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

10.1371/journal.pone.0187617
Identification of a t(3;4)(p1.3;q1.5) translocation breakpoint in pigs using somatic cell hybrid mapping and high-resolution mate-pair sequencing
Cited by: 2
Author(s): Katia Fève, Sylvain Foissac, Alain Pinton, Florence Mompart, Diane Esquerré, Thomas Faraut, Martine M. Yerle, Juliette Riquet
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.pone.0191570
Target discovery screens using pooled shRNA libraries and next-generation sequencing: A model workflow and analytical algorithm
Cited by: 10
Author(s): Christiane Schaefer, Nikhil Mallela, Jochen Seggewiß, Birgit Lechtape, Heymut Omran, Uta Dirksen, Eberhard Korsching, Jenny Potratz
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pone.0100572
Single-Step Selection of Bivalent Aptamers Validated by Comparison with SELEX Using High-Throughput Sequencing
Cited by: 24
Author(s): Robert Wilson, Christian Bourne, Roy R. Chaudhuri, Richard I. Gregory, John Kenny, Andrew R. Cossins
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0178483
ToNER: A tool for identifying nucleotide enrichment signals in feature-enriched RNA-seq data
Cited by: 4
Author(s): Yuttachon Promworn, Pavita Kaewprommal, Philip Shaw, Apichart Intarapanich, Sissades Tongsima, Jittima Piriyapongsa
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0094098
De Novo Transcriptome Hybrid Assembly and Validation in the European Earwig (Dermaptera, Forficula auricularia)
Cited by: 15
Author(s): Anne Roulin, Min Wu, Samuel Pichon, Roberto Arbore, Simone Kühn-Bühlmann, Mathias Kölliker, Jean‐Claude Walser
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0247180
Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1)
Cited by: 4
Author(s): Fu‐Jin Wei, S. Ueno, Tokuko Ujino‐Ihara, Maki Saito, Yoshihiko Tsumura, Yuumi Higuchi, Satoko Hirayama, Junji Iwai, Tetsuji Hakamata, Yoshinari Moriguchi
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0091851
Sequencing Degraded RNA Addressed by 3' Tag Counting
Cited by: 84
Author(s): Bárður Sigurgeirsson, Olof Emanuelsson, Joakim Lundeberg
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0145065
One Step Forward, Two Steps Back; Xeno-MicroRNAs Reported in Breast Milk Are Artifacts
Cited by: 26
Author(s): Caner Bağcı, Jens Allmer
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pone.0148698
Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies
Cited by: 91
Author(s): James L. O’Donnell, Ryan P. Kelly, Natalie Lowell, Jesse A. Port
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0161370
Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology
Cited by: 14
Author(s): Chandra Shekhar Pareek, Rafał Smoczyński, Haja N. Kadarmideen, Piotr Dziuba, Paweł Błaszczyk, Marcin Sikora, Paulina Walendzik, Tomasz Grzybowski, M. Pierzchała, Jarosław Olav Horbańczuk, Agnieszka Szostak, Magdalena Ogłuszka, L. Zwierzchowski, Urszula Czarnik, Leyland Fraser, Przemysław Sobiech, Krzysztof Wa̧sowicz, Brian Gelfand, Yaping Feng, Dibyendu Kumar
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0152322
Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments
Cited by: 12
Author(s): Gordon R. McInroy, Dario Beraldi, Eun‐Ang Raiber, Katarzyna Modrzynska, Pieter van Delft, Oliver Billker, Shankar Balasubramanian
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0078280
Evidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse
Cited by: 116
Author(s): Rebecca R. Bellone, Heather M. Holl, Vijayasaradhi Setaluri, Sulochana Devi, Nityanand Maddodi, Sheila Archer, Lynne S Sandmeyer, Arne Ludwig, Daniel W. Foerster, Mélanie Pruvost, Monika Reißmann, Ralf Bortfeldt, David L. Adelson, Seng Han Lim, Janelle Nelson, Bianca Haase, Martina Engensteiner, Tosso Leeb, G. W. Forsyth, Michael J. Mienaltowski, Padmanabhan Mahadevan, Michael Hofreiter, Johanna L. A. Paijmans, Gloria G. Fortes, Bruce H Grahn, Samantha A. Brooks
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0202022
Rare gene deletions in genetic generalized and Rolandic epilepsies
Cited by: 4
Author(s): Kamel Jabbari, Dheeraj Reddy Bobbili, Dennis Lal, Eva M. Reinthaler, Julian Schubert, Stefan Wolking, Vishal Sinha, Susanne Motameny, Holger Thiele, Amit Kawalia, Janine Altmüller, Mohammad Reza Toliat, Robert Kraaij, Jeroen van Rooij, André G. Uitterlinden, M. Arfan Ikram, Federico Zara, Anna‐Elina Lehesjoki, Roland Krause, Fritz Zimprich, Thomas Sander, Bernd A. Neubauer, Patrick May, Holger Lerche, Peter Nürnberg
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0109831
A Transcriptome for the Study of Early Processes of Retinal Regeneration in the Adult Newt, Cynops pyrrhogaster
Cited by: 36
Author(s): Kenta Nakamura, Md. Rafiqul Islam, Miyako Takayanagi, Hirofumi Yasumuro, Wataru Inami, Ailidana Kunahong, Roman Martin Casco-Robles, Fubito Toyama, Chikafumi Chiba
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pone.0200207
