pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.1186/s12864-016-2776-1

Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates
Cited by: 28
Author(s): Nathalia Flórez-Zapata, M. Humberto Reyes-Valdés, Octavio Martínez
Software Mentions: 4
Published: over 8 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 5 years ago

10.1186/s40168-020-00981-z

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome
Cited by: 17
Author(s): Hannes Petruschke, Christian Schori, Sebastian Canzler, Sarah Riesbeck, Anja Poehlein, Rolf Daniel, Daniel Frei, Tina Segessemann, Johannes Zimmerman, Γεώργιος Μαρίνος, Christoph Kaleta, Nico Jehmlich, Christian H. Ahrens, Martin von Bergen
Software Mentions: 4
Published: over 3 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 6 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: over 3 years ago

10.1186/s12864-021-07699-8

Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome
Cited by: 8
Author(s): Stefania Bertazzoni, Darcy A. B. Jones, H. Phan, Kar‐Chun Tan, James K. Hane
Software Mentions: 4
Published: over 3 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 3 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: over 5 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 3 years ago

10.7150/ijbs.60674

Ailanthus Altissima-derived Ailanthone enhances Gastric Cancer Cell Apoptosis by Inducing the Repression of Base Excision Repair by Downregulating p23 Expression
Cited by: 7
Author(s): Chunming Wang, Hua-Fu Li, Xiaokun Wang, Wu-Guo Li, Shan Qiao, Xing Xiao, Tong Hao, Wei Chen, Yawei Zhang, Haiyong Zhang, Wei Wu, Zhenran Hu, Guochao Zhao, Mingyu Huo, Yulong He, Changhua Zhang
Software Mentions: 4
Published: almost 4 years ago

10.3390/jof7030194

The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense
Cited by: 23
Author(s): Carmen Gómez-Lama Cabanás, Antonio José Fernández-González, Martina Cardoni, Antonio Valverde-Corredor, Javier López-Cepero Borrego, Manuel Fernández‐López, Jesús Mercado‐Blanco
Software Mentions: 4
Published: over 3 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 7 years ago

10.1128/mSystems.00471-20

Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors
Cited by: 14
Author(s): Ezequiel Santillan, Florentin Constancias, Stefan Wuertz
Software Mentions: 4
Published: about 4 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: almost 4 years ago

10.1186/s40168-018-0446-z

Reproducible protocols for metagenomic analysis of human faecal phageomes
Cited by: 127
Author(s): Andrey N. Shkoporov, Feargal J. Ryan, Lorraine A. Draper, Amanda Forde, Stephen R. Stockdale, Karen Daly, Siobhan A. McDonnell, James A. Nolan, Thomas D.S. Sutton, Marion Dalmasso, A. McCann, R. Paul Ross, Colin Hill
Software Mentions: 4
Published: over 6 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 3 years ago

10.1186/s40168-017-0356-5

Indoor microbiota in severely moisture damaged homes and the impact of interventions
Cited by: 38
Author(s): Balamuralikrishna Jayaprakash, Rachel I. Adams, Pirkka V. Kirjavainen, Anne M. Karvonen, Asko Vepsäläinen, Maria Valkonen, Kati Järvi, Michael Sulyok, Juha Pekkanen, Anne Hyvärinen, Martin Täubel
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: over 4 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 4 years ago

10.1186/s12915-020-00797-1

The roles of hybridization and habitat fragmentation in the evolution of Brazil’s enigmatic longwing butterflies, Heliconius nattereri and H. hermathena
Cited by: 14
Author(s): Darli Massardo, Nicholas W. VanKuren, Sumitha Nallu, Renato Rogner Ramos, Pedro G. Ribeiro, Karina Lucas Silva‐Brandão, Marcelo Mendes Brandão, Marília Bruzzi Lion, André Victor Lucci Freitas, Márcio Zikán Cardoso, Marcus R. Kronforst
Software Mentions: 4
Published: over 4 years ago

