Ecosyste.ms: Papers

10.3389/fmicb.2019.00805

Prevalence of Antibiotic and Heavy Metal Resistance Determinants and Virulence-Related Genetic Elements in Plasmids of Staphylococcus aureus
Cited by: 23
Author(s): Michał Bukowski, Rafał Piwowarczyk, Anna Mądry, Rafal Zagorski-Przybylo, Marcin Hydzik, Benedykt Władyka
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2019.01295

miRNAs Involved in M1/M2 Hyperpolarization Are Clustered and Coordinately Expressed in Alcoholic Hepatitis
Cited by: 18
Author(s): Adam Kim, Paramananda Saikia, Laura E. Nagy
Software Mentions: 3
Published: over 5 years ago

10.1186/s12866-019-1402-1

NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission
Cited by: 66
Author(s): Alexandra Dangel, Anja Berger, Regina Konrad, Andreas Sing
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-020-02450-z

Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars
Cited by: 21
Author(s): Heng Zhou, Ying He, Yu Cheng Zhu, Meiyu Li, Shuang Song, Wenhao Bo, Yingyue Li, Xiaoming Pang
Software Mentions: 3
Published: over 4 years ago

10.1186/s13104-016-2069-4

Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus
Cited by: 4
Author(s): Matteo Buti, Daniel J. Sargent, Khethani Mhelembe, Pietro Delfino, K. R. Tobutt, Riccardo Velasco
Software Mentions: 3
Published: over 8 years ago

10.1016/j.toxrep.2019.11.014

The impact of particulate matter (PM2.5) on skin barrier revealed by transcriptome analysis: Focusing on cholesterol metabolism
Cited by: 21
Author(s): Zhengzheng Liao, Jing Nie, Peng Sun
Software Mentions: 3
Published: almost 5 years ago

10.3758/s13428-018-1046-3

Testing moderator hypotheses in meta-analytic structural equation modeling using subgroup analysis
Cited by: 33
Author(s): Suzanne Jak, Mike W.‐L. Cheung
Software Mentions: 3
Published: over 6 years ago

10.3390/s20082208

Closed-Loop Attention Restoration Theory for Virtual Reality-Based Attentional Engagement Enhancement
Cited by: 12
Author(s): Gang Li, Shihong Zhou, Zhen Kong, Mengyuan Guo
Software Mentions: 3
Published: over 4 years ago

10.1002/lrh2.10214

The European medical information framework: A novel ecosystem for sharing healthcare data across Europe
Cited by: 18
Author(s): Simon Lovestone
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-020-6512-5

Transcriptomic response to three osmotic stresses in gills of hybrid tilapia (Oreochromis mossambicus female × O. urolepis hornorum male)
Cited by: 44
Author(s): Huanhuan Su, Dongmei Ma, Hai‐Lei Zhu, Zhigang Liu, Fengying Gao
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-017-4016-8

Characterization of mechanisms underlying degradation of sclerotia of Sclerotinia sclerotiorum by Aspergillus aculeatus Asp-4 using a combined qRT-PCR and proteomic approach
Cited by: 15
Author(s): Xiaojia Hu, Lü Qin, Daniel P. Roberts, Dilip K. Lakshman, Yiqin Gong, Jude E. Maul, Lin Xie, Chang Yeon Yu, Yinshui Li, Lei Hu, Liao Xiang-sheng, Lixin Xing
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-021-98708-z

AGO CLIP-based imputation of potent siRNA sequences targeting SARS-CoV-2 with antifibrotic miRNA-like activity
Cited by: 6
Author(s): Seung Hyun Ahn, Dowoon Gu, Yongjun Koh, Hye-Sook Lee, Sung Wook
Software Mentions: 3
Published: about 3 years ago

10.1038/s41380-018-0089-2

Stress peptides sensitize fear circuitry to promote passive coping
Cited by: 33
Author(s): Pinelopi Pliota, Vincent Böhm, Florian Grössl, Johannes Griessner, Ornella Valenti, Klaus Kraitsy, Joanna Kaczanowska, Manuel Pasieka, Thomas Lendl, Jan M. Deussing, Wulf Haubensak
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms21020426

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton
Cited by: 7
Author(s): Yuhang Fan, Xiaoman Yu, Huihui Guo, Junmei Wei, Haixia Guo, Li Zhang, Fanchang Zeng
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-87876-7