Expansion of Capsicum annum fruit is linked to dynamic tissue-specific differential expression of miRNA and siRNA profiles
Cited by: 8
Author(s): Dénes Taller, Jeannette Bálint, Péter Gyula, Tibor Nagy, Ivett Baksa, György Szittya, János Taller
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0197364
Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces)
Cited by: 14
Author(s): Ida-Maria Blåhed, Helena Königsson, Göran Ericsson, Göran Spong
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0165691
Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects
Cited by: 15
Author(s): Ruth R. Miller, Miguel Uyaguari, Mark McCabe, Vincent Montoya, Jennifer L. Gardy, Shoshana Parker, Theodore S. Steiner, William W. L. Hsiao, Matthew J. Nesbitt, Patrick Tang, David M. Patrick
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0256969
Is soil management system really important? comparison of microbial community diversity and structure in soils managed under organic and conventional regimes with some view on soil properties
Cited by: 6
Author(s): Kamila Rachwał, Klaudia Gustaw, Waldemar Kazimierczak, Adam Waśko
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0170199
Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing
Cited by: 100
Author(s): Mathis Hjort Hjelmsø, Maria Hellmér, Xavier Fernández-Cassi, Natàlia Timoneda, Oksana Lukjancenko, Michael Seidel, Dennis Elsäßer, Frank Møller Aarestrup, Charlotta Löfström, Sı́lvia Bofill-Mas, Josep F. Abril, Rosina Gironés, Anna Charlotte Schultz
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0201635
Response to early drought stress and identification of QTLs controlling biomass production under drought in pearl millet
Cited by: 37
Author(s): Maryline Debieu, Bassirou Sine, Sixtine Passot, Alexandre Grondin, Eyanawa A. Akata, Prakash Gangashetty, Vincent Vadez, Pascal Gantet, Daniel Foncéka, Laurent Cournac, C. T. Hash, Ndjido Ardo Kane, Yves Vigouroux, Laurent Laplaze
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0210586
Contrasting patterns of gene expression indicate differing pyrethroid resistance mechanisms across the range of the New World malaria vector Anopheles albimanus
Cited by: 19
Author(s): Lucy Mackenzie-Impoinvil, Gareth D. Weedall, Juan C. Lol, Jesús Pinto, Lucrecia Vizcaino, Nicole Dzuris, Jacob M. Riveron, Norma Padilla, Charles S. Wondji, Audrey Lenhart
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0196518
Differentially expressed microRNAs associated with changes of transcript levels in detoxification pathways and DDT-resistance in the Drosophila melanogaster strain 91-R
Cited by: 15
Author(s): Keon Mook Seong, Brad S. Coates, Do hyup Kim, Allison K. Hansen, Barry R. Pittendrigh
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0227067
Immunomodulatory function of the cystic fibrosis modifier gene BPIFA1
Cited by: 9
Author(s): Aabida Saferali, Allen Tang, Lisa J. Strug, Bradley S. Quon, James E. A. Zlosnik, Andrew J. Sandford, Stuart E. Turvey
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0234385
Ancestral mitogenome capture of the Southeast Asian banded linsang
Cited by: 9
Author(s): Johanna L. A. Paijmans, Axel Barlow, Kirstin Henneberger, Joerns Fickel, Michael Hofreiter, Daniel W. Foerster
Software Mentions: 2
Published: over 4 years ago
10.3390/cancers13020285
The Calcitriol/Vitamin D Receptor System Regulates Key Immune Signaling Pathways in Chronic Lymphocytic Leukemia
Cited by: 2
Author(s): Marina Gerousi, Fotis Psomopoulos, Konstantia Kotta, Maria Tsagiopoulou, Niki Stavroyianni, Αchilles Anagnostopoulos, Athanasios Anastasiadis, Maria Gkanidou, Ιoannis Kotsianidis, Stavroula Ntoufa, Kostas Stamatopoulos
Software Mentions: 2
Published: almost 4 years ago
10.3390/cancers12030769
Accessing a New Dimension in TP53 Biology: Multiplex Long Amplicon Digital PCR to Specifically Detect and Quantitate Individual TP53 Transcripts
Cited by: 8
Author(s): Annette Lasham, Peter Tsai, Sandra Fitzgerald, Sunali Mehta, Nicholas Knowlton, Antony W. Braithwaite, Cristin G. Print
Software Mentions: 2
Published: over 4 years ago
10.3390/cancers12051219
Novel Gene Fusions in Glioblastoma Tumor Tissue and Matched Patient Plasma
Cited by: 10
Author(s): Lan Wang, Anudeep Yekula, Koushik Muralidharan, Julia L. Small, Zachary S. Rosh, Keiko M. Kang, Bob S. Carter, Leonora Balaj
Software Mentions: 2
Published: over 4 years ago
10.1038/s41419-021-04016-9
The m6A mRNA demethylase FTO in granulosa cells retards FOS-dependent ovarian aging
Cited by: 30
Author(s): Zucheng Jiang, Yining Wang, Zi-Yuan Li, Zhihui Dai, Yi He, Kun Chu, Jiayi Gu, Yixuan Ji, Ning Sun, Li Wen
Software Mentions: 2
Published: over 3 years ago
10.1038/s41421-019-0116-8
Pwp1 regulates telomere length by stabilizing shelterin complex and maintaining histone H4K20 trimethylation
Cited by: 5
