago

10.1186/s10020-021-00325-z

CD36 deficiency ameliorates drug-induced acute liver injury in mice
Cited by: 5
Author(s): Chen Zhang, Shi Xiao, Zhongping Su, Chao Hu, Xiaoli Mu, Jinshun Pan, Mengjing Li, Fei Teng, Ling Tao, Ting Zhao, Chenjie Xu, Guozhong Ji, You Qin
Software Mentions: 1
Published: over 3 years ago

10.1128/mSystems.01211-20

Comprehensive Scanning of Prophages in Lactobacillus : Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems
Cited by: 28
Author(s): Zhangming Pei, Faizan Ahmed Sadiq, Xiao Han, Jianxin Zhao, Hao Zhang, R. Paul Ross, Wenwei Liu
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2018.01823

Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae
Cited by: 6
Author(s): Jiaying Li, Songping Zhan, Xuanzhen Liu, Qiang Lin, Jianping Jiang, Xiangzhen Li
Software Mentions: 1
Published: about 6 years ago

10.1038/s41396-018-0177-y

A gene transfer event suggests a long-term partnership between eustigmatophyte algae and a novel lineage of endosymbiotic bacteria
Cited by: 48
Author(s): Tatiana Yurchenko, Tereza Ševčíková, Pavel Přibyl, Khalid El Karkouri, Vladimír Klimeš, Raquel Amaral, Veronika Zbránková, Eun-Soo Kim, Didier Raoult, Lília M.A. Santos, Marek Eliáš
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2021.686298

Correlations Between the Characteristics of Alternative Splicing Events, Prognosis, and the Immune Microenvironment in Breast Cancer
Cited by: 3
Author(s): Youyuan Deng, Hongjun Zhao, Lifen Ye, Zhiya Hu, Kun Fang, Jianguo Wang
Software Mentions: 1
Published: over 3 years ago

10.2196/17687

What You Need to Know Before Implementing a Clinical Research Data Warehouse: Comparative Review of Integrated Data Repositories in Health Care Institutions
Cited by: 18
Author(s): Kristina K. Gagalova, M Angelica Leon Elizalde, Élodie Portales-Casamar, Matthias Görges
Software Mentions: 1
Published: about 4 years ago

10.3389/fgene.2020.00879

Genome-Wide Transcriptional Analysis Reveals Alternative Splicing Event Profiles in Hepatocellular Carcinoma and Their Prognostic Significance
Cited by: 10
Author(s): Yong Xiong, Gang Ye, Kang Wang, Muhammad Bilal Riaz, Jian Xu, Zhenbing Lv, He Zhou, Qiang Li, Weinan Li, Ji Sun, Tao Tang, Jingdong Li
Software Mentions: 1
Published: over 4 years ago

Projects: cran: UpSetR

Papers Mentioning UpSetR 319