Projects: pypi: cutadapt
https://packages.ecosyste.ms/registries/pypi.org/packages/cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
63 versions
Latest release: almost 3 years ago
14 dependent packages
40,808 downloads last month
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CITATION.cff
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CITATION.cff file
Contains citation file for academic attribution
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Very Likely Science (100)
Papers Mentioning cutadapt 1,562
10.1186/1471-2164-14-586
The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractionsCited by: 46
Author(s): Brian R. Johnson, Joel Atallah, David C. Plachetzki
Software Mentions: 4
Published: over 13 years ago
10.3389/fmicb.2021.643904
Predominant Microbial Colonizers in the Root Endosphere and Rhizosphere of Turfgrass Systems: Pseudomonas veronii, Janthinobacterium lividum, and Pseudogymnoascus spp.Cited by: 10
Author(s): Qing Xia, Thomas W. Rufty, Wei Shi
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-020-07072-1
B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processesCited by: 18
Author(s): Syed Farhan Ahmad, Maryam Jehangir, Adauto Lima Cardoso, Ivan Rodrigo Wolf, Vladimir Pavan Margarido, Diogo Cavalcanti Cabral-de-Mello, Rachel J. O’Neill, Guilherme Targino Valente, Cesar Martins
Software Mentions: 4
Published: almost 6 years ago
10.1111/pbi.12835
Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levelsCited by: 27
Author(s): M. Michelle Malmberg, Luke W. Pembleton, Rebecca C. Baillie, Michelle C. Drayton, Shimna Sudheesh, Sukhjiwan Kaur, Hiroshi Shinozuka, Preeti Verma, Germán Spangenberg, Hans D. Daetwyler, John W. Forster, Noel O. I. Cogan
Software Mentions: 4
Published: almost 9 years ago
10.3389/fmicb.2018.02094
Application of MootralTM Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation TechniqueCited by: 27
Author(s): Melanie Eger, Michael Graz, Susanne Riede, Gerhard Breves
Software Mentions: 4
Published: about 8 years ago
10.1098/rstb.2015.0040
Loss of neurogenesis in<i>Hydra</i>leads to compensatory regulation of neurogenic and neurotransmission genes in epithelial cellsCited by: 42
Author(s): Yvan Wenger, Wanda Christa Buzgariu, Brigitte Galliot
Software Mentions: 4
Published: over 10 years ago
10.7554/eLife.47891
Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylationCited by: 54
Author(s): Jered M. Wendte, Yinwen Zhang, Lexiang Ji, Xiulin Shi, Rashmi R. Hazarika, Yadollah Shahryary, Frank Johannes, Robert J. Schmitz
Software Mentions: 4
Published: about 7 years ago
10.3389/fmicb.2020.01305
Seasonal Dynamics of Pelagic Mycoplanktonic Communities: Interplay of Taxon Abundance, Temporal Occurrence, and Biotic InteractionsCited by: 21
Author(s): Stefanos Banos, Deisy Morselli Gysi, Tim Richter-Heitmann, Frank Oliver Glöckner, Maarten Boersma, Karen Helen Wiltshire, Gunnar Gerdts, Antje Wichels, M. Reich
Software Mentions: 4
Published: about 6 years ago
10.7717/peerj.8133
The impact of storage conditions on human stool 16S rRNA microbiome composition and diversityCited by: 19
Author(s): Lauren V. Carruthers, Moses Arinaitwe, Moses Adriko, Christina L. Faust, Edridah M. Tukahebwa, Lindsay J. Hall, Lisa Ranford-Cartwright, Poppy H. L. Lamberton
Software Mentions: 4
Published: almost 7 years ago
10.3389/fmicb.2019.01576
Fecal Microbiota Transplant From Highly Feed Efficient Donors Affects Cecal Physiology and Microbiota in Low- and High-Feed Efficient ChickensCited by: 30
Author(s): Barbara U. Metzler‐Zebeli, Sina-Catherine Siegerstetter, Elizabeth Magowan, Peadar G. Lawlor, Niamh O’Connell, Qendrim Zebeli
Software Mentions: 4
Published: about 7 years ago
10.1038/s41598-019-53892-x
Performance assessment of total RNA sequencing of human biofluids and extracellular vesiclesCited by: 46
Author(s): Celine Everaert, Hetty Helsmoortel, Anneleen Decock, Eva Hulstaert, Ruben Van Paemel, Kimberly Verniers, Justine Nuytens, Jasper Anckaert, Nele Nijs, Joeri Tulkens, Bert Dhondt, An Hendrix, Pieter Mestdagh, Jo Vandesompele
Software Mentions: 4
Published: almost 7 years ago