Author(s): Yangyang Yu, Wenwen Jia, Yao Lyu, Dingwen Su, Mingliang Bai, Junwei Shen, Jing Qiao, Tong Han, Wenqiang Liu, Jiayu Chen, Wen Chen, Dan Ye, Xudong Guo, Shifeng Zhu, Jiajie Xi, Rong Zhu, Xiaoping Wan, Shaorong Gao, Jiyue Zhu, Jiuhong Kang
Software Mentions: 2
Published: about 5 years ago
10.1007/s00018-019-03217-y
miR-221 and -222 target CACNA1C and KCNJ5 leading to altered cardiac ion channel expression and current density
Cited by: 20
Author(s): Stephanie Binas, Maria Knyrim, Julia Hupfeld, Udo Kloeckner, Sindy Rabe, Sigrid Mildenberger, Katja Quarch, Nicole Strätz, Danny Misiak, Michael Gekle, Claudia Großmann, Barbara Schreier
Software Mentions: 2
Published: over 5 years ago
10.1007/s00018-018-2842-8
Immune stimuli shape the small non-coding transcriptome of extracellular vesicles released by dendritic cells
Cited by: 49
Author(s): Tom A.P. Driedonks, Susanne G. van der Grein, Yavuz Ariyürek, Henk P.J. Buermans, Henrike Jekel, Wang Ngai Chow, Marca H. M. Wauben, Amy H. Buck, Peter A.C. ’t Hoen, Esther N. M. Nolte‐‘t Hoen
Software Mentions: 2
Published: over 6 years ago
10.1016/j.celrep.2020.108643
Transcription levels of a noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast
Cited by: 10
Author(s): Fabien Moretto, N. Ezgi Wood, Minghao Chia, Cai Li, Nicholas M. Luscombe, Folkert J. van Werven
Software Mentions: 2
Published: almost 4 years ago
10.1016/j.celrep.2020.107833
Labeling and Characterization of Human GLP-1-Secreting L-cells in Primary Ileal Organoid Culture
Cited by: 41
Author(s): Deborah A. Goldspink, Van B. Lu, Emily L Miedzybrodzka, Christopher A. Smith, Rachel E. Foreman, Lawrence J. Billing, Richard G. Kay, Frank Reimann, Fiona M. Gribble
Software Mentions: 2
Published: over 4 years ago
10.1038/cr.2017.25
De novo DNA methylation during monkey pre-implantation embryogenesis
Cited by: 42
Author(s): Fei Gao, Yuyu Niu, Yi Sun, Hanlin Lu, Yongchang Chen, Siguang Li, Yu Kang, Yuan Luo, Chenyang Si, Juehua Yu, Li Chang, Nianqin Sun, Wei Si, Hong Wang, Weizhi Ji, Tao Tan
Software Mentions: 2
Published: over 7 years ago
10.1038/s41422-021-00477-x
Formative pluripotent stem cells show features of epiblast cells poised for gastrulation
Cited by: 42
Author(s): Xiaoxiao Wang, Yunlong Xiang, Yang Yu, Ran Wang, Yu Zhang, Qianhua Xu, Hao Sun, Zhen Zhao, Xiangxiang Jiang, Xiaoqing Wang, Xukun Lu, Dandan Qin, Yujun Quan, Jiaqi Zhang, Ng Shyh‐Chang, Hongmei Wang, Naihe Jing, Wei Xie, Lei Li
Software Mentions: 2
Published: almost 4 years ago
10.3390/cells9092007
Tributyrin Attenuates Metabolic and Inflammatory Changes Associated with Obesity through a GPR109A-Dependent Mechanism
Cited by: 22
Author(s): Fábio Takeo Sato, Yu Anne Yap, Amanda Rabello Crisma, Mariana Portovedo, Gilson Masahiro Murata, Sandro Massao Hirabara, Willian R. Ribeiro, Caroline M. Ferreira, Maysa Mariana Cruz, Joice Naiara Bertaglia Pereira, Tanyara Baliani Payolla, Suzana Eiko Sato Guima, Andrew Maltez Thomas, João Carlos Setúbal, Maria Isabel Cardoso Alonso-Vale, Marinilce Fagundes dos Santos, Rui Curi, Eliana Mariño, Marco Aurélio Ramirez Vinolo
Software Mentions: 2
Published: about 4 years ago
10.3390/cells8111393
rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment
Cited by: 12
Author(s): Nickolai A. Tchurikov, Д. М. Федосеева, Elena S. Klushevskaya, I. Y. Slovohotov, V. R. Chechetkin, Yuri V. Kravatsky, О. В. Кретова
Software Mentions: 2
Published: about 5 years ago
10.1186/s13601-019-0267-6
A specific synbiotic-containing amino acid-based formula restores gut microbiota in non-IgE mediated cow’s milk allergic infants: a randomized controlled trial
Cited by: 21
Author(s): Harm Wopereis, Marleen T. J. van Ampting, Aysun Cetinyurek-Yavuz, R. A. Slump, D. C. A. Candy, Assad Butt, Diego Peroni, Yvan Vandenplas, Adam Fox, Neil Shah, Guus Roeselers, Lucien F. Harthoorn, Louise J. Michaelis, Jan Knol, Christina West
Software Mentions: 2
Published: over 5 years ago
10.1002/ctm2.200
The noncoding and coding transcriptional landscape of the peripheral immune response in patients with COVID‐19
Cited by: 101
Author(s): Hao Tang, Yuehan Gao, Zhaohuai Li, Yushan Miao, Zhaofeng Huang, Xiuxing Liu, Lihui Xie, Li He, Wen Wen, Yingfeng Zheng, Wenru Su
Software Mentions: 2
Published: about 4 years ago
10.1038/s42003-020-01543-7
Systemic viral spreading and defective host responses are associated with fatal Lassa fever in macaques
Cited by: 17
Author(s): Nicolas Baillet, Stéphanie Reynard, Émeline Perthame, Jimmy Hortion, Alexandra Journeaux, Mathieu Mateo, Xavier Carnec, Justine Schaeffer, Caroline Picard, Laura Barrot, Stéphane Barron, Audrey Vallvé, Aurélie Duthey, Frédéric Jacquot, Cathy Boehringer, Grégory Jouvion, Natalia Pietrosemoli, Rachel Legendre, Marie‐Agnès Dillies, Richard Allan, Catherine Legras-Lachuer, Caroline Carbonnelle, Hervé Raoul, Sylvain Baize
Software Mentions: 2
Published: almost 4 years ago
10.1093/dnares/dsz021
The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L.
