pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-73885-5

Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes
Cited by: 9
Author(s): Robert Mukiibi, Dayle Johnston, Michael Vinsky, Carolyn Fitzsimmons, Paul Stothard, Sinéad M. Waters, Changxi Li
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0095782

Extending the sRNAome of Apple by Next-Generation Sequencing
Cited by: 15
Author(s): Marike Visser, Van der Walt Anelda, Hans J. Maree, D. J. G. Rees, Johan T. Burger
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0224969

A fecal sequel: Testing the limits of a genetic assay for bat species identification
Cited by: 14
Author(s): Faith M. Walker, Abby Tobin, Nancy B. Simmons, Colin J. Sobek, Daniel E. Sanchez, Christopher P. Chambers, Viacheslav Y. Fofanov
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms20051018

Genomic Analysis of Shewanella sp. O23S—The Natural Host of the pSheB Plasmid Carrying Genes for Arsenic Resistance and Dissimilatory Reduction
Cited by: 17
Author(s): Witold Uhrynowski, Monika Radlińska, Łukasz Drewniak
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-77639-1

Secreted sphingomyelins modulate low mammary cancer incidence observed in certain mammals
Cited by: 7
Author(s): Melissa M. Ledet, Rebecca M. Harman, Jiwei Fan, Emily Schmitt-Matzen, M. Elena Díaz-Rubio, Sheng Zhang, Gerlinde R. Van de Walle
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0071609

Transcriptome and Peptidome Characterisation of the Main Neuropeptides and Peptidic Hormones of a Euphausiid: The Ice Krill, Euphausia crystallorophias
Cited by: 55
Author(s): Jean‐Yves Toullec, Matthieu Le Corre, Benoı̂t Bernay, Michael A. S. Thorne, Kévin Cascella, Céline Ollivaux, Joël Henry, Melody S. Clark
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0066662

Phylogenetic Analysis of a Microbialite-Forming Microbial Mat from a Hypersaline Lake of the Kiritimati Atoll, Central Pacific
Cited by: 134
Author(s): Dominik Schneider, Gernot Arp, Andreas Reimer, Joachim Reitner, Rolf Daniel
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0215658

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal
Cited by: 11
Author(s): Anneloes E. Groenenboom, Megan Parker, Anne de Vries, Suzette de Groot, Stephanie Zobrist, Kimberly Mansen, Peiman Milani, Remco Kort, Eddy J. Smid, Sijmen E. Schoustra
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-020-07026-7

Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1
Cited by: 10
Author(s): Umberto Rosani, Miriam Abbadi, Timothy Green, Changming Bai, Edoardo Turolla, Giuseppe Arcangeli, K. Mathias Wegner, Paola Venier
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-79332-9

Molecular patterns of isolated tubulitis differ from tubulitis with interstitial inflammation in early indication biopsies of kidney allografts
Cited by: 4
Author(s): Petra Hrubá, Katelynn S. Madill‐Thomsen, Martina Macková, Jǐŕı Kléma, Jana Malušková, Luděk Voska, Alena Paříková, Janka Slatinská, Philip F. Halloran, Ondřej Viklický
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0176343

Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding
Cited by: 159
Author(s): Elizabeth A. Andruszkiewicz, Hilary A. Starks, Francisco P. Chávez, Lauren M. Sassoubre, Barbara A. Block, Alexandria B. Boehm
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.9272

Piwi-interacting RNAs and PIWI genes as novel prognostic markers for breast cancer
Cited by: 74
Author(s): Preethi Krishnan, Sunita Ghosh, Kathryn Graham, John R. Mackey, Olga Kovalchuk, Sambasivarao Damaraju
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0121261

Identification of Candidate Odorant Receptors in Asian Corn Borer Ostrinia furnacalis
Cited by: 46
Author(s): Bin Yang, Katsuhisa Ozaki, Yukio Ishikawa, Takashi Matsuo
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0228483

Deep-sea amphipods around cobalt-rich ferromanganese crusts: Taxonomic diversity and selection of candidate species for connectivity analysis
Cited by: 7
Author(s): Akira Iguchi, Miyuki Nishijima, Yuki Yoshioka, Aika Miyagi, R. Miwa, Yuichiro Tanaka, Shogo Kato, Takaaki Matsui, Yoshiko Igarashi, Naoya Okamoto, Atsushi Suzuki
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms20122968

Integrated Analysis of the Altered lncRNAs and mRNAs Expression in 293T Cells after Ionizing Radiation Exposure
Cited by: 9
Author(s): Mengmeng Yang, Yuxiao Sun, Changyan Xiao, Kaihua Ji, Manman Zhang, Ningning He, Jinhan Wang, Qin Wang, Zhijuan Sun, Yan Wang, Liqing Du, Yang Liu, Chang Xu, Qiang Liu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0249229