Quantitative imaging of membrane contact sites for sterol transfer between endo-lysosomes and mitochondria in living cells
Cited by: 12
Author(s): Alice Dupont Juhl, Christian W. Heegaard, Stephan Werner, Gerd Schneider, Kathiresan Krishnan, Douglas F. Covey, Daniel Wüstner
Software Mentions: 3
Published: over 3 years ago

10.1111/j.1467-7652.2011.00625.x

Large‐scale transcriptome analysis in chickpea ( <i>Cicer arietinum</i> L.), an orphan legume crop of the semi‐arid tropics of Asia and Africa
Cited by: 239
Author(s): Pavana J Hiremath, Andrew Farmer, Steven B. Cannon, Jimmy E. Woodward, Himabindu Kudapa, Reetu Tuteja, Ashish Kumar, BhanuPrakash Amindala, Benjamin Mulaosmanovic, Neha Gujaria, L. Krishnamurthy, Pooran M. Gaur, Polavarapu B. KaviKishor, Trushar Shah, R. Srinivasan, Marc Lohse, Yongli Xiao, Christopher D. Town, Douglas R. Cook, Gregory D. May, Rajeev K. Varshney
Software Mentions: 3
Published: over 13 years ago

10.7554/eLife.64691

Disease-related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveal a path to selective inhibitors
Cited by: 23
Author(s): Manoj Kumar Rathinaswamy, Zied Gaieb, Kaelin D Fleming, Chiara Borsari, Noah J Harris, Brandon E Moeller, Matthias P. Wymann, Rommie E. Amaro, John E. Burke
Software Mentions: 3
Published: over 3 years ago

10.1073/pnas.2003724117

Genome mapping of a <i>LYST</i> mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles
Cited by: 28
Author(s): Asier Ullate-Agote, Ingrid Burgelin, Adrien Debry, Carine Langrez, Florent Montange, Rodrigue Peraldi, Jean Daraspe, Henrik Kaessmann, Michel C. Milinkovitch, Athanasia C. Tzika
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1003942

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data
Cited by: 122
Author(s): Krystyna Nadachowska‐Brzyska, Reto Burri, Pall I. Olason, Takeshi Kawakami, Linnéa Smeds, Hans Ellegren
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pgen.1008794

Exome-wide association study reveals largely distinct gene sets underlying specific resistance to dengue virus types 1 and 3 in Aedes aegypti
Cited by: 10
Author(s): Laura B. Dickson, Sarah H. Merkling, Mathieu Gautier, Amine Ghozlane, Davy Jiolle, Christophe Paupy, Diégo Ayala, Isabelle Moltini-Conclois, Albin Fontaine, Louis Lambrechts
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1003067

CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function
Cited by: 102
Author(s): Jacy L. Wagnon, Michael Briese, Wenzhi Sun, Connie L. Mahaffey, Tomaž Curk, Gregor Rot, Jernej Ule, Wayne N. Frankel
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0173020

Petri net-based approach to modeling and analysis of selected aspects of the molecular regulation of angiogenesis
Cited by: 11
Author(s): Dorota Formanowicz, Marcin Radom, Piotr Zawierucha, Piotr Formanowicz
Software Mentions: 3
Published: over 7 years ago

10.1128/JB.00607-20

Alkaline pH Increases Swimming Speed and Facilitates Mucus Penetration for Vibrio cholerae
Cited by: 9
Author(s): Nguyen T. Q. Nhu, John S. Lee, Helen J. Wang, Y. Dufour
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0041645

Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection
Cited by: 36
Author(s): Qinghua Nie, Erin Sandford, Xiquan Zhang, Lisa K. Nolan, Susan J. Lamont
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0202375

Genome-wide identification and functional analysis of circRNAs in Zea mays
Cited by: 28
Author(s): Baihua Tang, Zhiqiang Hao, Yanfeng Zhu, Hua Zhang, Guanglin Li
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-5893-9

Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression
Cited by: 21
Author(s): Mei Lan K. Han, Guifeng Wei, Catherine E. McManus, LaDeana W. Hillier, V Reinke
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0086976

Transcriptomic Analysis of Flower Development in Wintersweet (Chimonanthus praecox)
Cited by: 40
Author(s): Daofeng Liu, Shunzhao Sui, Jing Ma, Zhineng Li, Yanjun Guo, Dengpan Luo, Jingjing Yang, Mingyang Li
Software Mentions: 3
Published: almost 11 years ago

