pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.1002/prp2.632

Ascorbate sensitizes human osteosarcoma cells to the cytostatic effects of cisplatin
Cited by: 8
Author(s): Naohiro Oka, Akiyoshi Komuro, Hideharu Amano, Suman Dash, Masahiko Honda, Kyoko Ota, Shunji Nishimura, Takeshi Ueda, Masao Akagi, Hitoshi Okada
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-15-148

Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi
Cited by: 30
Author(s): Ester Feldmesser, Shilo Rosenwasser, Assaf Vardi, Shifra Ben‐Dor
Software Mentions: 3
Published: almost 11 years ago

10.3389/fmicb.2018.02559

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient
Cited by: 33
Author(s): Xin Fang, Jonathan M. Monk, Sergey Nurk, Margarita Akseshina, Quanyin Zhu, Christopher Gemmell, Connor Gianetto-Hill, Nelly Leung, Richard Szubin, Jon G. Sanders, Paul L. Beck, Weizhong Li, William J. Sandborn, Scott D. Gray-Owen, Rob Knight, Emma Allen‐Vercoe, Bernhard Ø. Palsson, Larry Smarr
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2018.00929

The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ
Cited by: 17
Author(s): Susanne Bury, Manonmani Soundararajan, Richa Bharti, Rudolf von Bünau, Konrad U. Förstner, Tobias A. Oelschlaeger
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.02606

Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach
Cited by: 36
Author(s): Valerie De Anda, Icoquih Zapata‐Peñasco, Jazmín Blaz, Augusto César Poot-Hernández, Bruno Contreras‐Moreira, Marcos González-Laffitte, Niza Gámez-Tamariz, Maribel Hernández-Rosales, Luis E. Eguiarte, Valeria Souza
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41396-020-0693-4

Changes in the transcriptome, ploidy, and optimal light intensity of a cryptomonad upon integration into a kleptoplastic dinoflagellate
Cited by: 10
Author(s): Ryo Onuma, Shunsuke Hirooka, Yu Kanesaki, Takayuki Fujiwara, Hideki Yoshikawa, Shin-ya Miyagishima
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 pathogen
Cited 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

10.1128/mSystems.00023-18

Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run
Cited by: 53
Author(s): Yi Chun Yeh, David M. Needham, Ella T. Sieradzki, Jed A. Fuhrman
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.5443

Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (Morus albaL.)
Cited by: 20
Author(s): Dujun Wang, Li Zhao, Dan Wang, Jia Liu, Xin Yu, Yuan Wei, Zhen Ouyang
Software Mentions: 3
Published: about 6 years ago

10.3390/biom9100516

Fish Oil, but Not Olive Oil, Ameliorates Depressive-Like Behavior and Gut Microbiota Dysbiosis in Rats under Chronic Mild Stress
Cited by: 18
Author(s): Te-Hsuan Tung, Yen-Ting Tung, I-Hsuan Lin, Chun Kuang Shih, Ngan Thi Kim Nguyen, Amalina Shabrina, Shih‐Yi Huang
Software Mentions: 3
Published: about 5 years ago

10.1128/mSystems.00136-17

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway
Cited by: 58
Author(s): Gourvendu Saxena, Suparna Mitra, Ezequiel M. Marzinelli, Chao Xie, Toh Jun Wei, Peter D. Steinberg, Rohan B. H. Williams, Staffan Kjelleberg, Federico M. Lauro, Sanjay Swarup
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.9085

Fast sequence-based microsatellite genotyping development workflow
Cited by: 24
Author(s): Olivier Lepais, Émilie Chancerel, Christophe Boury, Franck Salin, Aurélie Manicki, Laura Taillebois, Cyril Dutech, Abdeldjalil Aissi, Cecile F. E. Bacles, Françoise Daverat, Sophie Launey, Erwan Guichoux
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.629169

Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link
Cited by: 15
Author(s): Sara Fareed Mohamed Wahdan, Anna Heintz‐Buschart, Chakriya Sansupa, Benjawan Tanunchai, Yuting Wu, Martin Schädler, Matthias Noll, Witoon Purahong, François Buscot
Software Mentions: 3
Published: almost 4 years ago

