Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: cutadapt
https://packages.ecosyste.ms/registries/pypi.org/packages/cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
63 versions
Latest release: about 1 year ago
14 dependent packages
40,808 downloads last month
Papers Mentioning cutadapt 1,562
10.1093/molbev/msab061
The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in <i>Drosophila</i>Cited by: 11
Author(s): Tadeusz J. Kawecki, Berra Erkoşar, Cindy Dupuis, Brian Hollis, R. Craig Stillwell, Martin Kapun
Software Mentions: 3
Published: over 3 years ago
10.7554/eLife.20062
The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestionCited by: 122
Author(s): Damian Kao, Alvina G. Lai, Evangelia Stamataki, Silvana Rošić, Νικόλαος Κωνσταντινίδης, Erin Jarvis, Alessia Di Donfrancesco, Natalia Pouchkina-Stancheva, Marie Sémon, Marco Grillo, Heather S. Bruce, Suyash Kumar, Igor Siwanowicz, Andy Le, Andrew Lemire, Michael B. Eisen, Cassandra G. Extavour, William E. Browne, Carsten Wolff, Michalis Averof, Nipam H. Patel, Peter Sarkies, Anastasios Pavlopoulos, A. Aziz Aboobaker
Software Mentions: 3
Published: about 8 years ago
10.1186/s12870-014-0307-2
RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petuniasCited by: 39
Author(s): Shaun R. Broderick, Saranga Wijeratne, Asela J Wijeratn, Laura J. Chapin, Tea Meulia, Michelle L. Jones
Software Mentions: 3
Published: about 10 years ago
10.1371/journal.pgen.1009761
The CovR regulatory network drives the evolution of Group B Streptococcus virulenceCited 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
10.1093/dnares/dsaa005
Feeding exogenous dsRNA interferes with endogenous sRNA accumulation in <i>Paramecium</i>Cited by: 3
Author(s): Sivarajan Karunanithi, Vidya Oruganti, Raphaël de Wijn, Franziska Drews, Miriam Cheaib, Karl Nordström, Martín Simón, Marcel H. Schulz
Software Mentions: 3
Published: almost 5 years ago
10.1038/sdata.2017.67
Single-cell transcriptome of early embryos and cultured embryonic stem cells of cynomolgus monkeysCited by: 40
Author(s): Tomonori Nakamura, Yukihiro Yabuta, Ikuhiro Okamoto, Kotaro Sasaki, Chizuru Iwatani, Hideaki Tsuchiya, Mitinori Saitou
Software Mentions: 3
Published: over 7 years ago
10.1186/s13229-019-0285-1
RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulationCited by: 13
Author(s): Ayden Saffari, Matt Arno, Eric Nasser, Angelica Ronald, Chloe Wong, Leonard C Schalkwyk, Jonathan Mill, Frank Dudbridge, Emma L. Meaburn
Software Mentions: 3
Published: about 5 years ago
10.1186/s12915-016-0284-z
On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1Cited by: 34
Author(s): Feifei Xu, Jon Jerlström-Hultqvist, Martin Kolísko, Alastair G. B. Simpson, Andrew J. Roger, Staffan G. Svärd, Jan O. Andersson
Software Mentions: 3
Published: over 8 years ago
10.3390/microorganisms9091843
Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil MicrobiomeCited by: 9
Author(s): Kishan Mahmud, Kendall Lee, Nicholas S. Hill, Anaas Mergoum, Ali Missaoui
Software Mentions: 3
Published: about 3 years ago
10.1186/s12864-017-4141-4
Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodesCited by: 3
Author(s): Billy T. Lau, Hanlee P. Ji
Software Mentions: 3
Published: about 7 years ago
10.3390/microorganisms8060915
Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellumCited by: 12
Author(s): Regina Rettenmaier, Martina Schneider, Bernhard Munk, Michael Lebuhn, Sebastian Jünemann, Alexander Sczyrba, Irena Maus, Vladimir V. Zverlov, Wolfgang Liebl
Software Mentions: 3
Published: over 4 years ago
10.7554/eLife.52981
Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndromeCited by: 37
Author(s): Laura A. Lavery, Kerstin Ure, Ying-Wooi Wan, Chongyuan Luo, Alexander J Trostle, Wei Wang, Haijing Jin, José López López, Jacinta Lucero, Mark A. Durham, Rosa Castanon, Joseph R. Nery, Zhandong Liu, Margaret A. Goodell, Joseph R. Ecker, M. Margarita Behrens, Huda Y Zoghbi