10.3389/fmicb.2021.628437
Volatile Compounds From Bacillus, Serratia, and Pseudomonas Promote Growth and Alter the Transcriptional Landscape of Solanum tuberosum in a Passively Ventilated Growth SystemCited by: 8
Author(s): Darren Heenan-Daly, Simone Coughlan, Eileen Dillane, Barbara Doyle Prestwich
Software Mentions: 4
Published: about 5 years ago
10.1038/s41598-019-51056-5
Down-regulation of CK2α correlates with decreased expression levels of DNA replication minichromosome maintenance protein complex (MCM) genesCited by: 4
Author(s): Susanne Schaefer, Thomas Koed Doktor, Sabrina B Frederiksen, Kathleen Chea, Mirka Hlavacova, Georg M. Bruun, Maj Rabjerg, Brage S. Andresen, Isabel Domı́nguez, Bárbara Guerra
Software Mentions: 4
Published: almost 7 years ago
10.3389/fmicb.2017.01656
Linseed Oil Supplementation of Lambs’ Diet in Early Life Leads to Persistent Changes in Rumen Microbiome StructureCited by: 36
Author(s): Tamsin Lyons, T. M. Boland, Sean Storey, Evelyn Doyle
Software Mentions: 4
Published: about 9 years ago
10.1038/s41598-019-42865-9
Differences in resource use lead to coexistence of seed-transmitted microbial populationsCited by: 15
Author(s): Gloria Torres-Cortés, Benjamin J. Garcia, Stéphane Compant, Samir Rezki, Piet Jones, Anne Préveaux, Martial Briand, Alain Roulet, Olivier Bouchez, Daniel Jacobson, Matthieu Barret
Software Mentions: 4
Published: over 7 years ago
10.3389/fmicb.2021.675048
A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal SedimentsCited by: 6
Author(s): Zhongdong Huang, Shiqing Mo, Lifei Yan, Xiaomei Wei, Yangze Huang, Lizhen Zhang, Shuhui Zhang, Jianzong Liu, Qing Xiao, Hong Lin, Yu Guo
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-019-42560-9
De Novo Transcriptome Assembly and Functional Annotation in Five Species of BatsCited by: 22
Author(s): Diana D. Moreno-Santillán, Carlos Machaín-Williams, Georgina Hernández-Montes, Jorge Ortega
Software Mentions: 4
Published: over 7 years ago
10.3390/cancers13071494
Musashi1 Contribution to Glioblastoma Development via Regulation of a Network of DNA Replication, Cell Cycle and Division GenesCited by: 9
Author(s): Mirella Baroni, Caihong Yi, Saket Choudhary, Xiufen Lei, Adam Kosti, Denise Grieshober, Mitzli X. Velasco, Mu Qiao, Suzanne Burns, Patrícia Rosa de Araújo, Talia Delambre, Mi‐Young Son, Michelina Plateroti, Marco A. R. Ferreira, Paul Hasty, Luiz O. F. Penalva
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-019-42911-6
Habitat-dependent composition of bacterial and fungal communities in biological soil crusts from OmanCited by: 30
Author(s): Raeid M. M. Abed, Alexandra Tamm, Christiane Hassenrück, Ahmed Al‐Rawahi, Emilio Rodríguez‐Caballero, Sabine Fiedler, Stefanie Maier, Bettina Weber
Software Mentions: 4
Published: over 7 years ago
10.1155/2017/7183516
PEDF Is Associated with the Termination of Chondrocyte Phenotype and Catabolism of Cartilage TissueCited by: 6
Author(s): Patricia Klinger, Söeren Lukassen, Fulvia Ferrazzi, Arif B. Ekici, Thilo Hotfiel, B. Swoboda, Thomas Aigner, Kolja Gelse
Software Mentions: 4
Published: over 9 years ago
10.3390/pathogens10050555
Microeukaryotic Communities on the Fruit of Gardenia thunbergia Thunb. with a Focus on Pathogenic FungiCited by: 0
Author(s): Bastian Steudel, Himansu Baijnath, Thorben Schwedt, Armin O. Schmitt
Software Mentions: 4
Published: over 5 years ago
10.3390/cancers13184687
Bacteria-Derived Extracellular Vesicles in Urine as a Novel Biomarker for Gastric Cancer: Integration of Liquid Biopsy and Metagenome AnalysisCited by: 7
Author(s): Jae Yong Park, Chil Sung Kang, Ho Chan Seo, Jin Chul Shin, Sung Min Kym, Young Soo Park, Tae Seop Shin, Jae Gyu Kim, Yoon Keun Kim
Software Mentions: 4
Published: about 5 years ago
10.3389/fmed.2021.675842
Exosomal Circular RNA RNA-seq Profiling and the Carcinogenic Role of Exosomal circ-CYP24A1 in Cutaneous Squamous Cell CarcinomaCited by: 9
Author(s): Zheng Zhang, Hao Guo, Wen‐Jia Yang, Jiu‐Hong Li
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-017-15955-9
Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiomeCited by: 64
