Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: Sickle

https://packages.ecosyste.ms/registries/pypi.org/packages/Sickle

A lightweight OAI client library for Python
11 versions
Latest release: over 4 years ago
8 dependent packages
8,030 downloads last month

Papers Mentioning Sickle 740

10.1371/journal.pone.0172605
The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred
Cited by: 28
Author(s): Umer Zeeshan Ijaz, Christopher Quince, Laura Hanske, Nicholas J. Loman, Szymon T. Calus, Martin Bertz, Christine Edwards, Daniel R. Gaya, Richard Hansen, Paraic McGrogan, Richard K. Russell, Konstantinos Gerasimidis
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pone.0091918
RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence
Cited by: 34
Author(s): Bouabid Badaoui, Teresa Rutigliano, Anna Anselmo, Merijn Vanhee, Hans Nauwynck, Elisabetta Giuffra, Sara Botti
Software Mentions: 4
Published: over 10 years ago
10.1186/s12870-019-1653-x
Genome-wide association analysis of stalk biomass and anatomical traits in maize
Cited by: 68
Author(s): Mona Mazaheri, Marlies Heckwolf, Brieanne Vaillancourt, Joseph L. Gage, Brett Burdo, Sven Heckwolf, Kerrie Barry, Anna Lipzen, Cauê Ribeiro, Thomas J. Y. Kono, Heidi F. Kaeppler, Edgar P. Spalding, Candice N. Hirsch, C. Robin Buell, Natalia de León, Shawn M. Kaeppler
Software Mentions: 4
Published: almost 6 years ago
10.3389/fnmol.2017.00185
Optimized Method for Robust Transcriptome Profiling of Minute Tissues Using Laser Capture Microdissection and Low-Input RNA-Seq
Cited by: 18
Author(s): Shannon Farris, Yu Wang, James M. Ward, Serena M. Dudek
Software Mentions: 4
Published: over 7 years ago
10.1186/s12936-019-2826-7
Clinical expression and antigenic profiles of a Plasmodium vivax vaccine candidate: merozoite surface protein 7 (PvMSP-7)
Cited by: 7
Author(s): Chew Weng Cheng, Somchai Jongwutiwes, Chaturong Putaporntip, Andrew P. Jackson
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-015-1635-9
Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection
Cited by: 72
Author(s): James E. Koltes, Eric R. Fritz-Waters, Christopher J. Eisley, Igseo Choi, Hua Bao, Arun Kommadath, Nick V. L. Serão, Nicholas Boddicker, Samuel M. Abrams, Martine Schroyen, Hyelee Loyd, Christopher K. Tuggle, Graham Plastow, Leluo Guan, Paul Stothard, Joan K. Lunney, Peng Liu, Susan Carpenter, Raymond R. R. Rowland, Jack C. M. Dekkers, James M. Reecy
Software Mentions: 4
Published: over 9 years ago
10.1371/journal.pone.0094447
Analysis of the Salivary Gland Transcriptome of Frankliniella occidentalis
Cited by: 69
Author(s): Candice A. Stafford-Banks, Dorith Rotenberg, Brian R. Johnson, Anna E. Whitfield, Diane E. Ullman
Software Mentions: 4
Published: over 10 years ago
10.1371/journal.pone.0227882
Comparison of the myometrial transcriptome from singleton and twin pregnancies by RNA-Seq
Cited by: 5
Author(s): Sarah Arrowsmith, Yongxiang Fang, Andrew Sharp
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pone.0241889
Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide
Cited by: 2
Author(s): Takahiro Yamagishi, Haruyo Yamaguchi, Shigekatsu Suzuki, Mayumi Yoshikawa, Ian Jameson, Maike Lorenz, David R. Nobles, Christine Campbell, Masanori Seki, Masanobu Kawachi, Hiroshi Yamamoto
Software Mentions: 4
Published: about 4 years ago
10.3389/fphys.2021.655059
Transcriptomic and Metabolomic Data Reveal the Key Metabolic Pathways Affecting Streltzoviella insularis (Staudinger) (Lepidoptera: Cossidae) Larvae During Overwintering
Cited by: 5
Author(s): Jiahe Pei, Yecheng Xu, Shixiang Zong, Lili Ren
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0177739
Transcriptome profiling revealed novel transcriptional regulators in maize responses to Ostrinia furnacalis and jasmonic acid
Cited by: 15
Author(s): Wang Hai, Shengyan Li, Shouzhen Teng, Haisheng Liang, Hongjia Xin, Hongjiang Gao, Dafang Huang, Zhihong Lang
Software Mentions: 4
Published: over 7 years ago
10.3389/fmicb.2018.00093
Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method
Cited by: 17