Differential methylation and expression patterns of microRNAs in relation to breast cancer subtypes among American women of African and European ancestry
Cited by: 7
Author(s): Zhihong Gong, Jianhong Chen, Jie Wang, Song Liu, Christine B. Ambrosone, Michael J. Higgins
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0064393

Comparison of MicroRNA Deep Sequencing of Matched Formalin-Fixed Paraffin-Embedded and Fresh Frozen Cancer Tissues
Cited by: 63
Author(s): Meng Wang, Joseph P. McElroy, Stefano Volinia, Jeff Palatini, Sarah Warner, Leona W. Ayers, Kamalakannan Palanichamy, Arnab Chakravarti, Tim Lautenschlaeger
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-15-972

RNA-Seq reveals a xenobiotic stress response in the soybean aphid, Aphis glycines, when fed aphid-resistant soybean
Cited by: 70
Author(s): Raman Bansal, M. A. Rouf Mian, Omprakash Mittapalli, Andy Michel
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0219207

Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes
Cited by: 123
Author(s): Kerrigan B. Gilbert, Emily Holcomb, Robyn L Allscheid, James C. Carrington
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0143000

454 Pyrosequencing of Olive (Olea europaea L.) Transcriptome in Response to Salinity
Cited by: 22
Author(s): Christos Bazakos, Maria Manioudaki, Elena Sarropoulou, Spano Thodhoraq, Panagiotis Kalaitzis
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-018-4853-0

The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi
Cited by: 75
Author(s): Yuuki Kobayashi, Taro Maeda, Katsushi Yamaguchi, Hiromu Kameoka, Sachiko Tanaka, Tatsuhiro Ezawa, Shuji Shigenobu, Masayoshi Kawaguchi
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0095340

Effects of Silver Nitrate and Silver Nanoparticles on a Planktonic Community: General Trends after Short-Term Exposure
Cited by: 54
Author(s): Jens Boenigk, Daniela Beißer, Sonja Zimmermann, Christina Böck, Jurij Jakobi, Daniel Grabner, Lars Großmann, Sven Rahmann, Stephan Barcikowski, Bernd Sures
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-14-920

Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment
Cited by: 35
Author(s): Vincent P. Richards, Sang Chul Choi, Paulina D. Pavinski Bitar, Anagha Gurjar, Michael J. Stanhope
Software Mentions: 1
Published: almost 11 years ago

10.18632/oncotarget.13563

VENTX induces expansion of primitive erythroid cells and contributes to the development of acute myeloid leukemia in mice
Cited by: 6
Author(s): Gudumac Eva, Naidu M. Vegi, Medhanie Mulaw, Tamoghna Mandal, Shiva Bamezai, Rainer Claus, Alpaslan Tasdogan, Leticia Quintanilla-Martı́nez, Alexander Grunenberg, Konstanze Döhner, Hartmut Döhner, Lars Bullinger, Torsten Haferlach, Christian Buske, Vijay P.S. Rawat, Michaela Feuring‐Buske
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0211497

Vgsc-interacting proteins are genetically associated with pyrethroid resistance in Aedes aegypti
Cited by: 13
Author(s): Corey L. Campbell, Karla Saavedra-Rodríguez, Tristan D. Kubik, Audrey Lenhart, Saúl Lozano-Fuentes, William C. Black
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-021-93086-y

Acetaldehyde exposure underlies functional defects in monocytes induced by excessive alcohol consumption
Cited by: 5
Author(s): Shintaro Shiba, Nobuhiro Nakamoto, Po–Sung Chu, Keisuke Ojiro, Nobuhito Taniki, Akihiro Yamaguchi, Rei Morikawa, Tadashi Katayama, Aya Yoshida, Ryo Aoki, Toshiaki Teratani, Takahiro Suzuki, Takeshi Miyamoto, Sachiko Hara, Akira Yokoyama, Takanori Kanai
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0118339

RNA-Seq Analysis of the Response of the Halophyte, Mesembryanthemum crystallinum (Ice Plant) to High Salinity
Cited by: 54
Author(s): Hironaka Tsukagoshi, Takamasa Suzuki, Kyoji Nishikawa, Sakae Agarie, Sumie Ishiguro, Tetsuya Higashiyama
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0134310

The Identification of Circulating MiRNA in Bovine Serum and Their Potential as Novel Biomarkers of Early Mycobacterium avium subsp paratuberculosis Infection
Cited by: 47
Author(s): DJ Farrell, Ronan G. Shaughnessy, Louise Britton, David E. MacHugh, Bryan Markey, Stephen V. Gordon
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0113698