10.1111/1744-7917.12696

Co‐infection of <i>Wolbachia</i> and <i>Spiroplasma</i> in spider mite <i>Tetranychus truncatus</i> increases male fitness
Cited by: 8
Author(s): Kang Xie, Yi‐Jia Lu, Kun Yang, Shi‐Mei Huo, Xiao‐Yue Hong
Software Mentions: 3
Published: over 5 years ago

10.3390/healthcare8020154

AI Chatbot Design during an Epidemic like the Novel Coronavirus
Cited by: 88
Author(s): Gopi Battineni, Nalini Chintalapudi, Francesco Amenta
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-017-3775-6

The midgut transcriptome of Aedes aegypti fed with saline or protein meals containing chikungunya virus reveals genes potentially involved in viral midgut escape
Cited by: 42
Author(s): Shao-Jing Dong, Susanta K. Behura, Alexander W. E. Franz
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0199021

Transcriptomic response to GABA-producing Lactobacillus plantarum CGMCC 1.2437T induced by L-MSG
Cited by: 28
Author(s): Kejin Zhuang, Yujun Jiang, Xiaohan Feng, Li Li, Fangfang Dang, Wei Zhang, Chaoxin Man
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0020161

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
Cited by: 481
Author(s): Sarel J. Fleishman, Andrew Leaver‐Fay, Jacob E. Corn, Eva-Maria Strauch, Sagar D. Khare, Nobuyasu Koga, Justin Ashworth, Patricia Murphy, Florian Richter, Gordon Lemmon, Jens Meiler, David Baker
Software Mentions: 3
Published: over 13 years ago

10.1093/gigascience/giz129

Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop
Cited by: 65
Author(s): Gláucia Mendes Souza, Marie‐Anne Van Sluys, Carolina Gimiliani Lembke, Hayan Lee, Gabriel Rodrigues Alves Margarido, Carlos Takeshi Hotta, Jonas Weissmann Gaiarsa, Augusto Lima Diniz, Mona N. Oliveira, Sávio Siqueira Ferreira, Milton Yutaka Nishiyama, Felipe Ten Caten, Geovani Tolfo Ragagnin, Pablo de Morais Andrade, Robson Francisco de Souza, Gianlucca Gonçalves Nicastro, Ravi Pandya, Changsoo Kim, Hui Guo, Alan Mitchell Durham, Monalisa Sampaio Carneiro, Jisen Zhang, Xingtan Zhang, Qing Zhang, Ray Ming, Michael C. Schatz, Bob Davidson, Andrew H. Paterson, David Heckerman
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-9-311

Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge
Cited by: 5
Author(s): Don Armstrong, Chaim O. Jacob, Raphael Zidovetzki
Software Mentions: 3
Published: over 16 years ago

10.1002/mgg3.1115

Identification of novel differentially expressed genes in retinas of STZ‐induced long‐term diabetic rats through RNA sequencing
Cited by: 5
Author(s): Xindan Xing, Yan Jiang, Hanying Wang, Yuan Zhang, Tian Niu, Qing Yuan, Ching‐Yi Wang, Haiyan Wang, Kun Liu
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-9-70

GraphCrunch: A tool for large network analyses
Cited by: 103
Author(s): Tijana Milenković, Jih-Sheng Lai, Nataša Pržulj
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2105-14-77

GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures
Cited by: 24
Author(s): Björn Hammesfahr, Florian Odronitz, Stefanie Mühlhausen, Stephan Waack, Martin Kollmar
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-9-177

JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes
Cited by: 50
Author(s): Michael Richter, Thierry Lombardot, Ivaylo Kostadinov, Renzo Kottmann, Melissa B. Duhaime, Jörg Peplies, Frank Oliver Glöckner
Software Mentions: 2
Published: over 16 years ago

10.1186/s12859-021-04337-8

A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants
Cited by: 7
Author(s): Tim W McInerney, Brian Fulton-Howard, Christopher Patterson, Devashi Paliwal, Lars S. Jermiin, Hardip R. Patel, Judy Pa, Russell H. Swerdlow, Alison M. Goate, Simon Easteal, Shea J. Andrews
Software Mentions: 2
Published: about 3 years ago

10.1186/s12859-016-1366-1

PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms
Cited by: 5
Author(s): Richie Ruei-Chi Gan, Ting-Wen Chen, Timothy Wu, Po-Jung Huang, Chi-Ching Lee, Yuan-Ming Yeh, Cheng-Hsun Chiu, Hsien-Da Huang, Petrus Tang
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-020-03650-y

