Ecosyste.ms: Papers

10.1371/journal.pgen.1005265

The Developmental Intestinal Regulator ELT-2 Controls p38-Dependent Immune Responses in Adult C. elegans
Cited by: 42
Author(s): Dena H. S. Block, Kwame Twumasi-Boateng, Hae Sung Kang, Jolie A Carlisle, Alexandru Hanganu, Ty Yu-Jen Lai, Michael Y. Shapira
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1007810

Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing
Cited by: 70
Author(s): Kathryn J. Grive, Yang Hu, Eileen Shu, Andrew Grimson, Olivier Elemento, Jennifer K. Grenier, Paula E. Cohen
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-12-373

Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis
Cited by: 64
Author(s): Andrea Saß, Angela Marchbank, Elizabeth Tullis, John J. LiPuma, Eshwar Mahenthiralingam
Software Mentions: 3
Published: over 13 years ago

10.1038/s42003-021-02208-9

Systemic GLP-1R agonist treatment reverses mouse glial and neurovascular cell transcriptomic aging signatures in a genome-wide manner
Cited by: 5
Author(s): Zhongqi Li, Xinyi Chen, Joaquim S. L. Vong, Lei Zhao, Junzhe Huang, Leo Y. C. Yan, Bonaventure Ip, Yun Kwok Wing, H. M. Lai, Vincent Mok, Ho Ko
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-11-S1-S14

Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases
Cited by: 21
Author(s): П. А. Карпов, Е. С. Надеждина, А. І. Yemets, V. G. Matusov, A. Yu. Nyporko, Nadezhda Yu Shashina, Ya. B. Blume
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pgen.1001027

Reconstruction of the Core and Extended Regulons of Global Transcription Factors
Cited by: 65
Author(s): Y. Dufour, Patricia J. Kiley, Timothy J. Donohue
Software Mentions: 3
Published: over 14 years ago

10.1186/s12864-016-2444-5

Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva
Cited by: 12
Author(s): Kyle Tretina, Roger Pellé, Joana C. Silva
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1002531

A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis
Cited by: 34
Author(s): Brian W. Busser, Leila Taher, Yongsok Kim, Terese R. Tansey, Molly J. Bloom, Ivan Ovcharenko, Alan M. Michelson
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pgen.1005870

Systems Level Analyses Reveal Multiple Regulatory Activities of CodY Controlling Metabolism, Motility and Virulence in Listeria monocytogenes
Cited by: 55
Author(s): Lior Lobel, Anat A. Herskovits
Software Mentions: 3
Published: almost 9 years ago

10.1093/database/bau111

CBMAR: a comprehensive β-lactamase molecular annotation resource
Cited by: 35
Author(s): Abhishikha Srivastava, Neelja Singhal, Manisha Goel, Jugsharan Singh Virdi, Manish Kumar
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1004714

The Master Activator of IncA/C Conjugative Plasmids Stimulates Genomic Islands and Multidrug Resistance Dissemination
Cited by: 97
Author(s): Nicolas Carraro, Dominick Matteau, Peng Luo, Sébastien Rodrigue, Vincent Burrus
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-7-42

Gene expression profiling of Naïve sheep genetically resistant and susceptible to gastrointestinal nematodes
Cited by: 87
Author(s): Orla M. Keane, Amonida Zadissa, Theresa Wilson, D. L. Hyndman, G. J. Greer, David Baird, Alan McCulloch, A. M. Crawford, John C. McEwan
Software Mentions: 3
Published: over 18 years ago

10.1534/g3.116.032243

Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish
Cited by: 10
Author(s): Zaixuan Zhong, Kang Du, Yu Qian, Yong E. Zhang, Shunping He
Software Mentions: 3
Published: about 8 years ago

10.1186/1471-2164-9-582

Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva
Cited by: 12
Author(s): Xiang Guo, Joana C. Silva
Software Mentions: 3
Published: almost 17 years ago

10.1371/journal.pgen.1008965

Replication of the Salmonella Genomic Island 1 (SGI1) triggered by helper IncC conjugative plasmids promotes incompatibility and plasmid loss
Cited by: 18
Author(s): Kévin Huguet, Nicolas Rivard, Daniel Garneau, Jason Palanee, Vincent Burrus
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-7-126

Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria
Cited by: 97
Author(s): Roland J. Siezen, Jos Boekhorst, Lidia Muscariello, Douwe Molenaar, Bernadet Renckens, Michiel Kleerebezem
Software Mentions: 3
Published: over 18 years ago

10.1002/ece3.5185

Tree shape‐based approaches for the comparative study of cophylogeny
Cited by: 14
Author(s): Mariano Avino, Garway T Ng, Yiying He, Mathias S. Renaud, Bradley R. Jones, Art F. Y. Poon
Software Mentions: 3
Published: over 5 years ago

10.1155/2015/579417

Addenbrooke’s Cognitive Examination and Individual Domain Cut-Off Scores for Discriminating between Different Cognitive Subtypes of Parkinson’s Disease
Cited by: 15
Author(s): Dagmar Beránková, Eva Janoušová, Martina Mračková, Ilona Eliasova, Milena Košťálová, Světlana Skutilová, Irena Rektorová
Software Mentions: 3
Published: almost 10 years ago

10.1186/gb-2009-10-12-r142

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data
Cited by: 63
Author(s): Desmond S. Lun, Ashley M. Sherrid, Brian Weiner, David R. Sherman, James E. Galagan
Software Mentions: 3
Published: almost 16 years ago

10.1186/gb-2010-11-1-r7

Genome-wide prediction of transcription factor binding sites using an integrated model
Cited by: 111
Author(s): Kyoung Jae Won, Bing Ren, Weiwei Wang
Software Mentions: 3
Published: almost 15 years ago

10.1186/gb-2014-15-1-r10

Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens
Cited by: 79
Author(s): Huimin Wu, Yi-shin Su, Hsiu-Chen Chen, Yurong Chen, Chia-Hung Wu, Wen-Dar Lin, Shih-Long Tu
Software Mentions: 3
Published: almost 12 years ago

10.3390/ijms22094371

Connectivity Map Analysis of a Single-Cell RNA-Sequencing -Derived Transcriptional Signature of mTOR Signaling
Cited by: 8
Author(s): Naim Al Mahi, Erik Y. Zhang, Susan G. Sherman, Jane Yu, Mario Medvedovic
Software Mentions: 3
Published: over 3 years ago

10.1186/s12862-020-01734-0

The skeletome of the red coral Corallium rubrum indicates an independent evolution of biomineralization process in octocorals
Cited by: 35
Author(s): Nathalie Le Roy, Philippe Ganot, Manuel Aranda, Denis Allemand, Sylvie Tambutté
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1002585

Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription
Cited by: 45
Author(s): J. Gray Camp, Amelia L. Jazwa, Chad M. Trent, John F. Rawls
Software Mentions: 3
Published: over 12 years ago

10.1186/s13059-016-1077-y

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments
Cited by: 210
Author(s): Keegan Korthauer, Li‐Fang Chu, Michael A. Newton, Yuan Li, James A. Thomson, Ron Stewart, Christina Kendziorski
Software Mentions: 3
Published: about 8 years ago

10.1186/1756-8935-7-35

High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes
Cited by: 12
Author(s): Raghunath Chatterjee, Ximiao He, Di Huang, Peter Fitzgerald, Andrew D. Smith, Charles Vinson
Software Mentions: 3
Published: almost 10 years ago

10.1186/bcr3587

Progesterone receptor assembly of a transcriptional complex along with activator protein 1, signal transducer and activator of transcription 3 and ErbB-2 governs breast cancer growth and predicts response to endocrine therapy
Cited by: 30
Author(s): María Celeste Díaz Flaqué, Natalia M. Galigniana, Wendy Béguelin, Rocío Vicario, Cecilia J. Proietti, Rosalía Cordo Russo, Martín A. Rivas, Mercedes Tkach, Pablo Guzmán, Juan Carlos Roa, Esteban Maronna, Viviana Pineda, Sergio Muñoz, María F. Mercogliano, Eduardo H. Charreau, Patricio Yankilevich, Roxana Schillaci, Patricia V. Elizalde
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13059-017-1334-8

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq
Cited by: 102
Author(s): Florian Buettner, Naruemon Pratanwanich, Davis J. McCarthy, John C. Marioni, Oliver Stegle
Software Mentions: 3
Published: about 7 years ago

10.1186/1479-5876-11-74

In silico approaches for designing highly effective cell penetrating peptides
Cited by: 222
Author(s): Ankur Gautam, Kumardeep Chaudhary, Rahul Kumar, Arun Sharma, Pallavi Kapoor, Atul Tyagi, Gajendra P. S. Raghava
Software Mentions: 3
Published: over 11 years ago

