pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2018.02364

Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking
Cited by: 16
Author(s): Moa Hägglund, Stina Bäckman, Anna Macellaro, Petter Lindgren, Emmy Borgmästars, Karin Jacobsson, Rikard Dryselius, Per Stenberg, Andreas Sjödin, Mats Forsman, Jon Ahlinder
Software Mentions: 6
Published: about 8 years ago

10.3390/nu13092983

Supplementation of 1-Kestose Modulates the Gut Microbiota Composition to Ameliorate Glucose Metabolism in Obesity-Prone Hosts
Cited by: 10
Author(s): Ayako Watanabe, Takumi Tochio, Yasuhiro Kadota, Motoki Takahashi, Yasuyuki Kitaura, H. Ishikawa, Takanori Yasutake, Masahiro Nakano, Hiroe Shinohara, Toru Kudo, Yuichiro Nishimoto, Yoshinori Mizuguchi, Akihito Endo, Yoshiharu Shimomura
Software Mentions: 6
Published: about 5 years ago

10.1111/acel.13153

Epigenome signatures landscaped by histone H3K9me3 are associated with the synaptic dysfunction in Alzheimer's disease
Cited by: 44
Author(s): Min Young Lee, Jung‐Hee Lee, Seung Jae Hyeon, Hyesun Cho, Yu Jin Hwang, Jong Yeon Shin, Ann C. McKee, Neil W. Kowall, Jong‐Il Kim, Thor D. Stein, Daehee Hwang, Hoon Ryu
Software Mentions: 6
Published: over 6 years ago

10.1186/s40168-021-01136-4

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes
Cited by: 24
Author(s): Chhedi Lal Gupta, Shlomo E. Blum, Karuppasamy Kattusamy, Tali Daniel, S. Druyan, Roni Shapira, O. Krifucks, Yan Zhu, Xinyuan Zhou, Jian‐Qiang Su, Eddie Cytryn
Software Mentions: 6
Published: about 5 years ago

10.1523/JNEUROSCI.1675-19.2019

Midkine-a Is Required for Cell Cycle Progression of Müller Glia during Neuronal Regeneration in the Vertebrate Retina
Cited by: 28
Author(s): Mikiko Nagashima, Travis S. D’Cruz, Antoinette Eyram Danku, Doneen Hesse, Christopher J. Sifuentes, Pamela A. Raymond, Peter F. Hitchcock
Software Mentions: 6
Published: almost 7 years ago

10.3389/fmicb.2017.00744

Alterations in the Rumen Liquid-, Particle- and Epithelium-Associated Microbiota of Dairy Cows during the Transition from a Silage- and Concentrate-Based Ration to Pasture in Spring
Cited by: 36
Author(s): Melanie Schären, Kerstin Kiri, Susanne Riede, Mark C. Gardener, Ulrich Meyer, Jürgen Hummel, Tim Urich, Gerhard Breves, Sven Dänicke
Software Mentions: 6
Published: over 9 years ago

10.3390/ijms20061321

Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling
Cited by: 14
Author(s): Gesche K. Gerresheim, Jochen Bathke, Audrey M. Michel, Dmitry E. Andreev, Lyudmila Shalamova, Oliver Roßbach, Pan Hu, Dieter Glebe, Markus Fricke, Manja Marz, Alexander Goesmann, Stephen J Kiniry, Pavel V. Baranov, Ivan N. Shatsky, Michael Niepmann
Software Mentions: 6
Published: over 7 years ago

10.1186/s12974-021-02230-y

The role of interferon regulatory factor 8 for retinal tissue homeostasis and development of choroidal neovascularisation
Cited by: 9
Author(s): Peipei Zhang, Anja Schlecht, Julian Wolf, Stefaniya Boneva, Yannik Laich, Jana Koch, Franziska Ludwig, Myriam Boeck, Adrian Thien, Carmen Härdtner, Katrin Kierdorf, Hansjürgen Agostini, Günther Schlunck, Marco Prinz, Ingo Hilgendorf, Peter Wieghofer, Clemens Lange
Software Mentions: 6
Published: about 5 years ago

10.7554/eLife.09800

Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss
Cited by: 177
Author(s): Fredrick E. Henry, Ken Sugino, Adam Tozer, Tiago Branco, Scott M. Sternson
Software Mentions: 6
Published: about 11 years ago

10.3390/microorganisms8030405

Agroforestry Management Systems Drive the Composition, Diversity, and Function of Fungal and Bacterial Endophyte Communities in Theobroma Cacao Leaves
Cited by: 19
Author(s): Franziska Wemheuer, Dirk Hölscher, Bernd Wemheuer, Rolf Daniel, Stefan Vidal, Hervé Bertin Bisseleua Daghela
Software Mentions: 6
Published: over 6 years ago