Cited by: 22
Author(s): Ayasha Akter, Satoshi Takahashi, Wei‐Wei Deng, Daniel J. Shea, Etsuko Itabashi, Mitsuru Shimizu, Noriaki Miyaji, Kenji Osabe, Namiko Nishida, Yutaka Suzuki, Chris A. Helliwell, Motoaki Seki, W. James Peacock, Elizabeth S. Dennis, Ryo Fujimoto
Software Mentions: 2
Published: about 5 years ago
10.1016/j.dib.2018.09.038
Data on transcriptome profiling of circulating microRNAs in dairy cattle
Cited by: 0
Author(s): Kesavan Markkandan, Hyun-Joo Lim, Dong Jin Lee, In-gang Shin, Seung-il Yoo, Chang Gwon Dang, Chang Pyo Hong, Kung Ahn
Software Mentions: 2
Published: almost 6 years ago
10.1016/j.dib.2020.106570
RNA sequencing data from osteochondroprogenitor populations in synovial joints of mice during murine model of rheumatoid arthritis
Cited by: 2
Author(s): Nina Batorek-Lukač, Vedran Katavić, Alan Šućur, Maša Filipović, Danka Grčević, Nataša Kovačić
Software Mentions: 2
Published: almost 4 years ago
10.15252/embj.201694857
TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs
Cited by: 84
Author(s): Dmytro Ustianenko, Josef Pasulka, Zuzana Feketová, Lukas Bednarik, Dagmar Zigáčková, Andrea Fořtová, Mihaela Zavolan, Štěpánka Vaňáčová
Software Mentions: 2
Published: about 8 years ago
10.15252/embj.2020104579
Involvement of circulating factors in the transmission of paternal experiences through the germline
Cited by: 17
Author(s): Gretchen van Steenwyk, Katharina Gapp, Ali Jawaid, Pierre-Luc Germain, Francesca Manuella, Deepak K Tanwar, Nicola Zamboni, Niharika Gaur, Anastasiia Efimova, Kristina Thumfart, Eric A. Miska, Isabelle M. Mansuy
Software Mentions: 2
Published: about 4 years ago
10.15252/emmm.201505696
Accumulated common variants in the broader fragile X gene family modulate autistic phenotypes
Cited by: 35
Author(s): Beata Stepniak, Anne Kästner, Giulia Poggi, Marina Mitjans, Martin Begemann, Annette M. Hartmann, Sandra Van der Auwera, Farahnaz Sananbenesi, Dilja Krueger‐Burg, Gabriela Matuszko, Cornelia Brosi, Georg Homuth, Henry Völzke, Fritz Benseler, Claudia Bagni, Utz Fischer, Alexander Dityatev, Hans‐Jörgen Grabe, Dan Rujescu, André Fischer, Hannelore Ehrenreich
Software Mentions: 2
Published: almost 9 years ago
10.15252/emmm.202012523
Pharmacological reversal of synaptic and network pathology in human <i>MECP2</i> ‐KO neurons and cortical organoids
Cited by: 45
Author(s): Cleber A. Trujillo, Jason W Adams, Priscilla D. Negraes, Cassiano Carromeu, Leon Tejwani, Allan Acab, Ben Tsuda, Charles A. Thomas, Neha Sodhi, Katherine M Fichter, Sarah Romero, Fabian Zanella, Terrence J. Sejnowski, Henning Ulrich, Alysson R. Muotri
Software Mentions: 2
Published: almost 4 years ago
10.15252/emmm.202013545
Modeling, optimization, and comparable efficacy of T cell and hematopoietic stem cell gene editing for treating hyper‐IgM syndrome
Cited by: 28
Author(s): Valentina Vavassori, E. Mercuri, Genni Enza Marcovecchio, Maria Carmina Castiello, Giulia Schiroli, Luisa Albano, Carrie M Margulies, Frank A. Buquicchio, Elena Fontana, Stefano Beretta, Ivan Merelli, Andrea Cappelleri, Paola Mv Rancoita, Vassilios Lougaris, Alessandro Plebani, Maria Kanariou, Arjan C. Lankester, Francesca Ferrua, Eugenio Scanziani, Cecilia Cotta‐Ramusino, Anna Villa, Luigi Naldini, Pietro Genovese
Software Mentions: 2
Published: almost 4 years ago
10.1002/ece3.6082
Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA
Cited by: 11
Author(s): Grace Moore, Michael Tessler, Seth W. Cunningham, Julio L. Betancourt, Robert S. Harbert
Software Mentions: 2
Published: almost 5 years ago
10.1002/ece3.5614
Prokaryotic taxa play keystone roles in the soil microbiome associated with woody perennial plants in the genus<i>Buxus</i>
Cited by: 8
Author(s): Nicholas LeBlanc, Jo Anne Crouch
Software Mentions: 2
Published: about 5 years ago
10.1111/1462-2920.15064
Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value
Cited by: 14
Author(s): Güadalupe Piñar, Hakim Tafer, Manfred Schreiner, Heinz Miklas, Katja Sterflinger
Software Mentions: 2
Published: over 4 years ago
10.1186/s13072-021-00389-5
A cookbook for DNase Hi-C
Cited by: 9
Author(s): Maria Gridina, Evgeniy A. Mozheiko, Э. С. Валеев, Л. П. Назаренко, М. Е. Лопаткина, Ж. Г. Маркова, M. I. Yablonskaya, Viktoria Yu Voinova, N.V. Shilova, I. N. Lebedev, Veniamin Fishman