FluConvert and IniFlu: a suite of integrated software to identify novel signatures of emerging influenza viruses with increasing risk
Cited by: 2
Author(s): Chin-Rur Yang, Chwan-Chuen King, Liyu Liu, Chia-Chi Ku
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2148-12-217

Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D
Cited by: 104
Author(s): Jason T. Ladner, Daniel J. Barshis, Stephen R. Palumbi
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12864-020-06965-5

mRNA profile provides novel insights into stress adaptation in mud crab megalopa, Scylla paramamosain after salinity stress
Cited by: 18
Author(s): Yin Zhang, Qingping Wu, Shaobin Fang, Shengkang Li, Huaiping Zheng, Yueling Zhang, Mhd Ikhwanuddin, Hongyu Ma
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-020-6484-5

Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants
Cited by: 28
Author(s): Raphaël Leman, Hélène Tubeuf, Sabine Raad, Isabelle Tournier, Céline Derambure, Raphaël Lanos, Pascaline Gaildrat, G Castelain, Julie Hauchard, Audrey Killian, Stéphanie Baert‐Desurmont, Angélina Legros, Nicolas Goardon, Céline Quesnelle, Agathe Ricou, Laurent Castéra, Dominique Vaur, Gérald Le Gac, Chandran Ka, Yann Fichou, Françoise Bonnet‐Dorion, Nicolas Sévenet, Marine Guillaud‐Bataille, Nadia Boutry‐Kryza, Inès Schultz, Virginie Caux‐Moncoutier, Maria Rossing, Logan C. Walker, Amanda B. Spurdle, Claude Houdayer, Alexandra Martins, Sophie Krieger
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-015-2332-4

Transcriptome profiling of a Rhizobium leguminosarum bv. trifolii rosR mutant reveals the role of the transcriptional regulator RosR in motility, synthesis of cell-surface components, and other cellular processes
Cited by: 22
Author(s): Kamila Rachwał, Ewa Matczyńska, Monika Janczarek
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-021-07927-1

A graphical, interactive and GPU-enabled workflow to process long-read sequencing data
Cited by: 2
Author(s): Shishir Reddy, Ling Hong Hung, Olga Sala‐Torra, Jerald P. Radich, Cecilia C.S. Yeung, Ka Yee Yeung
Software Mentions: 2
Published: about 3 years ago

10.1186/s12864-016-2643-0

Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution
Cited by: 36
Author(s): Taya Forde, Roman Biek, Ruth N. Zadoks, Matthew L. Workentine, Jeroen De Buck, Susan Kutz, Tanja Opriessnig, Hannah Trewby, Frank van der Meer, Karin Orsel
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-020-07139-z

Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb (Puntius tetrazona)
Cited by: 31
Author(s): Huan Liu, Rong Zhang, Xiaowen Wang, Hua Zhu, Zhixi Tian
Software Mentions: 2
Published: about 4 years ago

10.1186/s12864-019-5655-8

Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states
Cited by: 4
Author(s): Kris A. Christensen, Dionne Sakhrani, Eric B. Rondeau, Jeffery Richards, Ben F. Koop, Robert H. Devlin
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-13-660

Downy mildew resistance induced by Trichoderma harzianum T39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes
Cited by: 126
Author(s): Michele Perazzolli, Marco Moretto, Paolo Fontana, Alberto Ferrarini, Riccardo Velasco, C. Moser, Massimo Delledonne, I. Pertot
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-14-849

The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum
Cited by: 50
Author(s): Keerthi P. Venkataramanan, Shawn W. Jones, Kevin McCormick, Sridhara G. Kunjeti, Matthew T. Ralston, Blake C. Meyers, Eleftherios T. Papoutsakis
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-018-5117-8

Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus
Cited by: 37
Author(s): Enhui Shen, Xintian Zhu, Shuijin Hua, Hongyu Chen, Chu-Yu Ye, Longhua Zhou, Qing Liu, Qian‐Hao Zhu, Longjiang Fan, Xi Chen
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2164-15-1090

Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism
Cited by: 54
Author(s): Henrik Stranneheim, Martin Engvall, K Naess, Nicole Lesko, Pontus Larsson, Mats Dahlberg, Robin Andeer, Anna Wredenberg, Christoph Freyer, Michela Barbaro, Helene Bruhn, Tesfail Emahazion, Måns Magnusson, Rolf Wibom, Rolf Zetterström, Valtteri Wirta, Ulrika von Döbeln, Anna Wedell
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12870-021-02880-3

Overexpression of a methyl-CpG-binding protein gene OsMBD707 leads to larger tiller angles and reduced photoperiod sensitivity in rice
Cited by: 10
Author(s): Mengyu Qu, Zhujian Zhang, Tingmin Liang, Peipei Niu, Mingji Wu, Wenchao Chi, Ziqiang Chen, Zaijie Chen, Shubiao Zhang, Songbiao Chen
Software Mentions: 2
Published: almost 4 years ago

10.1186/1472-6807-13-32

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
Cited by: 8
Author(s): Manuel Rueda, Modesto Orozco, Maxim Totrov, Ruben Abagyan
Software Mentions: 2
Published: almost 11 years ago

10.1186/1745-6150-4-12

Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans
Cited by: 2
Author(s): Karim Mezhoud, Haïtham Sghaier, Insaf Barkallah
Software Mentions: 2
Published: almost 16 years ago

10.1186/s13068-015-0246-7

Uniconazole-induced starch accumulation in the bioenergy crop duckweed (Landoltia punctata) I: transcriptome analysis of the effects of uniconazole on chlorophyll and endogenous hormone biosynthesis
Cited by: 37
Author(s): Liuyan Yang, Yang Fang, Mengjun Huang, Yanling Jin, Jiaolong Sun, Tao Xiang, Zhang Guo-hua, Kai He, Yun Zhao, Hai Zhao
Software Mentions: 2
Published: over 9 years ago

10.1186/s40575-015-0029-2

Evaluation of whole-genome sequencing of four Chinese crested dogs for variant detection using the ion proton system
Cited by: 5
Author(s): Agnese Viļuma, Shumaila Sayyab, Sofia Mikko, Gerhard Andersson, Tomas F. Bergström
Software Mentions: 2
Published: about 9 years ago

10.3390/microorganisms8010083

Inoculation with Rhizophagus irregularis Does Not Alter Arbuscular Mycorrhizal Fungal Community Structure within the Roots of Corn, Wheat, and Soybean Crops
Cited by: 27
Author(s): Sébastien Renaut, Rachid Daoud, Jacynthe Masse, Agathe Vialle, Mohamed Hijri
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.mcpro.2021.100052

New Proteomic Signatures to Distinguish Between Zika and Dengue Infections
Cited by: 10
Author(s): Kristina Allgoewer, Shuvadeep Maity, Alice Zhao, Lauren Lashua, Moti Ramgopal, B. Balkaran, Liyun Liu, Savita Purushwani, Maria T. Arévalo, Ted M. Ross, Hyungwon Choi, Elodie Ghedin, Christine Vogel
Software Mentions: 2
Published: almost 4 years ago

10.3390/molecules23040969

Self-Assembly Behavior of Amphiphilic Janus Dendrimers in Water: A Combined Experimental and Coarse-Grained Molecular Dynamics Simulation Approach
Cited by: 8
Author(s): Mariana E Elizondo-García, Valeria Márquez-Miranda, Ingrid Araya-Durán, Jesús A. Valencia-Gallegos, Fernando D. González-Nilo
Software Mentions: 2
Published: over 6 years ago

10.3390/vaccines9050432

Conformational and Immunogenicity Studies of the Shigella flexneri Serogroup 6 O-Antigen: The Effect of O-Acetylation
Cited by: 9
Author(s): Nicole I Richardson, Neil Ravenscroft, Vanessa Arato, Davide Oldrini, Francesca Micoli, Michelle M. Kuttel
Software Mentions: 2
Published: over 3 years ago

10.3390/v12070713

Long Term Delta-9-tetrahydrocannabinol Administration Inhibits Proinflammatory Responses in Minor Salivary Glands of Chronically Simian Immunodeficieny Virus Infected Rhesus Macaques
Cited by: 7
Author(s): Xavier Álvarez, Karol Sestak, Siddappa N. Byrareddy, Mahesh Mohan
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.11326