10.7554/eLife.24133

Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates
Cited by: 103
Author(s): Zachary Baker, Molly Schumer, Yuki Haba, Lisa Bashkirova, C. D. Holland, Gil G. Rosenthal, Molly Przeworski
Software Mentions: 6
Published: over 9 years ago

10.1111/1755-0998.13022

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring
Cited by: 64
Author(s): Jérôme Morinière, Michael Balke, Dieter Doczkal, Matthias F. Geiger, Laura A. Hardulak, Gerhard Haszprunar, Axel Hausmann, Lars Hendrich, Ledis Regalado, Björn Rulik, Stefan Schmidt, Johann‐Wolfgang Wägele, Paul D. N. Hebert
Software Mentions: 6
Published: over 7 years ago

10.1016/j.celrep.2020.108629

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide
Cited by: 10
Author(s): Kathrin Leppek, Gun Woo Byeon, Kotaro Fujii, Maria Barna
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1008822

An Africa-wide genomic evolution of insecticide resistance in the malaria vector Anopheles funestus involves selective sweeps, copy number variations, gene conversion and transposons
Cited by: 37
Author(s): Gareth D. Weedall, Jacob M. Riveron, Jack Hearn, Helen Irving, Colince Kamdem, Caroline Fouet, Bradley J. White, Charles S. Wondji
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.ppat.1007518

Comprehensive profiling of translation initiation in influenza virus infected cells
Cited by: 22
Author(s): Heather M. Machkovech, Jesse D. Bloom, Arvind R. Subramaniam
Software Mentions: 6
Published: over 7 years ago

10.1128/AEM.01285-16

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis
Cited by: 46
Author(s): Sagar M. Utturkar, W. Nathan Cude, Michael S. Robeson, Zamin K. Yang, Dawn M. Klingeman, Miriam Land, S. L. Allman, Tse-Yuan S. Lu, Steven D. Brown, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 6
Published: about 10 years ago

10.3389/fmicb.2020.571983

Large Enrichment of Anthropogenic Organic Matter Degrading Bacteria in the Sea-Surface Microlayer at Coastal Livingston Island (Antarctica)
Cited by: 12
Author(s): Alícia Martinez-Varela, Gemma Casas, Benjamı́n Piña, Jordi Dachs, Maria Vila‐Costa
Software Mentions: 6
Published: about 6 years ago

10.3390/ijms19020357

Genotyping by Sequencing Highlights a Polygenic Resistance to Ralstonia pseudosolanacearum in Eggplant (Solanum melongena L.)
Cited by: 28
Author(s): Sylvia Salgon, Morgane Raynal, Sylvain Lebon, Jean Michel Baptiste, M. C. Daunay, Jacques Dintinger, Cyril Jourda
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0223691

The bacterial community in potato is recruited from soil and partly inherited across generations
Cited by: 31
Author(s): Franziska Buchholz, Livio Antonielli, Tanja Kostić, Angela Sessitsch, Birgit Mitter
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12864-019-5511-x

RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions
Cited by: 35
Author(s): Kirti Shekhawat, Hugh-G. Patterton, Florian F. Bauer, Mathabatha Evodia Setati
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0175464

Identification of potential biomarkers in donor cows for in vitro embryo production by granulosa cell transcriptomics
Cited by: 12
Author(s): Gianluca Mazzoni, Suraya Mohamad Salleh, Kristine Freude, Helene Helboe Pedersen, Lotte Stroebech, Henrik Callesen, Poul Hyttel, Haja N. Kadarmideen
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.07295

Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100
Cited by: 179
Author(s): Shouan Liu, Barbara Kracher, J. Ziegler, Rainer P. Birkenbihl, Imre E. Somssich
Software Mentions: 5
Published: over 11 years ago

10.3389/fimmu.2021.633654

The SWI/SNF-Related, Matrix Associated, Actin-Dependent Regulator of Chromatin A4 Core Complex Represses Respiratory Syncytial Virus-Induced Syncytia Formation and Subepithelial Myofibroblast Transition
Cited by: 11
Author(s): Xiaofang Xu, Dianhua Qiao, Chenyang Dong, Morgan Mann, Roberto P. Garofalo, Sündüz Keleş, Allan R. Brasier
Software Mentions: 5
Published: over 5 years ago

10.1007/s10126-021-10033-8

Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions
Cited by: 5
Author(s): Magnus Alm Rosenblad, Anna Abramova, Ulrika Lind, Pall I. Olason, Stefania Giacomello, Björn Nystedt, Anders Blomberg
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2020.01095

