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.0116125
The Kidney Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling
Cited by: 46
Author(s): Masato Habuka, Linn Fagerberg, Björn M. Hallström, Caroline Kampf, Karolina Edlund, Åsa Sivertsson, Tadashi Yamamoto, Fredrik Pontén, Mathias Uhlén, Jacob Odeberg
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.pone.0178923
Comparative transcriptomics of genetically divergent lines of chickens in response to Marek’s disease virus challenge at cytolytic phase
Cited by: 4
Author(s): Kunzhe Dong, Shuang Chang, Qingmei Xie, Alexis Black-Pyrkosz, Huanmin Zhang
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0154674
NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes
Cited by: 24
Author(s): Anna Marriott, Olga Vasieva, Yongxiang Fang, Nikki A. Copeland, Alexander G. McLennan, Nigel J. Jones
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0215206
Scalp bacterial shift in Alopecia areata
Cited by: 42
Author(s): Daniela Pinto, Elisabetta Sorbellini, Barbara Mora, Mariangela Rucco, Giammaria Giuliani, Fabio Rinaldi
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0149301
Physiological and Transcriptome Responses to Combinations of Elevated CO2 and Magnesium in Arabidopsis thaliana
Cited by: 18
Author(s): Yaofang Niu, Golam Jalal Ahammed, Caixian Tang, Longbiao Guo, Jingquan Yu
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pone.0162573
Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster
Cited by: 4
Author(s): Jennifer Hackett, Xiaofei Wang, Brittny R. Smith, Stuart J. Macdonald
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0223786
Maize leaves drought-responsive genes revealed by comparative transcriptome of two cultivars during the filling stage
Cited by: 10
Author(s): Hongyu Jin, Songtao Liu, Tinashe Zenda, Xuan Wang, Guo Liu, Huijun Duan
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0082634
RNA-Seq Transcriptome Profiling of Upland Cotton (Gossypium hirsutum L.) Root Tissue under Water-Deficit Stress
Cited by: 56
Author(s): Megan J. Bowman, Wonkeun Park, Philip J. Bauer, Joshua A. Udall, Justin T. Page, Joshua A. Raney, Brian E. Scheffler, Don C. Jones, B. Todd Campbell
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0118321
Deep mRNA Sequencing of the Tritonia diomedea Brain Transcriptome Provides Access to Gene Homologues for Neuronal Excitability, Synaptic Transmission and Peptidergic Signalling
Cited by: 25
Author(s): Adriano Senatore, Neranjan Edirisinghe, Paul S. Katz
Software Mentions: 2
Published: over 9 years ago
10.1016/j.celrep.2014.12.008
Insights into the Evolution of Longevity from the Bowhead Whale Genome
Cited by: 261
Author(s): Michael P. Keane, Jeremy R. Semeiks, Andrew E. Webb, Yang Li, Vı́ctor Quesada, Thomas Craig, Lone Bruhn Madsen, Sipko van Dam, David Brawand, Patrícia Marques, Pawel Michalak, Lin Kang, Jong Bhak, Hyung-Soon Yim, Nick V. Grishin, Nynne H. Nielsen, Mads Peter Heide‐Jørgensen, Elias M. Oziolor, Cole W. Matson, George M. Church, Gary W. Stuart, James R. Patton, J. C. George, Robert Suydam, Knud Larsen, Carlos López-Otı́n, Mary J. O’Connell, John W. Bickham, Bo Thomsen, João Pedro de Magalhães
Software Mentions: 2
Published: almost 10 years ago
10.1016/j.csbj.2014.11.001
A case study for cloud based high throughput analysis of NGS data using the globus genomics system
Cited by: 23
Author(s): Krithika Bhuvaneshwar, Dinanath Sulakhe, Robinder Gauba, Álex Rodríguez, Ravi Madduri, Utpal J. Dave, Łukasz Łaciński, Ian Foster, Yuriy Gusev, Subha Madhavan
Software Mentions: 2
Published: almost 10 years ago
10.1016/j.cub.2018.05.058
Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia
Cited by: 67
Author(s): Zhemin Zhou, Inge Lundstrøm, Alicia Tran-Dien, Sebastián Duchêne, Nabil-Fareed Alikhan, Martin J. Sergeant, Gemma C. Langridge, Anna K. Fotakis, Satheesh Nair, Hans K. Stenøien, Stian S. Hamre, Sherwood Casjens, Axel Christophersen, Christopher Quince, Nicholas R. Thomson, François‐Xavier Weill, Simon Y. W. Ho, M. Thomas P. Gilbert, Mark Achtman
Software Mentions: 2
