pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.1126/sciadv.abd7459

Mechanisms of stearoyl CoA desaturase inhibitor sensitivity and acquired resistance in cancer
Cited by: 34
Author(s): Nicole Oatman, Nupur Dasgupta, Priyanka Arora, Kwangmin Choi, Mruniya V. Gawali, Neeraj Gupta, Sreeja Parameswaran, Joseph Salomone, Julie A. Reisz, Sean E. Lawler, Frank B. Furnari, Cameron Brennan, Jianqiang Wu, Larry Sallans, Gary A. Gudelsky, Pankaj B. Desai, Brian Gebelein, Matthew T. Weirauch, Angelo D’Alessandro, Kakajan Komurov, Biplab Dasgupta
Software Mentions: 2
Published: almost 4 years ago

10.1126/sciadv.abh2419

Ancient genomics reveals tripartite origins of Japanese populations
Cited by: 19
Author(s): Niall P. Cooke, Valeria Mattiangeli, Lara M. Cassidy, Ken Okazaki, Caroline A. Stokes, Shin Onbe, Satoshi Hatakeyama, Katsunosuke Machida, Kenji Kasai, Naoto Tomioka, Akihiko Matsumoto, Masafumi Ito, Yoshitaka Kojima, Daniel G. Bradley, Takashi Gakuhari, Shigeki Nakagome
Software Mentions: 2
Published: about 3 years ago

10.1038/sdata.2015.72

Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus
Cited by: 50
Author(s): Thomas Schmutzer, Birgit Samans, Emmanuelle Dyrszka, Chris Ulpinnis, Stéphan Weise, Doreen Stengel, Christian Colmsee, Denis Lespinasse, Zeljko Micic, Stefan Abel, Peter Duchscherer, Frank Breuer, Amine Abbadi, Gunhild Leckband, Rod J. Snowdon, Uwe Scholz
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41597-019-0077-7

Longitudinal 16S rRNA data derived from limb regenerative tissue samples of axolotl Ambystoma mexicanum
Cited by: 10
Author(s): Turan Demircan, Ayşe Elif İlhan, Guvanch Ovezmyradov, Gürkan Öztürk, Süleyman Yıldırım
Software Mentions: 2
Published: over 5 years ago

10.1038/s41597-021-00980-1

A curated dataset of modern and ancient high-coverage shotgun human genomes
Cited by: 2
Author(s): Pierpaolo Maisano Delser, Eppie R. Jones, Անահիտ Հովհաննիսյան, Lara M. Cassidy, Ron Pinhasi, Andrea Manica
Software Mentions: 2
Published: over 3 years ago

10.1038/srep11606

Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers
Cited by: 45
Author(s): Viia Kõiv, Märt Roosaare, Eve Vedler, Paula Ann Kivistik, Kristel Toppi, David W. Schryer, Maido Remm, Tanel Tenson, Andres Mäe
Software Mentions: 2
Published: over 9 years ago

10.1038/srep41529

The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes
Cited by: 10
Author(s): Daniel Fernandes, Kendra Sirak, Mario Novak, John A. Finarelli, John C. Byrne, E. Sander Connolly, Jens Carlsson, Edmondo Ferretti, Ron Pinhasi
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep43613

Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus
Cited by: 41
Author(s): Junko Yoshida, Keiko Akagi, Ryo Misawa, Chikara Kokubu, Junji Takeda, Kyoji Horie
Software Mentions: 2
Published: over 7 years ago

10.1038/srep45332

Activation of ERK1/2 Causes Pazopanib Resistance via Downregulation of DUSP6 in Synovial Sarcoma Cells
Cited by: 9
Author(s): Nobuhiko Yokoyama, Tomoya Matsunobu, Yoshihiro Matsumoto, Jun Ichi Fukushi, Makoto Endo, Masakazu Hatano, Akira Nabeshima, Sunao Fukushima, Seiji Okada, Yukihide Iwamoto
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-01181-w