10.7717/peerj.11166

Transcriptome analysis of the liver of Eospalax fontanierii under hypoxia
Cited by: 3
Author(s): Zhiqiang Hao, Lulu Xu, Li Zhao, Jianxing He, Guanglin Li, Jingang Li
Software Mentions: 3
Published: over 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 barcodes
Cited by: 3
Author(s): Billy T. Lau, Hanlee P. Ji
Software Mentions: 3
Published: about 7 years ago

10.1155/2018/2617432

Aberrantly Expressed Genes and miRNAs in Slow Transit Constipation Based on RNA-Seq Analysis
Cited by: 11
Author(s): Shushan Zhao, Qiang Chen, Xianwu Kang, Bin Kong, Zhuo Wang
Software Mentions: 3
Published: over 6 years ago

10.1128/mSphere.00186-20

Globally Abundant “ Candidatus Udaeobacter” Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas Scavenging
Cited 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

10.1128/mSystems.00587-19

The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities
Cited by: 2
Author(s): Thomas Yssing Michaelsen, Jakob Brandt, Caitlin M. Singleton, Rasmus Hansen Kirkegaard, Johanna Wiesinger, Nicola Segata, Mads Albertsen
Software Mentions: 3
Published: almost 5 years ago

10.1128/mBio.00217-20

Prebiotics and Community Composition Influence Gas Production of the Human Gut Microbiota
Cited 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

10.1128/mBio.03399-20

In Vivo Transcriptome of Lactobacillus acidophilus and Colonization Impact on Murine Host Intestinal Gene Expression
Cited by: 11
Author(s): Yong Jun Goh, Rodolphe Barrangou, Todd R. Klaenhammer
Software Mentions: 3
Published: over 3 years ago

10.1186/s13287-021-02585-2

In vitro genome editing rescues parkinsonism phenotypes in induced pluripotent stem cells-derived dopaminergic neurons carrying LRRK2 p.G2019S mutation
Cited by: 14
Author(s): Kuo‐Hsuan Chang, Cheng‐Yen Huang, Chih-Hsin Ou-Yang, Chang-Han Ho, Hon‐Yi Lin, Chih‐Cheng Hsu, You-Tzung Chen, Yu‐Chi Chou, Yijing Chen, Ying Chen, Jiali Lin, Ji-Kuan Wang, Pei‐Wen Lin, Ying-Ru Lin, Miao-Hsia Lin, C. K. Tseng, Chin-Hsien Lin
Software Mentions: 3
Published: about 3 years ago

10.1186/s40659-020-00282-7

Functional and genomic characterization of three novel cell lines derived from a metastatic gallbladder cancer tumor
Cited by: 4
Author(s): Patricia García, Carolina Bizama, Lorena Rosa, Jaime A. Espinoza, Helga Weber, Javier Cerda‐Infante, Marianela Sánchez, Viviana P. Montecinos, Justo Lorenzo Bermejo, Felix Boekstegers, Marcela Dávila-López, Francisca Alfaro, Claudia Leiva-Acevedo, Zasha Parra, Diego Romero, Sumie Kato, Pamela Leal, Marcela Lagos, Juan Carlos Roa
Software Mentions: 3
Published: over 4 years ago

10.1186/s40035-021-00249-y

Several miRNAs derived from serum extracellular vesicles are potential biomarkers for early diagnosis and progression of Parkinson’s disease
Cited by: 31
Author(s): Shulei He, Lu Huang, Ci Shao, Tiejian Nie, Xia Li, Bozhou Cui, Fangfang Lu, Lin Zhu, Bolin Chen, Qian Yang
Software Mentions: 3
Published: over 3 years ago

10.18632/aging.103683

Profiling of circular RNAs in age-related cataract reveals circZNF292 as an antioxidant by sponging miR-23b-3p
Cited by: 27
Author(s): Shijie Liang, Shengqian Dou, Wenfeng Li, Yusen Huang
Software Mentions: 3
Published: about 4 years ago

10.1002/yea.3211

Proteomic and genomic characterization of a yeast model for Ogden syndrome
Cited by: 14
Author(s): Max J. Dörfel, Fang Han, Jonathan Crain, Michael E Klingener, Jake Weiser, Gholson J. Lyon
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2021.643945