Peptidylarginine Deiminase 4 Promotes the Renal Infiltration of Neutrophils and Exacerbates the TLR7 Agonist-Induced Lupus Mice
Cited by: 14
Author(s): Norio Hanata, Hirofumi Shoda, Hiroaki Hatano, Yasuo Nagafuchi, Takashi Komai, Tomohisa Okamura, Akari Suzuki, I Ketut Gunarta, Katsuji Yoshioka, Kazuhiko Yamamoto, Keishi Fujio
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.63274

Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
Cited by: 68
Author(s): Steven Henikoff, Hatice S Kaya-Okur, Kami Ahmad
Software Mentions: 5
Published: almost 6 years ago

10.1136/jitc-2020-001657

Regorafenib enhances antitumor immunity via inhibition of p38 kinase/Creb1/Klf4 axis in tumor-associated macrophages
Cited by: 52
Author(s): Da-Liang Ou, Chia Wei Chen, Chia‐Lang Hsu, Chih‐Hung Chung, Zi Rui Feng, Bin Shyun Lee, Ann Lii Cheng, Muh Hwa Yang, Chiun Hsu
Software Mentions: 5
Published: over 5 years ago

10.1186/s12915-020-00769-5

Multiple links between 5-methylcytosine content of mRNA and translation
Cited by: 71
Author(s): Ulrike Schümann, He-Na Zhang, Tennille Sibbritt, Anyu Pan, Attila Horváth, Simon Gross, Susan J. Clark, Li Yang, Thomas Preiß
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2018.00671

UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes
Cited by: 20
Author(s): Santiago Radío, Rafael Sebastián Fort, Beatríz Garat, José Sotelo‐Silveira, Pablo Smircich
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.61894

Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis
Cited by: 45
Author(s): Michael Borg, Ranjith Papareddy, Rodolphe Dombey, Elin Axelsson, Michael D. Nodine, David Twell, Frédéric Berger
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2018.01561

A Single Vibrionales 16S rRNA Oligotype Dominates the Intestinal Microbiome in Two Geographically Separated Atlantic cod Populations
Cited by: 16
Author(s): Even Sannes Riiser, Thomas Haverkamp, Ørnulf Borgan, Kjetill S. Jakobsen, Sissel Jentoft, Bastiaan Star
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0169087

The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population
Cited by: 74
Author(s): Axel Künstner, Maria Hoffmann, Bonnie A. Fraser, Verena A. Kottler, Eshita Sharma, Detlef Weigel, Christine Dreyer
Software Mentions: 5
Published: almost 10 years ago

10.1084/jem.20171738

A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets
Cited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: over 8 years ago

10.1002/cam4.2632

Serial ultra‐deep sequencing of circulating tumor DNA reveals the clonal evolution in non‐small cell lung cancer patients treated with anti‐PD1 immunotherapy
Cited by: 27
Author(s): Li Li, Yübo Wang, Weiwei Shi, Mengxiao Zhu, Zhulin Liu, Nuo Luo, Yanwu Zeng, Yong He
Software Mentions: 5
Published: almost 7 years ago

10.1002/cam4.1791

Analysis of solid tumor mutation profiles in liquid biopsy
Cited by: 19
Author(s): Sai A. Balaji, Ashwini Shanmugam, Anuradha Chougule, Srikant Sridharan, Kumar Prabhash, Anuradha Arya, Aditya Chaubey, Arun K Hariharan, Pandurang Kolekar, Manimala Sen, Aarthi Ravichandran, Shanmukh Katragadda, Satish Sankaran, Satish Bhargava, Prashanth Kulkarni, Suchitra Rao, Chinnababu Sunkavalli, Shripad Banavali, Amit Joshi, Vanita Noronha, Amit Dutt, Urvashi Bahadur, Ramesh Hariharan, Vamsi Veeramachaneni, Vaijayanti Gupta
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pone.0222737

Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions
Cited by: 6
Author(s): Márton Szoboszlay, Astrid Näther, Ewen Mullins, Christoph C. Tebbe
Software Mentions: 5
Published: almost 7 years ago

10.3389/fimmu.2019.00330

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression
Cited by: 37
Author(s): Florian Kirchner, Katharina Littringer, Simon Altmeier, Van Du T. Tran, Franziska Annett Schönherr, Christina Braunsdorf, Marco Pagni, Dominique Sanglard, Nicole Joller, Salomé LeibundGut‐Landmann
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.54508

Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation
Cited by: 24
Author(s): Ava C. Carter, Jin Xu, Meagan Y Nakamoto, Yuning Wei, Brian Zarnegar, Quanming Shi, James P. Broughton, Ryan C. Ransom, Ankit Salhotra, Surya Nagaraja, Rui Li, Diana R. Dou, Kathryn E. Yost, Seung Woo Cho, Anil Mistry, Michael T. Longaker, Paul A. Khavari, Robert T. Batey, Deborah S. Wuttke, Howard Y. Chang
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.03549

Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment
Cited by: 21
Author(s): Brenda Y. Han, Shuang Wu, Chuan-Sheng Foo, Robert M. Horton, Craig N. Jenne, Susan R. Watson, Belinda Whittle, Christopher C. Goodnow, Jason G. Cyster
Software Mentions: 5
Published: almost 12 years ago

10.3389/fcell.2021.595744

A Highly Conserved Shh Enhancer Coordinates Hypothalamic and Craniofacial Development
Cited by: 2
Author(s): Zoe Crane-Smith, Jeffrey J. Schoenebeck, Katy A. Graham, Paul S. Devenney, Lorraine Rose, Mark Ditzell, E. S. Anderson, Joseph I. Thomson, Natalia Klenin, Deborah M. Kurrasch, Laura A. Lettice, Robert E. Hill
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0244341

Exposure to traffic-related air pollution and bacterial diversity in the lower respiratory tract of children
Cited by: 9
Author(s): Christine Niemeier‐Walsh, Patrick Ryan, Jarosław Meller, Nicholas J. Ollberding, Atin Adhikari, Tiina Reponen
Software Mentions: 5
Published: over 5 years ago

10.1128/mSystems.01306-20

Cultivating the Bacterial Microbiota of Populus Roots
Cited by: 12
Author(s): Dana L. Carper, David J. Weston, Aditya Barde, Collin M. Timm, Tse-Yuan S. Lu, Leah H. Burdick, Sara Jawdy, Dawn M. Klingeman, Michael S. Robeson, Allison M. Veach, Melissa Cregger, Udaya C. Kalluri, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2021.641987

Timing Does Matter: Nerve-Mediated HDAC1 Paces the Temporal Expression of Morphogenic Genes During Axolotl Limb Regeneration
Cited by: 3
Author(s): Mu-Hui Wang, Chih‐Cheng Hsu, Cheng‐Hsun Wu, Ling-Ling Chiou, Yi-Tzang Tsai, Hsuan-Shu Lee, Shau-Ping Lin
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2021.664178

Differential Transcriptomes and Methylomes of Trophoblast Stem Cells From Naturally-Fertilized and Somatic Cell Nuclear-Transferred Embryos
Cited by: 0
Author(s): Jin Sun, Weisheng Zheng, Wenqiang Liu, Xiaochen Kou, Yanhong Zhao, Zehang Liang, Lu Wang, Zihao Zhang, Jing Xiao, Rui Gao, Shaorong Gao, Cizhong Jiang
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2021.719192

PARP1 Inhibitor Combined With Oxaliplatin Efficiently Suppresses Oxaliplatin Resistance in Gastric Cancer-Derived Organoids via Homologous Recombination and the Base Excision Repair Pathway
Cited by: 1
Author(s): Huafu Li, Chunming Wang, Linxiang Lan, Wenhui Wu, Ian M. Evans, E Josue Ruiz, Le-Ping Yan, Zhijun Zhou, Joaquím M. Oliveira, Rui L. Reis, Zhenran Hu, Wei Chen, Axel Behrens, Yulong He, Changhua Zhang
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2020.580848

Adherent Intestinal Cells From Atlantic Salmon Show Phagocytic Ability and Express Macrophage-Specific Genes
Cited by: 5
Author(s): Youngjin Park, Qirui Zhang, G.F. Wiegertjes, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 5
Published: about 6 years ago

10.1038/s41396-019-0584-8

Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment
Cited by: 36
Author(s): Bennett J. Kapili, Samuel E. Barnett, Daniel H. Buckley, Anne E. Dekas
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-021-94761-w

Microbiome pattern of Lucilia sericata (Meigen) (Diptera: Calliphoridae) and feeding substrate in the presence of the foodborne pathogen Salmonella enterica
Cited by: 3
Author(s): Lavinia Iancu, Iulia Roxana Angelescu, Victoria Ioana Paun, Carlos Henríquez‐Castillo, Paris Lavín, Cristina Purcărea
Software Mentions: 5
Published: about 5 years ago

10.1002/bit.25990

Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time
Cited by: 109
Author(s): Julia Feichtinger, Inmaculada Hernández, Christoph Fischer, Michael Hanscho, Norbert Auer, Matthias Hackl, Vaibhav Jadhav, Martina Baumann, Peter M. Krempl, Christian Schmidl, Matthias Farlik, Michael Schuster, Angelika Merkel, Andreas Sommer, Simon Heath, Daniel Rico, Christoph Bock, Gerhard Thallinger, Nicole Borth
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-021-93863-9