Author(s): María‐Soledad Benítez, Shannon L. Osborne, R. Michael Lehman
Software Mentions: 4
Published: almost 9 years ago
10.3390/cancers13030527
Radiosensitizing Pancreatic Cancer with PARP Inhibitor and Gemcitabine: An In Vivo and a Whole-Transcriptome Analysis after Proton or Photon IrradiationCited by: 7
Author(s): Waisse Waissi, Anaïs Nicol, Matthieu Jung, M. Rousseau, D. Jarnet, Georges Noël, Hélène Burckel
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-017-01943-6
Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1Cited by: 16
Author(s): Tim-Michael Decker, Michael Kluge, Stefan Krebs, Nilay Shah, Helmut Blum, Caroline C. Friedel, Dirk Eick
Software Mentions: 4
Published: over 9 years ago
10.1186/1471-2164-15-221
From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolismCited by: 119
Author(s): Inès Zouari, Alessandra Salvioli, Matteo Chialva, Mara Novero, Laura Miozzi, Gian Carlo Tenore, Paolo Bagnaresi, Paola Bonfante
Software Mentions: 4
Published: over 12 years ago
10.3390/cancers13051126
Transformed Canine and Murine Mesenchymal Stem Cells as a Model for Sarcoma with Complex GenomicsCited by: 5
Author(s): Natasja Franceschini, Bas Verbruggen, Marianna A. Tryfonidou, Alwine B. Kruisselbrink, Hans J. Baelde, Karin E. de Visser, Károly Szuhai, Anne‐Marie Cleton‐Jansen, Judith V.M.G. Bovée
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-018-19684-5
Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomicsCited by: 23
Author(s): Jelle van Wesemael, Yann Hueber, Ewaut Kissel, Nádia Alves Campos, Rony Swennen, Sébastien Carpentier
Software Mentions: 4
Published: over 8 years ago
10.1242/bio.047829
Heterogeneous beta-catenin activation is sufficient to cause hepatocellular carcinoma in zebrafishCited by: 13
Author(s): Sharanya Maanasi Kalasekar, Srishti Kotiyal, Christopher J. Conley, Cindy Phan, Annika Young, Kimberley Evason
Software Mentions: 4
Published: over 7 years ago
10.3390/cancers12082210
Human FBXL8 Is a Novel E3 Ligase Which Promotes BRCA Metastasis by Stimulating Pro-Tumorigenic Cytokines and Inhibiting Tumor SuppressorsCited by: 10
Author(s): Shu Chun Chang, Wei‐Hsiu Hsu, Emily Chia Yu Su, Chin Sheng Hung, Jeak Ling Ding
Software Mentions: 4
Published: about 6 years ago
10.3389/fpls.2019.00235
Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAsCited by: 49
Author(s): Cristiane P. G. Calixto, Nikoleta A. Τzioutziou, Allan B. James, Csaba Hornyik, Wenbin Guo, Runxuan Zhang, Hugh G. Nimmo, John W. Brown
Software Mentions: 4
Published: over 7 years ago
10.1038/s41598-020-65638-1
Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levelsCited by: 11
Author(s): Saket Choudhary, Suzanne Perea Burns, Hoda Mirsafian, Wenzheng Li, Dat T. Vo, Mu Qiao, Xiufen Lei, Andrew D. Smith, Luiz O. F. Penalva
Software Mentions: 4
Published: over 6 years ago
10.7554/eLife.58041
Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondriaCited by: 52
Author(s): Sara M. Nowinski, Ashley Solmonson, Scott F. Rusin, J. Alan Maschek, Claire Bensard, Sarah Fogarty, Mi Young Jeong, Sandra Lettlová, Jordan A. Berg, Jeffrey T. Morgan, Yeyun Ouyang, Bradley C. Naylor, João A. Paulo, Katsuhiko Funai, James E. Cox, Steven P. Gygi, Dennis R. Winge, Ralph J. DeBerardinis, Jared Rutter
Software Mentions: 4
Published: about 6 years ago
10.3390/v11111041
Viruses in the Invasive Hornet Vespa velutinaCited by: 36
Author(s): Anne Dalmon, Philippe Gayral, Damien Decante, Christophe Klopp, Diane Bigot, Maxime Thomasson, Elisabeth A. Herniou, Cédric Alaux, Yves Le Conte
Software Mentions: 4
Published: almost 7 years ago
10.7717/peerj.10231
Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquacultureCited by: 22
Author(s): John K. Pearman, Nigel Keeley, Susanna A. Wood, Olivier Laroche, Anastasija Zaiko, Georgia Thomson‐Laing, Laura Biessy, Javier Atalah, Xavier Pochon
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12977-020-00544-y
Comparative analysis of human microglial models for studies of HIV replication and pathogenesisCited by: 34
Author(s): Ammara Mohammad, J. Hammonds, Mario Pujato, Christopher N. Mayhew, Krishna M. Roskin, Paul Spearman
