pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.3389/fphar.2020.00604

Distinct Responses of Gut Microbiota to Jian-Pi-Yi-Shen Decoction Are Associated With Improved Clinical Outcomes in 5/6 Nephrectomized Rats
Cited by: 14
Author(s): Lin Zheng, Shuo Chen, Fochang Wang, Shiying Huang, Xinhui Liu, Xiaotao Yang, Haokui Zhou, Guoping Zhao, Mingjing Luo, Shunmin Li, Jianping Chen
Software Mentions: 4
Published: over 4 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: over 3 years ago

10.3389/fonc.2019.00079

Time to Treatment Prediction in Chronic Lymphocytic Leukemia Based on New Transcriptional Patterns
Cited by: 8
Author(s): Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, Natalia Alonso Vence, Ángeles Bendaña López, José Ángel Díaz Arias, Nicolas Varela, Marta Sonia González Pérez, Manuel Pérez‐Encinas, José Luis Bello López
Software Mentions: 4
Published: almost 6 years ago

10.3389/fonc.2021.653902

Fucoidan Inhibits the Progression of Hepatocellular Carcinoma via Causing lncRNA LINC00261 Overexpression
Cited by: 10
Author(s): Danhui Ma, Jiayi Wei, Sinuo Chen, Heming Wang, Ning Lv, Shihua Luo, Chieh-Lun Liu, Guangqi Song, Qunyan Yao
Software Mentions: 4
Published: over 3 years ago

10.3389/fphys.2020.588313

High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress
Cited by: 21
Author(s): Heather Ikert, Michael Lynch, Andrew C. Doxey, John P. Giesy, Mark R. Servos, Barbara A. Katzenback, Paul M. Craig
Software Mentions: 4
Published: almost 4 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 5 years ago

10.1080/21505594.2021.1958057

Transcriptional response of <i>Aspergillus fumigatus</i> 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 3 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

10.3389/fonc.2020.556497

Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma
Cited by: 19
Author(s): Xing Niu, Jun Xu, Jinwen Liu, Lijie Chen, Xue Qin, Ming Zhong
Software Mentions: 4
Published: about 4 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: about 8 years ago

10.1016/j.isci.2021.102783

AMPK activation reverts mouse epiblast stem cells to naive state
Cited by: 4
Author(s): Yajing Liu, Junko Yamane, Akito Tanaka, Wataru Fujibuchi, Jun Yamashita
Software Mentions: 4
Published: over 3 years ago

10.1186/s12974-018-1170-0

Novel insights into neuroinflammation: bacterial lipopolysaccharide, tumor necrosis factor α, and Ureaplasma species differentially modulate atypical chemokine receptor 3 responses in human brain microvascular endothelial cells
Cited by: 15
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Mathias Buttmann, Kirsten Glaser
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21238898

MicroRNA Profiling in Oesophageal Adenocarcinoma Cell Lines and Patient Serum Samples Reveals a Role for miR-451a in Radiation Resistance
Cited by: 8
Author(s): Frederike Butz, Ann-Kathrin Eichelmann, George C. Mayne, Tingting Wang, Isabell Bastian, Karen Chiam, Shashikanth Marri, Pamela J. Sykes, Bas P. L. Wijnhoven, Eelke Toxopeus, Michael Michael, Christos S. Karapetis, Richard Hummel, David I. Watson, Damian J. Hussey
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12974-019-1413-8

More than just inflammation: Ureaplasma species induce apoptosis in human brain microvascular endothelial cells
Cited by: 18
Author(s): Christine Silwedel, Axel Haarmann, Markus Fehrholz, Heike Claus, Christian P. Speer, Kirsten Glaser
Software Mentions: 4
Published: almost 6 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: about 6 years ago

10.3390/ijms21093262

Whole-Genome Deep Sequencing Reveals Host-Driven in-planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations
Cited by: 5
Author(s): Parichate Tangkanchanapas, Annelies Haegeman, Tom Ruttink, Monica Höfte, Kris De Jonghe
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2021.666936

Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction
Cited by: 5
Author(s): Najoua Mghazli, Laila Sbabou, Rachid Hakkou, Ahmed Ouhammou, Mariam El Adnani, Odile Bruneel
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms21124453

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Cited by: 7
Author(s): Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan‐Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Software Mentions: 4
Published: over 4 years ago

10.3389/fpls.2021.643137

Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs
Cited by: 4
Author(s): А. В. Щенникова, Alexey V. Beletsky, M. A. Filyushin, М. А. Слугина, Eugeny V. Gruzdev, Andrey V. Mardanov, Е. З. Кочиева, Н. В. Равин
Software Mentions: 4
Published: over 3 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: about 8 years ago

10.3390/ijms21062079

Whole-Genome Uterine Artery Transcriptome Profiling and Alternative Splicing Analysis in Rat Pregnancy
Cited by: 4
Author(s): Kathirvel Gopalakrishnan, Sathish Kumar
Software Mentions: 4
Published: over 4 years ago