10.3390/cells8121592

Dietary Immunostimulant CpG Modulates MicroRNA Biomarkers Associated with Immune Responses in Atlantic Salmon (Salmo salar)
Cited by: 22
Author(s): Xi Xue, Nardos Tesfaye Woldemariam, Albert Caballero‐Solares, Navaneethaiyer Umasuthan, Mark D. Fast, Richard G. Taylor, Matthew L. Rise, Rune Andreassen
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSystems.00607-19

Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer
Cited by: 16
Author(s): Lauren M. Seyler, William J. Brazelton, Craig McLean, Lindsay I. Putman, Alex Hyer, M. D. Kubo, Tori M. Hoehler, D. Cardace, M. O. Schrenk
Software Mentions: 4
Published: over 4 years ago

10.1016/j.cmet.2020.09.001

Bone Marrow Mesenchymal Stem Cells Support Acute Myeloid Leukemia Bioenergetics and Enhance Antioxidant Defense and Escape from Chemotherapy
Cited by: 107
Author(s): Dorian Forte, María García-Fernández, Abel Sánchez-Aguilera, Vaia Stavropoulou, Claire Fielding, Daniel Martín-Pérez, Juan Antonio López, Ana S. H. Costa, Laura Tronci, Efterpi Nikitopoulou, M. Barber, Paolo Gallipoli, Ludovica Marando, Carlos L.F. de Castillejo, Alexandar Tzankov, Sabine Dietmann, Michèle Cavo, Lucia Catani, Antonio Curti, Jesús Vázquez, Christian Frezza, Brian J. P. Huntly, Juerg Schwaller, Simón Méndez-Ferrer
Software Mentions: 4
Published: about 4 years ago

10.1128/mSphere.00160-20

An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
Cited by: 43
Author(s): Lamia Wahba, Nikhil Jain, Andrew Fire, Massa J. Shoura, Karen L. Artiles, Matthew J. McCoy, Dae‐Eun Jeong
Software Mentions: 4
Published: over 4 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: over 5 years ago

10.1128/mSphere.00354-20

Light and Primary Production Shape Bacterial Activity and Community Composition of Aerobic Anoxygenic Phototrophic Bacteria in a Microcosm Experiment
Cited by: 14
Author(s): Kasia Piwosz, Ana Vrdoljak, Thijs Frenken, Juan Manuel González‐Olalla, Danijela Šantić, R. Michael L. McKay, Kristian Spilling, Louis Guttman, Petr Znachor, Izabela Mujakić, Lívia Kolesár Fecskeová, Luca Zoccarato, Martina Hanusová, Andrea Pessina, Tom Reich, Hans‐Peter Grossart, Michal Koblížek
Software Mentions: 4
Published: about 4 years ago

10.1186/1471-2164-15-631

Analysis of stranded information using an automated procedure for strand specific RNA sequencing
Cited by: 29
Author(s): Bárður Sigurgeirsson, Olof Emanuelsson, Joakim Lundeberg
Software Mentions: 4
Published: over 10 years ago

10.1038/s41398-017-0050-1

Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study
Cited by: 56
Author(s): Pei‐Fen Kuan, Monika A. Waszczuk, Roman Kotov, Sean Clouston, Xiaohua Yang, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 4
Published: almost 7 years ago

10.1128/mBio.02504-18

The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium
Cited by: 73
Author(s): Alexander J. Westermann, Elisa Venturini, Mikael E. Sellin, Konrad U. Förstner, Wolf‐Dietrich Hardt, Jörg Vogel
Software Mentions: 4
Published: over 5 years ago

10.1016/j.stemcr.2020.05.007

Modeling and Rescue of RP2 Retinitis Pigmentosa Using iPSC-Derived Retinal Organoids
Cited by: 100
Author(s): Amelia Lane, Katarina Jovanović, Ciara Shortall, Daniele Ottaviani, Anna Brugulat Panes, Nele Schwarz, Rosellina Guarascio, Matthew J. Hayes, Arpad Palfi, Naomi Chadderton, G. Jane Farrar, Alison J. Hardcastle, Michael E. Cheetham
Software Mentions: 4
Published: over 4 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 7 years ago

10.1128/mSphere.00451-20

Assessing the Variation within the Oral Microbiome of Healthy Adults
Cited by: 43
Author(s): Jacob T. Nearing, Vanessa DeClercq, Johan Van Limbergen, Morgan G. I. Langille
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-021-85909-9

Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using RAD-Seq
Cited by: 7
Author(s): Maddumage Dona Ginushika Priyadarshani Premarathne, Nami Fukutome, Kazuaki Yamasaki, Fumiyo Hayakawa, Atsushi J. Nagano, Hisataka Mizuno, Nobuo Ibaragi, Yukio Nagano
Software Mentions: 4
Published: over 3 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: about 9 years ago

10.1038/s41598-021-84691-y

Gene expression for secondary metabolite biosynthesis in hop (Humulus lupulus L.) leaf lupulin glands exposed to heat and low-water stress
Cited by: 12
Author(s): Renée L. Eriksen, Lillian K. Padgitt-Cobb, M. Shaun Townsend, Jimmy C. Henning
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-90863-7

Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea
Cited by: 12
Author(s): Danijela Šantić, Kasia Piwosz, Frano Matić, Ana Vrdoljak Tomaš, Jasna Arapov, Jason Dean, Mladen Šolić, Michal Koblížek, Grozdan Kušpilić, Stefanija Šestanović
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-77907-0

Integrated analyses of the microbiological, immunological and ontological transitions in the calf ileum during early life
Cited by: 6
Author(s): Tamsin Lyons, Hanne Jahns, Joseph Brady, Eóin O’Hara, Sinéad M. Waters, David A. Kenny, Evelyn Doyle, Kieran G. Meade
Software Mentions: 4
Published: almost 4 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 3 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 4 years ago

10.1038/s41598-020-77028-8

PRMT1 inhibition induces differentiation of colon cancer cells
Cited by: 19
Author(s): A.N. Plotnikov, Noga Kozer, Galit Cohen, Sílvia Carvalho, Shirly Duberstein, Ofir Almog, Leonardo J. Solmesky, Khriesto A. Shurrush, Ilana Babaev, Benjamin Schwessinger, Shlomit Gilad, Meital Kupervaser, Yishai Levin, Michael Gershovits, Danny Ben-Avraham, Haim Barr
Software Mentions: 4
Published: about 4 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 9 years ago

10.1002/mbo3.1217

Deciphering <i>Trifolium pratense</i> L. holobiont reveals a microbiome resilient to future climate changes
Cited by: 4
Author(s): Sara Fareed Mohamed Wahdan, Benjawan Tanunchai, Yuting Wu, Chakriya Sansupa, Martin Schädler, Turki M. Dawoud, François Buscot, Witoon Purahong
Software Mentions: 4
Published: over 3 years ago

10.1155/2018/1243858

Characterization of Transcription Termination-Associated RNAs: New Insights into their Biogenesis, Tailing, and Expression in Primary Tumors
Cited by: 4
Author(s): Ilaria Laudadio, Sara Formichetti, Silvia Gioiosa, Filippos Klironomos, Nikolaus Rajewsky, Giuseppe Macino, Claudia Carissimi, Valerio Fulci
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-68437-w

Injection of seminal fluid into the hemocoel of honey bee queens (Apis mellifera) can stimulate post-mating changes
Cited by: 9
Author(s): W. Cameron Jasper, Laura M. Brutscher, Christina M. Grozinger, Elina L. Niño
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2020.00133

Comparison of Adult Testis and Ovary MicroRNA Expression Profiles in Reeves’ Pond Turtles (Mauremys reevesii) With Temperature-Dependent Sex Determination
Cited by: 6
Author(s): Lei Xiong, Mengli Yang, Kai Zheng, Ziming Wang, Shengli Gu, Jiucui Tong, Jianjun Li, Nadar Ali Shah, Liuwang Nie
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0201851

Small RNAs detected in exosomes derived from the MH7A synovial fibroblast cell line with TNF-α stimulation
Cited by: 19
Author(s): Yosuke Takamura, Wataru Aoki, Atsushi Satomura, Seiji Shibasaki
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0194023

ER-positive breast cancer cells are poised for RET-mediated endocrine resistance
Cited by: 18
Author(s): Sachi Horibata, Edward J. Rice, Chinatsu Mukai, Brooke A. Marks, Kelly L. Sams, Hui Zheng, Lynne J. Anguish, Scott A. Coonrod, Charles G. Danko
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.625846