Software Mentions: 3
Published: over 4 years ago
10.1128/mSphere.00186-20
Globally Abundant “ <i>Candidatus</i> Udaeobacter” Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas ScavengingCited by: 25
Author(s): Inka M. Willms, Anina Y. Rudolph, Isabell Göschel, Simon Henning Bolz, Dominik Schneider, Caterina Penone, Anja Poehlein, Ingo Schöning, Heiko Nacke
Software Mentions: 3
Published: about 4 years ago
10.3390/ijms20194742
Causes and Consequences of A Glutamine Induced Normoxic HIF1 Activity for the Tumor MetabolismCited by: 17
Author(s): Matthias Kappler, Ulrike Pabst, Claus Weinholdt, Helge Täubert, Swetlana Rot, Tom Kaune, Johanna Kotrba, Martin Porsch, Antje Güttler, Matthias Bache, Knut Krohn, Fabian Bull, Anne Riemann, Claudia Wickenhauser, Barbara Seliger, Johannes Schubert, Bilal Al‐Nawas, Oliver Thews, Ivo Große, Dirk Vordermark, Alexander W. Eckert
Software Mentions: 3
Published: about 5 years ago
10.18632/aging.101446
Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 (IRS1) in miceCited 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
10.3390/microorganisms8040506
An Optimized Metabarcoding Method for MimiviridaeCited by: 6
Author(s): Florian Prodinger, Hisashi Endo, Yasuhiro Gotoh, Yanze Li, Daichi Morimoto, Kimiho Omae, Keiko Tominaga, Romain Blanc-Mathieu, Yoshihito Takano, Tetsuya Hayashi, Keisuke Nagasaki, Takashi Yoshida, Hiroyuki Ogata
Software Mentions: 3
Published: over 4 years ago
10.1186/s12864-020-06778-6
Impacts of local population history and ecology on the evolution of a globally dispersed pathogenCited by: 18
Author(s): Andreína I. Castillo, Carlos Chacón-Díaz, Neysa Rodríguez-Murillo, Helvécio Della Coletta-Filho, Rodrigo P. P. Almeida
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 dietCited 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
10.3390/microorganisms9071490
Composition and Functions of the Gut Microbiome in Pediatric Obesity: Relationships with Markers of Insulin ResistanceCited by: 13
Author(s): Camila E. Orsso, Ye Peng, Edward C. Deehan, Qiming Tan, Catherine J. Field, Karen Madsen, Jens Walter, Carla M. Prado, Hein Min Tun, Andrea M. Haqq
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2164-15-148
Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyiCited by: 30
Author(s): Ester Feldmesser, Shilo Rosenwasser, Assaf Vardi, Shifra Ben‐Dor
Software Mentions: 3
Published: almost 11 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 wheatCited 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
10.1186/s12860-020-00251-8
Identification of universal and cell-type specific p53 DNA bindingCited by: 14
Author(s): Antonina Hafner, Lyubov Kublo, Michael Tsabar, Galit Lahav, Jacob Stewart-Ornstein
Software Mentions: 3
Published: almost 5 years ago
10.1128/mBio.03549-20
Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence AttenuatorCited by: 23
Author(s): Shruti Nagaraja, Maggi W. Cai, Jingjing Sun, Hugo Varet, Lotem Sarid, Meirav Trebicz-Geffen, Yana Shaulov, Mohit Mazumdar, Rachel Legendre, Jean‐Yves Coppée, Thomas J. Begley, Peter C. Dedon, S. Gourinath, Nancy Guillén, Yumiko Saito‐Nakano, Chikako Shimokawa, Hajime Hisaeda, Serge Ankri
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pntd.0009297
Expression profiling of Echinococcus multilocularis miRNAs throughout metacestode development in vitroCited 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
10.3389/fimmu.2020.00661
Neutrophil Extracellular Trap Induced Dendritic Cell Activation Leads to Th1 Polarization in Type 1 DiabetesCited by: 40
Author(s): Zuzana Paračková, Irena Zentsová, Petra Vrabcová, Adam Klocperk, Zdenĕk Šumnı́k, Štěpánka Průhová, Lenka Petruželková, Robert Häsler, Anna Šedivá
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pntd.0007811
Comparative analysis of small RNAs released by the filarial nematode Litomosoides sigmodontis in vitro and in vivoCited 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