10.3390/ijms21186946

Proteomic and Transcriptomic Patterns during Lipid Remodeling in Nannochloropsis gaditana
Cited by: 13
Author(s): Chris J. Hulatt, Irina Smolina, Adam Dowle, Martina Kopp, Ghana Kalerammana Vasanth, Galice Hoarau, René H. Wijffels, Viswanath Kiron
Software Mentions: 4
Published: about 4 years ago

10.1080/20002297.2021.1946316

Microbial characteristics across different tongue coating types in a healthy population
Cited by: 5
Author(s): Hairong Chen, Qingwei Li, Min Li, Sheng Liu, Chensi Yao, Zixiong Wang, Zhixin Zhao, Ping Liu, Fan Yang, Xinjian Li, Jun Wang, Yi-Xin Zeng, Xiaolin Tong
Software Mentions: 4
Published: almost 4 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: over 3 years ago

10.7554/eLife.63545

Mutations in SKI in Shprintzen–Goldberg syndrome lead to attenuated TGF-β responses through SKI stabilization
Cited by: 20
Author(s): Ilaria Gori, Roger George, A. Purkiss, Stephanie Strohbuecker, Rebecca A. Randall, R.W. Ogrodowicz, Virginie Carmignac, Laurence Faivre, Dhira Joshi, Svend Kjær, Caroline S. Hill
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms19092500

Co-Expression Network Analysis Identifies miRNA–mRNA Networks Potentially Regulating Milk Traits and Blood Metabolites
Cited by: 12
Author(s): Adolf A. Ammah, Duy Ngoc, Nathalie Bissonnette, Nicolas Gévry, Eveline M. Ibeagha‐Awemu
Software Mentions: 4
Published: about 6 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

10.1371/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: almost 5 years ago

10.7554/eLife.50530

Viral miRNA adaptor differentially recruits miRNAs to target mRNAs through alternative base-pairing
Cited by: 5
Author(s): Carlos Gorbea, Tim Mosbruger, David A. Nix, Demián Cazalla
Software Mentions: 4
Published: about 5 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 5 years ago

10.3390/ijms20143583

Ureaplasma Species Modulate Cytokine and Chemokine Responses in Human Brain Microvascular Endothelial Cells
Cited by: 6
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Nicolas Schlegel, Kirsten Glaser
Software Mentions: 4
Published: over 5 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 6 years ago

10.3389/fmicb.2016.00603

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity
Cited by: 22
Author(s): Beverly E. Flood, Palmer Fliss, Daniel S. Jones, Gregory J. Dick, Sunit Jain, Anne‐Kristin Kaster, Matthias Winkel, Marc Mußmann, Jake V. Bailey
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.41337

Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni
Cited by: 83
Author(s): Wannaporn Ittiprasert, Victoria H. Mann, Shannon E. Karinshak, Avril Coghlan, Gabriel Rinaldi, Geetha Sankaranarayanan, Apisit Chaidee, Toshihiko Tanno, Chutima Kumkhaek, Pannathee Prangtaworn, Margaret M. Mentink–Kane, Christina J Cochran, Patrick Driguez, Nancy Holroyd, Alan S. Tracey, Rutchannee Rodpai, Bart Everts, Cornelis H. Hokke, Karl F. Hoffmann, Matthew Berriman, Paul J. Brindley
Software Mentions: 4
Published: almost 6 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 3 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 7 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: over 8 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

10.1093/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 3 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

10.3389/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 5 years ago

10.7554/eLife.38014

Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells
Cited by: 52
Author(s): Jacob W. Freimer, TJ Hu, Robert Blelloch
Software Mentions: 4
Published: over 6 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 7 years ago

10.7554/eLife.28625

The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis
Cited by: 30
Author(s): Sarah N. Deffit, Brian A. Yee, Aidan C. Manning, Suba Rajendren, Pranathi Vadlamani, Emily C. Wheeler, Alain Domissy, Michael C. Washburn, G Yeo, Heather A. Hundley
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms20236040

Whole Genome Expression Analyses of miRNAs and mRNAs Suggest the Involvement of miR-320a and miR-155-3p and their Targeted Genes in Lithium Response in Bipolar Disorder
Cited by: 27
Author(s): Claudia Pisanu, Eleni Merkouri Papadima, Carla Melis, Donatella Congiu, Annalisa Loizedda, Nicola Orrù, Stefano Calza, Sandro Orrù, Carlo Carcassi, Giovanni Severino, Raffaella Ardau, Caterina Chillotti, Maria Del Zompo, Alessio Squassina
Software Mentions: 4
Published: almost 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: over 4 years ago