Published: over 6 years ago
10.1007/s00125-017-4467-0
HbA1c is associated with altered expression in blood of cell cycle- and immune response-related genes
Cited by: 9
Author(s): Roderick C. Slieker, Amber A. W. A. van der Heijden, Nienke van Leeuwen, Hailiang Mei, Giel Nijpels, Joline W.J. Beulens, Leen M. ‘t Hart
Software Mentions: 2
Published: about 7 years ago
10.1002/ece3.1986
18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species
Cited by: 83
Author(s): Aitor Albaina, Mikel Aguirre, David Abad, M.B. Santos, Andone Estonba
Software Mentions: 2
Published: almost 9 years ago
10.1111/1462-2920.14590
Riding the wave of genomics to investigate aquatic coliphage diversity and activity
Cited by: 25
Author(s): Slawomir Michniewski, Tamsin Redgwell, Aurelija Grigonyte, Branko Rihtman, Maria del Mar Aguiló-Ferretjans, Joseph Alexander Christie-Oleza, Eleanor Jameson, David J. Scanlan, Andrew Millard
Software Mentions: 2
Published: over 5 years ago
10.1002/evl3.137
Compensatory<i>trans</i>-regulatory alleles minimizing variation in<i>TDH3</i>expression are common within<i>Saccharomyces cerevisiae</i>
Cited by: 21
Author(s): Brian P. H. Metzger, Patricia J. Wittkopp
Software Mentions: 2
Published: about 5 years ago
10.12688/f1000research.10040.1
YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools
Cited by: 8
Author(s): Sandeep Chakraborty, Pedro Manuel Martínez-García, Abhaya M. Dandekar
Software Mentions: 2
Published: about 8 years ago
10.12688/f1000research.6617.2
YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut
Cited by: 21
Author(s): Sandeep Chakraborty, Monica Britton, Jill L. Wegrzyn, Timothy Butterfield, Pedro J. Martínez-García, Russell L. Reagan, Basuthkar J. Rao, Charles A. Leslie, Mallikarjuna Aradhaya, David B. Neale, Keith Woeste, Abhaya M. Dandekar
Software Mentions: 2
Published: about 9 years ago
10.3389/fbioe.2020.01024
Characterization of Highly Mucus-Adherent Non-GMO Derivatives of Lacticaseibacillus rhamnosus GG
Cited by: 6
Author(s): Pia Rasinkangas, Hanne L. P. Tytgat, Jarmo Ritari, Justus Reunanen, Seppo Salminen, Airi Palva, François P. Douillard, Willem M. de Vos
Software Mentions: 2
Published: over 4 years ago
10.3389/fcell.2021.630228
Fibroblast Growth Factor 2 Promotes Bladder Hypertrophy Caused by Partial Bladder Outlet Obstruction
Cited by: 4
Author(s): Ye Gao, Peilin Liu, Fan He, Xingliang Yang, Ronghua Wu, Wei Chen, Longkun Li, Zhenxing Yang
Software Mentions: 2
Published: over 3 years ago
10.3389/fcell.2020.562940
Functional Characterization of the Lin28/let-7 Circuit During Forelimb Regeneration in Ambystoma mexicanum and Its Influence on Metabolic Reprogramming
Cited by: 5
Author(s): Hugo Varela-Rodríguez, Diana G. Abella-Quintana, Annie Espinal‐Centeno, Luis Varela-Rodríguez, David Gómez-Zepeda, Juan Caballero-Pérez, Paola L. García‐Medel, Luis G. Brieba, José Juan Ordaz-Ortíz, Alfredo Cruz‐Ramírez
Software Mentions: 2
Published: about 4 years ago
10.3389/fcell.2021.728352
Cochlear Sox2+ Glial Cells Are Potent Progenitors for Spiral Ganglion Neuron Reprogramming Induced by Small Molecules
Cited by: 8
Author(s): Zhe Chen, Yuhang Huang, Chaorong Yu, Qing Liu, Chen Qiu, Guoqiang Wan
Software Mentions: 2
Published: about 3 years ago
10.3389/fcell.2021.678190
Melatonin Regulates the Neurotransmitter Secretion Disorder Induced by Caffeine Through the Microbiota-Gut-Brain Axis in Zebrafish (Danio rerio)
Cited by: 12
Author(s): Zhen Zeng, Qingyun Peng, Dongxue Huo, Shuaiming Jiang, Chenchen Ma, Haibo Chang, Kaining Chen, Congfa Li, Pan Yingjie, Jiachao Zhang
Software Mentions: 2
Published: over 3 years ago
10.3389/fcell.2021.715733
SYMPK Is Required for Meiosis and Involved in Alternative Splicing in Male Germ Cells
Cited by: 1
Author(s): Rui Wu, Junfeng Zhan, Bo Zheng, Zhe Chen, Jianbo Li, Changrong Li, Rong Liu, Xinhua Zhang, Xiaoyan Huang, Mengcheng Luo
Software Mentions: 2
Published: over 3 years ago
10.3389/fcell.2021.680174
Integrated Metagenomic and Transcriptomic Analyses Reveal the Dietary Dependent Recovery of Host Metabolism From Antibiotic Exposure
Cited by: 5