10.1186/s13059-018-1431-3

GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection
Cited by: 53
Author(s): Daphne Tsoucas, Guo‐Cheng Yuan
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-14-830

HOXC9 directly regulates distinct sets of genes to coordinate diverse cellular processes during neuronal differentiation
Cited by: 23
Author(s): Xiangwei Wang, Jeong-Hyeon Choi, Jane Ding, Liqun Yang, Lambert C. M. Ngoka, Mi Kyung Lee, Yunhong Zha, Ling Mao, Boquan Jin, Mingqiang Ren, John K. Cowell, Shuang Huang, Huidong Shi, Hongjuan Cui, Han‐Fei Ding
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-13-256

A scalable method for identifying frequent subtrees in sets of large phylogenetic trees
Cited by: 5
Author(s): Avinash Ramu, Tamer Kahveci, J. Gordon Burleigh
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pgen.1006586

Discovery of a new family of relaxases in Firmicutes bacteria
Cited by: 31
Author(s): Gayetri Ramachandran, Andrés Miguel-Arribas, David Abia, Praveen Singh, Isidro Crespo, César Gago-Córdoba, Jia Hao, Juan Román Luque‐Ortega, Carlos Alfonso, Ling Juan Wu, Roeland Boer, Wilfried J. J. Meijer
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pgen.1001114

Chromatin Landscape Dictates HSF Binding to Target DNA Elements
Cited by: 193
Author(s): Michael J. Guertin, John T. Lis
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pgen.1005854

The Epigenomic Landscape of Prokaryotes
Cited by: 274
Author(s): Matthew J. Blow, Tyson A. Clark, Chris Daum, Adam M. Deutschbauer, Alexey Fomenkov, Roxanne Fries, Jeff Froula, Dongwan Kang, Rex R. Malmstrom, Richard D. Morgan, János Pósfai, Kanwar Pal Singh, Axel Visel, Kelly M. Wetmore, Zhiying Zhao, Edward M. Rubin, Jonas Korlach, Len A. Pennacchio, Richard J. Roberts
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2105-8-385

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm
Cited by: 94
Author(s): Emma Redhead, Timothy L. Bailey
Software Mentions: 3
Published: about 17 years ago

10.1093/gbe/evw094

Pooled Enrichment Sequencing Identifies Diversity and Evolutionary Pressures at NLR Resistance Genes within a Wild Tomato Population
Cited by: 47
Author(s): Remco Stam, Daniela Scheikl, Aurélien Tellier
Software Mentions: 3
Published: over 8 years ago

10.1093/gbe/evaa038

The Evolution History of Fe–S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs
Cited by: 3
Author(s): Hui‐Meng Lu, Jing-Di Li, Yu-Dan Zhang, Xiaoli Lü, Chang Xu, Yuan Huang, Michael Gribskov
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-7-S4-S16

Identification of new members of hydrophobin family using primary structure analysis
Cited by: 8
Author(s): Kuan Yang, Youping Deng, Chaoyang Zhang, Mohamed O. Elasri
Software Mentions: 3
Published: almost 18 years ago

10.3389/fcimb.2014.00159

The crimson conundrum: heme toxicity and tolerance in GAS
Cited by: 13
Author(s): Ankita J. Sachla, Yoann Le Breton, Fahmina Akhter, Kevin S. McIver, Zehava Eichenbaum
Software Mentions: 3
Published: about 10 years ago

10.1002/mgg3.859

The CLN3 gene and protein: What we know
Cited by: 40
Author(s): Myriam Mirza, Anna Vainshtein, Alberto DiRonza, Uma Chandrachud, Luke J. Haslett, Michela Palmieri, Stephan Storch, Janos Groh, Niv Dobzinski, Gennaro Napolitano, Carolin Schmidtke, Danielle Kerkovich
Software Mentions: 3
Published: about 5 years ago

10.3389/fcimb.2017.00186

RegA Plays a Key Role in Oxygen-Dependent Establishment of Persistence and in Isocitrate Lyase Activity, a Critical Determinant of In vivo Brucella suis Pathogenicity
Cited by: 10
Author(s): Elias Abdou, María Pilar Jiménez de Bagüés, Ignacio Martínez-Abadía, Safia Ouahrani‐Bettache, Véronique Pantesco, Alessandra Occhialini, Sascha Al Dahouk, Stephan Köhler, Véronique Jubier-Maurin
Software Mentions: 3
Published: over 7 years ago