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pone.0187150
RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningiomaCited by: 13
Author(s): Jennifer K. Grenier, Polly Foureman, Erica A. Sloma, Andrew D. Miller
Software Mentions: 4
Published: almost 9 years ago
10.3390/v10070388
Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial MicroorganismsCited by: 40
Author(s): Shaun T. Cross, Marylee Kapuscinski, Jacquelyn Perino, Bernadette L Maertens, James Weger-Lucarelli, Gregory D. Ebel, Mark D. Stenglein
Software Mentions: 4
Published: about 8 years ago
10.1098/rsos.180903
Bracketing phenogenotypic limits of mammalian hybridizationCited by: 26
Author(s): Yoland Savriama, Mia Valtonen, Juhana Kammonen, Pasi Rastas, Olli‐Pekka Smolander, Ari Löytynoja, Teemu J. Häkkinen, Ian J. Corfe, Sylvain Gerber, Isaac Salazar‐Ciudad, Lars Paulín, Liisa Holm, Ari Löytynoja, Petri Auvinen, Jukka Jernvall
Software Mentions: 4
Published: almost 8 years ago
10.1080/21505594.2021.1958057
Transcriptional response of <i>Aspergillus fumigatus</i> to copper and the role of the Cu chaperonesCited by: 6
Author(s): Duaa Anabosi, Zohar Meir, Yana Shadkchan, Mariana Handelman, Ammar Abou-Kandil, Annie Yap, Daniel Urlings, Morgan Gold, Sven Krappmann, Hubertus Haas, Nir Osherov
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.ppat.1009812
Mouse papillomavirus type 1 (MmuPV1) DNA is frequently integrated in benign tumors by microhomology-mediated end-joiningCited by: 12
Author(s): Lulu Yu, Vladimır Majerčiak, Xiangyang Xue, Aayushi Uberoi, Alexei V. Lobanov, Xiongfong Chen, Maggie Cam, Stephen H. Hughes, Paul F. Lambert, Zhi-Ming Zheng
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pone.0215986
Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-SeqCited by: 27
Author(s): Sebastian Laaß, Vivian Monzon, Jana Kliemt, M Hammelmann, Friedhelm Pfeiffer, Konrad U. Förstner, Jörg Soppa
Software Mentions: 4
Published: over 7 years ago
10.3389/fgene.2020.00867
Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic FibroblastsCited by: 13
Author(s): Wei Chen, Xuefei Wang, Gang Wei, Yin Huang, Yufang Shi, Dan Li, Shengnu Qiu, Bin Zhou, Junhong Cao, Meng Chen, Pengfei Qin, Wenfei Jin, Ting Ni
Software Mentions: 4
Published: about 6 years ago
10.1186/s12870-016-0926-x
Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seqCited by: 9
Author(s): Nikolay A. Shmakov, Gennady V. Vasiliev, Natalya V. Shatskaya, А. В. Дорошков, Е. И. Гордеева, D. A. Afonnikov, Е. К. Хлесткина
Software Mentions: 4
Published: almost 10 years ago
10.3389/fcimb.2020.594778
Biliary Microbial Structure of Gallstone Patients With a History of Endoscopic Sphincterotomy SurgeryCited by: 6
Author(s): Haikang Shen, Juanjuan Zhu, Fuqiang Ye, Danyi Xu, Liang Fang, Jianfeng Yang, Huijie Lv, Qifeng Lou, Hangbin Jin, Ming Ni, Xiaofeng Zhang
Software Mentions: 4
Published: over 5 years ago
10.3389/fgene.2019.00854
New Recurrent Structural Aberrations in the Genome of Chronic Lymphocytic Leukemia Based on Exome-Sequencing DataCited by: 7
Author(s): Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, José Ángel Díaz Arias, Marta Sonia González Pérez, José Luis Bello López
Software Mentions: 4
Published: about 7 years ago
10.3390/jcm8060849
MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV InfectionCited by: 10
Author(s): Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo, Pablo Ryan, Juan Macı́as, Joaquín Cabezas, Jesús Troya, Juan A Pineda, María Teresa Arias-Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa, Luz María Medrano, Isabel Cuesta de la Plaza, Sara Monzón, Salvador Resino, Amanda Fernández‐Rodríguez
Software Mentions: 4
Published: over 7 years ago
10.1038/s41380-018-0271-6
Alterations in sperm long RNA contribute to the epigenetic inheritance of the effects of postnatal traumaCited by: 106
Author(s): Katharina Gapp, Gretchen van Steenwyk, Pierre-Luc Germain, Wayo Matsushima, Konrad L. M. Rudolph, Francesca Manuella, Martin Roszkowski, Grégoire Vernaz, Tanay Ghosh, Paweł Pelczar, Isabelle M. Mansuy, Eric A. Miska
Software Mentions: 4
Published: almost 8 years ago
10.3389/fmicb.2016.02067
Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway SpruceCited by: 72
Author(s): Heiko Nacke, Kezia Goldmann, Ingo Schöning, Birgit Pfeiffer, Kristin Kaiser, Genis Castillo-Villamizar, Marion Schrumpf, François Buscot, Rolf Daniel, Tesfaye Wubet
Software Mentions: 4
Published: over 9 years ago
10.1371/journal.ppat.1006084
Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial InfectionCited by: 24
Author(s): Apollo Stacy, Nader Abraham, Peter Jorth, Marvin Whiteley
Software Mentions: 4
Published: almost 10 years ago
10.1007/s11105-017-1032-4
Drought-Tolerant Brassica rapa Shows Rapid Expression of Gene Networks for General Stress Responses and Programmed Cell Death Under Simulated Drought StressCited by: 25
Author(s): Yi Guo, Birgit Samans, Sheng Chen, Kidist B. Kibret, Sarah Hatzig, Neil C. Turner, Matthew N. Nelson, Wallace Cowling, Rod J. Snowdon
Software Mentions: 4
Published: over 9 years ago
10.1186/s12864-016-2694-2
RNA-Seq following PCR-based sorting reveals rare cell transcriptional signaturesCited by: 21
Author(s): Maurizio Pellegrino, Adam Sciambi, Jamie Yates, Joshua D. Mast, Charles Silver, Dennis J. Eastburn
Software Mentions: 4
Published: over 10 years ago
10.18632/aging.202780
circRNA expression profiling of colon tissue from mesalazine-treated mouse of inflammatory bowel disease reveals an important circRNA-miRNA-mRNA pathwayCited by: 8
Author(s): Wei Zhou, Haiyin Zhang, Y. B. Pan, Yingbin Xu, Yongqing Cao
Software Mentions: 4
Published: over 5 years ago
10.3389/fgene.2020.551065
Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in MiceCited by: 11
Author(s): Fang Cao, Yu Guo, Qiang Zhang, Yinchun Fan, Qian Liu, Jiancheng Song, Hua Zhong, Shengtao Yao
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12864-016-3227-8
Blood miRNomes and transcriptomes reveal novel longevity mechanisms in the long-lived bat, Myotis myotisCited by: 43
Author(s): Zixia Huang, David Jebb, Emma C. Teeling
Software Mentions: 4
Published: almost 10 years ago
10.3389/fimmu.2021.644350
Analysis of Bulk RNA Sequencing Data Reveals Novel Transcription Factors Associated With Immune Infiltration Among Multiple CancersCited by: 5
Author(s): Lei Liu, Qiuchen Zhao, Chao Cheng, Jingwen Yi, Hongyan Sun, Qi Wang, Weili Quan, Yaqiang Xue, Luguo Sun, Xianling Cong, Yi Zhang
Software Mentions: 4
Published: about 5 years ago
10.1172/JCI130809
A stress-responsive enhancer induces dynamic drug resistance in acute myeloid leukemiaCited by: 25
Author(s): Mark S. Williams, Fabio Amaral, Fabrizio Simeoni, Tim C. P. Somervaille
Software Mentions: 4
Published: over 6 years ago
10.1038/s41597-019-0141-3
Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspotCited by: 8
Author(s): Antônio Pedro Camargo, Rafael Soares Correa de Souza, Patrícia de Britto Costa, Isabel Rodrigues Gerhardt, Ricardo A. Dante, Grazielle Sales Teodoro, Anna Abrahão, Hans Lambers, Marcelo Falsarella Carazzolle, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Simon Roux, Krishna Palaniappan, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Alex Copeland, I. Min A. Chen, Natalia Ivanova, Nikos C. Kyrpides, Christa Pennacchio, Emiley A. Eloe‐Fadrosh, Paulo Arruda, Rafael S. Oliveira
Software Mentions: 4
Published: about 7 years ago
10.3389/fbioe.2020.00155
Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilisCited by: 9
Author(s): Richou Han, Katie Haning, Juan C. Gonzalez-Rivera, Yongqiang Yang, Runxia Li, Seung Hee Cho, Ju Huang, Bobi A. Simonsen, Shihui Yang, Lydia M. Contreras
Software Mentions: 4
Published: over 6 years ago
10.1186/s12866-021-02230-1
A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infantsCited by: 12
Author(s): Christophe Lay, Collins Wenhan Chu, Rikky W. Purbojati, Enzo Acerbi, Daniela I. Drautz–Moses, Paola Flórez de Sessions, Jié Song, Eliza Xin Pei Ho, Yee Jiun Kok, Xinyan Bi, Shuwen Chen, Shi Ya Mak, Mei Chien Chua, Angela Goh, Wen Chin Chiang, Rajeshwar Rao, Surasith Chaithongwongwatthana, Nipon Khemapech, Voranush Chongsrisawat, Rocı́o Martı́n, Yanqing Koh, Sachin R. Lohar, Ivan Chin Hin Tan, Wong Anng Anng, Jie Chen, Nana Bartke, Kaouther Ben-Amor, Ingrid B. Renes, Fiona Wong, Guus Roeselers, Ying Swan Ho, Martin L. Hibberd, Stephan C. Schuster, Jan Knol