White spot syndrome virus VP28 specific double-stranded RNA provides protection through a highly focused siRNA population
Cited by: 28
Author(s): Pål Nilsen, Marius Karlsen, Kallaya Sritunyalucksana, Siripong Thitamadee
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-07035-9

Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice
Cited by: 17
Author(s): Shin-Young Lee, Hyobin Jeong, Sichul Lee, Jinwon Lee, Sun-Ji Kim, Ji Won Park, Hye Ryun Woo, Pyung Ok Lim, Gynheung An, Hong Gil Nam, Daehee Hwang
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-15008-1

Mutation accumulation under UV radiation in Escherichia coli
Cited by: 50
Author(s): Atsushi Shibai, Yusuke Takahashi, Yuka Ishizawa, Daisuke Motooka, Shota Nakamura, Bei‐Wen Ying, Saburo Tsuru
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-19743-x

Drylands soil bacterial community is affected by land use change and different irrigation practices in the Mezquital Valley, Mexico
Cited by: 53
Author(s): Kathia Lüneberg, Dominik Schneider, Christina Siebe, Rolf Daniel
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-24935-6

Sauchinone controls hepatic cholesterol homeostasis by the negative regulation of PCSK9 transcriptional network
Cited by: 25
Author(s): Hee‐Sung Chae, Byoung Hoon You, Dong Yeop Kim, Hankyu Lee, Hyuk Wan Ko, Hyun Jeong Ko, Young Hee Choi, Sun Shim Choi, Young‐Won Chin
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-27980-3

HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa
Cited by: 53
Author(s): Heidi Tuominen, Samulii Rautava, Stina Syrjänen, María Carmen Collado, Jaana Rautava
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-29744-5

Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins
Cited by: 68
Author(s): Cláudia Marques, Iva Fernandes, Manuela Meireles, Ana Faria, Jeremy P.E. Spencer, Nuno Mateus, Conceição Calhau
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-35654-3

Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq
Cited by: 16
Author(s): Carolina Osuna‐Mascaró, Rafael Rubio de Casas, Francisco Perfectti
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-35940-0

Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India
Cited by: 37
Author(s): Avishek Dutta, Srimanti Dutta Gupta, Abhishek Gupta, Jayeeta Sarkar, Sukanta Roy, Abhijit Mukherjee, Pinaki Sar
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-019-40361-8

miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish
Cited by: 34
Author(s): Thomas Desvignes, Peter Batzel, Jason Sydes, B. Frank Eames, John H. Postlethwait
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-42455-9

Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater
Cited by: 68
Author(s): Gregory A. C. Singer, Nicole A Fahner, Joshua G Barnes, Avery McCarthy, Mehrdad Hajibabaei
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-42348-x

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming
Cited by: 17
Author(s): Nabeel Ahmed, Pietro Sormanni, Prajwal Ciryam, Michele Vendruscolo, Edward P. O’Brien
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-46914-1

Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago
Cited by: 56
Author(s): Stephen Sameroff, Rafal Tokarz, Roxanne A. Charles, Komal Jain, Alexandra Oleynik, Xiaoyu Che, Karla Georges, Christine V. F. Carrington, W. Ian Lipkin, C.A.L. Oura
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-47299-x

Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points
Cited by: 50
Author(s): Krista McGrath, Keri Rowsell, Christian Gates St-Pierre, Andrew Tedder, M. George B. Foody, Carolynne Roberts, Camilla Speller, Matthew J. Collins
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-48571-w

A hierarchy of environmental covariates control the global biogeography of soil bacterial richness
Cited by: 14
Author(s): Samuel Bickel, Xi Chen, Andreas Papritz, Dani Or
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-49118-9

A novel metabarcoding diagnostic tool to explore protozoan haemoparasite diversity in mammals: a proof-of-concept study using canines from the tropics
Cited by: 26
Author(s): Lucas G. Huggins, Anson V. Koehler, Dinh Ng-Nguyen, Stephen Wilcox, Bettina Schunack, Tawin Inpankaew, Rebecca J. Traub
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-49551-w