Author(s): Yonggang Yan, Qin Jiang, Jian-Gong Wang, Ting Zhu, Bin Zou, Qiongfen Qiu, Zhe‐Xue Quan
Software Mentions: 4
Published: almost 7 years ago
10.1534/g3.118.200880
Activation of the Bile Acid Pathway and No Observed Antimicrobial Peptide Sequences in the Skin of a Poison Frog
Cited by: 1
Author(s): Megan L. Civitello, Robert D. Denton, Michael Zasloff, John H. Malone
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12864-015-2277-7
Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome
Cited by: 42
Author(s): Erik A. Visser, Jill L. Wegrzyn, Emma T. Steenkmap, Alexander Andrew Myburg, Sanushka Naidoo
Software Mentions: 4
Published: almost 9 years ago
10.1534/g3.116.032805
Assessing the Gene Content of the Megagenome: Sugar Pine (<i>Pinus lambertiana</i>)
Cited by: 45
Author(s): Daniel González-Ibeas, Pedro Manuel Martínez-García, Randi Famula, Annette Delfino-Mix, Kristian Stevens, Carol A. Loopstra, Charles H. Langley, David B. Neale, Jill L. Wegrzyn
Software Mentions: 4
Published: almost 8 years ago
10.3390/pathogens9090723
Differences in the Endophytic Microbiome of Olive Cultivars Infected by Xylella fastidiosa across Seasons
Cited by: 35
Author(s): Annalisa Giampetruzzi, Paula Baptista, Massimiliano Morelli, Cristina Cameirão, Teresa Lino-Neto, Daniela Costa, Giusy D’Attoma, Raied Abou Kubaa, Giuseppe Altamura, María Saponari, José Alberto Pereira, P. Saldarelli
Software Mentions: 4
Published: about 4 years ago
10.3389/fmicb.2017.01656
Linseed Oil Supplementation of Lambs’ Diet in Early Life Leads to Persistent Changes in Rumen Microbiome Structure
Cited by: 36
Author(s): Tamsin Lyons, T. M. Boland, Sean Storey, Evelyn Doyle
Software Mentions: 4
Published: about 7 years ago
10.3390/ijms21197069
Human Fibroblasts In Vitro Exposed to 2.45 GHz Continuous and Pulsed Wave Signals: Evaluation of Biological Effects with a Multimethodological Approach
Cited by: 7
Author(s): Elisa Regalbuto, Anna Anselmo, Stefania De Sanctis, Valeria Franchini, Florigio Lista, Monica Benvenuto, Roberto Bei, Laura Masuelli, G. D’Inzeo, Alessandra Paffi, Eugenio Trodella, Antonella Sgura
Software Mentions: 4
Published: about 4 years ago
10.1186/s12920-020-0683-4
ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection
Cited by: 14
Author(s): Yuyu Li, Guangzhi Wang, Xiaofang Tan, Jian Ouyang, Menghuan Zhang, Xiaofeng Song, Qi Liu, Qibin Leng, Lanming Chen, Lu Xie
Software Mentions: 4
Published: over 4 years ago
10.1186/s12985-019-1211-z
The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites
Cited by: 9
Author(s): Heng Li, Hongzhe Li, Jingjing Wang, Lei Guo, Haitao Fan, Huiwen Zheng, Zening Yang, Xing Huang, Manman Chu, Fengmei Yang, Zhanlong He, Nan Li, Jun Yang, Qiongwen Wu, Hongzhe Shi, Longding Liu
Software Mentions: 4
Published: over 5 years ago
10.1093/molbev/msab096
Novelty and Convergence in Adaptation to Whole Genome Duplication
Cited by: 20
Author(s): Magdalena Bohutínská, Mark Alston, Patrick J. Monnahan, Terezie Mandáková, Sian Bray, Pirita Paajanen, Filip Kolář, Levi Yant
Software Mentions: 4
Published: over 3 years ago
10.3389/fimmu.2021.631472
An Inflammatory Loop Between Spleen-Derived Myeloid Cells and CD4+ T Cells Leads to Accumulation of Long-Lived Plasma Cells That Exacerbates Lupus Autoimmunity
Cited by: 4
Author(s): Eunkyeong Jang, Somi Cho, Sung-Jin Pyo, Jin Wu Nam, Jeehee Youn
Software Mentions: 4
Published: almost 4 years ago
10.1093/molbev/msaa323
Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence
Cited by: 40
Author(s): Gemma G. R. Murray, Jane Charlesworth, Eric L. Miller, Michael J. Casey, Catrin Lloyd, Marcelo Gottschalk, Alexander W. Tucker, John J. Welch, Lucy A. Weinert
Software Mentions: 4
Published: almost 4 years ago
10.3389/fimmu.2018.01624
Integration of RNAi and RNA-seq Reveals the Immune Responses of Epinephelus coioides to sigX Gene of Pseudomonas plecoglossicida
Cited by: 54
Author(s): Yujia Sun, Gang Luo, Lingmin Zhao, Lixing Huang, Yingxue Qin, Yongquan Su, Qingpi Yan
Software Mentions: 4
Published: over 6 years ago
10.1128/mSystems.00098-20
Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems
Cited by: 12