10.1128/mBio.03399-20
<i>In Vivo</i> Transcriptome of Lactobacillus acidophilus and Colonization Impact on Murine Host Intestinal Gene ExpressionCited by: 11
Author(s): Yong Jun Goh, Rodolphe Barrangou, Todd R. Klaenhammer
Software Mentions: 3
Published: almost 4 years ago
10.1186/s40168-021-01029-6
Xylitol enhances synthesis of propionate in the colon via cross-feeding of gut microbiotaCited by: 45
Author(s): Shasha Xiang, Kun Ye, Mian Li, Jian Ying, Huanhuan Wang, Jianzhong Han, Lihua Shi, Jie Xiao, Yubiao Shen, Xiao Feng, Xuan Bao, Yiqing Zheng, Guofu Yin, Yalin Zhang, Chang Liu, Jie Chen, Yuewen Chen, Shiping Tian, Xuan Zhu
Software Mentions: 3
Published: over 3 years ago
10.1128/mBio.00217-20
Prebiotics and Community Composition Influence Gas Production of the Human Gut MicrobiotaCited by: 19
Author(s): Xiaoqian Yu, Thomas Gurry, Le Thanh Tu Nguyen, Hunter S. Richardson, Eric J. Alm
Software Mentions: 3
Published: about 4 years ago
10.1186/s40168-021-01125-7
Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in miceCited by: 40
Author(s): Ryo Aoki, Masayoshi Onuki, Katsumi Hattori, Masato Ito, Takahiro Yamada, Kohei Kamikado, Yun Gi Kim, Nobuhiro Nakamoto, Ikuo Kimura, Julie Clarke, Takanori Kanai, Koji Hase
Software Mentions: 3
Published: about 3 years ago
10.1016/j.dib.2017.10.019
Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thalianaCited by: 11
Author(s): Daniel Lepe-Soltero, Alma Armenta-Medina, Daoquan Xiang, Raju Datla, C. Stewart Gillmor, Cei Abreu‐Goodger
Software Mentions: 3
Published: almost 7 years ago
10.1186/s13568-017-0490-2
Metagenomic analysis reveals potential interactions in an artificial cocultureCited by: 8
Author(s): Mei Ren, Guiying Zhang, Zi Ye, Zhixian Qiao, Meili Xie, Yan Lin, Tao Li, Jindong Zhao
Software Mentions: 2
Published: about 7 years ago
10.18632/aging.103560
Circular RNA hsa_circ_0076690 acts as a prognostic biomarker in osteoporosis and regulates osteogenic differentiation of hBMSCs via sponging miR-152Cited by: 17
Author(s): Shujuan Han, Ming-jie Kuang, Chao Sun, Haifeng Wang, Dachuan Wang, Qian Liu
Software Mentions: 2
Published: over 4 years ago
10.1016/j.ajpath.2018.04.008
ELABELA/APELA Levels Are Not Decreased in the Maternal Circulation or Placenta among Women with PreeclampsiaCited by: 34
Author(s): Natasha Pritchard, Tu’uhevaha J Kaitu’u-Lino, Sungsam Gong, Justyna Dopierała, Gordon C. S. Smith, D. Stephen Charnock-Jones, Stephen Tong
Software Mentions: 2
Published: over 6 years ago
10.1128/AAC.02356-17
Translation Elongation Factor 4 (LepA) Contributes to Tetracycline Susceptibility by Stalling Elongating RibosomesCited by: 7
Author(s): Bin Liu, Chunlai Chen
Software Mentions: 2
Published: over 6 years ago
10.3390/antiox10081232
Pterostilbene Changes Epigenetic Marks at Enhancer Regions of Oncogenes in Breast Cancer CellsCited by: 3
Author(s): Sadaf Harandi‐Zadeh, Cayla Boycott, Megan Beetch, T.Y. Yang, Bernice M. Martin, Kevin Ren, Anna Kwasniak, John H. Dupuis, Katarzyna Lubecka, Rickey Y. Yada, LeAnn Howe, Barbara Stefańska
Software Mentions: 2
Published: over 3 years ago
10.1128/AEM.00610-16
Contribution of Vegetation to the Microbial Composition of Nearby Outdoor AirCited by: 114
Author(s): Despoina S. Lymperopoulou, Rachel I. Adams, Steven E. Lindow
Software Mentions: 2
Published: over 8 years ago
10.1002/aps3.11398
TagSeq for gene expression in non‐model plants: A pilot study at the Santa Rita Experimental Range NEON core siteCited by: 3
Author(s): Hannah E. Marx, S. P. Scheidt, Michael S. Barker, Katrina M. Dlugosch
Software Mentions: 2
Published: about 4 years ago
10.1007/s00705-020-04832-y
Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA speciesCited by: 2
Author(s): Ramesh R. Vetukuri, Pruthvi B. Kalyandurg, Ganapathi Varma Saripella, Diya Sen, J. Gil, Nina I. Lukhovitskaya, Laura J. Grenville‐Briggs, Eugene I. Savenkov
Software Mentions: 2