10.1007/s00438-014-0959-5

RNase E in the γ-Proteobacteria: conservation of intrinsically disordered noncatalytic region and molecular evolution of microdomains
Cited by: 41
Author(s): Soraya Aït‐Bara, Agamemnon J. Carpousis, Yves Quentin
Software Mentions: 3
Published: almost 10 years ago

10.1111/j.1365-2958.2007.05827.x

A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis
Cited by: 186
Author(s): Sharon L. Kendall, Mike Withers, Catherine N. Soffair, Nicole J. Moreland, Sudagar S. Gurcha, Ben S. Sidders, Rosangela Frita, Annemieke Ten Bokum, Gurdyal S. Besra, J.S. Lott, Neil G. Stoker
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2164-8-330

Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing
Cited by: 125
Author(s): Jessica A. Schlueter, Jer-Young Lin, Shannon D. Schlueter, Iryna F. Vasylenko‐Sanders, Shweta Deshpande, Jing Yi, Majesta O’Bleness, Bruce A. Roe, Rex T. Nelson, Brian E. Scheffler, Scott A. Jackson, Randy C. Shoemaker
Software Mentions: 3
Published: about 17 years ago

10.3389/fgene.2020.633455

Dissecting the Invasion-Associated Long Non-coding RNAs Using Single-Cell RNA-Seq Data of Glioblastoma
Cited by: 4
Author(s): Bo Pang, Fei Quan, Yanyan Ping, Jing Hu, Yujia Lan, Lin Pang
Software Mentions: 3
Published: almost 4 years ago

10.3390/jcm10050960

Multiple Allergen Simultaneous Test-Immunoblot Assay for Immunoglobulin E Detection in Patients with Isolated Allergic Conjunctivitis
Cited by: 1
Author(s): Jung Yeob Han, Hun Lee, J. N. Chung, Young Jun Kim, Jae Yong Kim, Hungwon Tchah
Software Mentions: 3
Published: over 3 years ago

10.3390/jcm10143183

Review of Rhinitis: Classification, Types, Pathophysiology
Cited by: 37
Author(s): Georgia A Liva, Alexander D. Karatzanis, E Prokopakis
Software Mentions: 3
Published: over 3 years ago

10.1093/bib/bbw057

Comparison of methods to detect differentially expressed genes between single-cell populations
Cited by: 73
Author(s): Maria K. Jaakkola, Fatemeh Seyednasrollah, Arfa Mehmood, Laura L. Elo
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-021-07382-y

Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum)
Cited by: 25
Author(s): Ambika Dudhate, Harshraj Shinde, Pei Yu, Daisuke Tsugama, S. K. Gupta, Shenkui Liu, Tetsuo Takano
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.21856

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites
Cited by: 990
Author(s): Peter J. Skene, Steven Henikoff
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2164-14-493

Suppression of genetic recombination in the pseudoautosomal region and at subtelomeres in mice with a hypomorphic Spo11 allele
Cited by: 19
Author(s): Fátima Smagulova, Kevin Brick, Yongmei Pu, Uttara Sengupta, R. Daniel Camerini‐Otero, Galina V. Petukhova
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2105-7-280

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
Cited by: 240
Author(s): David J Reiss, Nitin S. Baliga, Richard Bonneau
Software Mentions: 3
Published: over 18 years ago

10.6026/97320630016293

COVID-19, Reduced Lung Function, and Increased Psycho-emotional Stress
Cited by: 3
Author(s): Dongyuan Wu, Dorothy Ellis, Susmita Datta
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2020.00942

Single Cell RNA-seq Data Analysis Reveals the Potential Risk of SARS-CoV-2 Infection Among Different Respiratory System Conditions
Cited by: 7
Author(s): Qiang Zhang, Yuanyi Yue, Huiwen Tan, Yishu Liu, Zhang Yin, Li Xiao
Software Mentions: 3
Published: over 4 years ago

10.1002/brb3.1188

Adaption and validation of the Mississippi Aphasia Screening Test to Estonian speakers with aphasia
Cited by: 3
Author(s): Aaro Nursi, Marika Padrik, Liisa Nursi, Maarja Pähkel, Liis Virkunen, Anne Küttim-Rips, Pille Taba
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0215492