Comprehensive Analysis of Differentially Expressed lncRNA, circRNA and mRNA and Their ceRNA Networks in Mice With Severe Acute Pancreatitis
Cited by: 14
Author(s): Bing Wang, Jun Wu, Qilin Huang, Xiaohui Yuan, Yi Yang, Wen Jiang, Yi Wen, Lijun Tang, Haiyan Sun
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2015.00340

Transfection of microRNA Mimics Should Be Used with Caution
Cited by: 124
Author(s): Hyun Yong Jin, Alicia González-Martín, Ana V. Miletic, Maoyi Lai, Sarah Knight, Mohsen Sabouri-Ghomi, Steven R. Head, Matthew S. Macauley, Robert C. Rickert, Changchun Xiao
Software Mentions: 3
Published: almost 9 years ago

10.3389/fgene.2020.00101

Skewed X-Chromosome Inactivation and Compensatory Upregulation of Escape Genes Precludes Major Clinical Symptoms in a Female With a Large Xq Deletion
Cited by: 15
Author(s): Cíntia Barros Santos-Rebouças, Raquel Boy, Evelyn Quintanilha Vianna, Andressa Pereira Gonçalves, Rafael Mina Piergiorge, Bianca Barbosa Abdala, J. M. Santos, Veluma Calassara, Filipe Brum Machado, Enrique Medina‐Acosta, Márcia Mattos Gonçalves Pimentel
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0095633

Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
Cited by: 39
Author(s): Kyriakos Tsangaras, Matthew C. Siracusa, Nikolas Nikolaidis, Yasuko Ishida, Pin Cui, Hanna Vielgrader, Kristofer M. Helgen, Alfred L. Roca, Alex D. Greenwood
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-020-65487-y

Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia
Cited by: 28
Author(s): Melak Weldenegodguad, Kisun Pokharel, Ming Yao, Mervi Honkatukia, Jaana Peippo, Tiina Reilas, Knut Røed, Juha Kantanen
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-52712-6

Whole blood transcriptome analysis in ewes fed with hemp seed supplemented diet
Cited by: 18
Author(s): Marco Iannaccone, Andrea Ianni, Felice Contaldi, Salvatore Esposito, Camillo Martino, Francesca Bennato, Elisabetta De Angelis, Lisa Grotta, Francesco Pomilio, Daniele Giansante, Giuseppe Martino
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-59407-3

MicroRNAs regulate innate immunity against uropathogenic and commensal-like Escherichia coli infections in the surrogate insect model Galleria mellonella
Cited by: 15
Author(s): Krishnendu Mukherjee, Daniel Amsel, Miriam Kalsy, André Billion, Ulrich Dobrindt, Andreas Vilcinskas
Software Mentions: 3
Published: almost 5 years ago

10.3390/metabo11060369

Plant Transcriptome Reprograming and Bacterial Extracellular Metabolites Underlying Tomato Drought Resistance Triggered by a Beneficial Soil Bacteria
Cited by: 17
Author(s): Rafael J. L. Morcillo, Juan Ignacio Vílchez, Song Zhang, Rajesh Kaushal, Danxia He, Hailing Zi, Renyi Liu, Karsten Niehaus, Avtar K. Handa, Huiming Zhang
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-42207-9

Parallel sequencing of porA reveals a complex pattern of Campylobacter genotypes that differs between broiler and broiler breeder chickens
Cited by: 12
Author(s): Frances M. Colles, Stephen G. Preston, Kenneth Klingenberg Barfod, Patrik G. Flammer, Maiden Mcj., Adrian L. Smith
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0007811

Comparative analysis of small RNAs released by the filarial nematode Litomosoides sigmodontis in vitro and in vivo
Cited by: 19
Author(s): Juan F. Quintana, Sujai Kumar, Alasdair Ivens, Wang Ngai Chow, Anna M. Hoy, Alison Fulton, Paul Dickinson, Coralie Martin, Matthew D. Taylor, Simon A. Babayan, Amy H. Buck
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pntd.0009297