A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes
Cited by: 44
Author(s): Carina Félix, Rodrigo Meneses, Micael F. M. Gonçalves, Laurentijn Tilleman, Ana Sofia Duarte, Jesús V. Jorrín Novo, Yves Van de Peer, Dieter Deforce, Filip Van Nieuwerburgh, Ana Cristina Esteves, Artur Alves
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-53105-5

Y-chromosome haplogroups from Hun, Avar and conquering Hungarian period nomadic people of the Carpathian Basin
Cited by: 26
Author(s): Endre Neparáczki, Zoltán Maróti, Tibor Kalmár, K Maár, István Nagy, Dóra Latinovics, Ágnes Kustár, György Paragh, Erika Molnár, Antónia Marcsik, Csılla Balogh, Gábor Lőrinczy, Szilárd Sándor Gál, Péter Tomka, Bernadett Kovacsóczy, László Kovács, István Raskó, Tibor Török
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-56438-3

Genomic and functional gene studies suggest a key role of beta-carotene oxygenase 1 like (bco1l) gene in salmon flesh color
Cited by: 22
Author(s): Hanna Helgeland, Marte Sodeland, Nina Zoric, Jacob Torgersen, Fabian Grammes, Johannes von Lintig, Thomas Moen, Sissel Kjøglum, Sigbjørn Lien, Dag Inge Våge
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-57450-8

Oropharyngeal microbiome of a college population following a meningococcal disease outbreak
Cited by: 6
Author(s): Adam C. Retchless, Cécilia B. Kretz, Lorraine D. Rodriguez‐Rivera, Alexander Chen, Heidi M. Soeters, Melissa Whaley, Xin Wang
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-019-57378-8

Genetic insights into the social organisation of the Avar period elite in the 7th century AD Carpathian Basin
Cited by: 21
Author(s): Veronika Csáky, Dániel Gerber, István Koncz, Gergely Csiky, Balázs Gusztáv Mende, Bea Szeifert, Balázs Egyed, Horolma Pamjav, Antónia Marcsik, Erika Molnár, György Paragh, András Gulyás, Bernadett Kovacsóczy, Gabriella M. Lezsák, Gábor Lőrinczy, Anna Szécsényi-Nagy, Tivadar Vida
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-58327-6

Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation
Cited by: 71
Author(s): Alan Selewa, Ryan Dohn, Heather Eckart, Stephanie Lozano, Bingqing Xie, Eric Gauchat, Reem Elorbany, Katherine Rhodes, Jonathan E. Burnett, Yoav Gilad, Sebastian Pott, Anindita Basu
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-60622-1

Effect of iron and magnesium addition on population dynamics and high value product of microalgae grown in anaerobic liquid digestate
Cited by: 16
Author(s): Hande Ermiş, Ünzile Güven-Gülhan, Tunahan Çakır, Mahmut Altınbaş
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-62990-0

Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis
Cited by: 15
Author(s): Yuichi I. Naito, Ioana N. Meleg, Marius Robu, Marius Vlaicu, Dorothée G. Drucker, Christoph Wißing, Michael Hofreiter, Axel Barlow, Hervé Bocherens
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-63664-7

Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map
Cited by: 42
Author(s): Estefanía Carrillo‐Perdomo, Adrien Vidal, Jonathan Kreplak, H. Duborjal, Magalie Leveugle, Jorge Duarte, Catherine Desmetz, Chrystel Deulvot, Blandine Raffiot, Pascal Marget, Nadim Tayeh, Jean-Philippe Pichon, Matthieu Falque, O. C. Martin, Judith Burstin, Grégoire Aubert
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-67798-6