Author(s): Bingbing Li, Huihui Qiu, Ningning Zheng, Gaosong Wu, Yu Gu, Jing Zhong, Ying Hong, Junli Ma, Wen Zhou, Lili Sheng, Houkai Li
Software Mentions: 2
Published: over 3 years ago
10.3389/fcimb.2021.733811
The Development of Ovine Gastric and Intestinal Organoids for Studying Ruminant Host-Pathogen Interactions
Cited by: 20
Author(s): David W. Smith, Daniel D. Price, Alison Burrells, Marc Faber, Katie A. Hildersley, Cosmin Chintoan-Uta, Ambre Chapuis, Mark P. Stevens, Karen Stevenson, Stewart T. G. Burgess, Elisabeth A. Innes, Alasdair J. Nisbet, Tom N. McNeilly
Software Mentions: 2
Published: about 3 years ago
10.3389/fcimb.2020.591751
cheA, cheB, cheR, cheV, and cheY Are Involved in Regulating the Adhesion of Vibrio harveyi
Cited by: 17
Author(s): Xiaojin Xu, Huiyao Li, Xin Qi, Yunong Chen, Yingxue Qin, Jiang Zheng, Xinglong Jiang
Software Mentions: 2
Published: almost 4 years ago
10.3389/fgene.2019.00082
Aneuploidy and Ethanol Tolerance in Saccharomyces cerevisiae
Cited by: 54
Author(s): Miguel Morard, Laura Graciela Chávez Macías, Ana Cristina Adam, María Lairón-Peris, Roberto Pérez‐Torrado, Christina Toft, Eladio Barrio
Software Mentions: 2
Published: almost 6 years ago
10.3389/fgene.2020.584817
Comparative Transcriptome Reveals the Genes’ Adaption to Herkogamy of Lumnitzera littorea (Jack) Voigt
Cited by: 4
Author(s): Ying Zhang, Yukai Chen, Yan Zhou, Jingwen Zhang, He Bai, Chunfang Zheng
Software Mentions: 2
Published: almost 4 years ago
10.3389/fimmu.2020.00305
Activation of the C-Type Lectin MGL by Terminal GalNAc Ligands Reduces the Glycolytic Activity of Human Dendritic Cells
Cited by: 17
Author(s): Anouk Zaal, R. J.Eveline Li, Joyce M. Lubbers, Sven C. M. Bruijns, Hakan Kalay, Yvette van Kooyk, Sandra J. van Vliet
Software Mentions: 2
Published: over 4 years ago
10.3389/fmicb.2017.02630
The Expressed MicroRNA—mRNA Interactions of Toxoplasma gondii
Cited by: 9
Author(s): İlhan E. Acar, Müşerref Duygu Saçar Demirci, Uwe Groß, Jens Allmer
Software Mentions: 2
Published: almost 7 years ago
10.3389/fmicb.2018.00965
Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts
Cited by: 25
Author(s): M. A. Eldarov, Alexey V. Beletsky, Tatiana N. Tanashchuk, Svetlana A. Kishkovskaya, Nikolai V. Ravin, Andrey V. Mardanov
Software Mentions: 2
Published: over 6 years ago
10.3389/fmicb.2018.00138
Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum
Cited by: 42
Author(s): Éric Duchaud, Tatiana Rochat, Christophe Habib, Paul Barbier, Valentin Loux, Cyprien Guérin, Inger Dalsgaard, Lone Madsen, Hanne Nilsen, Krister Sundell, Tom Wıklund, Nicole Strepparava, Thomas Wahli, Greta Caburlotto, Amedeo Manfrin, Gregory D. Wiens, Erina Fujiwara-Nagata, Rubén Avendaño‐Herrera, Jean‐François Bernardet, Pierre Nicolas
Software Mentions: 2
Published: almost 7 years ago
10.3389/fmicb.2021.680620
An Ecological Basis for Dual Genetic Code Expansion in Marine Deltaproteobacteria
Cited by: 2
Author(s): Veronika Kivenson, Blair G. Paul, David L. Valentine
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2018.02646
Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin
Cited by: 26
Author(s): Morgan V. Evans, Jenny Panescu, Andrea Hanson, Susan A. Welch, J. Sheets, Nicholas Nastasi, Rebecca A. Daly, David R. Cole, Thomas H. Darrah, Michael J. Wilkins, Kelly Wrighton, Paula J. Mouser
Software Mentions: 2
Published: about 6 years ago
10.3389/fmicb.2020.563885
Evolutionary Rescue of an Environmental Pseudomonas otitidis in Response to Anthropogenic Perturbation
Cited by: 4
Author(s): Manuel Ii García-Ulloa, Ana E. Escalante, Alejandra Moreno‐Letelier, Luis E. Eguiarte, Valeria Souza
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2021.739453
SUN-Family Protein UvSUN1 Regulates the Development and Virulence of Ustilaginoidea virens
Cited by: 4
Author(s): Mina Yu, Junjie Yu, Huijuan Cao, Tianqiao Song, Pan X, Zhongqiang Qi, Yan Du, Rongsheng Zhang, Shiwen Huang, Wende Liu, Yongfeng Liu
Software Mentions: 2
Published: about 3 years ago
10.3389/fmicb.2017.00664
Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors
Cited by: 33