Expression profiling of Echinococcus multilocularis miRNAs throughout metacestode development in vitro
Cited by: 7
Author(s): Natalia Macchiaroli, Matías Preza, Moira Pérez, Laura Kamenetzky, Marcela Alejandra Cucher, Uriel Koziol, Estela Castillo, Matthew Berriman, Klaus Brehm, Mara Cecília Rosenzvit
Software Mentions: 3
Published: over 3 years ago

10.18632/aging.101446

Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 (IRS1) in mice
Cited by: 7
Author(s): Melissa M. Page, Eugene F. Schuster, Manikhandan Mudaliar, Paweł Herzyk, Dominic J. Withers, Colin Selman
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.00321

Identification and Integrated Analysis of MicroRNA and mRNA Expression Profiles During Agonistic Behavior in Chinese Mitten Crab (Eriocheir sinensis) Using a Deep Sequencing Approach
Cited by: 4
Author(s): Yangyang Pang, Long He, Yameng Song, Xiaozhe Song, Jiahuan Lv, Yongxu Cheng, Xiaozhen Yang
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-63263-6

Circulating MicroRNA Profiling in Non-ST Elevated Coronary Artery Syndrome Highlights Genomic Associations with Serial Platelet Reactivity Measurements
Cited by: 14
Author(s): Kristian C. Becker, Lydia Coulter Kwee, Megan L. Neely, Elizabeth Grass, Joseph A. Jakubowski, Keith Fox, Harvey D. White, Simon Gregory, Paul A. Gurbel, Leonardo de Pinto Carvalho, Richard C. Becker, E. Magnus Ohman, Matthew T. Roe, Svati H. Shah, Mark Y. Chan
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-71913-y

Morphological and physiological factors contributing to early vigor in the elite rice cultivar 9,311
Cited by: 9
Author(s): Zai Shi, Tiangen Chang, Fa‐Ming Chen, Haichao Zhao, Qingfeng Song, Mengyao Wang, Yanjie Wang, Zhiwei Zhou, Chongrong Wang, Shungui Zhou, Baoshan Wang, Genyun Chen, Xin‐Guang Zhu
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-36866-3

Marine biogenics in sea spray aerosols interact with the mTOR signaling pathway
Cited by: 12
Author(s): Jana Asselman, Emmanuel Van Acker, Maarten De Rijcke, Laurentijn Tilleman, Filip Van Nieuwerburgh, Jan Mees, Karel A.C. De Schamphelaere, Colin R. Janssen
Software Mentions: 3
Published: almost 6 years ago

10.26508/lsa.202000659

Dynamic changes in RNA–protein interactions and RNA secondary structure in mammalian erythropoiesis
Cited by: 2
Author(s): Mengge Shan, Xinjun Ji, Kevin A. Janssen, Ian M. Silverman, Jesse Humenik, Ben Garcia, Stephen A. Liebhaber, Brian D. Gregory
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-38932-w

Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants
Cited by: 8
Author(s): Kun Yang, Xiaopeng Wen, Suresh B. Mudunuri, G. P. S. Varma, Gaurav Sablok
Software Mentions: 3
Published: almost 6 years ago

10.3389/fendo.2018.00158

Integrated Characterization of MicroRNA and mRNA Transcriptome in Papillary Thyroid Carcinoma
Cited by: 13
Author(s): Azliana Mohamad Yusof, A. Rahman A. Jamal, Rohaizak Muhammad, Shahrun Niza Abdullah Suhaimi, Isa Mohamed Rose, Sazuita Saidin, Nurul Syakima Ab Mutalib
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-36342-y

Gene expression profiles alteration after infection of virus, bacteria, and parasite in the Olive flounder (Paralichthys olivaceus)
Cited by: 8
Author(s): Gyu-Hwi Nam, Anshuman Mishra, Jeong‐An Gim, Hee-Eun Lee, Ara Jo, Dahye Yoon, Ahran Kim, Woo Jin Kim, Kung Ahn, Do-Hyung Kim, Suhkmann Kim, Hee‐Jae Cha, Yung Hyun Choi, Chan-Il Park, Heui‐Soo Kim
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-39880-1