Author(s): Robert Danczak, Rebecca A. Daly, Mikayla A. Borton, James C. Stegen, Simon Roux, Kelly Wrighton, Michael J. Wilkins
Software Mentions: 4
Published: over 4 years ago
10.1128/mSphere.00484-20
Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate
Cited by: 16
Author(s): Darío X. Ramírez-Villacís, Omri M. Finkel, Isai Salas-González, Connor R. Fitzpatrick, Jeffery L. Dangl, Corbin D. Jones, Antonio León-Reyes
Software Mentions: 4
Published: about 4 years ago
10.3390/microorganisms9040841
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
Cited by: 29
Author(s): Denis Kutnjak, Lucie Tamisier, Ian Adams, Neil Boonham, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Jan Kreuze, Marie Lefebvre, Gonçalo Silva, Martha Malapi‐Wight, Paolo Margaria, Irena Mavrič Pleško, Sam McGreig, Laura Miozzi, Benoît Remenant, Jean-Sébastien Reynard, Johan Rollin, M. Rott, Olivier Schumpp, Sébastien Massart, Annelies Haegeman
Software Mentions: 4
Published: over 3 years ago
10.1186/s12863-019-0790-4
Transcriptome, physiological and biochemical analysis of Triarrhena sacchariflora in response to flooding stress
Cited by: 17
Author(s): Jia Wang, Hao Sun, Jiajin Sheng, Surong Jin, Fangjian Zhou, Zhongli Hu, Youxiang Diao
Software Mentions: 4
Published: almost 5 years ago
10.3389/fgene.2021.645443
Global Transcriptome and Weighted Gene Co-expression Network Analyses of Growth-Stage-Specific Drought Stress Responses in Maize
Cited by: 21
Author(s): Songtao Liu, Tinashe Zenda, Anyi Dong, Yatong Yang, Nan Wang, Huijun Duan
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41396-017-0043-3
Energy limitation of cyanophage development: implications for marine carbon cycling
Cited by: 54
Author(s): Richard John Puxty, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 4
Published: almost 7 years ago
10.3389/fcell.2021.671806
Knockdown of Splicing Complex Protein PCBP2 Reduces Extravillous Trophoblast Differentiation Through Transcript Switching
Cited by: 6
Author(s): Danai Georgiadou, Souad Boussata, Remco Keijser, Dianta Janssen, Gijs B. Afink, Marie van Dijk
Software Mentions: 4
Published: over 3 years ago
10.1128/mBio.01718-20
The Role of Phosphorus Limitation in Shaping Soil Bacterial Communities and Their Metabolic Capabilities
Cited by: 49
Author(s): Angela M. Oliverio, Andrew Bissett, Krista L. McGuire, Kristin Saltonstall, Benjamín L. Turner, Noah Fierer
Software Mentions: 4
Published: about 4 years ago
10.1186/s40168-020-00799-9
Rhizosphere protists are key determinants of plant health
Cited by: 123
Author(s): Wu Xiong, Yuqi Song, Kun Yang, Yian Gu, Zhong Wei, George A. Kowalchuk, Yangchun Xu, Alexandre Jousset, Qirong Shen, Stefan Geisen
Software Mentions: 4
Published: over 4 years ago
10.3389/fcimb.2020.561761
LL-37-Induced Autophagy Contributed to the Elimination of Live Porphyromonas gingivalis Internalized in Keratinocytes
Cited by: 12
Author(s): Xue Yang, Li Na Niu, Yaping Pan, Xiaodong Feng, Jie Liu, Yan Guo, Chunyu Pan, Fei Geng, Xiaolin Tang
Software Mentions: 4
Published: about 4 years ago
10.1128/mSphereDirect.00120-18
Zika Virus Infection Preferentially Counterbalances Human Peripheral Monocyte and/or NK Cell Activity
Cited by: 26
Author(s): Fok‐Moon Lum, David Lee, Tze-Kwang Chua, Jeslin J. L. Tan, Cheryl Yi‐Pin Lee, Xuan Li, Yongxiang Fang, Bernett Lee, Wearn‐Xin Yee, Natasha Y. Rickett, Po Ying Chia, Vanessa Lim, Yee‐Sin Leo, David A. Matthews, Julian A. Hiscox, Lisa F. P. Ng
Software Mentions: 4
Published: over 6 years ago
10.3390/microorganisms8111679
Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
Cited by: 13
Author(s): Valentina Méndez, Matías A. Valenzuela, Francisco Salvà‐Serra, Daniel Jaén‐Luchoro, Ximena Besoaín, Edward R. B. Moore, Michael Seeger
Software Mentions: 4
Published: about 4 years ago
10.1186/s13059-016-1137-3
Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus
Cited by: 106