Bulked segregant analysis RNA-seq (BSR-Seq) validated a stem resistance locus in Aegilops umbellulata, a wild relative of wheat
Cited by: 19
Author(s): Erena A. Edae, Matthew N. Rouse
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-018-4781-z

Impact of growth pH and glucose concentrations on the CodY regulatory network in Streptococcus salivarius
Cited by: 3
Author(s): Jianing Geng, Szu-Chuan Huang, Yueh-Ying Chen, Cheng-Hsun Chiu, Songnian Hu, Yi-Ywan M. Chen
Software Mentions: 3
Published: over 6 years ago

10.1007/s00425-021-03717-x

Large-scale gene gains and losses molded the NLR defense arsenal during the Cucurbita evolution
Cited by: 5
Author(s): Giuseppe Andolfo, Cristina S. Sánchez, Joaquı́n Cañizares, María Belén Picó, Maria Raffaella Ercolano
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0150077

SMARTbot: A Behavioral Analysis Framework Augmented with Machine Learning to Identify Mobile Botnet Applications
Cited by: 39
Author(s): Ahmad Karim, Rosli Salleh, Muhammad Khurram Khan
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0160228

Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach
Cited by: 5
Author(s): Rajneesh Srivastava, Yang Zhang, Xin Xiong, Xiaoning Zhang, Xiaoyan Pan, X. Charlie Dong, Suthat Liangpunsakul, Sarath Chandra Janga
Software Mentions: 3
Published: over 8 years ago

10.1038/sdata.2016.54

High-throughput ab-initio dilute solute diffusion database
Cited by: 91
Author(s): Haonan Wu, Tam Mayeshiba, Dane Morgan
Software Mentions: 3
Published: over 8 years ago

10.1111/tpj.12307

Resistance gene enrichment sequencing (<scp>R</scp>en<scp>S</scp>eq) enables reannotation of the <scp>NB</scp>‐<scp>LRR</scp> gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
Cited by: 327
Author(s): Florian Jupe, Kamil Witek, Walter Verweij, Jadwiga Śliwka, Leighton Pritchard, Graham J. Etherington, Dan MacLean, Peter J. A. Cock, Richard M. Leggett, Glenn J. Bryan, Linda Cardle, Ingo Hein, Jonathan D. G. Jones
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0146643

Human Gut Bacteria Are Sensitive to Melatonin and Express Endogenous Circadian Rhythmicity
Cited by: 159
Author(s): Jiffin K. Paulose, John M. Wright, Akruti Patel, Vincent M. Cassone
Software Mentions: 3
Published: almost 9 years ago

10.1007/s00415-016-8170-8

Screening tests for aphasia in patients with stroke: a systematic review
Cited by: 66
Author(s): Hanane El Hachioui, Evy Visch-Brink, Lonneke M. L. de Lau, Mieke W. M. E. van de Sandt-Koenderman, Femke Nouwens, Peter J. Koudstaal, Diederik W.J. Dippel
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-13-S17-S26

Phylogenetic reconstruction in the Order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding
Cited by: 15
Author(s): Devendra Kumar Biswal, Manish Debnath, Sunil Kumar, Pramod Tandon
Software Mentions: 3
Published: almost 12 years ago

10.1038/srep27978

From multiple pathogenicity islands to a unique organized pathogenicity archipelago
Cited by: 12
Author(s): Costas Bouyioukos, Sylvie Reverchon, François Képès
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0060355

Regulatory Patterns of a Large Family of Defensin-Like Genes Expressed in Nodules of Medicago truncatula
Cited by: 42
Author(s): Sumitha Nallu, Kevin A.T. Silverstein, Deborah A. Samac, Bruna Bucciarelli, Carroll P. Vance, Kathryn A. VandenBosch
Software Mentions: 3
Published: over 11 years ago

10.1038/srep28995

Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos
Cited by: 30
Author(s): Elo Madissoon, Eeva-Mari Jouhilahti, Liselotte Vesterlund, Virpi Töhönen, Kaarel Krjutškov, Sophie Petropoulos, Elisabet Einarsdottir, Sten Linnarsson, Fredrik Lanner, Robert Månsson, Outi Hovatta, Thomas R. Bürglin, Shintaro Katayama, Juha Kere
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0066807