Unusual Ratio between Free Thyroxine and Free Triiodothyronine in a Long-Lived Mole-Rat Species with Bimodal Ageing
Cited by: 22
Author(s): Yoshiyuki Henning, Christiane Vole, Sabine Begall, Martin Bens, Martina Broecker-Preuß, Arne Sahm, Karol Szafranski, Hynek Burda, Philip Dammann
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0199010

MeDIP combined with in-solution targeted enrichment followed by NGS: Inter-individual methylation variability of fetal-specific biomarkers and their implementation in a proof of concept study for NIPT
Cited by: 7
Author(s): Anna Keravnou, Marios Ioannides, Charalambos Loizides, Kyriakos Tsangaras, Achilleas Achilleos, Petros Mina, Elena Kypri, Michael D. Hadjidaniel, Maria Neofytou, Skevi Kyriacou, Carolina Sismani, George Koumbaris, Philippos C. Patsalis
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0096793

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics
Cited by: 114
Author(s): Mandy M. Y. Tin, Evan P. Economo, Alexander S. Mikheyev
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-018-4581-5

Identification of novel putative causative genes and genetic marker for male sterility in Japanese cedar (Cryptomeria japonica D.Don)
Cited by: 34
Author(s): Kentaro Mishima, Tomonori Hirao, Miyoko Tsubomura, Miho Tamura, Masayuki Kurita, Masato Nose, So Hanaoka, Makoto Takahashi, Atsushi Watanabe
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.13816

MicroRNA-203 predicts human survival after resection of colorectal liver metastasis
Cited by: 16
Author(s): T. Peter Kingham, Hoang Cong Nguyen, Jianbao Zheng, Ioannis T. Konstantinidis, Eran Sadot, Jinru Shia, Deborah Kuk, Steven Zhang, Leonard Saltz, Michael I. D’Angelica, William R. Jarnagin, Hani Goodarzi, Sohail F. Tavazoie
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0130324

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol
Cited by: 500
Author(s): Vasco Elbrecht, Florian Leese
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-021-98168-5

The macronuclear genome of the Antarctic psychrophilic marine ciliate Euplotes focardii reveals new insights on molecular cold adaptation
Cited by: 12
Author(s): Matteo Mozzicafreddo, Sandra Pucciarelli, Estienne C. Swart, Angela Piersanti, Christiane Emmerich, Giovanna Migliorelli, Patrizia Ballarini, Cristina Miceli
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-021-98452-4

Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics
Cited by: 8
Author(s): Laila Sara Arroyo Mühr, Joakim Dillner, Agustín Enrique Ure, Karin Sundström, Emilie Hultin
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0162342

Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples
Cited by: 60
Author(s): Faith M. Walker, Charles H. D. Williamson, Daniel E. Sanchez, Colin J. Sobek, Christopher P. Chambers
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-021-98820-0

NEIL3-deficiency increases gut permeability and contributes to a pro-atherogenic metabolic phenotype
Cited by: 4
Author(s): Tom Rune Karlsen, Xiang Yi Kong, Sverre Holm, Ana Quiles‐Jiménez, Tuva B. Dahl, Kuan Yang, Ellen Lund Sagen, Tonje Skarpengland, Jonas Øgaard, Kristian Holm, Beate Vestad, Maria Belland Olsen, Pål Aukrust, Magnar Bjørås, Johannes R. Hov, Bente Halvorsen, Ida Gregersen
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0226654

Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan
Cited by: 22
Author(s): Rikai Sawafuji, Aiko Saso, Wataru Suda, Masahira Hattori, Shintaroh Ueda
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-15-S3-S5

A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders
Cited by: 17
Author(s): Margherita Mutarelli, Veer Singh Marwah, Rossella Rispoli, Diego Carrella, Gopuraja Dharmalingam, Gennaro Oliva, Diego di Bernardo
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0149541

Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Resistant to Fifth-Generation Cephalosporins Reveals Potential Non-mecA Mechanisms of Resistance
Cited by: 51
Author(s): Alexander L. Greninger, Som S. Chatterjee, Liana C. Chan, Stephanie M. Hamilton, Henry F. Chambers, Charles Y. Chiu
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.stemcr.2017.05.013

Fetal Therapy Model of Myelomeningocele with Three-Dimensional Skin Using Amniotic Fluid Cell-Derived Induced Pluripotent Stem Cells
Cited by: 29
Author(s): Kazuhiro Kajiwara, Tomohiro Tanemoto, Seiji Wada, Jurii Karibe, Norimasa Ihara, Yu Ikemoto, Tomoyuki Kawasaki, Yoshie Oishi, Osamu Samura, Koji Okamura, Shuji Takada, Hidenori Akutsu, Haruhiko Sago, Aikou Okamoto, Akihiro Umezawa
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0129102

Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone
Cited by: 310
Author(s): Ron Pinhasi, Daniel Fernandes, Kendra Sirak, Mario Novak, Sarah Connell, Songül Alpaslan-Roodenberg, Fokke Gerritsen, Vyacheslav Moiseyev, А. В. Громов, Pál Raczky, Alexandra Anders, Michael Pietrusewsky, Gary O. Rollefson, Marija Jovanovic, Trinhhoang Hiep, Guy Bar-Oz, Marc Oxenham, Hirofumi Matsumura, Michael Hofreiter
Software Mentions: 1
Published: over 9 years ago

10.18632/aging.103316

Integrative analysis of miRNAs-mRNAs reveals that miR-182 up-regulation contributes to proliferation and invasion of nasopharyngeal carcinoma by targeting PTEN
Cited by: 6
Author(s): Zhongqi Shi, Rushi Wang, Li-Gui Huang, Xiao Chen, Min Xu, Dingjun Zha, Yue Ma
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0092259

ZASP Interacts with the Mechanosensing Protein Ankrd2 and p53 in the Signalling Network of Striated Muscle
Cited by: 27
Author(s): Valentina Martinelli, W. Buck Kyle, Snežana Kojić, Nicola Vitulo, Zhaohui Li, Anna Belgrano, Paolo Maiuri, Lawrence Banks, Matteo Vatta, Giorgio Valle, Georgine Faulkner
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0191650

Effect of light wavelength on hot spring microbial mat biodiversity
Cited by: 10
Author(s): Akifumi Nishida, Vera Thiel, Mayuko Nakagawa, Shotaro Ayukawa, Masatoshi Yamamura
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13287-021-02384-9

Bone marrow mesenchymal stem cells and their derived exosomes resolve doxorubicin-induced chemobrain: critical role of their miRNA cargo
Cited by: 15
Author(s): Marwa O. El-Derany, Mohamed Noureldein
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0252534

Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses
Cited by: 27
Author(s): Isabelle Hardmeier, Nadja Aeberhard, Weihong Qi, Katja Schoenbaechler, Hubert Kraettli, Jean‐Michel Hatt, Cornel Fraefel, Jakub Kubacki
Software Mentions: 1
Published: over 3 years ago

10.1155/2017/4252974

Long Noncoding RNA uc001pwg.1 Is Downregulated in Neointima in Arteriovenous Fistulas and Mediates the Function of Endothelial Cells Derived from Pluripotent Stem Cells
Cited by: 4
Author(s): Lei Lv, Haozhe Qi, Xiaojia Guo, Qihong Ni, Zezhen Yan, Lan Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1007/s00122-019-03305-4

Genetic insights into morphometric inflorescence traits of wheat
Cited by: 31
Author(s): Gizaw M. Wolde, Corinna Trautewig, Martin Mascher, Thorsten Schnurbusch
Software Mentions: 1
Published: almost 6 years ago

10.1007/s00122-020-03743-5

Genome-wide identification of loci modifying spike-branching in tetraploid wheat
Cited by: 8
Author(s): Gizaw M. Wolde, Mona Schreiber, Corinna Trautewig, Axel Himmelbach, Shun Sakuma, Martin Mascher, Thorsten Schnurbusch
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-021-07904-8

Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation
Cited by: 10
Author(s): Ziyue Qin, Wencan Wang, Malik Ahsan Ali, Yihan Wang, Yan Zhang, Ming Zhang, Guangbin Zhou, Jiandong Yang, Changjun Zeng
Software Mentions: 1
Published: over 3 years ago

10.3390/toxins8120378

Transcriptome Analysis to Understand the Toxicity of Latrodectus tredecimguttatus Eggs
Cited by: 11
Author(s): Donghui Xu, Xianchun Wang
Software Mentions: 1
Published: almost 8 years ago

10.1186/2047-9158-3-17

In silico analysis of regulatory networks underlines the role of miR-10b-5p and its target BDNF in huntington’s disease
Cited by: 34
Author(s): Sören Müller
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0090599

Comprehensive Molecular Diagnosis of Bardet-Biedl Syndrome by High-Throughput Targeted Exome Sequencing
Cited by: 39
Author(s): Dongjun Xing, Hongxing Zhang, Na Huang, Kun Wu, Xiu‐Feng Huang, Fang Huang, Yi Tong, Chi‐Pui Pang, Jia Qu, Zi‐Bing Jin
Software Mentions: 1
Published: over 10 years ago