Author(s): Xuan Li, Emily Speranza, César Muñoz‐Fontela, Sam Haldenby, Natasha Y. Rickett, Isabel García-Dorival, Yongxiang Fang, Yper Hall, Elsa Gayle Zekeng, Anja Lüdtke, Dong Xia, Romy Kerber, Ralf Krumkamp, Sophie Duraffour, Daouda Sissoko, John Kenny, Nichola Rockliffe, E. Diane Williamson, Thomas R. Laws, N’Faly Magassouba, David A. Matthews, Stephan Günther, Andrew R. Cossins, Armand Sprecher, John H. Connor, Miles W. Carroll, Julian A. Hiscox
Software Mentions: 4
Published: almost 8 years ago
10.1186/s13100-018-0123-6
Extensive exchange of transposable elements in the Drosophila pseudoobscura group
Cited by: 25
Author(s): Tom Hill, Andrea J. Betancourt
Software Mentions: 4
Published: over 6 years ago
10.3389/fmicb.2021.627569
Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community
Cited by: 64
Author(s): Ziqin Pang, Fei Dong, Qiang Liu, Wenxiong Lin, Chaohua Hu, Zhaonian Yuan
Software Mentions: 4
Published: over 3 years ago
10.1128/mBio.00916-18
Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake
Cited by: 13
Author(s): Sari Peura, Moritz Buck, Sanni L. Aalto, Sergio E. Morales, Hannu Nykänen, Alexander Eiler
Software Mentions: 4
Published: about 6 years ago
10.1186/2049-2618-2-1
Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants
Cited by: 314
Author(s): Brandon Brooks, Brian Firek, Christopher S. Miller, Itai Sharon, Brian C. Thomas, Robyn Baker, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 4
Published: almost 11 years ago
10.1002/mbo3.871
Prevalence and proliferation of antibiotic resistance genes in the subtropical mangrove wetland ecosystem of South China Sea
Cited by: 21
Author(s): Huaxian Zhao, Bing Yan, Xueyan Mo, Pu Li, Baoqin Li, Quanwen Li, Nan Li, Shuming Mo, Qian Ou, Peihong Shen, Bo Wu, Chengjian Jiang
Software Mentions: 3
Published: over 5 years ago
10.1186/s12915-019-0674-0
RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting
Cited by: 24
Author(s): Bharati Jadhav, Ramin Monajemi, Kristina K. Gagalova, Daniel J. Ho, Harmen H.M. Draisma, Mark A. van de Wiel, Lude Franke, Bastiaan T. Heijmans, Joyce B. J. van Meurs, Rick Jansen, Peter A.C. ’t Hoen, Andrew J. Sharp, Szymon M. Kiełbasa
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-020-74814-2
Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia
Cited by: 17
Author(s): Tin Hang Hung, Thea So, Syneath Sreng, Bansa Thammavong, Chaloun Boounithiphonh, David Boshier, John Mackay
Software Mentions: 3
Published: about 4 years ago
10.1038/s41598-020-68187-9
Prostate cancer-derived holoclones: a novel and effective model for evaluating cancer stemness
Cited by: 9
Author(s): Louise Flynn, Martin P. Barr, Anne‐Marie Baird, Paul Smyth, Órla Casey, Gordon Blackshields, John Greene, Stephen R. Pennington, Emily Hams, Padraic G. Fallon, John O’Leary, Orla Sheils, Stephen Finn
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-020-65724-4
Simultaneous identification of animal-derived components in meats using high-throughput sequencing in combination with a custom-built mitochondrial genome database
Cited by: 6
Author(s): Yinan Zhang, Qinfeng Qu, RAO Mingzhen, Zhang Nana, Yu Zhao, Fei Tao
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-020-78934-7
DNA metabarcoding uncovers fungal diversity in soils of protected and non-protected areas on Deception Island, Antarctica
Cited by: 30
Author(s): Luiz Henrique Rosa, Thamar Holanda da Silva, Mayara Baptistucci Ogaki, Otávio Henrique Bezerra Pinto, Michael Stech, Peter Convey, Micheline Carvalho‐Silva, Carlos A. Rosa, Paulo Eduardo Aguiar Saraiva Câmara
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-021-89146-y
Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes
Cited by: 3
Author(s): Chris Smith
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-019-44974-x
DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies
Cited by: 40
Author(s): Alessandra Frau, John Kenny, Luca Lenzi, Barry J. Campbell, Umer Zeeshan Ijaz, Carrie A. Duckworth, Michael D. Burkitt, Neil Hall, Jim Anson, Alistair C. Darby, Chris Probert
Software Mentions: 3
Published: over 5 years ago
10.1186/1471-2164-14-872
Sequencing the transcriptome of milk production: milk trumps mammary tissue
Cited by: 43