Comparative transcriptome analysis reveals key insights into male sterility in <i>Salvia miltiorrhiza</i> Bunge
Cited by: 9
Author(s): Yan Yu, Yuanyuan Jiang, Long Wang, Yichao Wu, Jinqiu Liao, Mingzhi Zhong, Ruiwu Yang, Xingfu Chen, Qingmiao Li, Li Zhang
Software Mentions: 2
Published: over 3 years ago

10.1111/tpj.14895

Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross‐breeding
Cited by: 21
Author(s): Qingsong Liu, Xiaowei Yang, Vered Tzin, Yufa Peng, Jörg Romeis, Yunhe Li
Software Mentions: 2
Published: over 4 years ago

10.1186/s13007-019-0546-1

Fluctuating light experiments and semi-automated plant phenotyping enabled by self-built growth racks and simple upgrades to the IMAGING-PAM
Cited by: 9
Author(s): Dominik Schneider, Laura S. López, Meng Li, Joseph Crawford, Helmut Kirchhoff, Hans‐Henning Kunz
Software Mentions: 2
Published: almost 5 years ago

10.3390/plants10050991

Pan-Genome miRNomics in Brachypodium
Cited by: 2
Author(s): Tuğdem Muslu, Sezgi Biyiklioglu-Kaya, Bala Anı Akpınar, Meral Yüce, Hikmet Budak
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pbio.3000300

Genotype network intersections promote evolutionary innovation
Cited by: 28
Author(s): Devin P. Bendixsen, James Collet, Bjørn Østman, Eric J. Hayden
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1003056

Population Genomics of Inversion Polymorphisms in Drosophila melanogaster
Cited by: 173
Author(s): Russell Corbett-Detig, Daniel L. Hartl
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pgen.1003772

Cell Interactions and Patterned Intercalations Shape and Link Epithelial Tubes in C. elegans
Cited by: 25
Author(s): Jeffrey P. Rasmussen, Jessica L. Feldman, Sowmya Somashekar Reddy, James R Priess
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pntd.0000658

The Genome Sequence of Trypanosoma brucei gambiense, Causative Agent of Chronic Human African Trypanosomiasis
Cited by: 128
Author(s): Andrew P. Jackson, Mandy Sanders, Andrew Berry, Jacqueline A. McQuillan, Martin Aslett, Michael A. Quail, Bridget Chukualim, Paul Capewell, Annette MacLeod, Sara E. Melville, Wendy Gibson, J. David Barry, Matthew Berriman, Christiane Hertz‐Fowler
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0177791

Correlation between investment in sexual traits and valve sexual dimorphism in Cyprideis species (Ostracoda)
Cited by: 7
Author(s): Maria João Fernandes Martins, Gene Hunt, Rowan Lockwood, John P. Swaddle, David J. Horne
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0227780

Sonic Hedgehog upregulation does not enhance the survival and engraftment of stem cell-derived cardiomyocytes in infarcted hearts
Cited by: 4
Author(s): Jill J. Weyers, Jagadambika J. Gunaje, Benjamin Van Biber, Amy Martinson, Hans Reinecke, William M. Mahoney, Stephen M. Schwartz, Timothy C. Cox, Charles E. Murry
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0178077

Greenhouse gas emissions from dung pats vary with dung beetle species and with assemblage composition
Cited by: 39
Author(s): Irene Piccini, Fabrizio Arnieri, Enrico Caprio, Beatrice Nervo, Simone Pelissetti, Claudia Palestrini, Tomas Roslin, Antonio Rolando
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0085726

Oscillatory Behavior of Neutrophils under Opposing Chemoattractant Gradients Supports a Winner-Take-All Mechanism
Cited by: 26
Author(s): Matthew B. Byrne, Yuki Kimura, Ashish Kapoor, Yuan He, Kewin S. Mattam, Katherine M. Hasan, Luke N. Olson, Fei Wang, Paul J. A. Kenis, Christopher V. Rao
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0133901

An Integrative Approach for Mapping Differentially Expressed Genes and Network Components Using Novel Parameters to Elucidate Key Regulatory Genes in Colorectal Cancer
Cited by: 11
Author(s): Manika Sehgal, Rajinder K. Gupta, Ahmed Moussa, Tiratha Raj Singh
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0116696

Infection and Inflammation in Schizophrenia and Bipolar Disorder: A Genome Wide Study for Interactions with Genetic Variation
Cited by: 90
Author(s): Dimitrios Avramopoulos, Brad D. Pearce, John A. McGrath, Paula Wolyniec, Ruihua Wang, Nicole Eckart, Alexandros Hatzimanolis, Fernando S. Goes, Gerald Nestadt, Jennifer G. Mullé, Karen Coneely, Myfanwy Hopkins, Ingo Ruczinski, Robert H. Yolken, Ann E. Pulver
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0070564