10.7554/eLife.20983

A molecular portrait of maternal sepsis from Byzantine Troy
Cited by: 32
Author(s): Alison Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob Enk, G. Brian Golding, John Southon, Melanie Kuch, Ana T. Duggan, William Aylward, Shea N. Gardner, Jonathan Allen, Andrew King, Gerard D. Wright, Makoto Kuroda, Kengo Kato, Derek E. G. Briggs, Gino Fornaciari, Edward C. Holmes, Hendrik N. Poinar, Caitlin S. Pepperell
Software Mentions: 4
Published: almost 8 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

10.18632/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 3 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

10.3389/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: almost 8 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 8 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 3 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: about 4 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 7 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 5 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: over 7 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: over 8 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

10.1186/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: about 7 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

10.7554/eLife.67577

Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila
Cited by: 57
Author(s): Heather E. Machado, Alan O. Bergland, Ryan W. Taylor, Susanne Tilk, Emily L. Behrman, Kelly A. Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Bernard Kim, Iryna Kozeretska, Brian P. Lazzaro, Thomas J. S. Merritt, John E. Pool, Katherine R. O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul S. Schmidt, Dmitri A. Petrov
Software Mentions: 4
Published: over 3 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 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

10.3390/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 3 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

10.3390/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: almost 4 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 3 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 3 years ago

10.1186/s12864-019-5752-8

New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes
Cited by: 25
Author(s): Nikita I. Ershov, В. А. Мордвинов, Egor Prokhortchouk, Maria Y. Pakharukova, Konstantin Gunbin, Kirill Ustyantsev, Mikhail A. Genaev, А. Г. Блинов, Alexander Mazur, Eugenia Boulygina, Svetlana Tsygankova, Ekaterina Khrameeva, Nikolay Chekanov, Guangyi Fan, An Xiao, He Zhang, Xun Xu, Huanming Yang, Victor Solovyev, Simon Ming‐Yuen Lee, Xin Liu, D. A. Afonnikov, K. G. Skryabin
Software Mentions: 4
Published: over 5 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

10.3389/fmicb.2020.01012

The Gene Catalog and Comparative Analysis of Gut Microbiome of Big Cats Provide New Insights on Panthera Species
Cited by: 7
Author(s): Parul Mittal, Rituja Saxena, Atul Gupta, Shruti Mahajan, Vineet K. Sharma
Software Mentions: 4
Published: over 4 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: over 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: about 7 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: over 4 years ago

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

10.1186/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

10.3390/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: 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 3 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: over 5 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

10.1186/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

10.1186/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

10.1186/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

10.1186/s40303-016-0017-9

αT-catenin in restricted brain cell types and its potential connection to autism
Cited by: 20
Author(s): Stephen Sai Folmsbee, Douglas R. Wilcox, Koen Tyberghein, Pieter De Bleser, Warren G. Tourtellotte, Jolanda van Hengel, Frans van Roy, Cara J. Gottardi
Software Mentions: 4
Published: over 8 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

10.1186/s40168-018-0568-3

Fecal source identification using random forest
Cited by: 85
Author(s): Adélaïde Roguet, A. Murat Eren, Ryan J. Newton, Sandra L. McLellan
Software Mentions: 4
Published: about 6 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 4 years ago

10.3389/fpls.2021.653183

Transcriptome Analysis of Tetraploid and Octoploid Common Reed (Phragmites australis)
Cited by: 5
Author(s): Cui Wang, Tong Wang, Meiqi Yin, Franziska Eller, Lele Liu, Hans Brix, Weihua Guo
Software Mentions: 4
Published: over 3 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 5 years ago

10.3390/cancers13184518

The Tumor Microenvironment-Dependent Transcription Factors AHR and HIF-1α Are Dispensable for Leukemogenesis in the Eµ-TCL1 Mouse Model of Chronic Lymphocytic Leukemia
Cited by: 3
Author(s): Susanne Gonder, Anne Largeot, Ernesto Gargiulo, Sandrine Pierson, Iria Fernandez Botana, Giulia Pagano, Jérôme Paggetti, Etienne Moussay
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0236540

Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes
Cited by: 38
Author(s): Beverly McClenaghan, Nicole A Fahner, David Côté, Julek Chawarski, Avery McCarthy, Hoda Rajabi, Gregory A. C. Singer, Mehrdad Hajibabaei
Software Mentions: 4
Published: about 4 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

10.3389/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

10.7554/eLife.65760

Morphological and genomic shifts in mole-rat ‘queens’ increase fecundity but reduce skeletal integrity
Cited by: 8
Author(s): Rachel A Johnston, Philippe Vullioud, Jack Thorley, Henry Kirveslahti, Leyao Shen, Sayan Mukherjee, Courtney M. Karner, Tim Clutton‐Brock, Jenny Tung
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-018-5016-z

Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation
Cited by: 49
Author(s): Jing Wang, Yue Zhao, Xiaofan Zhou, Scott W. Hiebert, Qi Liu, Yu Shyr
Software Mentions: 4
Published: about 6 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: almost 5 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 5 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: about 6 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

Projects: pypi: cutadapt

Papers Mentioning cutadapt 1,562