Software Mentions: 4
Published: about 5 years ago
10.1186/s12866-017-1092-5
Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasoneCited by: 43
Author(s): Stephanie L. Bond, Edouard Timsit, Matthew L. Workentine, Trevor W. Alexander, Renaud Léguillette
Software Mentions: 4
Published: about 9 years ago
10.1186/s13073-021-00826-w
Comprehensive molecular characterization of gastric cancer patients from phase II second-line ramucirumab plus paclitaxel therapy trialCited by: 16
Author(s): Seung Tae Kim, K. Jason, Sung Yong Oh, Kyung Kim, Jung Yong Hong, Won Ki Kang, Jeeyun Lee
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pone.0246367
Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysisCited by: 6
Author(s): Lluís Revilla, Aida Mayorgas, A M Corraliza, Maria Carme Masamunt, Amira Metwaly, Dirk Haller, Eva Tristán, Anna Carrasco, María Esteve, Julián Panés, Elena Ricart, Juan José Lozano, Azucena Salas
Software Mentions: 4
Published: over 5 years ago
10.3389/fbioe.2015.00028
G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth MethodsCited by: 8
Author(s): Andrea Manconi, Elias Manca, Marco Moscatelli, Matteo Gnocchi, Alessandro Orro, Giuliano Armano, Luciano Milanesi
Software Mentions: 4
Published: over 11 years ago
10.1371/journal.pone.0223397
Brief communication: Long-term absence of Langerhans cells alters the gene expression profile of keratinocytes and dendritic epidermal T cellsCited by: 10
Author(s): Qingtai Su, Aurélie Bouteau, Jacob Cardenas, Uthra Balaji, Yuanyaun Wang, Cynthia Smitherman, Jin Gu, Botond Z. Igyártó
Software Mentions: 4
Published: over 6 years ago
10.12688/f1000research.10571.2
Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysisCited by: 332
Author(s): Jason L. Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu‐Jie Wang, David Buck, Kin Fai Au
Software Mentions: 4
Published: over 9 years ago
10.1016/j.molcel.2019.03.010
A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal JellyCited by: 35
Author(s): Eyal Maori, Isabela Cunha Navarro, Humberto Boncristiani, David J. Seilly, Konrad L. M. Rudolph, Alexandra Sapetschnig, Chi-Chuan Lin, John E. Ladbury, Jay D. Evans, Jonathan L. Heeney, Eric A. Miska
Software Mentions: 4
Published: over 7 years ago
10.1111/eva.12979
Estimating the contribution of Greenland Halibut (<i>Reinhardtius hippoglossoides</i>) stocks to nurseries by means of genotyping‐by‐sequencing: Sex and time matterCited by: 16
Author(s): Emilie Carrier, Anne‐Laure Ferchaud, Éric Normandeau, Pascal Sirois, Louis Bernatchez
Software Mentions: 4
Published: over 6 years ago
10.1093/gbe/evw262
Salmonid chromosome evolution as revealed by a novel method for comparing RADseq linkage mapsCited by: 38
Author(s): Ben J. G. Sutherland, Thierry Gosselin, Éric Normandeau, Manuel Lamothe, Nathalie Isabel, Céline Audet, Louis Bernatchez
Software Mentions: 4
Published: almost 10 years ago
10.1016/j.molcel.2018.10.018
Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription FactorCited by: 32
Author(s): Andrew Wu, Harshil Patel, Minghao Chia, Fabien Moretto, David Frith, Ambrosius P. Snijders, Folkert J. van Werven
Software Mentions: 4
Published: almost 8 years ago
10.1093/gbe/evy155
Pattern of DNA Methylation in Daphnia: Evolutionary PerspectiveCited by: 43
Author(s): Jouni Kvist, Camila Gonçalves Athanásio, Omid Shams Solari, James Brown, John K. Colbourne, Michael E. Pfrender, Leda Mirbahai
Software Mentions: 4
Published: about 8 years ago
10.1093/molbev/msab096
Novelty and Convergence in Adaptation to Whole Genome DuplicationCited by: 20
Author(s): Magdalena Bohutínská, Mark Alston, Patrick J. Monnahan, Terezie Mandáková, Sian Bray, Pirita Paajanen, Filip Kolář, Levi Yant
Software Mentions: 4
Published: over 5 years ago
10.1093/molbev/msx144
Recent Sex Chromosome Divergence despite Ancient Dioecy in the Willow Salix viminalisCited by: 55
Author(s): Pascal Pucholt, Alison E. Wright, Lei Liu Conze, Judith E. Mank, Sofia Berlin
Software Mentions: 4