Published: about 4 years ago
10.1186/s12859-017-1873-8
riboviz: analysis and visualization of ribosome profiling datasetsCited by: 35
Author(s): Oana Carja, Tongji Xing, Eric Wallace, Joshua B. Plotkin, Premal Shah
Software Mentions: 2
Published: about 7 years ago
10.1186/s12859-019-3073-1
Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assemblyCited by: 6
Author(s): Joyce B. Kang, Benjamin A. Siranosian, Eli L. Moss, Niaz Banaei, Tessa M. Andermann, Ami S. Bhatt
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12859-015-0454-y
TagDust2: a generic method to extract reads from sequencing dataCited by: 55
Author(s): Timo Lassmann
Software Mentions: 2
Published: almost 10 years ago
10.1186/s12915-017-0416-0
Ribosome signatures aid bacterial translation initiation site identificationCited by: 22
Author(s): Adam Giess, Veronique Jonckheere, Elvis Ndah, Katarzyna Chyżyńska, Petra Van Damme, Eivind Valen
Software Mentions: 2
Published: about 7 years ago
10.1186/s12915-021-01053-w
Methyltransferase-directed orthogonal tagging and sequencing of miRNAs and bacterial small RNAsCited by: 1
Author(s): Milda Mickutė, Kotryna Kvederavičiūtė, Aleksandr Osipenko, Raminta Mineikaitė, Saulius Klimašauskas, Giedrius Vilkaitis
Software Mentions: 2
Published: over 3 years ago
10.1186/s12915-020-00798-0
A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in riceCited by: 5
Author(s): Fengli Zhao, Yuexing Wang, Jianshu Zheng, Yanling Wen, Minghao Qu, Shujing Kang, Shigang Wu, Xiao‐Juan Deng, Kai Hong, Sanfeng Liu, Xing Qin, Zhichao Wu, Xiaobo Wang, Cheng Ai, Alun Li, Longjun Zeng, Jiang Hu, Dali Zeng, Lianguang Shang, Quan Wang, Qian Qian, Jue Ruan, Guosheng Xiong
Software Mentions: 2
Published: over 4 years ago
10.1186/s12915-019-0673-1
mTORC1/AMPK responses define a core gene set for developmental cell fate switchingCited by: 15
Author(s): Pundrik Jaiswal, Alan R. Kimmel
Software Mentions: 2
Published: over 5 years ago
10.1186/s12915-020-0763-0
Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific mannerCited by: 28
Author(s): Tess Cherlin, Rogan Magee, Jing Yi, Venetia Pliatsika, Phillipe Loher, Isidore Rigoutsos
Software Mentions: 2
Published: over 4 years ago
10.1186/s12896-020-00604-3
Integration, abundance, and transmission of mutations and transgenes in a series of CRISPR/Cas9 soybean linesCited by: 14
Author(s): Jean Michel Michno, Kamaldeep S. Virdi, Adrian O. Stec, Junqi Liu, Xiaobo Wang, Yer Xiong, Robert M. Stupar
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12885-018-4304-y
RNA-Seq reveals the existence of a CDKN1C-E2F1-TP53 axis that is altered in human T-cell lymphoblastic lymphomasCited by: 7
Author(s): Pilar López-Nieva, Pablo Fernández-Navarro, Concepción Vaquero-Lorenzo, María Villa‐Morales, Osvaldo Graña‐Castro, María Ángeles Cobos-Fernández, José Luis López-Lorenzo, Pilar Llamas, Laura González-Sánchez, Isabel Sastre, Marina Pollán, Marcos Malumbres, Javíer Santos, José Fernández‐Piqueras
Software Mentions: 2
Published: over 6 years ago
10.1186/s12885-020-07130-7
Defective migration and dysmorphology of neutrophil granulocytes in atypical chronic myeloid leukemia treated with ruxolitinibCited by: 6
Author(s): Lea Bornemann, Marc Schuster, Saskia Schmitz, Charlyn Sobczak, Clara Bessen, Simon F. Merz, Karl‐Heinz Jöckel, Thomas Haverkamp, Matthias Gunzer, Joachim R. Göthert
Software Mentions: 2
Published: over 4 years ago
10.1186/s12898-019-0269-1
FACEPAI: a script for fast and consistent environmental DNA processing and identificationCited by: 2
Author(s): Emma Wahlberg
Software Mentions: 2
Published: almost 5 years ago
10.1186/1471-2164-15-568
High-throughput sequencing reveals small RNAs involved in ASGV infectionCited by: 39
Author(s): Marike Visser, Hans J. Maree, D. J. G. Rees, Johan T. Burger
Software Mentions: 2
Published: over 10 years ago
10.1186/s12864-015-1792-x
The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeatCited by: 8