Author(s): Danielle G. Lemay, Russell C. Hovey, Stella R. Hartono, Katie Hinde, Jennifer T. Smilowitz, Frank Ventimiglia, Kimberli A. Schmidt, Joyce W.S. Lee, Alma Islas‐Trejo, Pedro Ivo Silva, Ian F Korf, Juan F. Medrano, Peter A. Barry, J. Bruce German
Software Mentions: 3
Published: almost 12 years ago
10.1038/s41598-019-50139-7
Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring
Cited by: 14
Author(s): Pedro Soares-Castro, Helena Araújo-Rodrigues, Filipa Godoy-Vitorino, Marisa Ferreira, Pablo Covelo, Alfredo López, José Vingada, Catarina Eira, Pedro M. Santos
Software Mentions: 3
Published: about 5 years ago
10.1038/s41598-019-39323-x
16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan
Cited by: 102
Author(s): Medelin Ocejo, Beatriz Oporto, Ana Hurtado
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-018-33693-4
RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways
Cited by: 17
Author(s): Adil Lateef, Sudheesh K. Prabhudas, Purushothaman Natarajan
Software Mentions: 3
Published: about 6 years ago
10.1111/eva.12799
Divergent transcriptomic signatures in response to salinity exposure in two populations of an estuarine fish
Cited by: 35
Author(s): Ken M. Jeffries, Richard E. Connon, Christine E. Verhille, Theresa F. Dabruzzi, Monica Britton, Blythe Durbin‐Johnson, Nann A. Fangue
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-018-36364-6
Impact of CFTR modulation with Ivacaftor on Gut Microbiota and Intestinal Inflammation
Cited by: 88
Author(s): Chee Y. Ooi, Saad Syed, Laura Rossi, Millie Garg, Bronwen Needham, Julie Avolio, Kelsey Young, Michael G. Surette, Tanja Gonska
Software Mentions: 3
Published: almost 6 years ago
10.3390/md19060286
An Integrative Bioinformatic Analysis for Keratinase Detection in Marine-Derived Streptomyces
Cited by: 2
Author(s): Ricardo Valencia, Valentina González, Agustina Undabarrena, Leonardo Zamora-Leiva, Juan A. Ugalde, Beatríz Cámara
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-017-06099-x
Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum
Cited by: 18
Author(s): Amy Kenyon, Daria Gavriouchkina, Jernej Zorman, Giorgio Napolitani, Vincenzo Cerundolo, Tatjana Sauka‐Spengler
Software Mentions: 3
Published: over 7 years ago
10.1038/srep28984
An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis
Cited by: 37
Author(s): Niels Willemse, Kate J. Howell, Lucy A. Weinert, Annet Heuvelink, Yvonne Pannekoek, Jaap A. Wagenaar, Hilde E. Smith, Arie van der Ende, Constance Schultsz
Software Mentions: 3
Published: over 8 years ago
10.18632/aging.202738
Hydrogen sulfide treatment at the late growth stage of Saccharomyces cerevisiae extends chronological lifespan
Cited by: 3
Author(s): Arman Ali Shah, Binghua Liu, Zhihuai Tang, Wang Wang, Wenjie Yang, Quanjun Hu, Yan Liu, Nianhui Zhang, Ke Liu
Software Mentions: 3
Published: over 3 years ago
10.1186/s12864-017-4430-y
The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes
Cited by: 38
Author(s): Deepak Kumar Gupta, Martin Rühl, Bagdevi Mishra, Vanessa Kleofas, Martin Hofrichter, Robert Herzog, Marek J. Pecyna, Rahul Sharma, Harald Kellner, Florian Hennicke, Marco Thines
Software Mentions: 3
Published: almost 7 years ago
10.1016/j.stem.2020.05.004
Human-iPSC-Derived Cardiac Stromal Cells Enhance Maturation in 3D Cardiac Microtissues and Reveal Non-cardiomyocyte Contributions to Heart Disease
Cited by: 302
Author(s): Elisa Giacomelli, Viviana Meraviglia, Giulia Campostrini, Amy Cochrane, Xu Cao, Ruben W.J. van Helden, Ana Krotenberg Garcia, Maria Mircea, Sarantos Kostidis, Richard P. Davis, Berend J. van Meer, Carolina R. Jost, Abraham J. Koster, Hailiang Mei, David G. Míguez, Aat A. Mulder, Mario Ledesma-Terrón, Giulio Pompilio, Luca Sala, Daniela Salvatori, Roderick C. Slieker, Elena Sommariva, Antoine A.F. de Vries, Martin Giera, Stefan Semrau, Leon G.J. Tertoolen, Valeria V. Orlova, Milena Bellin, Christine L. Mummery
Software Mentions: 3
Published: over 4 years ago
10.1093/gigascience/giz138
Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)
Cited by: 64