Published: over 9 years ago
10.1093/molbev/msw161
Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural VariationCited by: 82
Author(s): Sara Pinosio, Stefania Giacomello, Patricia Faivre-Rampant, Gail Taylor, Véronique Jorge, Marie Christine Le Paslier, Giusi Zaina, Catherine Bastien, Federica Cattonaro, Fabio Marroni, Michèle Morgante
Software Mentions: 4
Published: about 10 years ago
10.1371/journal.pone.0232715
PIWI-interacting RNAs are differentially expressed during cardiac differentiation of human pluripotent stem cellsCited by: 11
Author(s): Alejandro La Greca, María Agustina Scarafia, María Clara Hernández Cañás, Nelba Pérez, Sheila Castañeda, Carolina Colli, Alan Miqueas Möbbs, Natalia Lucía Santín Velazque, Gabriel Neiman, Ximena Garate, Cyntia Abán, Ariel Waisman, Lucía Moro, Gustavo Sevlever, Carlos Luzzani, Santiago Gabriel Miriuka
Software Mentions: 4
Published: over 6 years ago
10.1093/molbev/msab141
Rapid Parallel Adaptation to Anthropogenic Heavy Metal PollutionCited by: 14
Author(s): Alexander S. T. Papadopulos, Andrew J. Helmstetter, Owen G. Osborne, Aaron A. Comeault, Daniel P. Wood, Edward A. Straw, Laurence Mason, Michael F. Fay, Joe Parker, Luke T. Dunning, Andrew Foote, Rhian J. Smith, Jackie Lighten
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pone.0216366
Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern CroatiaCited by: 11
Author(s): Daniel Fernandes, Kendra Sirak, Olivia Cheronet, Rachel Howcroft, Mislav Čavka, Dženi Los, Josip Burmaz, Ron Pinhasi, Mario Novak
Software Mentions: 4
Published: about 7 years ago
10.1093/gigascience/giaa158
ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome dataCited by: 4
Author(s): Pavankumar Videm, Anup Kumar, Oleg Zharkov, Björn Grüning, Rolf Backofen
Software Mentions: 4
Published: over 5 years ago
10.1093/molbev/msaa172
Gene Loss Predictably Drives Evolutionary AdaptationCited by: 49
Author(s): Jana Helsen, Karin Voordeckers, Laura Vanderwaeren, Toon Santermans, Maria Tsontaki, Kevin J. Verstrepen, Rob Jelier
Software Mentions: 4
Published: about 6 years ago
10.1002/ece3.1720
The transcriptomic and evolutionary signature of social interactions regulating honey bee caste developmentCited by: 34
Author(s): Svjetlana Vojvodic, Brian R. Johnson, Brock A. Harpur, Clement F. Kent, Amro Zayed, Kirk E. Anderson, Timothy A. Linksvayer
Software Mentions: 4
Published: almost 11 years ago
10.1002/ece3.3976
Brain gene expression analyses in virgin and mated queens of fire ants reveal mating-independent and socially regulated changesCited by: 14
Author(s): Travis L. Calkins, Mei Er Chen, Arinder K. Arora, Chloë Hawkings, Cécilia Tamborindeguy, Patricia V. Pietrantonio
Software Mentions: 4
Published: over 8 years ago
10.1186/s13059-021-02272-8
A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesisCited by: 16
Author(s): Li Li, Alejandro P. Ugalde, Colinda L.G.J. Scheele, Sebastian M. Dieter, Remco Nagel, Jin Ma, Abhijeet Pataskar, Gözde Korkmaz, Ran Elkon, Miao‐Ping Chien, You Li, Pin-Rui Su, Onno B. Bleijerveld, Maarten Altelaar, Lyubomir Momchev, Zohar Manber, Ruiqi Han, Pieter C. van Breugel, Rui Lopes, Peter ten Dijke, Jacco van Rheenen, Reuven Agami
Software Mentions: 4
Published: over 5 years ago
10.1002/ece3.4559
Table for five, please: Dietary partitioning in boreal batsCited by: 62
Author(s): Eero J. Vesterinen, Anna I. E. Puisto, Anna Blomberg, Thomas M. Lilley
Software Mentions: 4
Published: almost 8 years ago
10.1186/s40793-020-00364-9
Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomatoCited by: 12
Author(s): Peter Kusstatscher, Wisnu Adi Wicaksono, Alessandro Bergna, Tomislav Cernava, Nick Bergau, Alain Tissier, Bettina Hause, Gabriele Berg
Software Mentions: 4
Published: about 6 years ago
10.1186/s12885-021-08388-1
Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transitionCited by: 10
Author(s): Ryne C. Ramaker, Andrew A. Hardigan, Emily R. Gordon, Carter A Wright, R Myers, Sara J. Cooper
Software Mentions: 4
Published: over 5 years ago
10.1186/s13059-020-02062-8
Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in ArabidopsisCited by: 26