Author(s): Nicolas J. Tourasse, Nastassia Shtaida, Inna Khozin‐Goldberg, Sammy Boussiba, Olivier Vallon
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-016-3114-3
Novel microRNA discovery using small RNA sequencing in post-mortem human brainCited by: 29
Author(s): Christian Wake, Adam Labadorf, Alexandra Dumitriu, Andrew G. Hoss, Joli Bregu, Kenneth H. Albrecht, Anita L. DeStefano, Richard H. Myers
Software Mentions: 2
Published: about 8 years ago
10.1186/s12864-018-5355-9
Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptationCited by: 35
Author(s): Ning Li, Lisui Bao, Tao Zhou, Zihao Yuan, Shikai Liu, Rex A. Dunham, Yuanning Li, Kun Wang, Xiaoyan Xu, Yulin Jin, Qifan Zeng, Sen Gao, Qiang Fu, Liu Yang, Yujia Yang, Qi Li, Axel Meyer, Dongya Gao, Zhanjiang Liu
Software Mentions: 2
Published: almost 6 years ago
10.1186/s12864-018-4561-9
UDiTaS™, a genome editing detection method for indels and genome rearrangementsCited by: 87
Author(s): Georgia Giannoukos, Dawn Ciulla, Eugenio Marco, Hayat Abdulkerim, Luis Barrera, Anne Bothmer, Vidya Dhanapal, Sebastian Gloskowski, Hariharan Jayaram, Morgan L. Maeder, Maxwell N. Skor, Tongyao Wang, Vic E. Myer, Christopher J. Wilson
Software Mentions: 2
Published: over 6 years ago
10.1186/s12864-018-5119-6
Characterization and expression profiling of microRNAs in response to plant feeding in two host-plant strains of the lepidopteran pest Spodoptera frugiperdaCited by: 20
Author(s): Yves Moné, Sandra Nhim, Sylvie Gimenez, Fabrice Legeai, Imène Séninet, Hugues Parrinello, Nicolas Nègre, Emmanuelle d’Alençon
Software Mentions: 2
Published: about 6 years ago
10.1186/s12864-019-5712-3
Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterizationCited by: 36
Author(s): Sara Montanari, Luca Bianco, Brian Allen, Pedro J. Martínez-García, Nahla V. Bassil, Joseph D. Postman, Mareike Knäbel, Biff Kitson, Cecilia Deng, David Chagné, Marc W. Crepeau, Charles H. Langley, Kate Evans, Amit Dhingra, Michela Troggio, David B. Neale
Software Mentions: 2
Published: over 5 years ago
10.1186/s12864-015-2132-x
Deciphering the molecular adaptation of the king scallop (Pecten maximus) to heat stress using transcriptomics and proteomicsCited by: 32
Author(s): Sébastien Artigaud, Joëlle Richard, Michael A. S. Thorne, Romain Lavaud, Jonathan Flye-Sainte-Marie, Fred Jean, Lloyd S. Peck, Melody S. Clark, Vianney Pichereau
Software Mentions: 2
Published: about 9 years ago
10.1186/s12864-016-3398-3
Temperature-dependent sRNA transcriptome of the Lyme disease spirocheteCited by: 36
Author(s): Niko Popitsch, Ivana Bilusic, Philipp Rescheneder, Renée Schroeder, Meghan Lybecker
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12864-016-2977-7
Analysis of ethanol fermentation mechanism of ethanol producing white-rot fungus Phlebia sp. MG-60 by RNA-seqCited by: 20
Author(s): Jianqiao Wang, Tomohiro Suzuki, Hideo Dohra, Shoko Takigami, Hiroko Kako, Ayumi Soga, Ichiro Kamei, Toshio Mori, Hirokazu Kawagishi, Hirofumi Hirai
Software Mentions: 2
Published: over 8 years ago
10.1186/s12864-021-07905-7
Integrated miRNA and transcriptome profiling to explore the molecular determinism of convergent adaptation to corn in two lepidopteran pests of agricultureCited by: 0
Author(s): Sylvie Gimenez, Imène Séninet, Marion Orsucci, Philippe Audiot, Nicolas Nègre, Kiwoong Nam, Réjane Streiff, Emmanuelle d’Alençon
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-020-6740-8
Genomic characterization of Lactobacillus fermentum DSM 20052Cited by: 13
Author(s): Katelyn Brandt, Matthew A. Nethery, Sarah O’Flaherty, Rodolphe Barrangou
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-015-1490-8
An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stressCited by: 23
Author(s): Zahra Agharbaoui, Mickaël Leclercq, Mohamed Amine Remita, Mohamed Badawi, Étienne Lord, Mario Houde, Jean Danyluk, Abdoulaye Baniré Diallo, Fathey Sarhan