MYCN-induced nucleolar stress drives an early senescence-like transcriptional program in hTERT-immortalized RPE cells
Cited by: 6
Author(s): Sofia Zanotti, Suzanne Vanhauwaert, Christophe Van Neste, Volodimir Olexiouk, Jolien Van Laere, Marlies Verschuuren, Joni Van der Meulen, Liselot Mus, Kaat Durinck, Laurentijn Tilleman, Dieter Deforce, Filip Van Nieuwerburgh, Michael D. Hogarty, Bieke Decaesteker, Winnok H. De Vos, Frank Speleman
Software Mentions: 5
Published: over 5 years ago

10.1186/s13072-020-00359-3

UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells
Cited by: 5
Author(s): Beisi Xu, Brett B. Mulvey, Muneeb Salie, Xiaoyang Yang, Yurika Matsui, Anjana Nityanandam, Yiping Fan, Jamy C. Peng
Software Mentions: 5
Published: about 6 years ago

10.1186/s13024-021-00481-0

Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer’s disease brains
Cited by: 9
Author(s): Julio Barrera, Lingyun Song, Julia Gamache, Melanie E. Garrett, Alexias Safi, Young Won Yun, Ivana Premasinghe, Daniel J. Sprague, Danielle Chipman, Jeffrey Li, Hélène Fradin, Karen Soldano, Raluca Gordân, Allison Ashley‐Koch, Gregory E. Crawford, Ornit Chiba‐Falek
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0092663

Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome Sequencing
Cited by: 48
Author(s): Chong Wang, Markus A. Grohme, Brahim Mali, Ralph O. Schill, Marcus Frohme
Software Mentions: 5
Published: over 12 years ago

10.1038/s41385-020-0305-7

γδ T cells compose a developmentally regulated intrauterine population and protect against vaginal candidiasis
Cited by: 32
Author(s): Leticia Monin, Dmitry S. Ushakov, Henriette Arnesen, Nourdine Bah, Anett Jandke, Miguel Muñoz-Ruiz, Joana Carvalho, Susan Joseph, Bruna Almeida, M. J. Green, Emma Nye, Shoji Hatano, Yasunobu Yoshikai, Michael Curtis, Harald Carlsen, Ulrich Steinhoff, Preben Boysen, Adrian Hayday
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12936-020-3137-8

Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago
Cited by: 25
Author(s): Andrew P. Morgan, Nicholas F. Brazeau, Billy Ngasala, Lwidiko E. Mhamilawa, Madeline Denton, Mwinyi Msellem, Ulrika Morris, Dayne L. Filer, Özkan Aydemir, Jeffrey A. Bailey, Jonathan B. Parr, Andreas Mårtensson, Anders Björkman, Jonathan J. Juliano
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0238557

eDNA metabarcoding as a biomonitoring tool for marine protected areas
Cited by: 67
Author(s): Zachary Gold, Joshua Sprague, David J. Kushner, Erick Zerecero Marin, Paul H. Barber
Software Mentions: 5
Published: over 5 years ago

10.1111/eva.12647

Population genomics of the introduced and cultivated Pacific kelpUndaria pinnatifida: Marinas-not farms-drive regional connectivity and establishment in natural rocky reefs
Cited by: 43
Author(s): Jaromir Guzinski, Marion Ballenghien, Claire Daguin‐Thiébaut, Laurent Lévêque, Frédérique Viard
Software Mentions: 5
Published: over 8 years ago

10.7150/ijbs.37399

Gut microbiome associated with APC gene mutation in patients with intestinal adenomatous polyps
Cited by: 38
Author(s): Sai Liang, Yan Mao, Ming Liao, Yali Xu, Ying‐Chun Chen, Xiaoliang Huang, Chuangyi Wei, Changtao Wu, Qiuyan Wang, Xiaoyan Pan, Weizhong Tang
Software Mentions: 5
Published: almost 7 years ago

10.3390/v13081647

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner
Cited by: 25
Author(s): Devon A. Gregory, Chris G. Wieberg, Jeff Wenzel, Chung‐Ho Lin, Marc C. Johnson
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.42499

A combination of transcription factors mediates inducible interchromosomal contacts
Cited by: 15
Author(s): Seungsoo Kim, Maitreya J. Dunham, Jay Shendure
Software Mentions: 5
Published: over 7 years ago

10.1093/bioinformatics/btw088

fqtools: an efficient software suite for modern FASTQ file manipulation
Cited by: 21
Author(s): Alastair Droop
Software Mentions: 5
Published: over 10 years ago