Author(s): Lejon E. M. Kralemann, S. Liu, Minerva S. Trejo-Arellano, Rafael Muñoz‐Viana, Claudia Köhler, Lars Hennig
Software Mentions: 4
Published: over 6 years ago
10.3390/microorganisms8101506
Microbiome Management by Biological and Chemical Treatments in Maize Is Linked to Plant HealthCited by: 16
Author(s): Peter Kusstatscher, Wisnu Adi Wicaksono, Dhivya Priya Thenappan, Eveline Adam, Henry Müller, Gabriele Berg
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12864-017-3622-9
RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattleCited by: 73
Author(s): Mohd Shukor Salleh, Gianluca Mazzoni, Johanna Höglund, D.W. Olijhoek, Peter Lund, Peter Løvendahl, Haja N. Kadarmideen
Software Mentions: 4
Published: over 9 years ago
10.3390/microorganisms7120635
Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria SymbiosesCited by: 12
Author(s): Anoop Alex, Agostinho Antunes
Software Mentions: 4
Published: almost 7 years ago
10.1186/s12859-017-1772-z
Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneumCited by: 13
Author(s): Daniel Amsel, Andreas Vilcinskas, André Billion
Software Mentions: 4
Published: about 9 years ago
10.1186/s12864-016-2925-6
Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroiCited by: 74
Author(s): S. Matić, Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Greice Amaral Carneiro, Ilenia Siciliano, Giampiero Valè, M. L. Gullino, D. Spadaro
Software Mentions: 4
Published: about 10 years ago
10.1186/s12864-017-4168-6
TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganismsCited by: 7
Author(s): Daniela Beißer, Nadine Graupner, Lars Großmann, Henning Timm, Jens Boenigk, Sven Rahmann
Software Mentions: 4
Published: almost 9 years ago
10.1371/journal.pone.0143496
Human Breast Milk miRNA, Maternal Probiotic Supplementation and Atopic Dermatitis in OffspringCited by: 56
Author(s): Melanie Rae Simpson, Gaute Brede, Jostein Johansen, Roar Johnsen, Ola Storrø, Pål Sætrom, Torbjørn Øien
Software Mentions: 4
Published: almost 11 years ago
10.3390/microorganisms9051069
Study of the Vaginal Microbiota in Healthy Women of Reproductive AgeCited by: 7
Author(s): Melanie Cristine Alonzo Martínez, Eduardo Cazorla, Esther Cánovas, Juan F. Martínez-Blanch, Empar Chenoll, Eric Climent, Vicente Navarro-López
Software Mentions: 4
Published: over 5 years ago
10.3390/microorganisms9040816
CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial EcosystemsCited by: 8
Author(s): Matthew G. Links, Tim J. Dumonceaux, Erin McCarthy, Sean M. Hemmingsen, Edward Topp, Jennifer Town
Software Mentions: 4
Published: over 5 years ago
10.3390/microorganisms9010157
The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic FungiCited by: 13
Author(s): K. Fliegerová, Sabine Marie Podmirseg, Julia Vinzelj, Diego Grilli, Simona Kvasnová, Dagmar Schierová, Hana Sechovcová, Jakub Mrázek, Giuliana Siddi, Graciela Nora Arenas, Giuseppe Moniello
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-021-07747-3
Downregulated luteolytic pathways in the transcriptome of early pregnancy bovine corpus luteum are mimicked by interferon-tau in vitroCited by: 6
Author(s): Raghavendra Basavaraja, J. N. Drum, Jackson Sapuleni, Lonice Bibi, Gilgi Friedlander, Sai Kumar, Roberto Sartori, Rina Meidan
Software Mentions: 4
Published: over 5 years ago
10.3390/microorganisms9091842
The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’IvoireCited by: 5
Author(s): Sara Laetitia Elphège Gnangui, Romain Kouakou Fossou, Anicet Ebou, Chiguié Estelle Raïssa Amon, Dominique Koua, Claude Ghislaine Kouadjo, Don A. Cowan, Adolphe Zézé
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pmed.1002204
The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program “CASCADE”Cited by: 111
Author(s): Peter Savas, Zhi L. Teo, Christophe Lefèvre, Christoffer Flensburg, Franco Caramia, Kathryn Alsop, Mariam Mansour, Prudence A. Francis, Heather Thorne, Maria João Silva, Nnennaya Kanu, Michelle Dietzen, Andrew Rowan, Maik Kschischo, Stephen B. Fox, David D.L. Bowtell, Sarah-Jane Dawson, Terence P. Speed, Charles Swanton, Sherene Loi
Software Mentions: 4
Published: over 9 years ago