Author(s): Gareth Linsmith, Stéphane Rombauts, Sara Montanari, Cecilia Deng, Jean‐Marc Celton, Philippe Guérif, Chang Liu, Rolf Lohaus, Jason D. Zurn, Alessandro Cestaro, Nahla V. Bassil, Linda V. Bakker, Elio Schijlen, Susan E. Gardiner, Yves Lespinasse, Charles‐Eric Durel, Riccardo Velasco, David B. Neale, David Chagné, Yves Van de Peer, Michela Troggio, Luca Bianco
Software Mentions: 3
Published: almost 5 years ago
10.1038/srep40218
Identifying a gene expression signature of cluster headache in blood
Cited by: 19
Author(s): Else Eising, Nadine Pelzer, Lisanne S. Vijfhuizen, Boukje de Vries, Michel D. Ferrari, Peter A.C. ’t Hoen, Gisela M. Terwindt, Arn M. J. M. van den Maagdenberg
Software Mentions: 3
Published: almost 8 years ago
10.1534/g3.119.400669
Molecular Profiling of the<i>Drosophila</i>Antenna Reveals Conserved Genes Underlying Olfaction in Insects
Cited by: 24
Author(s): Pratyajit Mohapatra, Karen Menuz
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.pone.0227886
Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses
Cited by: 57
Author(s): Youn Wook Chung, Ho Jin Gwak, Sungmin Moon, Mina Rho, Ji Hwan Ryu
Software Mentions: 3
Published: almost 5 years ago
10.3390/genes8060152
DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age
Cited by: 62
Author(s): Alexey Kozlenkov, Andrew E. Jaffe, Alisa Timashpolsky, Pasha Apontes, Sergei Rudchenko, Mihaela Barbu, William Byne, Yasmin L. Hurd, Steve Horvath, Stella Dracheva
Software Mentions: 3
Published: over 7 years ago
10.3389/fpls.2021.697889
Identification of a New Giant Emrbryo Allele, and Integrated Transcriptomics and Metabolomics Analysis of Giant Embryo Development in Rice
Cited by: 7
Author(s): Zejun Hu, Qiangqiang Xiong, Kai Wang, Lixia Zhang, Ying Yan, Liming Cao, Fuan Niu, Zhu Jun, Jinlong Hu, Shujun Wu
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0204629
Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing
Cited by: 64
Author(s): Simon Poirier, Olivier Rué, R. Peguilhan, Gwendoline Coeuret, Monique Zagorec, Marie‐Christine Champomier‐Vergès, Valentin Loux, Stéphane Chaillou
Software Mentions: 3
Published: about 6 years ago
10.3389/fpls.2016.01083
De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development
Cited by: 21
Author(s): Hong Yue, Le Wang, Hui Liu, Wenjie Yue, Xianghong Du, Weining Song, Xiaojun Nie
Software Mentions: 3
Published: over 8 years ago
10.1534/g3.117.1137
Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease
Cited by: 17
Author(s): Joseph R. Owen, Noelle Noyes, Amy Young, Daniel J. Prince, Patricia C Blanchard, Terry W. Lehenbauer, Sharif S. Aly, Jessica Hoffmann Davis, Sean O’Rourke, Zaid Abdo, K. E. Belk, Michael R. Miller, Paul S. Morley, Alison L. Van Eenennaam
Software Mentions: 3
Published: about 7 years ago
10.1371/journal.pone.0183859
Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms
Cited by: 35
Author(s): Kevin A. Meyer, Timothy W. Davis, Susan B. Watson, Vincent J. Denef, Michelle A. Berry, Gregory J. Dick
Software Mentions: 3
Published: about 7 years ago
10.1186/s12870-015-0643-x
Changes in Lolium perenne transcriptome during cold acclimation in two genotypes adapted to different climatic conditions
Cited by: 29
Author(s): Shamila Abeynayake, Stephen Byrne, Istvàn Nagy, Kristina Jonavičienė, Thomas Etzerodt, Birte Boelt, Torben Asp
Software Mentions: 3
Published: about 9 years ago
10.3389/fmicb.2020.612257
Diversity and Genomic Characterization of a Novel Parvarchaeota Family in Acid Mine Drainage Sediments
Cited by: 20
Author(s): Zhen-Hao Luo, Qi Li, Yan Lai, Hao Chen, Bin Liao, Li-Nan Huang
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0224379
Molecular characterization of lung adenocarcinoma from Korean patients using next generation sequencing
Cited by: 12
Author(s): Youngsub Chun, Jae Woo Choi, Min Hee Hong, Dongmin Jung, Hyeonju Son, Eun Kyung Cho, Young Joo Min, Sang‐We Kim, Keunchil Park, Sung Sook Lee, Sang Woo Kim, Hye Ryun Kim, Byoung Chul Cho
Software Mentions: 3
Published: almost 5 years ago
10.3389/fpls.2018.00771
Molecular Profiling of Pierce’s Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection
Cited by: 28
Author(s): Paulo A. Zaini, Rafael Nascimento, Hossein Gouran, Dario Cantu, Sandeep Chakraborty, My L. Phu, Luíz Ricardo Goulart, Abhaya M. Dandekar