Evaluation of Three Prokaryote Primers for Identification of Prokaryote Community Structure and Their Abode Preference in Three Distinct Wetland Ecosystems
Cited by: 2
Author(s): Kavita Kumari, Malay Naskar, Md. Aftabuddin, Soma Das Sarkar, Bandana Das Ghosh, Uttam Kumar Sarkar, Subir Nag, Chayna Jana, Basanta Kumar Das
Software Mentions: 3
Published: over 3 years ago

10.1128/mBio.03549-20

Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator
Cited 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

10.1186/s40793-015-0069-y

Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata
Cited by: 9
Author(s): Julie Meyer, Brian A. Dillard, J. Michael Rodgers, Kim B. Ritchie, Valerie J. Paul, Max Teplitski
Software Mentions: 3
Published: about 9 years ago

10.1186/s13287-019-1191-3

In vitro expansion affects the response of human bone marrow stromal cells to irradiation
Cited by: 8
Author(s): Yang Xiang, Chun Wu, Jiang Wu, Weili Quan, Chao Cheng, Jian Zhou, Li Chen, Lan Xiang, Fengjie Li, Kebin Zhang, Qian Ran, Yi Zhang, Zhongjun Li
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2016.00893

Epimicrobiota Associated with the Decay and Recovery of Orbicella Corals Exhibiting Dark Spot Syndrome
Cited by: 16
Author(s): Julie Meyer, J. Michael Rodgers, Brian A. Dillard, Valerie J. Paul, Max Teplitski
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-020-03576-5

Deconvolution of bulk blood eQTL effects into immune cell subpopulations
Cited by: 32
Author(s): Raúl Aguirre-Gamboa, Nigel Klein, Jennifer di Tommaso, Annique Claringbould, Monique G. P. van der Wijst, Dylan de Vries, Harm Brugge, Roy Oelen, Urmo Võsa, Maria M. Zorro, Xiaojin Chu, Olivier B. Bakker, Z Borek, Isis Ricaño-Ponce, Patrick Deelen, Cheng-Jiang Xu, Morris A. Swertz, Iris Jonkers, Sebo Withoff, Irma Joosten, Serena Sanna, Vinod Kumar, Hans J. P. M. Koenen, Leo A. B. Joosten, Mihai G. Netea, Cisca Wijmenga, Lude Franke, Yang Li
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2017.00238

Fungal ITS1 Deep-Sequencing Strategies to Reconstruct the Composition of a 26-Species Community and Evaluation of the Gut Mycobiota of Healthy Japanese Individuals
Cited by: 55
Author(s): Daisuke Motooka, Kosuke Fujimoto, Reiko Tanaka, Takashi Yaguchi, Kazuyoshi Gotoh, Yukihide Maeda, Yoshikazu Furuta, Takashi Kurakawa, Naohisa Goto, Teruo Yasunaga, Masashi Narazaki, Atsushi Kumanogoh, Toshihiro Horii, Tetsuya Iida, Kiyoshi Takeda, Shota Nakamura
Software Mentions: 3
Published: almost 8 years ago

10.1093/bioinformatics/btab171

Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq
Cited by: 5
Author(s): Ferhat Alkan, Joana Silva, Eric Pintó Barberà, William J. Faller
Software Mentions: 3
Published: over 3 years ago

10.1186/s13287-020-01619-5

Genetic barcoding reveals clonal dominance in iPSC-derived mesenchymal stromal cells
Cited by: 12
Author(s): Jonathan Hollmann, Johanna Brecht, Roman Goetzke, Julia Franzen, Anton Selich, Marco F. Schmidt, Monika Eipel, Alina Ostrowska, Jan Hapala, Eduardo Fernández-Rebollo, Gerhard Müller‐Newen, Michael Rothe, Thomas Eggermann, Martin Zenke, Wolfgang Wagner
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.596156

Substrate Pre-loading Influences Initial Colonization of GAC Biofilter Biofilms
Cited by: 1
Author(s): Wen Qin, Frederik Hammes
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-90255-x

Modular barcode beads for microfluidic single cell genomics
Cited by: 12
Author(s): Cyrille L. Delley, Adam R. Abate
Software Mentions: 3
Published: over 3 years ago