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-33627-0

Blood immune transcriptome analysis of artificially fed dairy calves and naturally suckled beef calves from birth to 7 days of age
Cited by: 8
Author(s): Carla Surlis, Bernadette Earley, M. McGee, Kate Keogh, Paul Cormican, Gordon Blackshields, K. Tiernan, Amanda Dunn, Steven Morrison, A. Argüello, Sinéad M. Waters
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-33964-0

Amyotrophic Lateral Sclerosis associated FUS mutation shortens mitochondria and induces neurotoxicity
Cited by: 54
Author(s): Tadashi Nakaya, Manolis Maragkakis
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pgen.1009761

The CovR regulatory network drives the evolution of Group B Streptococcus virulence
Cited by: 11
Author(s): Maria-Vittoria Mazzuoli, Maëlle Daunesse, Hugo Varet, Isabelle Rosinski‐Chupin, Rachel Legendre, Odile Sismeiro, Myriam Gominet, P.A. Kaminski, Philippe Glaser, Claudia Chica, Patrick Trieu-Cuot, Arnaud Firon
Software Mentions: 3
Published: about 3 years ago

10.3389/fcell.2021.697832

A Novel Mechanism of Cannabidiol in Suppressing Hepatocellular Carcinoma by Inducing GSDME Dependent Pyroptosis
Cited by: 36
Author(s): Fugen Shangguan, Hongfei Zhou, Nengfang Ma, Shanshan Wu, Huimin Huang, Guihua Jin, Shijia Wu, Weilong Hong, Weiwei Zhuang, Hongping Xia, Linhua Lan
Software Mentions: 3
Published: over 3 years ago

10.3390/life11060558

The Effect of a Total Fishmeal Replacement by Arthrospira platensis on the Microbiome of African Catfish (Clarias gariepinus)
Cited by: 6
Author(s): Simon Rosenau, Elisa Oertel, Alexander C. Mott, Jens Tetens
Software Mentions: 3
Published: over 3 years ago

10.3389/fcell.2020.00842

Epitranscriptomic N4-Acetylcytidine Profiling in CD4+ T Cells of Systemic Lupus Erythematosus
Cited by: 18
Author(s): Gangqiang Guo, Xinyu Shi, Huijing Wang, Lele Ye, Xinya Tong, Kejing Yan, Ning Ding, Chaosheng Chen, Huidi Zhang, Xiangyang Xue
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-26453-x

Blood lipid-related low-frequency variants in LDLR and PCSK9 are associated with onset age and risk of myocardial infarction in Japanese
Cited by: 14
Author(s): Tomoyuki Tajima, Hiroyuki Morita, Kei Ito, Tsutomu Yamazaki, Michiaki Kubo, Issei Komuro, Yukihide Momozawa
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1008582

Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality
Cited by: 32
Author(s): Katherine Lagree, Carol A. Woolford, Manning Y. Huang, Gemma E. May, C. Joel McManus, Norma V. Solis, Scott G. Filler, Aaron P. Mitchell
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-016-2704-4

Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Cited by: 30
Author(s): Nikol Voutsina, Adrienne Payne, Robert D. Hancock, Graham J. J. Clarkson, Steve D. Rothwell, Mark A. Chapman, Gail Taylor
Software Mentions: 3
Published: over 8 years ago

10.1038/s41375-020-0762-8

Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing
Cited by: 38
Author(s): Wibowo Arindrarto, Daniel Borràs, Ruben A.L. De Groen, Redmar R van den Berg, Irene J. Locher, Saskia A.M.E. van Diessen, Rosalie van der Holst, Edith D. van der Meijden, M. Willy Honders, Rick H. de Leeuw, Wina Verlaat, Inge Jedema, Wilma G. M. Kroes, Jeroen Knijnenburg, Tom van Wezel, Joost S.P. Vermaat, Peter J.M. Valk, Bart Janssen, Peter de Knijff, Cornelis A.M. van Bergen, Erik B. van den Akker, Peter A C ‘t Hoen, Szymon M. Kiełbasa, Jeroen F. J. Laros, Marieke Griffioen, Hendrik Veelken
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1007309

miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs
Cited by: 8
Author(s): Jimmy D. Bell, Maureen K. Larson, Michelle Anne Kutzler, Massimo Bionaz, Christiane V. Löhr, David A. Hendrix
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-015-2111-2

Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome
Cited by: 15
Author(s): Christelle Robert, Ronan Kapétanovic, Dario Beraldi, Michael Watson, Alan Archibald, David Hume
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pbio.3001121

CD74 is a regulator of hematopoietic stem cell maintenance
Cited by: 13
Author(s): Shirly Becker-Herman, Milena Rozenberg, Carmit Hillel-Karniel, Naama Gil-Yarom, Matthias P. Kramer, Avital Barak, Lital Sever, Keren David, Lihi Radomir, Hadas Lewinsky, Michal Levi, Gilgi Friedlander, Richard Bucala, Amnon Peled, Idit Shachar
Software Mentions: 3
Published: over 3 years ago

10.1002/cam4.3006

Downregulated hsa_circ_0077837 and hsa_circ_0004826, facilitate bladder cancer progression and predict poor prognosis for bladder cancer patients
Cited by: 31
Author(s): Chong Shen, Zhouliang Wu, Yujie Wang, Shen Gao, La Da, Linguo Xie, Yunkai Qie, Dan Tian, Hailong Hu
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2021.663130

Androgen Activity Is Associated With PD-L1 Downregulation in Thyroid Cancer
Cited by: 10
Author(s): Timmy O’Connell, Sina Dadafarin, Melanie Jones, Tomás Rodríguez, Anvita Gupta, Edward J. Shin, Augustine Moscatello, Codrin Iacob, Humayun Islam, Raj K. Tiwari, Jan Geliebter
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-39608-1

Field transcriptome revealed a novel relationship between nitrate transport and flowering in Japanese beech
Cited by: 16
Author(s): Akiko Satake, Kazutaka Kawatsu, Kenjiro Teshima, Daisuke Kabeya, Qingmin Han
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-021-01784-4

Re-expression of miR-200s in claudin‐low mammary tumor cells alters cell shape and reduces proliferation and invasion potentially through modulating other miRNAs and SUZ12 regulated genes
Cited by: 8
Author(s): Kaitlyn E. Simpson, Garret Conquer-Van Heumen, Katrina L. Watson, Majesta J Roth, Courtney J. Martin, Roger A. Moorehead
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-14301-3

Exosomal microRNA signatures in multiple sclerosis reflect disease status
Cited by: 178
Author(s): Saeideh Ebrahimkhani, Fatemeh Vafaee, Paul E. Young, Suzy S J Hur, Simon Hawke, Emma Devenney, Heidi Beadnall, Michael Barnett, Catherine M. Suter, Michael E. Buckland
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-015-2252-3

Construction of relatedness matrices using genotyping-by-sequencing data
Cited by: 104
Author(s): K. G. Dodds, John C. McEwan, Rüdiger Bräuning, R. M. Anderson, Tracey C. van Stijn, Theódór Kristjánsson, Shannon Clarke
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.ccell.2019.05.015

RAC1P29S Induces a Mesenchymal Phenotypic Switch via Serum Response Factor to Promote Melanoma Development and Therapy Resistance
Cited by: 86
Author(s): Daniël A. Lionarons, David C. Hancock, Sareena Rana, Philip East, Christopher Moore, Miguel Murillo, Joana Carvalho, Bradley Spencer–Dene, Eleanor Herbert, Gordon Stamp, Djamil Damry, Dinis Pedro Calado, Ian Rosewell, Ralph Fritsch, Richard R. Neubig, Míriam Molina‐Arcas, Julian Downward
Software Mentions: 3
Published: over 5 years ago

10.3389/fbioe.2020.603145

No Tangible Effects of Field-Grown Cisgenic Potatoes on Soil Microbial Communities
Cited by: 9
Author(s): Sascha Krause, Astrid Näther, Vilma Ortiz Cortes, Ewen Mullins, G.J.T. Kessel, L.A.P. Lotz, Christoph C. Tebbe
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pbio.3000739