Software Mentions: 3
Published: over 6 years ago
10.1186/s13059-014-0540-x
Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity
Cited by: 33
Author(s): Stuart Dowall, David A. Matthews, Isabel García-Dorival, Irene Taylor, John Kenny, Christiane Hertz‐Fowler, Neil Hall, Kara Corbin-Lickfett, Cyril Empig, Kyle Schlunegger, John N. Barr, Miles W. Carroll, Roger Hewson, Julian A. Hiscox
Software Mentions: 3
Published: about 10 years ago
10.1186/s12870-016-0844-y
Markers associated with heading and aftermath heading in perennial ryegrass full-sib families
Cited by: 16
Author(s): Sai Krishna Arojju, Susanne Barth, Dan Milbourne, Philip G. Conaghan, Janaki Velmurugan, Trevor R. Hodkinson, Stephen Byrne
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0132642
Spontaneous Deletion of an “ORFanage” Region Facilitates Host Adaptation in a “Photosynthetic” Cyanophage
Cited by: 12
Author(s): Richard John Puxty, Blanca Perez-Sepulveda, Branko Rihtman, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 3
Published: over 9 years ago
10.3389/fmicb.2020.02075
Sodium New Houttuyfonate Inhibits Candida albicans Biofilm Formation by Inhibiting the Ras1-cAMP-Efg1 Pathway Revealed by RNA-seq
Cited by: 21
Author(s): Jiadi Wu, Donghui Wu, Yeye Zhao, Yuanqing Si, Longfei Mei, Jing Shao, Tianming Wang, Yan Ge, Changzhong Wang
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pone.0115911
The Transcriptomic and Proteomic Landscapes of Bone Marrow and Secondary Lymphoid Tissues
Cited by: 14
Author(s): Sandra Andersson, Kenneth Nilsson, Linn Fagerberg, Björn M. Hallström, Christer Sundström, Anna Danielsson, Karolina Edlund, Mathias Uhlén, Anna Asplund
Software Mentions: 3
Published: almost 10 years ago
10.1186/s12864-015-2157-1
Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq
Cited by: 51
Author(s): Sabina Bajda, Wannes Dermauw, Robert Greenhalgh, Ralf Nauen, Luc Tirry, Richard M. Clark, Thomas Van Leeuwen
Software Mentions: 3
Published: about 9 years ago
10.3389/fmicb.2021.720967
The Effect of tonB Gene on the Virulence of Pseudomonas plecoglossicida and the Immune Response of Epinephelus coioides
Cited by: 7
Author(s): Lingfei Hu, Lingmin Zhao, Zhixia Zhuang, Xiaoru Wang, Qi Fu, Huabin Huang, Lili Lin, Lixing Huang, Yingxue Qin, Jiaonan Zhang, Qingpi Yan
Software Mentions: 3
Published: over 3 years ago
10.1186/s12870-019-1795-x
Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)
Cited by: 19
Author(s): Daniel R. Kohlhase, Jamie A. O’Rourke, Micheal D. K. Owen, Michelle A. Graham
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pgen.1006909
Termination factor Rho: From the control of pervasive transcription to cell fate determination in Bacillus subtilis
Cited by: 48
Author(s): Vladimir Bidnenko, Pierre Nicolas, Aleksandra Grylak-Mielnicka, Olivier Delumeau, Sandrine Auger, Anne Aucouturier, Cyprien Guérin, Francis Repoila, Jacek Bardowski, Stéphane Aymerich, Elena Bidnenko
Software Mentions: 3
Published: over 7 years ago
10.1186/s42523-020-00062-4
Changes in the faecal microbiome of pied tamarins (Saguinus bicolor) associated with chronic, recurrent diarrhoea and weight loss
Cited by: 4
Author(s): Peter Richards‐Rios, Paul Wigley, Javier López, Dominic Wormell, Alberto Rodríguez Barbón
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0202844
Predicting provenance of forensic soil samples: Linking soil to ecological habitats by metabarcoding and supervised classification
Cited by: 35
Author(s): Camilla Fløjgaard, Tobias Guldberg Frøslev, Ane Kirstine Brunbjerg, Hans Henrik Bruun, Jesper Erenskjold Moeslund, Anders J. Hansen, Rasmus Ejrnæs
Software Mentions: 3
Published: over 5 years ago
10.3389/fmicb.2020.02069
Transcriptomic Analysis and Functional Characterization Reveal the Duck Interferon Regulatory Factor 1 as an Important Restriction Factor in the Replication of Tembusu Virus
Cited by: 8
Author(s): Chengwei Xiang, Mei Huang, Tingting Xiong, Rong Fang, Linyu Li, Ding Xiang Liu, Rui Ai Chen
Software Mentions: 3
Published: about 4 years ago
10.1534/g3.118.200815