The earliest domestic cat on the Silk Road
Cited by: 8
Author(s): Ashleigh Haruda, Alicia R. Ventresca Miller, Johanna L. A. Paijmans, Axel Barlow, Azilkhan Tazhekeyev, С. Билалов, Y Hesse, Michaela Preick, Turi King, Richard M. Thomas, Heinrich Härke, Ирина Аржанцева
Software Mentions: 2
Published: over 4 years ago

10.18632/oncotarget.25988

Differential signaling pathway activation in 7,12-dimethylbenz[a] anthracene (DMBA)-treated mammary stem/progenitor cells from species with varying mammary cancer incidence
Cited by: 9
Author(s): Melissa M. Ledet, Meghan Oswald, Robert Anderson, Gerlinde R. Van de Walle
Software Mentions: 2
Published: about 6 years ago

10.18632/oncotarget.27400

A pan-cancer transcriptome analysis identifies replication fork and innate immunity genes as modifiers of response to the CHK1 inhibitor prexasertib
Cited by: 11
Author(s): Wayne Blosser, Jack Dempsey, Ann M. McNulty, Xi Rao, Philip J. Ebert, Caitlin D. Lowery, Philip W. Iversen, Yue Webster, Gregory P. Donoho, Xueqian Gong, Farhana F. Merzoug, Sean G. Buchanan, Karsten Boehnke, Chunping Yu, Xintian You, Richard P. Beckmann, Wenjuan Wu, Samuel C. McNeely, Aimee Bence Lin, Ricardo Martínez
Software Mentions: 2
Published: almost 5 years ago

10.1128/JVI.01515-20

Identification of a Functional Small Noncoding RNA of African Swine Fever Virus
Cited by: 8
Author(s): Laura Dunn, Alasdair Ivens, Christopher L. Netherton, Dave Chapman, Philippa M. Beard
Software Mentions: 2
Published: about 4 years ago

10.1186/s12967-021-02848-9

Inhibition of CPT1a as a prognostic marker can synergistically enhance the antileukemic activity of ABT199
Cited by: 9
Author(s): Shihui Mao, Qing Ling, Jiajia Pan, Fenglin Li, Shujuan Huang, Wenle Ye, Wuran Wei, Xiangjie Lin, Yu Qin, Yungui Wang, Xin Huang, Jiansong Huang, Jinghan Wang, Jie Jin
Software Mentions: 2
Published: over 3 years ago

10.1098/rsos.150196

Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation
Cited by: 44
Author(s): Jessica A. Goodheart, Adam L. Bazinet, Allen G. Collins, Michael P. Cummings
Software Mentions: 2
Published: about 9 years ago

10.18632/aging.103560

Circular RNA hsa_circ_0076690 acts as a prognostic biomarker in osteoporosis and regulates osteogenic differentiation of hBMSCs via sponging miR-152
Cited by: 17
Author(s): Shujuan Han, Ming-jie Kuang, Chao Sun, Haifeng Wang, Dachuan Wang, Qian Liu
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.1847

Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome
Cited by: 14
Author(s): Pin Cui, Ulrike Löber, David E. Alquezar‐Planas, Yasuko Ishida, Alexandre Courtiol, Peter Timms, Rebecca N. Johnson, Dorina Lenz, Kristofer M. Helgen, Alfred L. Roca, Stefanie Hartman, Alex D. Greenwood
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.22750

Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis
Cited by: 95
Author(s): Shengben Li, Brandon H. Le, Xuan Ma, Shaofang Li, Chenjiang You, Yu Yu, Bailong Zhang, Lin Liu, Lei Gao, Ting Shi, Yue Zhao, Beixin Mo, Xiaofeng Cao, Xuemei Chen
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.11285

Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples
Cited by: 4
Author(s): Robert S. Cornman, Jennifer A. Fike, Sara J. Oyler‐McCance, Paul M. Cryan
Software Mentions: 2
Published: over 3 years ago