Author(s): Stephanie Connelly, Seung Gu Shin, Robert J. Dillon, Umer Zeeshan Ijaz, Christopher Quince, William T. Sloan, Gavin Collins
Software Mentions: 2
Published: over 7 years ago
10.3389/fmicb.2021.653873
Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats
Cited by: 9
Author(s): Wenqiao He, Yuhan Gao, Yiping Wen, Xuemei Ke, Zejin Ou, Yongzhi Li, Huan He, Qing Chen
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2020.568457
The Effect of Xylooligosaccharide, Xylan, and Whole Wheat Bran on the Human Gut Bacteria
Cited by: 8
Author(s): Miao Chen, Shujun Liu, Khandaker Md Sharif Uddin Imam, Lichao Sun, Yulu Wang, Tianyi Gu, Bin Wen, Fengjiao Xin
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2018.01982
Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils
Cited by: 21
Author(s): Ngoc‐Loi Nguyen, Woon-Jong Yu, Joo-Han Gwak, So-Jeong Kim, Soo-Je Park, Craig W. Herbold, Jong-Geol Kim, Man‐Young Jung, Sung‐Keun Rhee
Software Mentions: 2
Published: about 6 years ago
10.3389/fmicb.2015.00716
H2O2 production rate in Lactobacillus johnsonii is modulated via the interplay of a heterodimeric flavin oxidoreductase with a soluble 28 Kd PAS domain containing protein
Cited by: 12
Author(s): Ricardo Valladares, Christina Graves, Kaitlyn Wright, C. L. Gardner, Graciela L. Lorca, Claudio F. González
Software Mentions: 2
Published: over 9 years ago
10.3389/fmicb.2016.01546
Photosynthetic Versatility in the Genome of Geitlerinema sp. PCC 9228 (Formerly Oscillatoria limnetica ‘Solar Lake’), a Model Anoxygenic Photosynthetic Cyanobacterium
Cited by: 27
Author(s): Sharon L. Grim, Gregory J. Dick
Software Mentions: 2
Published: about 8 years ago
10.3389/fmicb.2021.627099
De novo Sequencing and Comparative Transcriptome Analyses Provide First Insights Into Polysaccharide Biosynthesis During Fruiting Body Development of Lentinula edodes
Cited by: 2
Author(s): Qiaozhen Li, Jing Chen, Jianyu Liu, Hailong Yu, Lujun Zhang, Chunyan Song, Li Yu, Ning Jiang, Qian Tan, Xiaodong Shang, Yunfu Gu
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2018.03009
Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture
Cited by: 41
Author(s): Lucy Peters, Sofie Spatharis, Maria Augusta Dario, Toni Dwyer, Inaki J. T. Roca, Anna Kintner, Øyvind Kanstad-Hanssen, Martin S. Llewellyn, Kim Præbel
Software Mentions: 2
Published: almost 6 years ago
10.3389/fmicb.2020.573969
A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease
Cited by: 8
Author(s): Lydia Luise Bach, Asha Ram, Umer Zeeshan Ijaz, Thomas J. Evans, Jan Lindström
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2020.570825
Data-Driven Modeling for Species-Level Taxonomic Assignment From 16S rRNA: Application to Human Microbiomes
Cited by: 11
Author(s): Ho Jin Gwak, Mina Rho
Software Mentions: 2
Published: about 4 years ago
10.3389/fmicb.2020.588410
Acinetobacter Plasmids: Diversity and Development of Classification Strategies
Cited by: 11
Author(s): S. Z. Mindlin, Alexey V. Beletsky, Andrey L. Rakitin, Andrey V. Mardanov, Mayya Petrova
Software Mentions: 2
Published: about 4 years ago
10.3389/fmicb.2019.02004
Taxonomy, Diet, and Developmental Stage Contribute to the Structuring of Gut-Associated Bacterial Communities in Tephritid Pest Species
Cited by: 24
Author(s): Antonios A. Augustinos, George Tsiamis, Carlos Cáceres, Adly M. M. Abd-Alla, Kostas Bourtzis
Software Mentions: 2
Published: about 5 years ago
10.3389/fmicb.2019.01258
Presence, Diversity, and Enrichment of Respiratory Reductive Dehalogenase and Non-respiratory Hydrolytic and Oxidative Dehalogenase Genes in Terrestrial Environments
Cited by: 17
Author(s): Hanna R. Temme, Aaron Carlson, Paige J. Novak
Software Mentions: 2
Published: over 5 years ago
10.3389/fmicb.2019.00928
Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems
Cited by: 34
Author(s): Lin-Xing Chen, Basem Al-Shayeb, Raphaël Méheust, Wenjun Li, Jennifer A. Doudna, Jillian F. Banfield
Software Mentions: 2
Published: over 5 years ago
10.3389/fmicb.2021.656306
Genomic Analysis of Antibiotic-Resistant Staphylococcus epidermidis Isolates From Clinical Sources in the Kwazulu-Natal Province, South Africa