10.1002/advs.201903727

Germline Polymorphisms and Length of Survival of Nasopharyngeal Carcinoma: An Exome‐Wide Association Study in Multiple Cohorts
Cited by: 12
Author(s): Yun‐Miao Guo, Jie‐Rong Chen, Yang Feng, Melvin L.K. Chua, Yanni Zeng, Edwin P. Hui, Allen Chan, Lin‐Quan Tang, Lin Wang, Qian Cui, Huiqiong Han, Chunling Luo, Guo‐Wang Lin, Yan Liang, Yang Liu, Z. He, Yu‐Xiang Liu, Panpan Wei, Chu‐Jun Liu, Peng Wan, Bo‐Wei Han, Xiaoyu Zuo, Enya Hui Wen Ong, Eugenia Li Ling Yeo, Kay Soon Low, Gek San Tan, Tony Kiat Hon Lim, Jacqueline Siok Gek Hwang, Bo Li, Feng Qian, Xiaojun Xia, Yunfei Xia, Josephine Mun Yee Ko, Wei Dai, Maria Li Lung, Anthony Tak-cheung Chan, Dennis Lo, Mu‐Sheng Zeng, Hai‐Qiang Mai, Jianjun Li, Yi‐Xin Zeng, Jin‐Xin Bei
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0048607

Prediction of Altered 3′- UTR miRNA-Binding Sites from RNA-Seq Data: The Swine Leukocyte Antigen Complex (SLA) as a Model Region
Cited by: 15
Author(s): Marie-Laure Endale Ahanda, Eric Fritz, Jordi Estellé, Zhi Liang Hu, Ole Madsen, Martien A. M. Groenen, Dario Beraldi, Ronan Kapétanovic, David Hume, R. Rowland, Joan K. Lunney, Claire Rogel‐Gaillard, James M. Reecy, Elisabetta Giuffra
Software Mentions: 1
Published: about 12 years ago

10.1186/s12864-015-1806-8

Reducing amplification artifacts in high multiplex amplicon sequencing by using molecular barcodes
Cited by: 103
Author(s): Peng Quan, Ravi Vijaya Satya, Marcus Lewis, Pranay Randad, Yexun Wang
Software Mentions: 1
Published: over 9 years ago

10.1007/s11250-021-02877-y

Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi
Cited by: 10
Author(s): J.N. Hakizimana, Jean‐Bosco Ntirandekura, Clara M. Yona, Lionel Nyabongo, Gladson Kamwendo, Julius L.C. Chulu, Désiré Ntakirutimana, Olivier Kamana, Hans Nauwynck, Gerald Misinzo
Software Mentions: 1
Published: over 3 years ago

10.1101/2021.03.11.435000

ChAdOx1 nCoV-19 (AZD1222) protects Syrian hamsters against SARS-CoV-2 B.1.351 and B.1.1.7
Cited by: 18
Author(s): Robert J. Fischer, Neeltje van Doremalen, Danielle R. Adney, Claude Kwe Yinda, Julia R Port, Myndi G. Holbrook, Jonathan Schulz, Brandi N. Williamson, Tina Thomas, Kent D. Barbian, Sarah L. Anzick, Stacy Ricklefs, Brian J Smith, Dan Long, Craig Martens, Greg Saturday, Emmie de Wit, Sarah C. Gilbert, Teresa Lambe, Vincent J. Munster
Software Mentions: 1
Published: over 3 years ago

10.1101/2021.06.17.448814

Western diet increases COVID-19 disease severity in the Syrian hamster
Cited by: 9
Author(s): Julia R Port, Danielle R. Adney, Benjamin Schwarz, Jonathan Schulz, Daniel E. Sturdevant, Brian J Smith, Victoria A. Avanzato, Myndi G. Holbrook, Jyothi N. Purushotham, Kaitlin A. Stromberg, Ian Leighton, Catharine M. Bosio, Carl Shaia, Vincent J. Munster
Software Mentions: 1
Published: over 3 years ago

10.18632/oncotarget.17448

Characterization of mouse serum exosomal small RNA content: The origins and their roles in modulating inflammatory response
Cited by: 25
Author(s): Xin Zhou, Zinan Jiao, Juling Ji, Shuyuan Li, Xiaodi Huang, Xiaoshuang Lu, Heng Zhao, Jingwen Peng, Xinya Chen, Qiuhong Ji, Yuhua Ji
Software Mentions: 1
Published: over 7 years ago

10.1101/2021.05.07.443115

Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques
Cited by: 6
Author(s): Vincent J. Munster, Meaghan Flagg, Manmeet Singh, Brandi N. Williamson, Friederike Feldmann, Lizzette Pérez-Pérez, Beniah Brumbaugh, Myndi G. Holbrook, Danielle R. Adney, Atsushi Okumura, Patrick W. Hanley, Brian J Smith, Jamie Lovaglio, Sarah L. Anzick, Craig Martens, Neeltje van Doremalen, Greg Saturday, Emmie de Wit
Software Mentions: 1
Published: over 3 years ago