Patterns of Population Differentiation and Natural Selection on the Celiac Disease Background Risk Network
Cited by: 7
Author(s): Aaron J. Sams, John Hawks
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0152569

QTLs for Woolly Poplar Aphid (Phloeomyzus passerinii L.) Resistance Detected in an Inter-Specific Populus deltoides x P. nigra Mapping Population
Cited by: 11
Author(s): Giorgia Carletti, Andrea Carrà, Gianni Allegro, Lorenzo Vietto, Francesca Desiderio, Paolo Bagnaresi, Alberto Gianinetti, Luigi Cattivelli, Giampiero Valè, G. Nervo
Software Mentions: 2
Published: over 8 years ago

10.3390/cancers12061572

Quantitative Analysis of Differential Expression of HOX Genes in Multiple Cancers
Cited by: 4
Author(s): Orit Adato, Yaron Orenstein, Juri Kopolovic, Tamar Juven‐Gershon, Ron Unger
Software Mentions: 2
Published: over 4 years ago

10.1002/ece3.3076

Environmental stress linked to consumption of maternally derived carotenoids in brown trout embryos ( <i>Salmo trutta</i> )
Cited by: 13
Author(s): Laetitia G. E. Wilkins, Lucas Marques da Cunha, Gaëtan Glauser, Armelle Vallat, Claus Wedekind
Software Mentions: 2
Published: over 7 years ago

10.1002/2211-5463.12925

Cracking of jujube fruits is associated with differential expression of metabolic genes
Cited by: 5
Author(s): Yaling Liu, Peng-Fei Zhang, Yaping Geng, Xinglong Xie, Pengfei Wen
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2020.00506

Characterization of Burkholderia cepacia Complex Core Genome and the Underlying Recombination and Positive Selection
Cited by: 10
Author(s): Jianglin Zhou, Hongguang Ren, Mingda Hu, Jing Zhou, Beiping Li, Na Kong, Qi Zhang, Jianmin Yuan, Long Liang, Junjie Yue
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2019.00471

Subspecies Typing of Streptococcus agalactiae Based on Ribosomal Subunit Protein Mass Variation by MALDI-TOF MS
Cited by: 16
Author(s): Julian Rothen, Joël F. Pothier, Frédéric Foucault, Jochen Blom, Dulmini Nanayakkara, Carmen Li, Margaret Ip, Marcel Tanner, Guido Vogel, Valentin Pflüger, Claudia Daubenberger
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2015.00818

Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression
Cited by: 24
Author(s): Jia Yi Har, Tim Helbig, Jae S. Lim, Samodha C. Fernando, Adam M. Reitzel, Kevin Penn, Janelle R. Thompson
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2019.01659

MicroRNA Expression Profiling in Newcastle Disease Virus-Infected DF-1 Cells by Deep Sequencing
Cited by: 13
Author(s): Yu Chen, Wen Liu, Haixu Xu, Jingjing Liu, Yifan Deng, Hao Cheng, Shanshan Zhu, Yuru Pei, Jiao Hu, Zenglei Hu, Xiaowen Liu, Xiaoquan Wang, Minghong Gu, Shunlin Hu
Software Mentions: 2
Published: over 5 years ago

10.3389/fnana.2017.00047

Lower Functional Connectivity of the Periaqueductal Gray Is Related to Negative Affect and Clinical Manifestations of Fibromyalgia
Cited by: 36
Author(s): Marie‐Andrée Coulombe, Keith St. Lawrence, Dwight E. Moulin, Patricia Morley‐Forster, Mahsa Shokouhi, Warren R. Nielson, Karen D. Davis
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2019.00333

Salt-Enhanced Reproductive Development of Suaeda salsa L. Coincided With Ion Transporter Gene Upregulation in Flowers and Increased Pollen K+ Content
Cited by: 28
Author(s): Jianrong Guo, Xiao-Qiao Dong, Guoliang Han, Baoshan Wang
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2019.01705

Defensive Responses of Tea Plants (Camellia sinensis) Against Tea Green Leafhopper Attack: A Multi-Omics Study
Cited by: 50
Author(s): Xiujuan Zhao, Si Chen, Shanshan Wang, Wenna Shan, Xiaoxia Wang, Yunting Lin, Feng Su, Zhenbiao Yang, Xiaomin Yu
Software Mentions: 2
Published: almost 5 years ago