Cited by: 9
Author(s): Jonathan Asante, Bakoena Ashton Hetsa, Daniel G. Amoako, Akebe Luther King Abia, Linda A. Bester, Sabiha Y. Essack
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2014.00678
Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes
Cited by: 220
Author(s): Austin G. Davis-Richardson, Alexandria N. Ardissone, Raquel Dias, Ville Simell, Michael T. Leonard, Kaisa Kemppainen, Jennifer C. Drew, Desmond Schatz, Mark A. Atkinson, Bryan Kolaczkowski, Jorma Ilonen, Mikael Knip, Jorma Toppari, Noora Nurminen, Heikki Hyöty, Riitta Veijola, Tuula Simell, Juha Mykkänen, Olli Simell, Eric W. Triplett
Software Mentions: 2
Published: almost 10 years ago
10.3389/fmicb.2018.00214
Characterization of Asymptomatic Bacteriuria Escherichia coli Isolates in Search of Alternative Strains for Efficient Bacterial Interference against Uropathogens
Cited by: 21
Author(s): Christoph Stork, Beáta Kovács, Barnabás Rózsai, Johannes Putze, Matthias Kiel, Ágnes Dorn, Judit Kovács, Szilvia Melegh, Andreas Leimbach, Tamás Kovács, G. Schneider, Mónika Kerényi, Levente Emődy, Ulrich Dobrindt
Software Mentions: 2
Published: almost 7 years ago
10.3389/fmicb.2021.642125
Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli
Cited by: 6
Author(s): Ama Szmolka, Haleluya Wami, Ulrich Dobrindt
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2017.00791
Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin
Cited by: 28
Author(s): Allison Sharrar, Beverly E. Flood, Jake V. Bailey, Daniel S. Jones, Bopaiah A. Biddanda, Steven A. Ruberg, Daniel N. Marcus, Gregory J. Dick
Software Mentions: 2
Published: over 7 years ago
10.3389/fmicb.2020.00286
Identification of Persistent Sulfidogenic Bacteria in Shale Gas Produced Waters
Cited by: 11
Author(s): Lisa Cliffe, Sophie L. Nixon, Rebecca A. Daly, Bob Eden, Kevin G. Taylor, Christopher Boothman, Michael J. Wilkins, Kelly Wrighton, Jonathan R. Lloyd
Software Mentions: 2
Published: almost 5 years ago
10.3389/fmicb.2020.01588
The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens
Cited by: 3
Author(s): Jessica C. A. Friedersdorff, Alison H. Kingston‐Smith, Justin A. Pachebat, Alan Cookson, David Rooke, Christopher J. Creevey
Software Mentions: 2
Published: over 4 years ago
10.3389/fphys.2018.01833
A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus
Cited by: 11
Author(s): Qilin Zhang, Guanling Zhang, Ming Yüan, Zhi-Xiang Dong, Hongwei Li, Jun Guo, Feng Wang, Xian-Yu Deng, Jun-Yuan Chen, Lin Lü
Software Mentions: 2
Published: almost 6 years ago
10.3389/fphys.2018.00812
Transcriptional and Translational Relationship in Environmental Stress: RNAseq and ITRAQ Proteomic Analysis Between Sexually Reproducing and Parthenogenetic Females in Moina micrura
Cited by: 14
Author(s): Jingyi Jia, Xiangjiang Liu, Lü Li, Lei Chen, Ying Dong, Guoqiang Wu, Guangfu Hu
Software Mentions: 2
Published: over 6 years ago
10.3389/fpls.2021.667678
Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development
Cited by: 9
Author(s): Parul Gupta, Matthew Geniza, Sushma Naithani, Jeremy Phillips, Ebaad Haq, Pankaj Jaiswal
Software Mentions: 2
Published: over 3 years ago
10.3389/fpls.2017.00553
Comprehensive Transcriptome Analyses Reveal Differential Gene Expression Profiles of Camellia sinensis Axillary Buds at Para-, Endo-, Ecodormancy, and Bud Flush Stages
Cited by: 62
Author(s): Xinyuan Hao, Yajun Yang, Chuan Yue, Lu Wang, David P. Horvath, Xinchao Wang
Software Mentions: 2
Published: over 7 years ago
10.3389/fvets.2020.00017
Development of the Ileal Microbiota in Three Broiler Breeds
Cited by: 51
Author(s): Peter Richards, Joanne L. Fothergill, Marion Bernardeau, Paul Wigley
Software Mentions: 2
Published: almost 5 years ago
10.3389/fvets.2019.00201
Development of the Caecal Microbiota in Three Broiler Breeds
Cited by: 68
Author(s): Peter Richards, Joanne L. Fothergill, Marion Bernardeau, Paul Wigley
Software Mentions: 2
Published: over 5 years ago
10.3389/fvets.2019.00371
The Effect of Milk Replacer Composition on the Intestinal Microbiota of Pre-ruminant Dairy Calves
