pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-14-586

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions
Cited 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 processes
Cited 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 levels
Cited 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 Technique
Cited 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 inHydraleads to compensatory regulation of neurogenic and neurotransmission genes in epithelial cells
Cited 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 methylation
Cited 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 Interactions
Cited 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 diversity
Cited 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 Chickens
Cited 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 vesicles
Cited 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 System
Cited 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) genes
Cited 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 Structure
Cited 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 populations
Cited 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 Sediments
Cited 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 Bats
Cited 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 Genes
Cited 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 Oman
Cited 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 Tissue
Cited 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 Fungi
Cited 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 Analysis
Cited 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 Carcinoma
Cited 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 microbiome
Cited 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 Irradiation
Cited 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 JQ1
Cited 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 metabolism
Cited 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 Genomics
Cited 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 proteomics
Cited 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 zebrafish
Cited 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 Suppressors
Cited 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 RNAs
Cited 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 levels
Cited 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 mitochondria
Cited 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 velutina
Cited 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 aquaculture
Cited 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 pathogenesis
Cited 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 meningioma
Cited 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 Microorganisms
Cited 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 hybridization
Cited 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 Aspergillus fumigatus to copper and the role of the Cu chaperones
Cited 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-joining
Cited 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-Seq
Cited 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 Fibroblasts
Cited 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-seq
Cited 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 Surgery
Cited 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 Data
Cited 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 Infection
Cited 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 trauma
Cited 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 Spruce
Cited 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 Infection
Cited 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 Stress
Cited 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 signatures
Cited 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 pathway
Cited 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 Mice
Cited 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 myotis
Cited 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 Cancers
Cited 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 leukemia
Cited 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 hotspot
Cited 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 mobilis
Cited 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 infants
Cited 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 dexamethasone
Cited 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 trial
Cited 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 analysis
Cited 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 Methods
Cited 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 cells
Cited 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 analysis
Cited 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 Jelly
Cited 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 (Reinhardtius hippoglossoides) stocks to nurseries by means of genotyping‐by‐sequencing: Sex and time matter
Cited 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 maps
Cited 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 Factor
Cited 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 Perspective
Cited 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 Duplication
Cited 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 viminalis
Cited 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 Variation
Cited 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 cells
Cited 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 Pollution
Cited 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 Croatia
Cited 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 data
Cited 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 Adaptation
Cited 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 development
Cited 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 changes
Cited 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 oncogenesis
Cited 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 bats
Cited 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 tomato
Cited 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 transition
Cited 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 Arabidopsis
Cited 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 Health
Cited 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 cattle
Cited 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 Symbioses
Cited 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 castaneum
Cited 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 fujikuroi
Cited 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 microorganisms
Cited 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 Offspring
Cited 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 Age
Cited 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 Ecosystems
Cited 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 Fungi
Cited 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 vitro
Cited 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’Ivoire
Cited 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

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Papers Mentioning cutadapt 1,562