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-015-1503-7
Temperature during early development has long-term effects on microRNA expression in Atlantic codCited by: 76
Author(s): Teshome Tilahun Bizuayehu, Steinar Johansen, Velmurugu Puvanendran, Hilde Toften, Igor Babiak
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-016-2563-z
Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafishCited by: 17
Author(s): Isabel Brocal, Richard White, Christopher M. Dooley, Samantha Carruthers, Richard Clark, Amanda Hall, Elisabeth M Busch-Nentwich, Derek L. Stemple, Ross Kettleborough
Software Mentions: 2
Published: over 8 years ago
10.1186/s12864-017-4143-2
Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genesCited by: 19
Author(s): Roland Akakpo, Nora Scarcelli, Hâna Chaïr, Alexandre Dansi, Gustave Djèdatin, Anne-Céline Thuillet, Bénédicte Rhoné, F. Ochsenbein, Karine Alix, Yves Vigouroux
Software Mentions: 2
Published: about 7 years ago
10.1186/s12864-020-6462-y
Transcriptome-wide map of m6A circRNAs identified in a rat model of hypoxia mediated pulmonary hypertensionCited by: 48
Author(s): Hua Su, Guowen Wang, Lingfang Wu, Xiaochun Ma, Kejing Ying, Ruifeng Zhang
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12864-015-1392-9
NMDA receptor activation upstream of methyl farnesoate signaling for short day-induced male offspring production in the water flea, Daphnia pulexCited by: 41
Author(s): Kenji Toyota, Hitoshi Miyakawa, Katsushi Yamaguchi, Shuji Shigenobu, Yukiko Ogino, Norihisa Tatarazako, Shinichi Miyagawa, Taisen Iguchi
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-015-1355-1
Learning-induced gene expression in the heads of two Nasonia species that differ in long-term memory formationCited by: 17
Author(s): Katja M. Hoedjes, Hans M. Smid, Elio Schijlen, Louise E. M. Vet, Joke J.F.A. van Vugt
Software Mentions: 2
Published: over 9 years ago
10.1186/s12920-019-0526-3
Transient multifocal genomic crisis creating chromothriptic and non-chromothriptic rearrangements in prezygotic testicular germ cellsCited by: 8
Author(s): Atsushi Hattori, Koji Okamura, Yasuhiko Terada, Rika Tanaka, Yuko Katoh‐Fukui, Yoichi Matsubara, Kazuo Matsubara, Masayo Kagami, Reiko Horikawa, Maki Fukami
Software Mentions: 2
Published: over 5 years ago
10.1186/s12866-020-02027-8
Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluidCited by: 5
Author(s): Katelyn Brandt, Rodolphe Barrangou
Software Mentions: 2
Published: about 4 years ago
10.1186/s12860-021-00363-9
Impact of uORFs in mediating regulation of translation in stress conditionsCited by: 12
Author(s): Simone G. Moro, Cédric Hermans, Jorge Ruiz-Orera, M. Mar Albà
Software Mentions: 2
Published: over 3 years ago
10.1186/s12870-018-1438-7
Rice stripe virus-derived siRNAs play different regulatory roles in rice and in the insect vector Laodelphax striatellusCited by: 32
Author(s): Meiling Yang, Zhongtian Xu, Wan Zhao, Qing Liu, Qiong Li, Lu Lu, Renyi Liu, Xiaoming Zhang, Feng Cui
Software Mentions: 2
Published: about 6 years ago
10.1186/s12870-021-03148-6
Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogenCited by: 7
Author(s): Roshan Regmi, Toby E. Newman, Lars G. Kamphuis, Mark Derbyshire
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2229-14-4
Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflightCited by: 70
Author(s): Mineharu Sugimoto, Youko Oono, Oleg Gusev, Takashi Matsumoto, Takayuki Yazawa, Margarita Levinskikh, Vladimir Sychev, Gail E. Bingham, Raymond M. Wheeler, Mary E. Hummerick
Software Mentions: 2
Published: almost 11 years ago
10.1186/s12917-018-1696-5
Metagenomic analysis of captive Amur tiger faecal microbiomeCited by: 17
Author(s): Fengping He, Dan Liú, Le Zhang, Jiancheng Zhai, Yue Ma, Yanchun Xu, Guangshun Jiang, Ke Rong, Jingyun Ma
Software Mentions: 2
Published: almost 6 years ago
10.1155/2021/6673010
Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F5 Population of Pepper with Contrasting Powdery Mildew Resistance TraitCited by: 6
Author(s): Abinaya Manivannan, Sena Choi, Tae-Hwan Jun, Eun-Young Yang, Jinhee Kim, Eun-Su Lee, Hye-Eun Lee, Do-Sun Kim, Yul-Kyun Ahn
Software Mentions: 2
Published: over 3 years ago
10.3390/biom11050688
Molecular Targets and Biological Functions of cAMP Signaling in ArabidopsisCited by: 17
Author(s): Ruqiang Xu, Yanjuan Guo, Peng Song, Jinrui Liu, Panyu Li, Wenjing Jia, Junheng Zhao
Software Mentions: 2
Published: over 3 years ago
10.1042/BSR20201590
Profiling and bioinformatics analyses reveal differential circular RNA expression in NK/T-cell lymphoma-associated hemophagocytic syndromeCited by: 0
Author(s): Changfeng Man, Yu Fan, Guangli Yin, Jiayu Huang, Jujuan Wang, Hai-Rong Qiu
Software Mentions: 2
Published: about 4 years ago
10.1186/s13068-016-0565-3
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plantsCited by: 87
Author(s): Yvonne Stolze, Andreas Bremges, Madis Rumming, Christian Henke, Irena Maus, Alfred Pühler, Alexander Sczyrba, Andreas Schlüter
Software Mentions: 2
Published: over 8 years ago
10.1186/s13068-015-0381-1
The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applicationsCited by: 93
Author(s): Arne van Hoeck, Nele Horemans, Pieter Monsieurs, Hieu X. Cao, Hildegarde Vandenhove, Ronny Blust
Software Mentions: 2
Published: about 9 years ago
10.1186/s13058-020-01306-6
Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancerCited by: 6
Author(s): Laura A. Baker, Holly Holliday, Daniel Roden, Christoph Krisp, Sunny Z. Wu, Simon Junankar, Aurélien A. Sérandour, Hisham Mohammed, Radhika Nair, Geetha Sankaranarayanan, Andrew M. K. Law, Andrea McFarland, Peter T. Simpson, Sunil R. Lakhani, Eoin Dodson, Christina Selinger, Lyndal Anderson, Goli Samimi, Neville F. Hacker, Elgene Lim, Christopher J. Ormandy, Matthew J. Naylor, Kaylene J. Simpson, Iva Nikolić, Sandra A. O’Toole, Warren Kaplan, Mark J. Cowley, Jason S. Carroll, Mark P. Molloy, Alexander Swarbrick
Software Mentions: 2
Published: over 4 years ago
10.1186/s13058-020-01328-0
Clinical implications of prospective genomic profiling of metastatic breast cancer patientsCited by: 29
Author(s): Courtney T. van Geelen, Peter Savas, Zhi L. Teo, Stephen J. Luen, Chen-Fang Weng, Yi-An Ko, Keilly Kuykhoven, Franco Caramia, Roberto Salgado, Prudence A. Francis, Sarah-Jane Dawson, Stephen B. Fox, Andrew Fellowes, Sherene Loi
Software Mentions: 2
Published: over 4 years ago
10.1093/bib/bbab021
Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysisCited by: 11
Author(s): Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger
Software Mentions: 2
Published: almost 4 years ago
10.26508/lsa.202000902
A novel <i>canis lupus familiaris</i> reference genome improves variant resolution for use in breed-specific GWASCited by: 8
Author(s): Robert A. Player, Ellen R. Forsyth, Kathleen Verratti, David Mohr, Alan F. Scott, Christopher Bradburne
Software Mentions: 2
Published: almost 4 years ago
10.3390/md19040183
Effect of Supplementing Seaweed Extracts to Pigs until d35 Post-Weaning on Performance and Aspects of Intestinal HealthCited by: 12
Author(s): Stafford Vigors, John V. O’Doherty, Ruth Rattigan, T. Sweeney
Software Mentions: 2
Published: over 3 years ago
10.1186/s12934-021-01682-4
Multivalent poultry vaccine development using Protein Glycan Coupling TechnologyCited by: 7
Author(s): Marta Mauri, Thippeswamy H. Sannasiddappa, Prerna Vohra, Ricardo Corona-Torres, Adam Smith, Cosmin Chintoan-Uta, Abi Bremner, Vanessa S. Terra, Sherif Abouelhadid, Mark P. Stevens, A. Grant, Jon Cuccui, Brendan W. Wren
Software Mentions: 2
Published: about 3 years ago
10.1099/mgen.0.000181
An outbreak of a rare Shiga-toxin-producing Escherichia coli serotype (O117:H7) among men who have sex with menCited by: 13
Author(s): Kate S. Baker, Timothy J. Dallman, Nicholas R. Thomson, Claire Jenkins
Software Mentions: 2
Published: over 6 years ago