Dosage Compensation and Gene Expression of the X Chromosome in Sheep
Cited by: 9
Author(s): Jianan Duan, Kaleigh Flock, Nathanial Jue, Mingyuan Zhang, A. K. Jones, Sahar Al Seesi, Ion Măndoiu, S. M. Pillai, M. L. Hoffman, Rachel J. O’Neill, S. A. Zinn, Kristen E Govoni, Sarah Reed, Hesheng Jiang, Zongliang Jiang, X. Cindy Tian
Software Mentions: 3
Published: almost 6 years ago
10.1371/journal.pone.0163148
Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota
Cited by: 64
Author(s): A. Christina Gill, Janneke van de Wijgert, Frances Blow, Alistair C. Darby
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pgen.1005122
SERPINB11 Frameshift Variant Associated with Novel Hoof Specific Phenotype in Connemara Ponies
Cited by: 22
Author(s): Carrie J. Finno, Carlynn Stevens, Amy Young, Verena K. Affolter, Nikhil Joshi, Sheila Ramsay, Danika L. Bannasch
Software Mentions: 3
Published: over 9 years ago
10.3389/fmicb.2021.693574
Integrated Analysis of microRNA and mRNA Transcriptome Reveals the Molecular Mechanism of Solanum lycopersicum Response to Bemisia tabaci and Tomato chlorosis virus
Cited by: 3
Author(s): Ya Hao, Liping Huang, Ding-Yi-Hui Lu, Zhanhong Zhang, Zhuo Zhang, Deyong Zhang, Limin Zheng, Yang Gao, Xinqiu Tan, Xuguo Zhou, Xiaolu Shi, Yong Liu
Software Mentions: 3
Published: over 3 years ago
10.3389/fmicb.2017.00732
A Meta-Transcriptomics Survey Reveals Changes in the Microbiota of the Chinese Mitten Crab Eriocheir sinensis Infected with Hepatopancreatic Necrosis Disease
Cited by: 30
Author(s): Huangxuan Shen, Yanan Zang, Kun Song, Yuanchao Ma, Tianhao Dai, Ali Serwadda
Software Mentions: 3
Published: over 7 years ago
10.1111/pbi.12685
Indel‐seq: a fast‐forward genetics approach for identification of trait‐associated putative candidate genomic regions and its application in pigeonpea (<i>Cajanus cajan</i>)
Cited by: 57
Author(s): Vikas K. Singh, Aamir W. Khan, Rachit K. Saxena, Pallavi Sinha, Sandip M. Kale, Swathi Parupalli, Vinay Kumar, Annapurna Chitikineni, Suryanarayana Vechalapu, C.V. Sameer Kumar, Mamta Sharma, G. Anuradha, K.N. Yamini, S. Muniswamy, Rajeev K. Varshney
Software Mentions: 3
Published: almost 8 years ago
10.1007/s10482-018-1040-x
Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach
Cited by: 83
Author(s): Loo Wee Chia, Bastian Hornung, Steven Aalvink, Peter J. Schaap, Willem M. de Vos, Jan Knol, Clara Belzer
Software Mentions: 3
Published: almost 7 years ago
10.3390/plants9010063
Comparative Analysis between Wild and Cultivated Cucumbers Reveals Transcriptional Changes during Domestication Process
Cited by: 6
Author(s): Eslam M. Abdel-Salam, Abdulrahman A. Alatar, Quaiser Saquib, Hend A. Alwathnani
Software Mentions: 3
Published: almost 5 years ago
10.7717/peerj.11465
Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of <i>Cinnamomum camphora</i> induced by mechanical damage
Cited by: 9
Author(s): Zerui Yang, Chunzhu Xie, Yuying Huang, Wenli An, Shanshan Liu, Song Huang, Xiasheng Zheng
Software Mentions: 3
Published: over 3 years ago
10.1186/s12864-020-06980-6
Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae
Cited by: 8
Author(s): Hanna Kehlet-Delgado, Claudia C. Häse, Robert F. Mueller
Software Mentions: 3
Published: about 4 years ago
10.3390/v11090792
Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour
Cited by: 20
Author(s): Christine N. Palermo, Roberta R. Fulthorpe, Rosemary Saati, Steven M. Short
Software Mentions: 3
Published: about 5 years ago
10.3389/fimmu.2021.678699
The Zinc Nutritional Immunity of Epinephelus coioides Contributes to the Importance of znuC During Pseudomonas plecoglossicida Infection
Cited by: 12
Author(s): Lixing Huang, Yanfei Zuo, Yingxue Qin, Lingmin Zhao, Mao Lin, Qingpi Yan
Software Mentions: 3
Published: over 3 years ago
10.3389/fimmu.2020.598636
Early Cytokine Induction Upon Pseudomonas aeruginosa Infection in Murine Precision Cut Lung Slices Depends on Sensing of Bacterial Viability
Cited by: 11
Author(s): Ulrike Kolbe, Buqing Yi, Tanja Poth, Amy E. Saunders, Sébastien Boutin, Alexander H. Dalpke
Software Mentions: 3
Published: about 4 years ago