10.1101/2021.08.25.457626

The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters
Cited by: 3
Author(s): Timothy D. Carroll, Douglas Fox, Neeltje van Doremalen, Erin E. Ball, Mary Kate Morris, Alicia Sotomayor-González, Venice Servellita, Arjun Rustagi, Claude Kwe Yinda, Linda Fritts, Julia R Port, Zhien Ma, Myndi G. Holbrook, Jonathan Schulz, Catherine A. Blish, Carl V. Hanson, Charles Y. Chiu, Vincent J. Munster, Sarah A. Stanley, Christopher J. Miller
Software Mentions: 1
Published: about 3 years ago

10.3390/ijms21165753

Alterations of Rice (Oryza sativa L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus
Cited by: 6
Author(s): Linying Li, Yuqing He, Xueying Zhang, Hehong Zhang, Zongtao Sun, Junmin Li, Gaojie Hong
Software Mentions: 1
Published: over 4 years ago

10.1128/mBio.00844-17

Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity
Cited by: 23
Author(s): Ivaylo P. Ivanov, Jiajie Wei, Stephen Z. Caster, Kristina M. Smith, Audrey M. Michel, Ying Zhang, Andrew E. Firth, Michael Freitag, Jay C. Dunlap, Deborah Bell-Pedersen, John F. Atkins, Matthew S. Sachs
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.00419-18

A Viral Suppressor Modulates the Plant Immune Response Early in Infection by Regulating MicroRNA Activity
Cited by: 28
Author(s): Robert Pertermann, Selvaraj Tamilarasan, Torsten Gursinsky, Giorgio Gambino, Jana Schuck, Claus Weinholdt, Hauke Lilie, Ivo Große, Ralph Golbik, Vitantonio Pantaleo, Sven-Erik Behrens
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-017-4348-4

Alternative patterns of sex chromosome differentiation in Aedes aegypti (L)
Cited by: 9
Author(s): Corey L. Campbell, Laura B. Dickson, Saúl Lozano-Fuentes, Punita Juneja, Francis M. Jiggins, William C. Black
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0074938

Signatures of Rapid Evolution in Urban and Rural Transcriptomes of White-Footed Mice (Peromyscus leucopus) in the New York Metropolitan Area
Cited by: 65
Author(s): S. E. Harris, Jason Munshi‐South, Craig Obergfell, Rachel J. O’Neill
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0143472

Whole-Genome Sequencing of Three Clonal Clinical Isolates of B. cenocepacia from a Patient with Cystic Fibrosis
Cited by: 9
Author(s): Ruth R. Miller, Trevor J. Hird, Patrick Tang, James E. A. Zlosnik
Software Mentions: 1
Published: almost 9 years ago

10.1128/mBio.01315-19

Crypt- and Mucosa-Associated Core Microbiotas in Humans and Their Alteration in Colon Cancer Patients
Cited by: 87
Author(s): Azadeh Saffarian, Céline Mulet, Béatrice Regnault, Aurélien Amiot, J. Tran-Van-Nhieu, Jacques Ravel, Iradj Sobhani, Philippe J. Sansonetti, Thierry Pédron
Software Mentions: 1
Published: about 5 years ago

10.1128/mBio.00600-20

“ Candidatus Ethanoperedens,” a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane
Cited by: 59
Author(s): Cedric Jasper Hahn, Rafael Laso-Pérez, Francesca Vulcano, Konstantinos-Marios Vaziourakis, Runar Stokke, Ida Helene Steen, Andreas Teske, Antje Boetius, Manuel Liebeke, Rudolf Amann, Katrin Knittel, Gunter Wegener
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-020-06882-7

Transcriptome analysis of the uterus of hens laying eggs differing in cuticle deposition
Cited by: 14
Author(s): Sandra Poyatos Pertiñez, Peter W.F. Wilson, W. Icken, D. Cavero, M. Bain, Anita C. Jones, Ian C. Dunn
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0252930

Disruption of the pro-inflammatory, anti-inflammatory cytokines and tight junction proteins expression, associated with changes of the composition of the gut microbiota in patients with irritable bowel syndrome
Cited by: 16
Author(s): В. Т. Ивашкин, Yuri M. Poluektov, Evgeniya Kogan, О. С. Шифрин, А. А. Шептулин, А. Л. Ковалева, А. А. Курбатова, George S. Krasnov, Elena Poluektova
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.02052-20

Phase Transitions by an Abundant Protein in the Anammox Extracellular Matrix Mediate Cell-to-Cell Aggregation and Biofilm Formation
Cited by: 8
Author(s): Thomas Seviour, Lan Li Wong, Yang Lü, Sudarsan Mugunthan, Qiaohui Yang, Uma Shankari, Irina Bessarab, David Liebl, Rohan B. H. Williams, Yingyu Law, Staffan Kjelleberg
Software Mentions: 1
Published: about 4 years ago