10.1093/gigascience/giaa008

GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms
Cited by: 77
Author(s): Patrick Browne, Tue Kjærgaard Nielsen, Witold Kot, Anni Aggerholm, M. Thomas P. Gilbert, Lara Puetz, Morten Rasmussen, Athanasios Zervas, Lars Hestbjerg Hansen
Software Mentions: 5
Published: over 6 years ago

10.1002/ece3.6662

Major histocompatibility complex variation is similar in little brown bats before and after white‐nose syndrome outbreak
Cited by: 3
Author(s): Xueling Yi, Deahn M. Donner, Paula E. Marquardt, Jonathan M. Palmer, Michelle A. Jusino, Jacqueline L. Frair, Daniel L. Lindner, Emily K. Latch
Software Mentions: 5
Published: about 6 years ago

10.1093/gigascience/giaa088

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning
Cited by: 16
Author(s): Eugenie C Yen, Shane McCarthy, Juan A. Galarza, Tomas N Generalovic, Sarah Pelan, Petr Nguyen, Joana I. Meier, Ian A. Warren, Johanna Mappes, Richard Durbin, Chris D. Jiggins
Software Mentions: 5
Published: about 6 years ago

10.1002/ece3.3404

Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces
Cited by: 62
Author(s): Kari Kaunisto, Tomas Roslin, Ilari E. Sääksjärvi, Eero J. Vesterinen
Software Mentions: 5
Published: about 9 years ago

10.1186/s12864-017-3936-7

Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
Cited by: 35
Author(s): Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D. G. Jones, Matt Clark
Software Mentions: 5
Published: about 9 years ago

10.15252/emmm.201809456

Alternative oxidase‐mediated respiration prevents lethal mitochondrial cardiomyopathy
Cited by: 47
Author(s): Jayasimman Rajendran, Janne Purhonen, Saara Tegelberg, Olli‐Pekka Smolander, Matthias Mörgelin, Jan Rozman, Valérie Gailus‐Durner, Helmut Fuchs, Martin Hrabě de Angelis, Petri Auvinen, Eero Mervaala, Howard T. Jacobs, Marten Szibor, Vineta Fellman, Jukka Kallijärvi
Software Mentions: 5
Published: almost 8 years ago

10.1016/j.devcel.2018.12.026

Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis
Cited by: 32
Author(s): Toni Beltran, Consuelo Barroso, T. Y. Birkle, Lewis Stevens, Hillel T. Schwartz, Paul W. Sternberg, Hélène Fradin, Kristin C. Gunsalus, Fabio Piano, Garima Sharma, Chiara Cerrato, Julie Ahringer, Enrique Martínez-Pérez, Mark Blaxter, Peter Sarkies
Software Mentions: 5
Published: over 7 years ago

10.1002/mbo3.1133

A low‐cost pipeline for soil microbiome profiling
Cited by: 5
Author(s): Anita Bollmann‐Giolai, Michael Giolai, Darren Heavens, Iain C. Macaulay, Jacob G. Malone, Matt Clark
Software Mentions: 5
Published: almost 6 years ago

10.1002/ece3.5711

Site‐specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales
Cited by: 15
Author(s): Candice Y. Lumibao, Elizabeth T. Borer, Bradford Condon, Linda L. Kinkel, Georgiana May, Eric W. Seabloom
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-021-02494-w

Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization
Cited by: 12
Author(s): Sarah L. Gillen, Chiara Giacomelli, Kelly Hodge, Sara Zanivan, Martin Bushell, Ania Wilczynska
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pbio.3000719

Discovery of genes required for body axis and limb formation by global identification of retinoic acid–regulated epigenetic marks
Cited by: 22
Author(s): Marie Berenguer, Karolin F Meyer, Jun Yin, Gregg Duester
Software Mentions: 5
Published: over 6 years ago

10.1093/gbe/evaa187

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)
Cited by: 29
Author(s): Bonnie A. Fraser, James R. Whiting, Josephine R. Paris, Cameron J. Weadick, Paul J. Parsons, Deborah Charlesworth, Roberta Bergero, Felix Bemm, Maria Hoffmann, Verena A. Kottler, Chang Liu, Christine Dreyer, Detlef Weigel
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-015-2135-7

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish
Cited by: 27
Author(s): Candida Vaz, Choon Wei Wee, Gek Ping Serene Lee, Philip W. Ingham, Vivek Tanavde, Sinnakaruppan Mathavan
Software Mentions: 5
Published: almost 11 years ago

10.3390/curroncol28040214

Targeted Next-Generation Sequencing of Circulating Tumor DNA Mutations among Metastatic Breast Cancer Patients
Cited by: 1
Author(s): Ming Sun, Fangqin Lin, Lu-Jia Chen, Hong Li, Wei‐De Lin, Hongwu Du, Xiaobo Yang, Ming Li
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02446-4

Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea
Cited by: 20
Author(s): Antoine Porquier, Constance Tisserant, F. Salinas, Carla Glassl, Lucas E. Wange, Wolfgang Enard, Andreas Hauser, Matthias Hahn, Arne Weiberg
Software Mentions: 5
Published: about 5 years ago

10.1186/s12916-020-01898-y

Development and validation of a novel circular RNA as an independent prognostic factor in acute myeloid leukemia
Cited by: 9
Author(s): Jinghan Wang, Jiajia Pan, Shujuan Huang, Fenglin Li, Jiansong Huang, Xia Li, Qing Ling, Wenle Ye, Yungui Wang, Wenjuan Yu, Jie Jin
Software Mentions: 5
Published: over 5 years ago

10.3390/plants10020267

Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover
Cited by: 5
Author(s): Axel J Giudicatti, Ariel Hernán Tomassi, Pablo Andrés Manavella, Agustín Lucas Arce
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02302-5

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics
Cited by: 31
Author(s): Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez‐Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, A. Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós, Jordi Solana
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-015-2124-x

De novo transcriptome reconstruction and annotation of the Egyptian rousette bat
Cited by: 34
Author(s): Albert Kim Lee, Kirsten A. Kulcsar, Oliver Elliott, Hossein Khiabanian, Elyse R. Nagle, Megan E. B. Jones, Brian R. Amman, Mariano Sánchez-Lockhart, Jonathan S. Towner, Gustavo Palacios, Raúl Rabadán
Software Mentions: 5
Published: almost 11 years ago

10.1111/mec.13481

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental <scp>DNA</scp>
Cited by: 318
Author(s): Jesse A. Port, James L. O’Donnell, Ofelia C. Romero‐Maraccini, Paul Leary, Steven Y. Litvin, Kerry J. Nickols, Kevan M. Yamahara, Ryan P. Kelly
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12898-020-00326-2

Family matters: skin microbiome reflects the social group and spatial proximity in wild zebra finches
Cited by: 12
Author(s): Kathrin Engel, Helga Pankoke, Sebastian Jünemann, Hanja B. Brandl, Jan Sauer, Simon C. Griffith, Jörn Kalinowski, Barbara A. Caspers
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-019-5892-x

Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization
Cited by: 25
Author(s): Petya Berger, Ivan U. Kouzel, Michael Berger, Nadja Haarmann, Ulrich Dobrindt, Gerald B. Koudelka, Alexander Mellmann
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pbio.3000396

Inverted translational control of eukaryotic gene expression by ribosome collisions
Cited by: 39
Author(s): Heungwon Park, Arvind R. Subramaniam
Software Mentions: 5
Published: about 7 years ago

10.1186/s13073-020-00747-0

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale
Cited by: 37
Author(s): Soumaya Zlitni, Alex Bishara, Eli L. Moss, Е. И. Ткаченко, Joyce B. Kang, Rebecca Culver, Tessa M. Andermann, Ziming Weng, Christina M. Wood, Christine Handy, Hanlee P. Ji, Serafim Batzoglou, Ami S. Bhatt
Software Mentions: 5
Published: over 6 years ago

10.1172/JCI133187

Mesenchymal niche remodeling impairs hematopoiesis via stanniocalcin 1 in acute myeloid leukemia
Cited by: 45
Author(s): Alexander Waclawiczek, Ashley Hamilton, Kevin Rouault-Pierre, Ander Abarrategi, Manuel Garcia-Albornoz, Farideh Miraki-Moud, Nourdine Bah, John G. Gribben, Jude Fitzgibbon, David Taussig, Dominique Bonnet
Software Mentions: 5
Published: over 6 years ago

10.1002/pld3.239

N6‐methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis
Cited by: 35
Author(s): Marianne C. Kramer, Kevin A. Janssen, Kyle Palos, Andrew D. L. Nelson, Lee E. Vandivier, Benjamin A. García, Eric Lyons, Mark A. Beilstein, Brian D. Gregory
Software Mentions: 5
Published: over 6 years ago

10.3390/cells8101196

Genome-Wide Distribution of Nascent Transcripts in Sperm DNA, Products of a Late Wave of General Transcription
Cited by: 6
Author(s): Leila Kianmehr, Homayoun Khazali, Hassan Rajabi‐Maham, Ali Sharifi‐Zarchi, François Cuzin, Minoo Rassoulzadegan
Software Mentions: 5
Published: about 7 years ago