The Rice NAD+-Dependent Histone Deacetylase OsSRT1 Targets Preferentially to Stress- and Metabolism-Related Genes and Transposable Elements
Cited by: 38
Author(s): Xiaochao Zhong, Hua Zhang, Yu Zhao, Qianwen Sun, Yongfeng Hu, Hai Peng, Dao‐Xiu Zhou
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-9-330

An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters
Cited by: 43
Author(s): Michiel Wels, Tom Groot Kormelink, Michiel Kleerebezem, Roland J. Siezen, Christof Francke
Software Mentions: 3
Published: almost 17 years ago

10.1038/srep29311

Genome-wide analysis of HIF-2α chromatin binding sites under normoxia in human bronchial epithelial cells (BEAS-2B) suggests its diverse functions
Cited by: 9
Author(s): Meng Chang Lee, Hsin Ju Huang, Tzu Hao Chang, Hung‐Tsai Huang, Shen Yuan Hsieh, Yi Siou Chen, Wei-Yuan Chou, Chiao–Hsi Chiang, Chao Hung Lai, Chia Yang Shiau
Software Mentions: 2
Published: over 8 years ago

10.1038/srep32474

Identification of p53-target genes in Danio rerio
Cited by: 10
Author(s): Barbara Mandriani, Stefano Castellana, Carmela Rinaldi, Marta Manzoni, Santina Venuto, Eva Rodriguez-Aznar, Juan Galceran, M. Ángela Nieto, Giuseppe Borsani, Eugenio Monti, Tommaso Mazza, Giuseppe Merla, Lucia Micale
Software Mentions: 2
Published: about 8 years ago

10.1038/srep32517

Identification and characterization of the GhHsp20 gene family in Gossypium hirsutum
Cited by: 27
Author(s): Wei Ma, Ting Zhao, Jie Li, Bingliang Liu, Lei Fang, Yan Hu, Tianzhen Zhang
Software Mentions: 2
Published: about 8 years ago

10.1038/srep32673

Genome-wide identification and comparison of legume MLO gene family
Cited by: 37
Author(s): Nicolás Rispail, Diego Rubiales
Software Mentions: 2
Published: about 8 years ago

10.1038/srep45456

Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi
Cited by: 37
Author(s): Juan Li, Fangyi Gu, Ru‐Nian Wu, Jinkui Yang, Ke‐Qin Zhang
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-00951-w

Identification and Characterization of Differentially-Regulated Type IVb Pilin Genes Necessary for Predation in Obligate Bacterial Predators
Cited by: 25
Author(s): Ofir Avidan, Margarita Petrenko, René Becker, Sebastian Beck, Michael Linscheid, Shmuel Pietrokovski, Édouard Jurkevitch
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-05405-x

A Novel Dual Eigen-Analysis of Mouse Multi-Tissues’ Expression Profiles Unveils New Perspectives into Type 2 Diabetes
Cited by: 4
Author(s): Lei M. Li, Xiuxiu Liu, Lin Wang, Yong Wang, Xiuqin Liu, Tian Xue, Fuzhou Gong, Li Shen, Xiao Peng
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-09121-4

Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato
Cited by: 17
Author(s): Bhaskar Sharma, Tarun Kumar Bhatt
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-09199-w

Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection
Cited by: 210
Author(s): Mudassar Ali, Rajan Kumar Pandey, Nazia Khatoon, Aruna Narula, Amit Mishra, Vijay Kumar Prajapati
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-15354-0

Novel Plasmodium antigens identified via genome-based antibody screen induce protection associated with polyfunctional T cell responses
Cited by: 14
Author(s): Sophie Schussek, Angela Trieu, Simon H. Apte, John Sidney, Alessandro Sette, Denise L. Doolan
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-18629-8

Large-scale sill emplacement in Brazil as a trigger for the end-Triassic crisis
Cited by: 49
Author(s): Thea Hatlen Heimdal, Henrik Svensen, Jahandar Ramezani, Karthik Iyer, Egberto Pereira, R. F. Rodrigues, Morgan T. Jones, Sara Callegaro
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2105-12-204

Tree edit distance for leaf-labelled trees on free leafset and its comparison with frequent subsplit dissimilarity and popular distance measures
Cited by: 6
Author(s): Jakub Koperwas, Krzysztof Walczak
Software Mentions: 2
Published: over 13 years ago