Software Mentions: 2
Published: over 3 years ago
10.1186/s13072-018-0211-3
DNA methylation analysis on purified neurons and glia dissects age and Alzheimer’s disease-specific changes in the human cortex
Cited by: 158
Author(s): Gilles Gasparoni, Sebastian Bultmann, Pavlo Lutsik, Theo Kraus, Sabrina Sordon, Julia Vlcek, Vanessa Dietinger, Martina Steinmaurer, Melanie Haider, Christopher B. Mulholland, Thomas Arzberger, Sigrun Roeber, Matthias Riemenschneider, Hans A. Kretzschmar, Armin Giese, Heinrich Leonhardt, Jörn Walter
Software Mentions: 2
Published: over 6 years ago
10.1186/s13072-019-0278-5
MYC deregulates TET1 and TET2 expression to control global DNA (hydroxy)methylation and gene expression to maintain a neoplastic phenotype in T-ALL
Cited by: 20
Author(s): Candace J. Poole, Atul Lodh, Jeong Hyeon Choi, Jan van Riggelen
Software Mentions: 2
Published: over 5 years ago
10.1111/eva.12954
Transcriptional differentiation of UV‐B protectant genes in maize landraces spanning an elevational gradient in Chiapas, Mexico
Cited by: 6
Author(s): Matthew A. Kost, Hugo Perales, Saranga Wijeratne, Asela J. Wijeratne, Eric J. Stockinger, Kristin L. Mercer
Software Mentions: 2
Published: over 4 years ago
10.1111/eva.12566
Predicting the genetic impact of stocking in Brook Charr (<i>Salvelinus fontinalis</i>) by combining <scp>RAD</scp> sequencing and modeling of explanatory variables
Cited by: 37
Author(s): Justine Létourneau, Anne‐Laure Ferchaud, Jérémy Le Luyer, Martin Laporte, Dany Garant, Louis Bernatchez
Software Mentions: 2
Published: about 7 years ago
10.1096/fj.201900071R
<i>APOE</i>genotype influences the gut microbiome structure and function in humans and mice: relevance for Alzheimer's disease pathophysiology
Cited by: 114
Author(s): Tam Tran, Simone Corsini, Lee Kellingray, Claire Hegarty, Gwénaëlle Le Gall, Arjan Narbad, Michael Müller, Noemı́ Tejera, Paul W. O’Toole, Anne‐Marie Minihane, David Vauzour
Software Mentions: 2
Published: over 5 years ago
10.1002/2211-5463.12803
Potential prognostic impact of EBV RNA‐seq reads in gastric cancer: a reanalysis of The Cancer Genome Atlas cohort
Cited by: 4
Author(s): Daichi Sadato, Mina Ogawa, Chizuko Hirama, Tsunekazu Hishima, Shinichiro Horiguchi, Yuka Harada, Tatsu Shimoyama, Masanari Itokawa, Kazuteru Ohashi, Keisuke Oboki
Software Mentions: 2
Published: almost 5 years ago
10.3389/fnbeh.2015.00255
Differentially expressed genes linked to natural variation in long-term memory formation in Cotesia parasitic wasps
Cited by: 7
Author(s): Joke J.F.A. van Vugt, Katja M. Hoedjes, H.C. van de Geest, Elio W. G. M. Schijlen, Louise E. M. Vet, Hans M. Smid
Software Mentions: 2
Published: about 9 years ago
10.3389/fbioe.2020.582052
Production of the Fragrance Geraniol in Peroxisomes of a Product-Tolerant Baker’s Yeast
Cited by: 17
Author(s): Jennifer Gerke, Holm Frauendorf, Dominik Schneider, Maxim Wintergoller, Thomas Hofmeister, Anja Poehlein, Žiga Zebec, Eriko Takano, Nigel S. Scrutton, Gerhard H. Braus
Software Mentions: 2
Published: about 4 years ago
10.3389/fbioe.2018.00202
The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan
Cited by: 24
Author(s): Eri Nishiyama, Koichi Higashi, Hiroshi Mori, K. Suda, Hitomi Nakamura, Soichi Omori, Shigenori Maruyama, Yuichi Hongoh, Ken Kurokawa
Software Mentions: 2
Published: almost 6 years ago
10.3389/fcell.2019.00264
TRIBE Uncovers the Role of Dis3 in Shaping the Dynamic Transcriptome in Malaria Parasites
Cited by: 9
Author(s): Meng Liu, Binbin Lu, Yanting Fan, Xiaohong He, Shijun Shen, Cizhong Jiang, Qingfeng Zhang
Software Mentions: 2
Published: about 5 years ago
10.3389/fcell.2021.705986
N6 -Methyladenosine Modification in Chronic Stress Response Due to Social Hierarchy Positioning of Mice
Cited by: 3
Author(s): Malena dos Santos Guilherme, Theodora Tsoutsouli, Hristo Todorov, Sina Teifel, Vu Thu Thuy Nguyen, Susanne Gerber, Kristina Endres
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2021.627347
Multi-Omics Analysis to Examine Gene Expression and Metabolites From Multisite Adipose-Derived Mesenchymal Stem Cells
Cited by: 3