10.1093/ve/veaa010

Linking influenza virus evolution within and between human hosts
Cited by: 39
Author(s): Katherine S Xue, Jesse D. Bloom
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-016-3168-2

Novel equine tissue miRNAs and breed-related miRNA expressed in serum
Cited by: 27
Author(s): Alicja Pacholewska, Núria Mach, Xavier Mata, Anne Vaiman, Laurent Schibler, Éric Barrey, V. Gerber
Software Mentions: 3
Published: about 8 years ago

10.3390/ani11041150

Whole Blood Transcriptome Profiling Reveals Positive Effects of Olive Leaves-Supplemented Diet on Cholesterol in Goats
Cited by: 1
Author(s): Andrea Ianni, Francesca Bennato, Camillo Martino, Martina Colapietro, Giuseppe Martino
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-80732-0

Application of wood ash leads to strong vertical gradients in soil pH changing prokaryotic community structure in forest top soil
Cited by: 11
Author(s): Toke Bang‐Andreasen, Mette Peltre, Lea Ellegaard-Jensen, Lars Hestbjerg Hansen, Morten Ingerslev, Regin Rønn, Carsten Suhr Jacobsen, Rasmus Kjøller
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-89175-7

Concurrent X chromosome inactivation and upregulation during non-human primate preimplantation development revealed by single-cell RNA-sequencing
Cited by: 2
Author(s): Ana Luíza Cidral, Joana Carvalho Moreira de Mello, Joost Gribnau, Lygia V. Pereira
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-76229-5

Effects of set cathode potentials on microbial electrosynthesis system performance and biocathode methanogen function at a metatranscriptional level
Cited by: 8
Author(s): Ala’a Ragab, Dario Rangel Shaw, Krishna P. Katuri, Pascal E. Saikaly
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-77402-6

Mycosporine-like amino acid and aromatic amino acid transcriptome response to UV and far-red light in the cyanobacterium Chlorogloeopsis fritschii PCC 6912
Cited by: 16
Author(s): Carole A. Llewellyn, Carolyn Greig, Alla Silkina, Bethan Kultschar, Matthew D. Hitchings, Garry Farnham
Software Mentions: 3
Published: almost 4 years ago

10.3389/fimmu.2021.695148

CD32+CD4+ T Cells Sharing B Cell Properties Increase With Simian Immunodeficiency Virus Replication in Lymphoid Tissues
Cited by: 8
Author(s): Nicolas Huot, Philippe Rascle, Cyril Planchais, Vanessa Contreras, Caroline Passaes, Roger Le Grand, Anne-Sophie Beignon, Étienne Kornobis, Rachel Legendre, Hugo Varet, Asier Sáez‐Cirión, Hugo Mouquet, Béatrice Jacquelin, Michaela Müller‐Trutwin
Software Mentions: 3
Published: over 3 years ago

10.1186/s12870-014-0307-2

RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petunias
Cited 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

10.1038/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

10.3390/ani11051433

Faecal Microbiome Transplantation as a Solution to Chronic Enteropathies in Dogs: A Case Study of Beneficial Microbial Evolution
Cited by: 11
Author(s): Michele Berlanda, Giada Innocente, Barbara Simionati, Barbara Di Camillo, Sonia Facchin, Maria Cecilia Giron, Edoardo Savarino, Federico Sebastiani, Francesca Fiorio, Ilaria Patuzzi
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-77221-9

DNA aptamers against bacterial cells can be efficiently selected by a SELEX process using state-of-the art qPCR and ultra-deep sequencing
Cited by: 24
Author(s): Claudia Kolm, Isabella Cervenka, Ulrich J Aschl, Niklas Baumann, Stefan Jakwerth, Rudolf Krska, Robert L. Mach, Regina Sommer, Maria C. DeRosa, Alexander K. T. Kirschner, Andreas H. Farnleitner, Georg H. Reischer
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12860-020-00251-8

Identification of universal and cell-type specific p53 DNA binding
Cited by: 14
Author(s): Antonina Hafner, Lyubov Kublo, Michael Tsabar, Galit Lahav, Jacob Stewart-Ornstein
Software Mentions: 3
Published: almost 5 years ago