10.1186/s12934-021-01682-4

Multivalent poultry vaccine development using Protein Glycan Coupling Technology
Cited by: 7
Author(s): Marta Mauri, Thippeswamy H. Sannasiddappa, Prerna Vohra, Ricardo Corona-Torres, Adam Smith, Cosmin Chintoan-Uta, Abi Bremner, Vanessa S. Terra, Sherif Abouelhadid, Mark P. Stevens, A. Grant, Jon Cuccui, Brendan W. Wren
Software Mentions: 2
Published: about 3 years ago

10.1111/pbi.12997

Tracking disease resistance deployment in potato breeding by enrichment sequencing
Cited by: 50
Author(s): Miles Armstrong, Jack H. Vossen, Joanne Tze-Yin Lim, R.C.B. Hutten, Jianfei Xu, Shona Strachan, Brian Harrower, Nicolas Champouret, Eleanor M. Gilroy, Ingo Hein
Software Mentions: 2
Published: about 6 years ago

10.1111/pbi.12664

RNAi-mediated endogene silencing in strawberry fruit: detection of primary and secondary siRNAs by deep sequencing
Cited by: 9
Author(s): Katja Härtl, Gregor Kalinowski, Thomas Hoffmann, Anja Preuß, Wilfried Schwab
Software Mentions: 2
Published: over 7 years ago

10.18632/oncotarget.21918

Integrated analysis of mRNA and miRNA expression profiles in livers of Yimeng black pigs with extreme phenotypes for backfat thickness
Cited by: 8
Author(s): Wentong Li, Yalan Yang, Ying Liu, Shuai Liu, Xiuxiu Li, Ying‐Ping Wang, Yanmin Zhang, Hui Tang, Rong Zhou, Kui Li
Software Mentions: 2
Published: about 7 years ago

10.1080/20002297.2019.1663084

Composition and maternal origin of the neonatal oral cavity microbiota
Cited by: 25
Author(s): Heidi Tuominen, María Carmen Collado, Jaana Rautava, Stina Syrjänen, Samuli Rautava
Software Mentions: 2
Published: almost 6 years ago

10.3390/md19040183

Effect of Supplementing Seaweed Extracts to Pigs until d35 Post-Weaning on Performance and Aspects of Intestinal Health
Cited by: 12
Author(s): Stafford Vigors, John V. O’Doherty, Ruth Rattigan, T. Sweeney
Software Mentions: 2
Published: over 3 years ago

10.26508/lsa.202000902

A novel <i>canis lupus familiaris</i> reference genome improves variant resolution for use in breed-specific GWAS
Cited by: 8
Author(s): Robert A. Player, Ellen R. Forsyth, Kathleen Verratti, David Mohr, Alan F. Scott, Christopher Bradburne
Software Mentions: 2
Published: almost 4 years ago

10.3390/antiox10081232

Pterostilbene Changes Epigenetic Marks at Enhancer Regions of Oncogenes in Breast Cancer Cells
Cited by: 3
Author(s): Sadaf Harandi‐Zadeh, Cayla Boycott, Megan Beetch, T.Y. Yang, Bernice M. Martin, Kevin Ren, Anna Kwasniak, John H. Dupuis, Katarzyna Lubecka, Rickey Y. Yada, LeAnn Howe, Barbara Stefańska
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pbio.3000004

Similarities and differences in the regulation of HoxD genes during chick and mouse limb development
Cited by: 25
Author(s): Nayuta Yakushiji-Kaminatsui, Lucille Lopez-Delisle, Christopher Chase Bolt, Guillaume Andrey, Léonardo Beccari, Denis Duboule
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pbio.3001043

Systematic analyses of the MIR172 family members of Arabidopsis define their distinct roles in regulation of APETALA2 during floral transition
Cited by: 40
Author(s): Diarmuid S. Ó’Maoiléidigh, Annabel D. van Driel, Anamika Singh, Qing Sang, N. Le Bec, Coral Vincent, E. Bertrán, Alice Vayssières, Maida Romera-Branchat, Edouard Severing, Rafael Martinez Gallegos, George Coupland
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1008469