10.3389/fpls.2016.00371

Transcriptomic Changes Drive Physiological Responses to Progressive Drought Stress and Rehydration in Tomato
Cited by: 85
Author(s): Paolo Iovieno, Paola Punzo, Gianpiero Guida, Carmela Mistretta, Michael James Van Oosten, Roberta Nurcato, Hamed Bostan, Chiara Colantuono, Antonello Costa, Paolo Bagnaresi, Maria Luisa Chiusano, Rossella Albrizio, P. Giorio, Giorgia Batelli, Stefania Grillo
Software Mentions: 2
Published: over 8 years ago

10.3389/fpsyt.2018.00090

Brain Structural Covariance Network Topology in Remitted Posttraumatic Stress Disorder
Cited by: 11
Author(s): Delin Sun, S. Lindsey Davis, Courtney C. Haswell, Chelsea Swanson, Mid-Atlantic Mirecc Workgroup, Kevin S. LaBar, John A. Fairbank, Rajendra A. Morey
Software Mentions: 2
Published: over 6 years ago

10.3389/fvets.2021.598691

Changes of Intestinal Oxidative Stress, Inflammation, and Gene Expression in Neonatal Diarrhoea Kids
Cited by: 14
Author(s): Yan Cheng, Chao Yang, Zhiliang Tan, Zhixiong He
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13059-019-1832-y

OrthoFinder: phylogenetic orthology inference for comparative genomics
Cited by: 2,683
Author(s): David Emms, Steven Kelly
Software Mentions: 2
Published: about 5 years ago

10.1093/gigascience/giy161

Calcium imaging, MEA recordings, and immunostaining images dataset of neuron-astrocyte networks in culture under the effect of norepinephrine
Cited by: 5
Author(s): Yasmin Bar El, Sivan Kanner, Ari Barzilai, Yael Hanein
Software Mentions: 2
Published: almost 6 years ago

10.3390/insects11100693

High-Throughput Genotyping of Common Chromosomal Inversions in the Afrotropical Malaria Mosquito Anopheles Funestus
Cited by: 7
Author(s): Martin Lukindu, R. Rebecca Love, Moussa W. Guelbeogo, Scott T. Small, Melissa Stephens, Nathan R. Campbell, N’Falé Sagnon, Carlo Costantini, Nora J. Besansky
Software Mentions: 2
Published: about 4 years ago

10.1186/s13321-018-0279-6

Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database
Cited by: 112
Author(s): Miguel Quirós, S. Gražulis, Saulė Girdzijauskaitė, Andrius Merkys, Antanas Vaitkus
Software Mentions: 2
Published: over 6 years ago

10.1038/srep26035

Marked variation between winter and spring gut microbiota in free-ranging Tibetan Macaques (Macaca thibetana)
Cited by: 129
Author(s): Binghua Sun, Xi Wang, Sofi Bernstein, Michael A. Huffman, Dong Xia, Zhiyuan Gu, Rui Chen, Lori K. Sheeran, R. Steven Wagner, Jinhua Li
Software Mentions: 2
Published: over 8 years ago

10.1038/srep28130

Distinct transcriptome profiles reveal gene expression patterns during fruit development and maturation in five main cultivated species of pear (Pyrus L.)
Cited by: 48
Author(s): Mingyue Zhang, Cheng Xue, Li Xu, Honghe Sun, Mengfan Qin, Shaoling Zhang, Wu Jun
Software Mentions: 2
Published: over 8 years ago

10.1038/srep46487

The evolutionary history of bears is characterized by gene flow across species
Cited by: 166
Author(s): Vikas Kumar, Fritjof Lammers, Tobias Bidon, Markus Pfenninger, Lydia Kolter, Maria A. Nilsson, Axel Janke
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-07476-2

Disturbance and mosquito diversity in the lowland tropical rainforest of central Panama
Cited by: 40
Author(s): José R. Loaiza, Larissa C. Dutari, José Rovira, Oris I. Sanjur, Gabriel Zorello Laporta, James E. Pecor, Desmond H. Foley, Gillian Eastwood, Laura D. Kramer, Meghan Radtke, Montira J. Pongsiri
Software Mentions: 2
Published: over 7 years ago