10.1002/1878-0261.12828

TGFBI modulates tumour hypoxia and promotes breast cancer metastasis
Cited by: 30
Author(s): Flavia Fico, Albert Santamaria-Martínez
Software Mentions: 3
Published: about 4 years ago

10.1098/rspb.2020.3169

Conservation and turnover of miRNAs and their highly complementary targets in early branching animals
Cited by: 5
Author(s): Daniela Praher, Bob Zimmermann, Rohit Dnyansagar, David J. Miller, Aurélie Moya, Vengamanaidu Modepalli, Arie Fridrich, Daniel Sher, Lene Friis-Møller, Per Sundberg, Sylvain Forêt, Regan Ashby, Yehu Moran, Ulrich Technau
Software Mentions: 3
Published: over 3 years ago

10.1111/mmi.14237

Systematic analysis of Type I‐E Escherichia coli CRISPR‐Cas PAM sequences ability to promote interference and primed adaptation
Cited by: 26
Author(s): Olga Musharova, Vasily Sitnik, Marnix Vlot, Ekaterina Savitskaya, Kirill A. Datsenko, Andrey Krivoy, Ivan Fedorov, Ekaterina Semenova, Stan J. J. Brouns, Konstantin Severinov
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2020.01033

Adjuvanting Allergen Extracts for Sublingual Immunotherapy: Calcitriol Downregulates CXCL8 Production in Primary Sublingual Epithelial Cells
Cited by: 3
Author(s): Michael Pelst, Clara Hôbart, Charlotte Wallaeys, H. de Rooster, Yannick Gansemans, Filip Van Nieuwerburgh, Bert Devriendt, Eric Cox
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2021.707217

Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients
Cited by: 9
Author(s): Miranda Houtman, Espen Hesselberg, Lars Rönnblom, Lars Klareskog, Vivianne Malmström, Leonid Padyukov
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-97430-0

Comparative transcriptional profiling of canine acanthomatous ameloblastoma and homology with human ameloblastoma
Cited by: 6
Author(s): Santiago Peralta, G Duhamel, William P. Katt, Kristiina Heikinheimo, Andrew D. Miller, Faraz Ahmed, Angela L. McCleary‐Wheeler, Jennifer K. Grenier
Software Mentions: 3
Published: about 3 years ago

10.15252/embr.201948155

Redistribution of <scp>EZH</scp> 2 promotes malignant phenotypes by rewiring developmental programmes
Cited by: 9
Author(s): Thomas Mortimer, Elanor N. Wainwright, Harshil Patel, Bernard Siow, Zane Jaunmuktane, Sebastian Brandner, Paola Scaffidi
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-018-4651-8

Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry
Cited by: 11
Author(s): Yang Jin, Rolf Erik Olsen, Mari‐Ann Östensen, Gareth Benjamin Gillard, Sven Arild Korsvoll, Nina Santi, Arne B. Gjuvsland, Jon Olav Vik, Jacob Torgersen, Simen Rød Sandve, Yngvar Ôlsen
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1008562

High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms
Cited by: 22
Author(s): Manja Czech-Sioli, Thomas Guenther, Marlin Therre, Michael Spohn, Daniela Indenbirken, Juliane Theiß, Sabine Riethdorf, Minyue Qi, Malik Alawi, Corinna Wülbeck, Irene Fernández-Cuesta, Franziska M. Esmek, Jürgen C. Becker, Adam Grundhoff, Nicole Fischer
Software Mentions: 3
Published: about 4 years ago

10.1186/s42523-021-00110-7

The link between broiler flock heterogeneity and cecal microbiome composition
Cited by: 13
Author(s): Randi Lundberg, Christian Scharch, Dorthe Sandvang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1005857

Staphylococcus aureus Exploits a Non-ribosomal Cyclic Dipeptide to Modulate Survival within Epithelial Cells and Phagocytes
Cited by: 47
Author(s): Sebastian Blättner, Sudip Das, Kerstin Paprotka, Ursula Eilers, Markus Krischke, Dorothee Kretschmer, Christian W. Remmele, Marcus Dittrich, Tobias Müller, Christina Sakarikou, Tobias Hertlein, Martin J. Mueller, Bruno Huettel, Richard Reinhardt, Knut Ohlsen, Thomas Rudel, Martin Fraunholz
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.ppat.1004156

Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model
Cited by: 71
Author(s): Pejman Mohammadi, Julia di Iulio, Miguel Muñoz, Raquel Martínez, István Bartha, Matthias Cavassini, Christian W. Thorball, Jacques Fellay, Niko Beerenwinkel, Angela Ciuffi, Amalio Telenti
Software Mentions: 3
Published: over 10 years ago

10.1016/j.devcel.2017.05.021

Distinct Roles of RNA Helicases MVH and TDRD9 in PIWI Slicing-Triggered Mammalian piRNA Biogenesis and Function
Cited by: 60
Author(s): Joanna M. Wenda, David Homolka, Zhaolin Yang, Pietro Spinelli, Ravi Sachidanandam, Radha Raman Pandey, Ramesh S. Pillai
Software Mentions: 3
Published: over 7 years ago

10.7150/jca.59348

Long non-coding RNA RP4-694A7.2 Promotes Hepatocellular Carcinoma Cell Proliferation and Metastasis through the Regulation of PSAT1
Cited by: 5
Author(s): Yaoxin Fan, Lin Wang, Yang Ding, Qiuju Sheng, Chong Zhang, Yanwei Li, Chao Han, Bao-Liang Lu, Xiao-guang Dou
Software Mentions: 3
Published: almost 4 years ago

10.3390/insects12040327

Gut Bacterial and Fungal Communities of the Wild and Laboratory-Reared Thitarodes Larvae, Host of the Chinese Medicinal Fungus Ophiocordyceps sinensis on Tibetan Plateau
Cited by: 11
Author(s): Guiqing Liu, Xin Zheng, Hailin Long, Zhongchen Rao, Li Cao, Richou Han
Software Mentions: 3
Published: over 3 years ago

10.1111/jam.13590

16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria
Cited by: 41
Author(s): George S. Watts, Ken Youens‐Clark, Marvin J. Slepian, Donna M. Wolk, Marc M. Oshiro, Gregory S. Metzger, Dalia Dhingra, Lee D. Cranmer, Bonnie Hurwitz
Software Mentions: 3
Published: about 7 years ago

10.1111/jcmm.16750

Identification and characterization of N6‐methyladenosine modification of circRNAs in glioblastoma
Cited by: 8
Author(s): Yuhao Zhang, Xiuchao Geng, Jintao Xu, Qiang Li, Liangchao Hao, Zhaomu Zeng, Menglin Xiao, Jia Song, Fulin Liu, Chuan Fang, Hong Wang
Software Mentions: 3
Published: over 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 thaliana
Cited 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

10.3389/fimmu.2020.02113

miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection
Cited by: 20
Author(s): Nardos Tesfaye Woldemariam, Oleg Agafonov, Hilde Sindre, Bjørn Høyheim, Ross D. Houston, Diego Robledo, James E. Bron, Rune Andreassen
Software Mentions: 3
Published: about 4 years ago

10.1080/19490976.2021.1951113

The effect of early probiotic exposure on the preterm infant gut microbiome development
Cited by: 19
Author(s): Yan Hui, Birgitte Smith, Martin Steen Mortensen, Łukasz Krych, Søren J. Sørensen, Gorm Greisen, Karen A. Krogfelt, Dennis Sandris Nielsen
Software Mentions: 3
Published: almost 4 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

10.1186/s12859-014-0357-3

NeatFreq: reference-free data reduction and coverage normalization for De Novosequence assembly
Cited by: 16
Author(s): Jamison McCorrison, Pratap Venepally, Indresh Singh, Derrick E. Fouts, Roger S. Lasken, Barbara A. Methé
Software Mentions: 3
Published: about 10 years ago

10.3389/fimmu.2020.00661

Neutrophil Extracellular Trap Induced Dendritic Cell Activation Leads to Th1 Polarization in Type 1 Diabetes
Cited 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