Genome-wide identification of short 2′,3′-cyclic phosphate-containing RNAs and their regulation in aging
Cited by: 24
Author(s): Megumi Shigematsu, Keisuke Morichika, Takahiro Kawamura, Syuta Honda, Yohei Kirino
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1005475

SmD1 Modulates the miRNA Pathway Independently of Its Pre-mRNA Splicing Function
Cited by: 24
Author(s): Xi Xiong, Georg Vogler, Krishna Kurthkoti, Anastasia Samsonova, Rui Zhou
Software Mentions: 2
Published: about 9 years ago

10.1128/AAC.02356-17

Translation Elongation Factor 4 (LepA) Contributes to Tetracycline Susceptibility by Stalling Elongating Ribosomes
Cited by: 7
Author(s): Bin Liu, Chunlai Chen
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1004090

Defining NELF-E RNA Binding in HIV-1 and Promoter-Proximal Pause Regions
Cited by: 55
Author(s): John M. Pagano, Ho Young Kwak, Colin T. Waters, Rebekka O. Sprouse, Brian S. White, Abdullah Ozer, Kylan Szeto, David Shalloway, Harold G. Craighead, John T. Lis
Software Mentions: 2
Published: almost 11 years ago

10.1093/bib/bbab021

Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis
Cited by: 11
Author(s): Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1006275

Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions
Cited by: 10
Author(s): Lai Hong Wong, Sunita Sinha, Julien R. C. Bergeron, Joseph Mellor, Guri Giaever, Patrick Flaherty, Corey Nislow
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1006956

Recruitment of Armitage and Yb to a transcript triggers its phased processing into primary piRNAs in Drosophila ovaries
Cited by: 60
Author(s): Radha Raman Pandey, David Homolka, Kuan-Ming Chen, Ravi Sachidanandam, Marie-Odile Fauvarque, Ramesh S. Pillai
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1004915

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress
Cited by: 315
Author(s): Irina Makarevitch, Amanda J. Waters, Patrick T. West, Michelle C. Stitzer, Candice N. Hirsch, Jeffrey Ross‐Ibarra, Nathan M. Springer
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pntd.0004452

Small RNA Profiling in Dengue Virus 2-Infected Aedes Mosquito Cells Reveals Viral piRNAs and Novel Host miRNAs
Cited by: 111
Author(s): Pascal Miesen, Alasdair Ivens, Amy H. Buck, Ronald P. van Rij
Software Mentions: 2
Published: over 8 years ago

10.1186/s13058-020-01328-0

Clinical implications of prospective genomic profiling of metastatic breast cancer patients
Cited by: 29
Author(s): Courtney T. van Geelen, Peter Savas, Zhi L. Teo, Stephen J. Luen, Chen-Fang Weng, Yi-An Ko, Keilly Kuykhoven, Franco Caramia, Roberto Salgado, Prudence A. Francis, Sarah-Jane Dawson, Stephen B. Fox, Andrew Fellowes, Sherene Loi
Software Mentions: 2
Published: over 4 years ago

10.1371/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

10.7554/eLife.40037

The RNA interactome of human telomerase RNA reveals a coding-independent role for a histone mRNA in telomere homeostasis
Cited by: 12
Author(s): Roland Iványi-Nagy, Syed Moiz Ahmed, Sabrina Peter, Priya Dharshana Ramani, P.P. Ong, Oliver Dreesen, Peter Dröge
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.68068

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator
Cited by: 71
Author(s): Adrian L. Sanborn, Benjamin Yeh, Jordan T. Feigerle, Cynthia V. Hao, Raphael J.L. Townshend, E Aiden, Ron O. Dror, Barbara Maier-Davis
Software Mentions: 2
Published: over 3 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