Author(s): Chuanxi Yang, Jing Zhang, Tingting Wu, Kun Zhao, Xiaoguang Wu, Jing Shi, Wei Sun, Xiangqing Kong
Software Mentions: 2
Published: almost 4 years ago
10.3389/fgene.2021.724527
High-Throughput Sequencing-Based Identification of miRNAs and Their Target mRNAs in Wheat Variety Qing Mai 6 Under Salt Stress Condition
Cited by: 2
Author(s): Xiaoyan He, Zhen Han, Huayan Yin, Fan Chen, Yihuan Dong, Lufei Zhang, Xiaoyan Lu, Jianbin Zeng, Wujun Ma, Mu Peng
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2021.642602
Comprehensive Identification and Alternative Splicing of Microexons in Drosophila
Cited by: 3
Author(s): Ting-Lin Pang, Zhan Ding, Shuli Liang, Liang Li, Bei Zhang, Yu Zhang, Yujie Fan, Yan Xu
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2020.561566
The N6-Methyladenosine Features of mRNA and Aberrant Expression of m6A Modified Genes in Gastric Cancer and Their Potential Impact on the Risk and Prognosis
Cited by: 6
Author(s): Shuli Liang, Liping Sun, Ang Wang, Han Zhang, Yuan Yuan
Software Mentions: 2
Published: about 4 years ago
10.3389/fgene.2021.633125
Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus
Cited by: 3
Author(s): Dayle Johnston, Bernadette Earley, Matthew S. McCabe, Jae-Woo Kim, Jeremy F. Taylor, Ken Lemon, Michael McMenamy, Catherine Duffy, S. L. Cosby, Sinéad M. Waters
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2021.695178
Changthangi Pashmina Goat Genome: Sequencing, Assembly, and Annotation
Cited by: 0
Author(s): Basharat Ahmad Bhat, Nazir Ahmad Ganai, Ashutosh Singh, Rakeeb Ahmad Mir, Syed Mudasir Ahmad, Sajad Majeed Zargar, Firdose Ahmad Malik
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2020.00166
Upstream ORFs Influence Translation Efficiency in the Parasite Trypanosoma cruzi
Cited by: 7
Author(s): Santiago Radío, Beatríz Garat, José Sotelo‐Silveira, Pablo Smircich
Software Mentions: 2
Published: over 4 years ago
10.3389/fimmu.2018.00638
Immunization Elicits Antigen-Specific Antibody Sequestration in Dorsal Root Ganglia Sensory Neurons
Cited by: 14
Author(s): Manojkumar Gunasekaran, Prodyot K. Chatterjee, Andrew Shih, Gavin H. Imperato, Meghan Addorisio, Gopal Kumar, Annette Lee, John Graf, Dan E. Meyer, Michael Marino, Christopher M. Puleo, Jeffrey Ashe, Maureen A. Cox, Tak W. Mak, Chad Bouton, Barbara Sherry, Betty Diamond, Ulf Andersson, Thomas R. Coleman, Christine N. Metz, Kevin J. Tracey, Sangeeta S. Chavan
Software Mentions: 2
Published: over 6 years ago
10.3389/fimmu.2021.690817
Impact of Interleukin 10 Deficiency on Intestinal Epithelium Responses to Inflammatory Signals
Cited by: 9
Author(s): Σταματια Παπουτσοπουλου, Liam Pollock, Catherine Walker, William D. Tench, Sakim Shakh Samad, François Bergey, Luca Lenzi, Raheleh Sheibani-Tezerji, P Rosenstiel, Mohammad Tauqeer Alam, Vítor A. P. Martins dos Santos, Werner Müller, Barry J. Campbell
Software Mentions: 2
Published: over 3 years ago
10.3389/fimmu.2021.641886
The Chromatin Accessibility Landscape of Peripheral Blood Mononuclear Cells in Patients With Systemic Lupus Erythematosus at Single-Cell Resolution
Cited by: 5
Author(s): Haiyan Yu, Xiaoping Hong, Hongwei Wu, Fengping Zheng, Zhipeng Zeng, Weier Dai, Yin Li, Dongzhou Liu, Donge Tang, Yong Dai
Software Mentions: 2
Published: over 3 years ago
10.3389/fimmu.2018.00035
TGF-β-Induced CD8+CD103+ Regulatory T Cells Show Potent Therapeutic Effect on Chronic Graft-versus-Host Disease Lupus by Suppressing B Cells
Cited by: 41
Author(s): Haowen Zhong, Ya Liu, Zhenjian Xu, Peifeng Liang, Hui Yang, Xiao Zhang, Jun Zhao, Junzhen Chen, Sha Fu, Ying Tang, Jun Lv, Julie Wang, Nancy J. Olsen, Anping Xu, Song Guo Zheng
Software Mentions: 2
Published: almost 7 years ago
10.3389/fimmu.2018.03185
TCR Repertoire Analysis Reveals Mobilization of Novel CD8+ T Cell Clones Into the Cancer-Immunity Cycle Following Anti-CD4 Antibody Administration
Cited by: 20
Author(s): Hatsuo Aoki, Satoshi Ueha, Shigeyuki Shichino, Haru Ogiwara, Shin Ichi Hashimoto, Kazuhiro Kakimi, Satoru Ito, Kouji Matsushima
Software Mentions: 2
Published: almost 6 years ago
10.3389/fimmu.2018.00251
High-Throughput Sequencing of the Expressed Torafugu (Takifugu rubripes) Antibody Sequences Distinguishes IgM and IgT Repertoires and Reveals Evidence of Convergent Evolution