10.1128/IAI.00331-18

Genome Plasticity of agr -Defective Staphylococcus aureus during Clinical Infection
Cited by: 45
Author(s): Deena R. Altman, Mitchell J. Sullivan, Kieran I. Chacko, Divya Balasubramanian, Theodore R. Pak, William E. Sause, Krishan Kumar, Robert Sebra, Gintaras Deikus, Oliver Attie, Hannah Rose, Martha Lewis, Yi Fulmer, Ali Kashif Bashir, Andrew Kasarskis, Eric E. Schadt, Anthony R. Richardson, Victor J. Torres, Bo Shopsin, Harm van Bakel
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.ppat.1009494

The multi-functional reovirus σ3 protein is a virulence factor that suppresses stress granule formation and is associated with myocardial injury
Cited by: 14
Author(s): Yingying Guo, Meleana M. Hinchman, Mercedes Lewandrowski, Shaun T. Cross, Danica M. Sutherland, Olivia L. Welsh, Terence S. Dermody, John S. L. Parker
Software Mentions: 3
Published: over 3 years ago

10.1093/dnares/dsaa005

Feeding exogenous dsRNA interferes with endogenous sRNA accumulation in Paramecium
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

10.3389/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

10.1093/gigascience/giz059

A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)
Cited by: 13
Author(s): Bruno Louro, Gianluca De Moro, Carlos M.E.V.R. Garcia, Cymon J. Cox, Ana Veríssimo, Stephen J. Sabatino, António M. Santos, Adelino V.M. Canário
Software Mentions: 3
Published: over 5 years ago

10.1016/j.molcel.2020.03.017

Division of Labor between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment
Cited by: 39
Author(s): Hon Wing Liu, Céline Bouchoux, Mélanie Panarotto, Yasutaka Kakui, Harshil Patel, Frank Uhlmann
Software Mentions: 3
Published: over 4 years ago

10.1038/s42003-020-01289-2

The E3 ubiquitin ligase HectD3 attenuates cardiac hypertrophy and inflammation in mice
Cited by: 14
Author(s): Ashraf Yusuf Rangrez, Ankush Borlepawar, Nesrin Schmiedel, Anushka Deshpande, Anca Remes, Manju Kumari, Alexander Bernt, Lynn Christen, Andreas O. Helbig, Andreas Jungmann, Samuel Sossalla, Andreas Tholey, Oliver Müller, Norbert Frey
Software Mentions: 3
Published: about 4 years ago

10.1093/gigascience/gix040

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation
Cited by: 52
Author(s): Peter R. Sternes, Danna Lee, Dariusz R. Kutyna, Anthony R. Borneman
Software Mentions: 3
Published: over 7 years ago

10.1093/gigascience/giy084

SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data
Cited by: 11
Author(s): Carlo Yague-Sanz, Damien Hermand
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.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

10.1186/s12862-017-0888-0

Phylogeography of red muntjacs reveals three distinct mitochondrial lineages
Cited by: 23
Author(s): Raquel A. Martins, Jörns Fickel, Minh Đức Lê, Thanh Van Nguyen, Ha L. Nguyen, Robert J. Timmins, Han Ming Gan, Jeffrine J. Rovie-Ryan, Dorina Lenz, Daniel W. Förster, Andreas Wilting
Software Mentions: 3
Published: almost 8 years ago

10.1002/ctm2.201

Long noncoding RNA lncGALM increases risk of liver metastasis in gallbladder cancer through facilitating N‐cadherin and IL‐1β‐dependent liver arrest and tumor extravasation
Cited by: 8
Author(s): Huaifeng Li, Yunping Hu, Yunpeng Jin, Yi Zhu, Yajuan Hao, Fatao Liu, Yang Yang, Guoqiang Li, Xiaoling Song, Yuanyuan Ye, Sheng Xiang, Yuan Gao, Jinhui Zhu, Yijian Zhang, Lin Jiang, Wen Huang, Jian Zhu, Xiangsong Wu, Yingbin Liu
Software Mentions: 3
Published: about 4 years ago

10.1186/s13073-015-0251-2

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly
Cited by: 39
Author(s): Rendong Yang, Andrew C. Nelson, Christine Henzler, Bharat Thyagarajan, Kevin A.T. Silverstein
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13148-021-01121-6