Cited by: 14
Author(s): James Badman, Kristian Daly, Jennifer Kelly, Andrew W. Moran, John Cameron, Ian Watson, J.R. Newbold, Soraya P. Shirazi-Beechey
Software Mentions: 2
Published: about 5 years ago
10.1007/s10142-020-00752-x
Comparative transcriptomic analysis reveals the mechanistic basis of Pib-mediated broad spectrum resistance against Magnaporthe oryzae
Cited by: 3
Author(s): Jian Qiu, Feifei Lu, Min Xiong, Shuai Meng, Xiangqian Shen, Yanjun Kou
Software Mentions: 2
Published: about 4 years ago
10.1007/s10142-017-0585-5
A large-scale multiomics analysis of wheat stem solidness and the wheat stem sawfly feeding response, and syntenic associations in barley, Brachypodium, and rice
Cited by: 17
Author(s): Sezgi Biyiklioglu, Burcu Alptekin, Bala Anı Akpınar, Andrea C. Varella, Megan L. Hofland, David K. Weaver, Brian Bothner, Hikmet Budak
Software Mentions: 2
Published: almost 7 years ago
10.3390/genes12030389
Filling the Gaps in the Cyanobacterial Tree of Life—Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014
Cited by: 5
Author(s): Pia Marter, Sixing Huang, Henner Brinkmann, Silke Pradella, Michael Jarek, Manfred Rohde, Boyke Bunk, Jörn Petersen
Software Mentions: 2
Published: over 3 years ago
10.3390/genes12060833
The Genes of Freedom: Genome-Wide Insights into Marronage, Admixture and Ethnogenesis in the Gulf of Guinea
Cited by: 4
Author(s): João Nóbrega de Almeida, Anne-Maria Fehn, Margarida Ferreira, Teresa M. Machado, Tjerk Hagemeijer, Jorge Rocha, Magdalena Gayà-Vidal
Software Mentions: 2
Published: over 3 years ago
10.1590/1678-4685-GMB-2020-0155
Genomic sequencing of two isolates of Ralstonia solanacearum causing Sergipe facies and comparative analysis with Bugtok disease isolates
Cited by: 3
Author(s): Jéssica Rodrigues da Silva, Ana Karolina Leite Pais, Greecy Mirian Rodrigues Albuquerque, Adriano Márcio Freire Silva, Wilson José Silva, Valdir de Queiroz Balbino, M. E. N. Fonseca, Marco Aurélio Siqueira da Gama, Elineide Barbosa de Souza, Rosa de Lima Ramos Mariano
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12711-018-0390-1
A survey of functional genomic variation in domesticated chickens
Cited by: 25
Author(s): Martijn F.L. Derks, Hendrik‐Jan Megens, Mirte Bosse, J. Visscher, Katrijn Peeters, M.C.A.M. Bink, Addie Vereijken, Christian Groß, Dick de Ridder, Marcel J. T. Reinders, Martien A. M. Groenen
Software Mentions: 2
Published: over 6 years ago
10.1128/genomeA.01646-15
Complete Genome Sequence of Bovine Polyomavirus Type 1 from Aborted Cattle, Isolated in Belgium in 2014
Cited by: 7
Author(s): Steven Van Borm, Toon Rosseel, Isabelle Behaeghel, Marc Saulmont, Laurent Delooz, T. Petitjean, Élisabeth Mathijs, Frank Vandenbussche
Software Mentions: 2
Published: over 8 years ago
10.1128/genomeA.01243-16
Complete Genome Sequence of a Vaccinal Newcastle Disease Virus Strain Isolated from an Owl ( Rhinoptynx clamator )
Cited by: 2
Author(s): Steven Van Borm, Laís Santos Rizotto, Leila Sabrina Ullmann, Guilherme Pereira Scagion, Camila Dantas Malossi, Raphael Mausbach Simão, João Pessoa Araújo, Izabelle M. Cordeiro, Lara Borges Keid, Tiago Marcelo Oliveira, Rodrigo Martins Soares, Matheus Cavalheiro Martini, Maria Ângela Orsi, Clarice Weis Arns, Helena Lage Ferreira
Software Mentions: 2
Published: almost 8 years ago
10.1128/genomeA.00042-17
Complete Coding Sequence of Usutu Virus Strain Gracula religiosa/U1609393/Belgium/2016 Obtained from the Brain Tissue of an Infected Captive Common Hill Myna ( Gracula religiosa )
Cited by: 4
Author(s): Steven Van Borm, Bénédicte Lambrecht, Frank Vandenbussche, Mieke Steensels
Software Mentions: 2
Published: over 7 years ago
10.1186/s13059-014-0504-1
Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires’ disease outbreak
Cited by: 23
Author(s): Paul R. McAdam, Charles W. Vander Broek, Diane Lindsay, Melissa J. Ward, Mary Hanson, Michael Gillies, Mick Watson, Joanne M. Stevens, Giles Edwards, J. Ross Fitzgerald
Software Mentions: 2
Published: about 10 years ago
10.1186/s13059-019-1746-8