Cited by: 5
Author(s): Fu Xi, Jianqiang Sun, Engkong Tan, Kentaro Shimizu, Md. Shaheed Reza, Shugo Watabe, Shuichi Asakawa
Software Mentions: 2
Published: over 6 years ago
10.3389/fimmu.2017.01386
Critical Role for Very-Long Chain Sphingolipids in Invariant Natural Killer T Cell Development and Homeostasis
Cited by: 18
Author(s): Ashish Saroha, Yael Pewzner-Jung, Natália Santos Ferreira, Piyush Sharma, Youenn Jouan, Samuel Kelly, Ester Feldmesser, Alfred H. Merrill, François Trottein, Christophe Paget, Karl S. Lang, Anthony H. Futerman
Software Mentions: 2
Published: about 7 years ago
10.3389/fimmu.2017.01407
Structure and Diversity of the Rhesus Macaque Immunoglobulin Loci through Multiple De Novo Genome Assemblies
Cited by: 60
Author(s): Akshaya Ramesh, Sam Darko, Axin Hua, Glenn Overman, Amy Ransier, Joseph R. Francica, Ashley M. Trama, Georgia D. Tomaras, Barton F. Haynes, Daniel C. Douek, Thomas B. Kepler
Software Mentions: 2
Published: about 7 years ago
10.3389/fmicb.2018.02887
Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry
Cited by: 24
Author(s): Christina Jil Fiedler, Christoph Schönher, Philipp Proksch, David Kerschbaumer, Ernest Mayr, Marija Žunabović-Pichler, Konrad J. Domig, Reinhard Perfler
Software Mentions: 2
Published: almost 6 years ago
10.3389/fmicb.2020.588906
Chitin Attenuates Expression of Listeria monocytogenes Virulence Genes in vitro
Cited by: 0
Author(s): Miguel Villoria Recio, Bo-Hyung Lee, Eva Maria Sternkopf Lillebæk, Birgitte H. Kallipolitis, Cormac G. M. Gahan, Hanne Ingmer, Mona Larsen
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2020.01031
Single-Cell Genomics of Novel Actinobacteria With the Wood–Ljungdahl Pathway Discovered in a Serpentinizing System
Cited by: 38
Author(s): Nancy Merino, Mikihiko Kawai, Eric S. Boyd, Daniel R. Colman, Shawn E. McGlynn, Kenneth H. Nealson, Ken Kurokawa, Yuichi Hongoh
Software Mentions: 2
Published: over 4 years ago
10.3389/fmicb.2020.01889
Cross-Species Transmission and Evolution of SIV Chimpanzee Progenitor Viruses Toward HIV-1 in Humanized Mice
Cited by: 7
Author(s): Kimberly Schmitt, James Curlin, Leila Remling‐Mulder, Ryan V. Moriarty, Kelly Goff, Shelby L. O’Connor, Mark D. Stenglein, Preston A. Marx, Ramesh Akkina
Software Mentions: 2
Published: over 4 years ago
10.3389/fmicb.2016.02171
Bacillus thuringiensis and Bacillus weihenstephanensis Inhibit the Growth of Phytopathogenic Verticillium Species
Cited by: 49
Author(s): Jacqueline Hollensteiner, Franziska Wemheuer, Rebekka Harting, Anna M. Kolarzyk, Stefani Maria Díaz Valerio, Anja Poehlein, Elżbieta Brzuszkiewicz, Kai Nesemann, Susanna A. Braus‐Stromeyer, Gerhard H. Braus, Rolf Daniel, Heiko Liesegang
Software Mentions: 2
Published: almost 8 years ago
10.3389/fmicb.2020.00448
Combination Analysis of Metatranscriptome and Metagenome Reveal the Composition and Functional Response of Coral Symbionts to Bleaching During an El Niño Event
Cited by: 9
Author(s): Fu-Lin Sun, Hongqiang Yang, Guan Wang, Quan Shi
Software Mentions: 2
Published: over 4 years ago
10.3389/fmicb.2020.01807
Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding
Cited by: 2
Author(s): Julien Fouret, Frédéric Brunet, Martin Binet, Noémie Aurine, François Enchéry, Séverine Croze, Marie Guinier, Abdelghafar Goumaidi, Doris Preininger, Jean‐Nicolas Volff, Marc Bailly‐Bechet, Joël Lachuer, Branka Horvat, Catherine Legras-Lachuer
Software Mentions: 2
Published: over 4 years ago
10.3389/fmicb.2021.646273
Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings
Cited by: 5
Author(s): Tyler Dang, Irene Lavagi-Craddock, Sohrab Bodaghi, Georgios Vidalakis
Software Mentions: 2
Published: over 3 years ago
10.1186/s13059-014-0420-4
Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
Cited by: 24
Author(s): Erin N. Smith, Kristen Jepsen, Mahdieh Khosroheidari, Laura Z. Rassenti, Matteo D’Antonio, Emanuela M. Ghia, Dennis A. Carson, Catriona Jamieson, Thomas J. Kipps, Kelly A. Frazer
Software Mentions: 2
Published: over 10 years ago
10.1186/s13059-014-0504-1
Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires’ disease outbreak
Cited by: 23