10.1128/MRA.00835-19
Draft Whole-Genome Sequences of Xylella fastidiosa subsp. fastidiosa Strains TPD3 and TPD4, Isolated from Grapevines in Hou-li, TaiwanCited by: 7
Author(s): Andreína I. Castillo, Shu‐Jen Tuan, Adam C. Retchless, Fei-Ting Hu, Hsun-Yin Chang, Rodrigo P. P. Almeida
Software Mentions: 2
Published: about 5 years ago
10.1186/s40168-019-0665-y
Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic dataCited by: 68
Author(s): Krithika Arumugam, Caner Bağcı, Irina Bessarab, Sina Beier, Benjamin Buchfink, Anna Górska, Guanglei Qiu, Daniel H. Huson, Rohan B. H. Williams
Software Mentions: 2
Published: over 5 years ago
10.1186/s40168-018-0598-x
Long-term colonisation with donor bacteriophages following successful faecal microbial transplantationCited by: 105
Author(s): Lorraine A. Draper, Feargal J. Ryan, Muireann K. Smith, Jonna Jalanka, Eero Mattila, Perttu Arkkila, R. Paul Ross, Reetta Satokari, Colin Hill
Software Mentions: 2
Published: almost 6 years ago
10.1186/s40168-020-00989-5
Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sitesCited by: 12
Author(s): Alexandra Kristin Bashir, Lisa Wink, Stefanie Duller, Petra Schwendner, Charles S. Cockell, Petra Rettberg, Alexander Mahnert, Kristina Beblo‐Vranesevic, Maria Bohmeier, Elke Rabbow, F. Gaboyer, Francès Westall, Nicolas Walter, P. Cabezas, L. García-Descalzo, Felipe Gómez, M. Malki, Ricardo Amils, P. Ehrenfreund, E. Monaghan, P. Vannier, V. Marteinsson, Armin Erlacher, George Tanski, Jens Strauß, Mina Bashir, Andreas Riedo, Christine Moissl-Eichinger
Software Mentions: 2
Published: almost 4 years ago
10.3390/microorganisms9040769
Ocean Acidification Induces Changes in Virus–Host Relationships in Mediterranean Benthic EcosystemsCited by: 8
Author(s): Michael Tangherlini, Cinzia Corinaldesi, Francesca Ape, Silvestro Greco, Teresa Romeo, Franco Andaloro, Roberto Danovaro
Software Mentions: 2
Published: over 3 years ago
10.1038/s41379-020-0596-y
Targeted sequencing of FH-deficient uterine leiomyomas reveals biallelic inactivating somatic fumarase variants and allows characterization of missense variantsCited by: 17
Author(s): Bernt Popp, Ramona Erber, Cornelia Kraus, Georgia Vasileiou, Juliane Hoyer, Stefanie Burghaus, Arndt Hartmann, Matthias W. Beckmann, André Reis, Abbas Agaimy
Software Mentions: 2
Published: about 4 years ago
10.1093/molbev/msaa290
Genomic Architecture of Rapid Parallel Adaptation to Fresh Water in a Wild FishCited by: 14
Author(s): Shao-Bing Zong, Yulong Li, Jinxian Liu
Software Mentions: 2
Published: about 4 years ago
10.1186/s12943-021-01340-8
FBW7 suppresses ovarian cancer development by targeting the N6-methyladenosine binding protein YTHDF2Cited by: 62
Author(s): Fei Xu, Jiajia Li, Ming Ni, Jingyi Cheng, Hong Zhao, Shanshan Wang, Xiang Zhou, Xiaohua Wu
Software Mentions: 2
Published: over 3 years ago
10.1016/j.molcel.2018.03.010
Cell-Cycle Modulation of Transcription Termination Factor Sen1Cited by: 18
Author(s): Hannah E. Mischo, Yujin Chun, Kevin Harlen, Brendan M Smalec, Somdutta Dhir, L. Stirling Churchman, Stephen Buratowski
Software Mentions: 2
Published: over 6 years ago
10.1016/j.molcel.2019.07.037
Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome StabilityCited by: 71
Author(s): Diana Zatreanu, Zhong Chao Han, Richard Mitter, Emanuela Tumini, Hannah Williams, Lea H. Gregersen, A. Barbara Dirac-Svejstrup, Stefania Roma, Aengus Stewart, Andrés Aguilera, Jesper Q. Svejstrup
Software Mentions: 2
Published: about 5 years ago
10.1186/s13039-021-00565-y
A rare familial rearrangement of chromosomes 9 and 15 associated with intellectual disability: a clinical and molecular studyCited by: 0
Author(s): Natalya A. Lemskaya, Svetlana A. Romanenko, Mariia A Rezakova, Elena Filimonova, Dmitry Prokopov, Alexander A. Dolskiy, Polina L. Perelman, Yulia V. Maksimova, Asia R. Shorina, Dmitry V. Yudkin
Software Mentions: 2
Published: about 3 years ago