Methylation status of genes escaping from X-chromosome inactivation in patients with X-chromosome rearrangements
Cited by: 1
Author(s): Sayaka Kawashima, Atsushi Hattori, Erina Suzuki, Kazuo Matsubara, Machiko Toki, Rika Kosaki, Yukihiro Hasegawa, Kazuhiko Nakabayashi, Maki Fukami, Masayo Kagami
Software Mentions: 3
Published: over 3 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

10.1186/s13148-018-0565-1

Prediction of smoking by multiplex bisulfite PCR with long amplicons considering allele-specific effects on DNA methylation
Cited by: 11
Author(s): Nikolay Kondratyev, Arkadiy K. Golov, М. В. Алфимова, Т. В. Лежейко, В. Е. Голимбет
Software Mentions: 3
Published: about 6 years ago

10.3389/fimmu.2012.00386

Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing
Cited by: 13
Author(s): Miri Michaeli, Hila Noga, Hilla Tabibian‐Keissar, Iris Barshack, Ramit Mehr
Software Mentions: 3
Published: almost 13 years ago

10.3390/cells10071718

Epigenetic Drifts during Long-Term Intestinal Organoid Culture
Cited by: 5
Author(s): Torsten Thalheim, Susann Siebert, Marianne Quaas, Maria Herberg, Michal R. Schweiger, Gabriela Aust, Joerg Galle
Software Mentions: 3
Published: over 3 years ago

10.1093/molbev/msab061

The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in Drosophila
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

10.1093/gbe/evab042

A De Novo Transcriptome Assembly ofCeratopteris richardiiProvides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants
Cited by: 21
Author(s): Yichao Geng, Chao Cai, Scott A. M. McAdam, Jo Ann Banks, Jennifer H. Wisecaver, Yun Zhou
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-98018-4

Handling of targeted amplicon sequencing data focusing on index hopping and demultiplexing using a nested metabarcoding approach in ecology
Cited by: 13
Author(s): Yasemin Guenay-Greunke, David Bohan, Michael Traugott, Corinna Wallinger
Software Mentions: 3
Published: about 3 years ago

10.3390/cells10071730

Pathophysiological Effects of Overactive STIM1 on Murine Muscle Function and Structure
Cited by: 9
Author(s): Roberto Silva‐Rojas, Anne Charles, Sarah Djeddi, Bernard Gény, Jocelyn Laporte
Software Mentions: 3
Published: over 3 years ago

10.3390/cells9051272

Secretome of Mesenchymal Stromal Cells Prevents Myofibroblasts Differentiation by Transferring Fibrosis-Associated microRNAs within Extracellular Vesicles
Cited by: 40
Author(s): Nataliya Basalova, Georgy Sagaradze, Mikhail Arbatskiy, Evgeniy G. Evtushenko, Konstantin Kulebyakin, Olga Grigorieva, Zhanna Akopyan, Kalinina Ni, Anastasia Efimenko
Software Mentions: 3
Published: over 4 years ago

10.1186/s13229-019-0285-1

RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation
Cited 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/s12885-018-4567-3

Deep sequencing of human papillomavirus positive loco-regionally advanced oropharyngeal squamous cell carcinomas reveals novel mutational signature
Cited by: 13
Author(s): Christian Grónhøj Larsen, David Hebbelstrup Jensen, Tina Klitmøller Agander, Katalin Kiss, Estrid Høgdall, Lena Specht, Frederik Otzen Bagger, Finn Cilius Nielsen
Software Mentions: 3
Published: over 6 years ago

10.1016/j.celrep.2019.02.077

Oxidative Stress Triggers Selective tRNA Retrograde Transport in Human Cells during the Integrated Stress Response
Cited by: 32
Author(s): Hagen Schwenzer, Frank Jühling, Alexander L. Chu, Laura J. Pallett, Thomas F. Baumert, Mala K. Maini, Ariberto Fassati
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2995-5

RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.)
Cited by: 57
Author(s): Kazuma Suzuki, Tomohiro Suzuki, Takashi Nakatsuka, Hideo Dohra, Masumi Yamagishi, Kohei Matsuyama, Hideyuki Matsuura
Software Mentions: 3
Published: over 8 years ago

Projects: pypi: cutadapt

Papers Mentioning cutadapt 1,562