10.1186/s13058-020-01306-6

Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer
Cited by: 6
Author(s): Laura A. Baker, Holly Holliday, Daniel Roden, Christoph Krisp, Sunny Z. Wu, Simon Junankar, Aurélien A. Sérandour, Hisham Mohammed, Radhika Nair, Geetha Sankaranarayanan, Andrew M. K. Law, Andrea McFarland, Peter T. Simpson, Sunil R. Lakhani, Eoin Dodson, Christina Selinger, Lyndal Anderson, Goli Samimi, Neville F. Hacker, Elgene Lim, Christopher J. Ormandy, Matthew J. Naylor, Kaylene J. Simpson, Iva Nikolić, Sandra A. O’Toole, Warren Kaplan, Mark J. Cowley, Jason S. Carroll, Mark P. Molloy, Alexander Swarbrick
Software Mentions: 2
Published: over 4 years ago

10.1371/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

10.1186/s13068-015-0381-1

The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications
Cited by: 93
Author(s): Arne van Hoeck, Nele Horemans, Pieter Monsieurs, Hieu X. Cao, Hildegarde Vandenhove, Ronny Blust
Software Mentions: 2
Published: almost 9 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

10.1186/s13068-016-0565-3

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
Cited by: 87
Author(s): Yvonne Stolze, Andreas Bremges, Madis Rumming, Christian Henke, Irena Maus, Alfred Pühler, Alexander Sczyrba, Andreas Schlüter
Software Mentions: 2
Published: over 8 years ago

10.1371/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

10.1042/BSR20201590

Profiling and bioinformatics analyses reveal differential circular RNA expression in NK/T-cell lymphoma-associated hemophagocytic syndrome
Cited by: 0
Author(s): Changfeng Man, Yu Fan, Guangli Yin, Jiayu Huang, Jujuan Wang, Hai-Rong Qiu
Software Mentions: 2
Published: about 4 years ago

10.1371/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

10.3390/biom11050688

Molecular Targets and Biological Functions of cAMP Signaling in Arabidopsis
Cited by: 17
Author(s): Ruqiang Xu, Yanjuan Guo, Peng Song, Jinrui Liu, Panyu Li, Wenjing Jia, Junheng Zhao
Software Mentions: 2
Published: over 3 years ago

10.1371/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

10.1016/j.ajpath.2018.04.008

ELABELA/APELA Levels Are Not Decreased in the Maternal Circulation or Placenta among Women with Preeclampsia
Cited by: 34
Author(s): Natasha Pritchard, Tu’uhevaha J Kaitu’u-Lino, Sungsam Gong, Justyna Dopierała, Gordon C. S. Smith, D. Stephen Charnock-Jones, Stephen Tong
Software Mentions: 2
Published: over 6 years ago

10.1371/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

10.7554/eLife.42549

Circular synthesized CRISPR/Cas gRNAs for functional interrogations in the coding and noncoding genome
Cited by: 32
Author(s): Martin Wegner, Valentina Diehl, Verena Bittl, Rahel de Bruyn, Svenja Wiechmann, Yves Matthess, Marie Hebel, Michael Hayes, Simone Schaubeck, Chris Benner, Sven Heinz, Anja Bremm, Ivan Đikić, Andreas Ernst, Manuel Kaulich
Software Mentions: 2
Published: over 5 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

10.1155/2021/6673010

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F5 Population of Pepper with Contrasting Powdery Mildew Resistance Trait
Cited by: 6
Author(s): Abinaya Manivannan, Sena Choi, Tae-Hwan Jun, Eun-Young Yang, Jinhee Kim, Eun-Su Lee, Hye-Eun Lee, Do-Sun Kim, Yul-Kyun Ahn
Software Mentions: 2
Published: over 3 years ago

10.1371/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

10.7554/eLife.26875

Parallel evolution of influenza across multiple spatiotemporal scales
Cited by: 107
Author(s): Katherine S Xue, Terry Stevens-Ayers, Angela P Campbell, Janet A. Englund, Steven A. Pergam, Michael Boeckh, Jesse D. Bloom
Software Mentions: 2
Published: over 7 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

Projects: pypi: cutadapt

Papers Mentioning cutadapt 1,562