Author(s): Paul R. McAdam, Charles W. Vander Broek, Diane Lindsay, Melissa J. Ward, Mary Hanson, Michael Gillies, Mick Watson, Joanne M. Stevens, Giles Edwards, J. Ross Fitzgerald
Software Mentions: 2
Published: about 10 years ago
10.1186/s13059-017-1150-1
Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania
Cited by: 47
Author(s): Fumiko Kawasaki, Dario Beraldi, Robyn Hardisty, Gordon R. McInroy, Pieter van Delft, Shankar Balasubramanian
Software Mentions: 2
Published: almost 8 years ago
10.1186/s13059-017-1291-2
Conservation and divergence of small RNA pathways and microRNAs in land plants
Cited by: 76
Author(s): Chenjiang You, Jie Cui, Hui Wang, Xun Qi, Li Chung Kuo, Hong Mā, Lei Gao, Beixin Mo, Xuemei Chen
Software Mentions: 2
Published: about 7 years ago
10.1186/s13059-018-1618-7
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Cited by: 623
Author(s): Nathan D. Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L. Matteson, Jaqueline Góes de Jesus, Bradley J. Main, Amanda L Tan, Lauren M. Paul, Doug E. Brackney, Saran Grewal, Nikos Gurfield, Koen K. A. Van Rompay, Sharon Isern, Scott F. Michael, Lark L. Coffey, Nicholas J. Loman, Kristian G. Andersen
Software Mentions: 2
Published: almost 6 years ago
10.1186/s13059-021-02319-w
Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes
Cited by: 3
Author(s): Brayon J. Fremin, Ami S. Bhatt
Software Mentions: 2
Published: over 3 years ago
10.1093/gbe/evz125
Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths
Cited by: 23
Author(s): David A. Ray, Jenna Grimshaw, Michaela K. Halsey, Jennifer M. Korstian, Austin Osmanski, Kevin A. Sullivan, Kristen A. Wolf, Harsith Reddy, Nicole M. Foley, Richard D. Stevens, Binyamin A. Knisbacher, Orr Levy, Brian A. Counterman, Nathaniel B. Edelman, James Mallet
Software Mentions: 2
Published: over 5 years ago
10.1093/gbe/evaa175
Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids
Cited by: 29
Author(s): Atsushi Nakabachi, Jörn Piel, Igor Malenovský, Yuu Hirose
Software Mentions: 2
Published: over 4 years ago
10.1186/s13073-015-0235-2
Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing
Cited by: 97
Author(s): Alexander L. Greninger, Kevin Messacar, Thelma H. Dunnebacke, Samia N. Naccache, Scot Federman, Jérôme Bouquet, David M. Mirsky, Yoshihiko Nomura, Shigeo Yagi, Carol Glaser, Michael Vollmer, Craig A. Press, Bette K. Kleinschmidt‐DeMasters, Samuel R. Dominguez, Charles Y. Chiu
Software Mentions: 2
Published: almost 9 years ago
10.1186/s13073-016-0375-z
Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
Cited by: 36
Author(s): Tanjina Kader, David Goode, Stephen Q. Wong, Jacquie Connaughton, Simone M. Rowley, Lisa Devereux, David Byrne, Stephen B. Fox, Gisela Mir Arnau, Richard W. Tothill, Ian Campbell, Kylie L. Gorringe
Software Mentions: 2
Published: about 8 years ago
10.1186/s13073-017-0442-0
The genomic road to invasion—examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples
Cited by: 30
Author(s): Henry M. Wood, Catherine Daly, Rebecca Chalkley, Burcu Şengüven, Lisa Ross, Philip Egan, Preetha Chengot, Jennifer Graham, Neeraj Sethi, T.K. Ong, Kenneth MacLennan, Pamela Rabbitts, Caroline Conway
Software Mentions: 2
Published: over 7 years ago
10.1007/s00251-020-01181-7
High-throughput immunogenetic typing of koalas suggests possible link between MHC alleles and cancers
Cited by: 2
Author(s): Bonnie Chaban, Galit Tzipori, Kjell Nilsson, Peter Timms
Software Mentions: 2
Published: about 4 years ago
10.1111/imm.13158
Depletion of Foxp3 <sup>+</sup> regulatory T cells is accompanied by an increase in the relative abundance of Firmicutes in the murine gut microbiome
Cited by: 21
Author(s): Jan Kehrmann, Laura Effenberg, C. Matthias Wilk, Davina Schoemer, Nhi Ngo Thi Phuong, Alexandra Adamczyk, Eva Pastille, René Scholtysik, Ludger Klein-Hitpaß, Robert Klopfleisch, Astrid M. Westendorf, Jan Buer
Software Mentions: 2
Published: almost 5 years ago
10.1093/jas/sky260
Analysis of temporal fecal microbiota dynamics in weaner pigs with and without exposure to enterotoxigenic Escherichia coli1,2
Cited by: 31
Author(s): Jolinda Pollock, David L. Gally, Laura Glendinning, Raksha Tiwari, Michael R. Hutchings, J.G.M. Houdijk
Software Mentions: 2
Published: over 6 years ago