10.1186/s40478-017-0414-z

Serum microRNA miR-501-3p as a potential biomarker related to the progression of Alzheimer’s disease
Cited by: 118
Author(s): Norikazu Hara, Masataka Kikuchi, Akinori Miyashita, Hiroyuki Hatsuta, Yuko Saito, Kensaku Kasuga, Shigeo Murayama, Takeshi Ikeuchi, Ryozo Kuwano
Software Mentions: 5
Published: over 9 years ago

10.1186/s13229-020-00369-8

Chd8 haploinsufficiency impairs early brain development and protein homeostasis later in life
Cited by: 18
Author(s): Jessica A. Jiménez, Travis Ptacek, Alex H. Tuttle, Ralf S. Schmid, Sheryl S. Moy, Jeremy M. Simon, Mark J. Zylka
Software Mentions: 5
Published: about 6 years ago

10.1534/genetics.120.303038

Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean
Cited by: 22
Author(s): Alice MacQueen, Jeffrey W. White, Rian Lee, Juan M. Osorno, Jeremy Schmutz, Phillip N. Miklas, James R. Myers, Phillip E. McClean, Thomas E. Juenger
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-016-0902-7

Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants
Cited by: 67
Author(s): Claire Morandin, Mandy M. Y. Tin, Sílvia Abril, Crisanto Gómez, Luigi Pontieri, Morten Schiøtt, Liselotte Sundström, Kazuki Tsuji, Jes S. Pedersen, Heikki Helanterä, Alexander S. Mikheyev
Software Mentions: 5
Published: over 10 years ago

10.3390/microorganisms9071374

The Microbiome Associated with the Reef Builder Neogoniolithon sp. in the Eastern Mediterranean
Cited by: 2
Author(s): Shany Gefen-Treves, Alexander Bartholomäus, Fabian Horn, Adam Boleslaw Zaborowski, Dan Tchernov, Dirk Wagner, Aharon Oren, Aaron Kaplan
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms8121977

Alteration of Bacterial Communities in Anterior Nares and Skin Sites of Patients Undergoing Arthroplasty Surgery: Analysis by 16S rRNA and Staphylococcal-Specific tuf Gene Sequencing
Cited by: 8
Author(s): Søren Iversen, Thor Bech Johannesen, Anna Cäcilia Ingham, Sofie Marie Edslev, Staffan Tevell, Emeli Månsson, Åsa Nilsdotter-Augustinsson, Bo Söderquist, Marc Stegger, Paal Skytt Andersen
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.stem.2020.09.001

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder
Cited by: 86
Author(s): Hannah K. Long, Marco Osterwalder, Ian Welsh, Karissa Hansen, James O. J. Davies, Yiran E. Liu, Mervenaz Koska, Alexander T. Adams, Robert Aho, Neiha Arora, Kazuya Ikeda, Ruth M. Williams, Tatjana Sauka‐Spengler, Matthew H. Porteus, Tim Mohun, Diane E. Dickel, Tomek Swigut, Jim R. Hughes, Douglas R. Higgs, Axel Visel, Licia Selleri, Joanna Wysocka
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41422-018-0128-1

A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis
Cited by: 46
Author(s): Marcos Morgan, Yuka Kabayama, Christian Much, Ivayla Ivanova, Monica Di Giacomo, Tatsiana Auchynnikava, Jack Monahan, Dimitrios Vitsios, Lina Vasiliauskaitė, Stefano Comazzetto, Juri Rappsilber, Robin C. Allshire, Bo T. Porse, Anton J. Enright, Dónal O’Carroll
Software Mentions: 5
Published: almost 8 years ago

10.1016/j.celrep.2018.04.047

Influenza Virus Mounts a Two-Pronged Attack on Host RNA Polymerase II Transcription
Cited by: 68
Author(s): David L.V. Bauer, Michael Tellier, Maira Martínez-Alonso, Takayuki Nojima, Nick J. Proudfoot, Shona Murphy, Ervin Fodor
Software Mentions: 5
Published: over 8 years ago

10.3390/microorganisms8060868

Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig
Cited by: 34
Author(s): Ann M. Arfken, Juli Foster Frey, Katie Lynn Summers
Software Mentions: 5
Published: over 6 years ago

10.1002/pld3.220

Identification of nodulation‐related genes in Medicago truncatula using genome‐wide association studies and co‐expression networks
Cited by: 4
Author(s): Jean Michel Michno, Junqi Liu, Joseph Jeffers, Robert M. Stupar, Chad L. Myers
Software Mentions: 5
Published: over 6 years ago

10.1534/g3.120.401345

Reference Genome for the Highly Transformable Setaria viridis ME034V
Cited by: 30
Author(s): Peter Thielen, Amanda L. Pendleton, Robert A. Player, Kenneth V. Bowden, Thomas J. Lawton, Jennifer H. Wisecaver
Software Mentions: 5
Published: about 6 years ago

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