The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements
Cited by: 80
Author(s): Zijuan Li, Meiyue Wang, Kande Lin, Yilin Xie, Jingyu Guo, Luhuan Ye, Yili Zhuang, Wan Teng, Xiaojuan Ran, Yiping Tong, Yongbiao Xue, Wenli Zhang, Yijing Zhang
Software Mentions: 2
Published: over 5 years ago
10.1186/s13059-019-1748-6
BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis
Cited by: 18
Author(s): Fatma Uzbaş, Florian Opperer, Can Sönmezer, Dmitry Shaposhnikov, Steffen Sass, Christian Krendl, Philipp Angerer, Fabian J. Theis, Nikola S. Mueller, Micha Drukker
Software Mentions: 2
Published: over 5 years ago
10.1186/s13059-020-02225-7
Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression
Cited by: 35
Author(s): Jizeng Jia, Yilin Xie, Jingfei Cheng, Chuizheng Kong, Meiyue Wang, Lifeng Gao, Fei Zhao, Jingyu Guo, Kai Wang, Guangwei Li, Dangqun Cui, Tiezhu Hu, Guangyao Zhao, Daowen Wang, Zhengang Ru, Yijing Zhang
Software Mentions: 2
Published: almost 4 years ago
10.5808/GI.2019.17.4.e40
Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data
Cited by: 1
Author(s): Yu Na Lee, Kiejung Park, Insong Koh
Software Mentions: 2
Published: almost 5 years ago
10.1093/gigascience/gix008
Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history
Cited by: 34
Author(s): Xiaofeng Dong, Stuart D. Armstrong, Dong Xia, Benjamin L. Makepeace, Alistair C. Darby, Tatsuhiko Kadowaki
Software Mentions: 2
Published: almost 8 years ago
10.1093/gigascience/giy127
Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism
Cited by: 27
Author(s): Xiaofeng Dong, Kittipong Chaisiri, Dong Xia, Stuart D. Armstrong, Yongxiang Fang, Martin J. Donnelly, Tatsuhiko Kadowaki, John McGarry, Alistair C. Darby, Benjamin L. Makepeace
Software Mentions: 2
Published: about 6 years ago
10.1038/s41438-018-0115-1
Wide transcriptional investigation unravel novel insights of the on-tree maturation and postharvest ripening of ‘Abate Fetel’ pear fruit
Cited by: 13
Author(s): Nicola Busatto, Brian Farneti, Alice Tadiello, Vicky Oberkofler, Antonio Cellini, Franco Biasioli, Massimo Delledonne, Alessandro Cestaro, Christos Noutsos, Fabrizio Costa
Software Mentions: 2
Published: over 5 years ago
10.1016/j.meegid.2016.07.010
Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus
Cited by: 16
Author(s): David J. King, Graham Freimanis, Richard Orton, Ryan Waters, Daniel T. Haydon, Donald P. King
Software Mentions: 2
Published: about 8 years ago
10.1111/jcmm.16569
RNA‐seq analysis of ageing human retinal pigment epithelium: Unexpected up‐regulation of visual cycle gene transcription
Cited by: 20
Author(s): Joe Butler, Wasu Supharattanasitthi, Yit Yang, Luminita Paraoan
Software Mentions: 2
Published: over 3 years ago
10.1111/jeb.13722
Compost spatial heterogeneity promotes evolutionary diversification of a bacterium
Cited by: 4
Author(s): Stineke van Houte, Daniel Padfield, Pedro Sánchez Gómez, Adela M. Luján, Michael A. Brockhurst, Steve Paterson, Angus Buckling
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.ppat.1009416
Viral genomic, metagenomic and human transcriptomic characterization and prediction of the clinical forms of COVID-19
Cited by: 23
Author(s): Christophe Rodriguez, Nicolas de Prost, Slim Fourati, Claudie Lamoureux, Guillaume Gricourt, Mélissa N’Debi, Florence Canouï‐Poitrine, Isaac Désveaux, Oriane Picard, Vanessa Démontant, Elisabeth Trawinski, R. Lepeule, Laure Surgers, William Vindrios, Jean‐Daniel Lelièvre, Nicolas Mongardon, Olivier Langeron, José L. Cohen, Armand Mekontso-Dessap, Paul‐Louis Woerther, Jean‐Michel Pawlotsky
Software Mentions: 2
Published: over 3 years ago
10.1530/REP-16-0484
Hormone-sensitive lipase deficiency alters gene expression and cholesterol content of mouse testis
Cited by: 18
Author(s): Wei Feng, Zheng Chen, Xiaofang Ren, Ye Tian, Fucheng Wang, Chao Liu, Pengcheng Jin, Zongyue Li, Feixiong Zhang, Beiwei Zhu
Software Mentions: 2
Published: almost 8 years ago
10.1038/sdata.2018.69
The draft genome sequence of cork oak
Cited by: 78