Increased prostaglandin-D2 in male STAT3-deficient hearts shifts cardiac progenitor cells from endothelial to white adipocyte differentiation
Cited by: 3
Author(s): Elisabeth Stelling, Melanie Ricke‐Hoch, Sergej Erschow, Steve Hoffmann, Anke Bergmann, Maren Heimerl, Stefan Pietzsch, Karin Battmer, Alexandra Haase, Britta Stapel, Michaela Scherr, Jean‐Luc Balligand, Ofer Binah, Denise Hilfiker‐Kleiner
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-16193-9

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens
Cited by: 66
Author(s): Philipp N. Spahn, Tyler Bath, Ryan J. Weiss, Jihoon Kim, Jeffrey D. Esko, Nathan E. Lewis, Olivier Harismendy
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pbio.3000689

Telomeric TART elements target the piRNA machinery in Drosophila
Cited by: 7
Author(s): Chris Ellison, Meenakshi S. Kagda, Weihuan Cao
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-019-52444-7

A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat
Cited by: 27
Author(s): Darcy A. B. Jones, Evan John, Kasia Rybak, H. Phan, Karam B. Singh, Shao-Yu Lin, Peter S. Solomon, Richard P. Oliver, Kar‐Chun Tan
Software Mentions: 3
Published: about 5 years ago

10.1038/srep28984

An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis
Cited by: 37
Author(s): Niels Willemse, Kate J. Howell, Lucy A. Weinert, Annet Heuvelink, Yvonne Pannekoek, Jaap A. Wagenaar, Hilde E. Smith, Arie van der Ende, Constance Schultsz
Software Mentions: 3
Published: over 8 years ago

10.1038/srep35436

Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping
Cited by: 34
Author(s): Ranjith Rajendran, Ali May, Leighann Sherry, Ryan Kean, Craig Williams, Brian Jones, Karl Burgess, Jaap Heringa, Sanne Abeln, Bernd W. Brandt, Carol A. Munro, Gordon Ramage
Software Mentions: 3
Published: about 8 years ago

10.3390/plants9010060

Analysis of Small RNAs of Barley Genotypes Associated with Resistance to Barley Yellow Dwarf Virus
Cited by: 8
Author(s): Jana Jarošová, Kundan Singh, J. Chrpová, Jiban Kumar Kundu
Software Mentions: 3
Published: almost 5 years ago

10.3390/plants9091080

Transcriptome-Wide N6-Methyladenosine (m6A) Methylome Profiling of Heat Stress in Pak-choi (Brassica rapa ssp. chinensis)
Cited by: 30
Author(s): Gaofeng Liu, Jin Wang, Xilin Hou
Software Mentions: 3
Published: over 4 years ago

10.18632/aging.101536

A Drosophila model of cigarette smoke induced COPD identifies Nrf2 signaling as an expedient target for intervention
Cited by: 21
Author(s): R. Prange, Marcus Thiedmann, Anita Bhandari, Neha Mishra, Anupam Sinha, Robert Häsler, Philip Rosenstiel, Karin Uliczka, Christina Wagner, Ali Önder Yildirim, Christine Fink, Thomas Roeder
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0211978

Testing of library preparation methods for transcriptome sequencing of real life glioblastoma and brain tissue specimens: A comparative study with special focus on long non-coding RNAs
Cited by: 7
Author(s): Marek Večeřa, Jiří Šána, Jan Oppelt, Boris Tichý, Alena Kopková, Radim Lipina, Martin Smrčka, Radim Jančálek, Markéta Hermanová, Leoš Křen, Ondřej Slabý
Software Mentions: 3
Published: almost 6 years ago

10.3390/plants8020047

Intrusive Growth of Phloem Fibers in Flax Stem: Integrated Analysis of miRNA and mRNA Expression Profiles
Cited by: 16
Author(s): Oleg Gorshkov, Tatyana Chernova, Natalia Mokshina, Natalia Gogoleva, Dmitry Suslov, А.А. Ткаченко, Т. А. Горшкова
Software Mentions: 3
Published: almost 6 years ago

Projects: pypi: cutadapt

Papers Mentioning cutadapt 1,562