10.1128/mBio.01492-20

CaaX-Like Protease of Cyanobacterial Origin Is Required for Complex Plastid Biogenesis in Malaria Parasites
Cited by: 3
Author(s): Thomas R. Meister, Yong Tang, Michael J. Pulkoski-Gross, Ellen Yeh
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pntd.0002701

Parasite-Derived MicroRNAs in Host Serum As Novel Biomarkers of Helminth Infection
Cited by: 121
Author(s): Anna M. Hoy, Rachel J. Lundie, Alasdair Ivens, Juan F. Quintana, Norman Nausch, Thorsten Forster, Frances M. Jones, Narcis B. Kabatereine, David W. Dunne, Francisca Mutapi, Andrew S. MacDonald, Amy H. Buck
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pntd.0007189

Parasite specific 7SL-derived small RNA is an effective target for diagnosis of active trypanosomiasis infection
Cited by: 12
Author(s): Stephen Chiweshe, Pieter C. Steketee, Siddharth Jayaraman, Edith Paxton, Kyriaki Neophytou, Heidi Erasmus, M. T. Labuschagne, Anneli Cooper, Annette MacLeod, Finn Grey, Liam J. Morrison
Software Mentions: 1
Published: almost 6 years ago

10.1128/mBio.00972-21

Expression of the Ebola Virus VP24 Protein Compromises the Integrity of the Nuclear Envelope and Induces a Laminopathy-Like Cellular Phenotype
Cited by: 5
Author(s): Santiago Vidal, María Teresa Sánchez-Aparicio, Rocio Castro Seoane, Ahmed El Motiam, Emily V Nelson, Yanis Hichem Bouzaher, Maite Baz-Martínez, Isabel García-Dorival, Susana Gonzalo, Enrique Vázquez, Anxo Vidal, César Muñoz‐Fontela, Adolfo Garcı́a-Sastre, Carmen Rivas
Software Mentions: 1
Published: about 3 years ago

10.1186/1471-2164-15-219

Transcriptome sequencing and profiling of expressed genes in cambial zone and differentiating xylem of Japanese cedar (Cryptomeria japonica)
Cited by: 45
Author(s): Kentaro Mishima, Takeshi Fujiwara, Taiichi Iki, Katsushi Kuroda, Kana Yamashita, Miho Tamura, Yoshitake Fujisawa, Atsushi Watanabe
Software Mentions: 1
Published: over 10 years ago

10.1128/mSphere.00615-17

Heterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients
Cited by: 16
Author(s): Xuan Qin, Chuan Zhou, Danielle M. Zerr, Amanda Adler, Amin Addetia, Shuo Yuan, Alexander L. Greninger
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-016-2690-6

Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements
Cited by: 135
Author(s): Kentaro Yoshida, Diane G. O. Saunders, Chikako Mitsuoka, Satoshi Natsume, Shunichi Kosugi, Hiromasa Saitoh, Yushi Inoue, Izumi Chuma, Yukio Tosa, Liliana Cano, Sophien Kamoun, Ryohei Terauchi
Software Mentions: 1
Published: over 8 years ago

10.1128/mSphere.00090-18

Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis
Cited by: 31
Author(s): Clement K. M. Tsui, Ruth R. Miller, Miguel Uyaguari, Patrick Tang, Cédric Chauve, William W. L. Hsiao, Judith L. Isaac-Renton, Natalie Prystajecky
Software Mentions: 1
Published: over 6 years ago

10.1128/mSphere.00311-18

Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches
Cited by: 16
Author(s): Simon H. Williams, Samuel Cordey, Nishit Bhuva, Florian Laubscher, Mary-Anne Hartley, Noémie Boillat‐Blanco, Zainab Mbarack, Josephine Samaka, Tarsis Mlaganile, Komal Jain, Valérie D’Acremont, Laurent Kaiser, W. Ian Lipkin
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.16788

Next-generation sequencing reveals microRNA markers of adrenocortical tumors malignancy
Cited by: 31
Author(s): Łukasz Koperski, Marta Kotlarek, Michał Świerniak, Monika Kolanowska, Anna Klinke, Barbara Górnicka, Krystian Jażdżewski, Anna Wójcicka
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pntd.0004018

Differential Gene Expression and Infection Profiles of Cutaneous and Mucosal Leishmania braziliensis Isolates from the Same Patient
Cited by: 28
Author(s): Eliza V.C. Alves-Ferreira, Juliano Simões de Toledo, Arthur Henrique Cavalcante de Oliveira, Tiago Luiz Ferreira, Patrícia de Cássia Ruy, Camila Figueiredo Pinzan, Ramon F. Santos, Viviane Boaventura, David Rojo, Ángeles López‐Gonzálvez, José César Rosa, Coral Barbas, Manoel Barral‐Netto, Aldina Barral, Ângela K. Cruz
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1009444

Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure
Cited by: 7
Author(s): Heinrich Bente, Andrea M. Foerster, Nicole Lettner, Ortrun Mittelsten Scheid
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1008094

Canonical cytosolic iron-sulfur cluster assembly and non-canonical functions of DRE2 in Arabidopsis
Cited by: 5
Author(s): Xiaokang Wang, Xudong Chen, Landi Sun, Weiqiang Qian
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1006539

Genomic Footprints of Selective Sweeps from Metabolic Resistance to Pyrethroids in African Malaria Vectors Are Driven by Scale up of Insecticide-Based Vector Control
Cited by: 57
Author(s): Kayla G. Barnes, Gareth D. Weedall, Miranda Ndula, Helen Irving, Themba Mzihalowa, Janet Hemingway, Charles S. Wondji
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms22041792

Signatures of Dermal Fibroblasts from RDEB Pediatric Patients
Cited by: 4
Author(s): A. Beilin, Н. А. Евтушенко, Daniil K. Lukyanov, Н. Н. Мурашкин, Э. Т. Амбарчян, Alexander Pushkov, Kirill Savostyanov, А. П. Фисенко, O. S. Rogovaya, A. V. Vasiliev, E. A. Vorotelyak, Nadya G. Gurskaya
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-017-4159-7

dCATCH-Seq: improved sequencing of large continuous genomic targets with double-hybridization
Cited by: 4
Author(s): Yan Feng Zhang, Jun Song, Kenneth Day, Devin Absher
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pgen.1007590

The methyltransferase HEN1 is required in Nematostella vectensis for microRNA and piRNA stability as well as larval metamorphosis
Cited by: 20
Author(s): Vengamanaidu Modepalli, Arie Fridrich, Maayan Agron, Yehu Moran
Software Mentions: 1
Published: over 6 years ago

10.1128/mSystems.00040-17

Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology
Cited by: 58
Author(s): Kirk J. Grubbs, Rachel M. Bleich, Kevin C. Santa Maria, Scott E. Allen, Sherif Farag, AgBiome Team, Elizabeth A. Shank, A. Bowers
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pcbi.1007206

PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting
Cited by: 13
Author(s): Annett Erkes, Stefanie Mücke, Maik Reschke, Jens Boch, Jan Grau
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.2000779

Alteration of protein function by a silent polymorphism linked to tRNA abundance
Cited by: 97
Author(s): Sebastian Kirchner, Zhiwei Cai, Robert Rauscher, Nicolai Kastelic, Melanie Anding, Andreas Czech, Bertrand Kleizen, Lynda S. Ostedgaard, Ineke Braakman, David N. Sheppard, Zoya Ignatova
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22084161

Integrated Analysis of the Transcriptome and Metabolome Revealed Candidate Genes Involved in GA3-Induced Dormancy Release in Leymus chinensis Seeds
Cited by: 10
Author(s): Bing Li, Pan Zhang, Fengdan Wang, Ran Li, Jian Liu, Qiannan Wang, Wei Liu, Bo Wang, Guofu Hu
Software Mentions: 1
Published: over 3 years ago

10.1186/s12862-017-0904-4

Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system
Cited by: 14
Author(s): Sandy Richter, Conrad Helm, Frédéric A. Meunier, Lars Hering, Lahcen I. Campbell, Stephan Drukewitz, Eivind A. B. Undheim, Ronald A. Jenner, Giampietro Schiavo, Christoph Bleidorn
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pbio.3000969

Pseudomonas aeruginosa cleaves the decoding center of Caenorhabditis elegans ribosomes
Cited by: 8
Author(s): Alejandro Vasquez-Rifo, Emiliano P. Ricci, Victor R. Ambros
Software Mentions: 1
Published: almost 4 years ago

10.3390/plants10010144

Genotype-by-Sequencing Analysis of Mutations and Recombination in Pepper Progeny of Gamma-Irradiated Gametophytes
Cited by: 5
Author(s): Yeong Deuk Jo, Hoyoul Kang, Hong‐Il Choi, Jin Baek Kim
Software Mentions: 1
Published: almost 4 years ago

10.3390/plants9080951

Transcriptome Response of Metallicolous and a Non-Metallicolous Ecotypes of Noccaea goesingensis to Nickel Excess
Cited by: 2
Author(s): Agnieszka Domka, Piotr Rozpądek, Rafał Ważny, Roman J. Jędrzejczyk, Magdalena Hubalewska-Mazgaj, Cristina Gonnelli, Jubina Benny, Federico Martinelli, Markus Puschenreiter, Katarzyna Turnau
Software Mentions: 1
Published: over 4 years ago

Projects: pypi: cutadapt

Papers Mentioning cutadapt 1,562