Author(s): António Marcos Ramos, Ana Usié, Pedro Barbosa, Pedro M. Barros, Tiago Capote, Inês Chaves, Fernanda Simões, Isabel A. Abreu, Isabel Carrasquinho, Carlos Faro, Joana Bagoin Guimarães, Diogo Mendonça, Filomena Nóbrega, L. Rodrigues, Nelson J. M. Saibo, Maria Carolina Varela, Conceição Egas, José Matos, Celia María Gonzalo Miguel, M. Margarida Oliveira, Cândido Pinto Ricardo, Sónia Gonçalves
Software Mentions: 2
Published: over 6 years ago
10.1038/s41597-020-0387-9
Genome-wide gene expression profiling of the melon fly, Zeugodacus cucurbitae, during thirteen life stages
Cited by: 13
Author(s): Dong Wei, Hui-Qian Xu, Chen Dong, Suyun Zhang, Weijun Li, Guy Smagghe, Jinjun Wang
Software Mentions: 2
Published: almost 5 years ago
10.1038/srep16498
Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
Cited by: 118
Author(s): Kirsten A. Ziesemer, Allison E. Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea L. Waters‐Rist, Menno L. P. Hoogland, Domingo C. Salazar‐García, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy MacDonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis, Corinne L. Hofman, Christina Warinner
Software Mentions: 2
Published: about 9 years ago
10.1038/srep25211
Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions
Cited by: 54
Author(s): Monica Hongrø Solbakken, Ole K. Tørresen, Alexander J. Nederbragt, Marit Seppola, Tone F. Gregers, Kjetill S. Jakobsen, Sissel Jentoft
Software Mentions: 2
Published: over 8 years ago
10.1038/srep43558
Serum snoRNAs as biomarkers for joint ageing and post traumatic osteoarthritis
Cited by: 41
Author(s): M.M. Steinbusch, Yongxiang Fang, Peter Milner, Peter Clegg, David A. Young, Tim J. M. Welting, Mandy J. Peffers
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-10867-0
Integrated analysis of microRNA and mRNA expression profiles during the sex-differentiation sensitive period in oriental river prawn, Macrobrachium nipponense
Cited by: 18
Author(s): Shubo Jin, Hongtuo Fu, Shengming Sun, Sufei Jiang, Yiwei Xiong, Yongsheng Gong, Hui Qiao, Wenyi Zhang, Yan Wu
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-018-21992-9
The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish
Cited by: 18
Author(s): Alexandros Tsakogiannis, Tereza Manousaki, Jacques Lagnel, Aspasia Sterioti, M. Pavlidis, Nikos Papandroulakis, Constantinos C. Mylonas, Costas S. Tsigenopoulos
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/s41598-018-35844-z
The NnaR orphan response regulator is essential for the utilization of nitrate and nitrite as sole nitrogen sources in mycobacteria
Cited by: 6
Author(s): Magdalena Antczak, Renata Płocińska, Przemysław Płociński, Anna Rumijowska-Galewicz, Anna Żaczek, Dominik Strapagiel, Jarosław Dziadek
Software Mentions: 2
Published: almost 6 years ago
10.1038/s41598-019-40719-y
Clinical utility of androgen receptor gene aberrations in circulating cell-free DNA as a biomarker for treatment of castration-resistant prostate cancer
Cited by: 50
Author(s): Takayuki Sumiyoshi, Kei Mizuno, Toshinari Yamasaki, Yu Miyazaki, Yuki Makino, Kosuke Okasho, Xin Li, Noriaki Utsunomiya, Takayuki Goto, Takashi Kobayashi, Naoki Terada, Takahiro Inoue, Tomomi Kamba, Akihiro Fujimoto, Osamu Ogawa, Shusuke Akamatsu
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-42779-6
ASYMMETRIC LEAVES1 and REVOLUTA are the key regulatory genes associated with pitcher development in Nepenthes khasiana
Cited by: 9
Author(s): Jeremy Dkhar, Ashwani Pareek
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-48047-x
Functional Transcriptome Analysis in ARSACS KO Cell Model Reveals a Role of Sacsin in Autophagy
Cited by: 24
Author(s): Federica Morani, Stefano Doccini, Roberto Sirica, Marta Paterno, Francesco Pezzini, Ivana Ricca, Alessandro Simonati, Massimo Delledonne, Filippo M. Santorelli
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-50561-x
RNA Sequencing revealed differentially expressed genes functionally associated with immunity and tumor suppression during latent phase infection of a vv + MDV in chickens
Cited by: 0
Author(s): Kunzhe Dong, Shuang Chang, Qingmei Xie, Peng Zhao, Huanmin Zhang
Software Mentions: 2
Published: about 5 years ago