10.1038/s41598-019-42487-1

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
Cited by: 35
Author(s): Mike Sieracki, Nicole Poulton, Olivier Jaillon, Patrick Wincker, Colomban de Vargas, Laura Rubinat-Ripoll, Ramunas Stepanauskas, Ramiro Logares, Ramón Massana
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-45128-9

Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum
Cited by: 30
Author(s): Bart van de Vossenberg, Sven Warris, Hai D. T. Nguyen, M.P.E. van Gent-Pelzer, David L. Joly, H.C. van de Geest, P.J.M. Bonants, Donna S. Smith, C. André Lévesque, Theo A. J. van der Lee
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-49826-2

A Functional Near-Infrared Spectroscopy Study on the Cortical Haemodynamic Responses During the Maastricht Acute Stress Test
Cited by: 16
Author(s): Nora K. Schaal, Philip Hepp, Adam Schweda, Oliver T. Wolf, Caspar Krampe
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-86740-y

Carbohydrate-controlled serine protease inhibitor (serpin) production in Bifidobacterium longum subsp. longum
Cited by: 12
Author(s): Stéphane Duboux, Mireille Golliard, Jeroen Muller, Gabriela Bergonzelli, Christoph J. Bolten, Annick Mercenier, Michiel Kleerebezem
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-14-S6-S4

AllerTOP - a server for in silico prediction of allergens
Cited by: 261
Author(s): Иван Димитров, Darren R. Flower, Irini Doytchinova
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-021-86827-6

Decision support for the quickest detection of critical COVID-19 phases
Cited by: 10
Author(s): Paolo Braca, Domenico Gaglione, Stefano Maranò, Leonardo M. Millefiori, Peter Willett, Krishna R. Pattipati
Software Mentions: 2
Published: over 3 years ago

10.1155/2014/980572

Identification of Family Specific Fingerprints in<b><i>β</i></b>-Lactamase Families
Cited by: 9
Author(s): Abhishikha Srivastava, Neelja Singhal, Manisha Goel, Jugsharan Singh Virdi, Manish Kumar
Software Mentions: 2
Published: almost 11 years ago

10.1155/2015/986262

Recent Advances in General Game Playing
Cited by: 32
Author(s): Maciej Świechowski, Hyunsoo Park, Jacek Mańdziuk, Kyung Joong Kim
Software Mentions: 2
Published: almost 10 years ago

10.3390/s16091491

Design and Experimental Validation of a USBL Underwater Acoustic Positioning System
Cited by: 27
Author(s): Joel Reis, Manuel Morgado, Pedro Batista, Paulo Oliveira, Carlos Silvestre
Software Mentions: 2
Published: about 8 years ago

10.3390/s20226516

Study of the Vertical Structure of the Coastal Boundary Layer Integrating Surface Measurements and Ground-Based Remote Sensing
Cited by: 10
Author(s): Teresa Lo Feudo, Claudia Roberta Calidonna, Elenio Avolio, Anna Maria Sempreviva
Software Mentions: 2
Published: about 4 years ago

10.1186/s40463-015-0111-5

Detection of bacteria in middle ear effusions based on the presence of allergy: does allergy augment bacterial infection in the middle ear?
Cited by: 5
Author(s): Woo Jin Kim, Byung Guk Kim, Ki‐Hong Chang, Jong-Ryool Oh
Software Mentions: 2
Published: almost 9 years ago

10.1186/1747-597X-7-42

The alcohol use disorders identification test (AUDIT): validation of a Nepali version for the detection of alcohol use disorders and hazardous drinking in medical settings
Cited by: 63
Author(s): Bickram Pradhan, François Chappuis, Dharanidhar Baral, Prahlad Karki, Suman Rijal, Antoine Hadengue, Pascal Gache
Software Mentions: 2
Published: about 12 years ago

10.3390/toxins8020044

An Insight into the Triabin Protein Family of American Hematophagous Reduviids: Functional, Structural and Phylogenetic Analysis
Cited by: 12
Author(s): Maria José Hernández-Vargas, Carlos E. Santibáñez‐López, Gerardo Corzo
Software Mentions: 2
Published: almost 9 years ago

10.1111/tme.12659

Pre‐hospital transfusion of red blood cells. Part 2: A systematic review of treatment effects on outcomes
Cited by: 24
Author(s): Elisabeth C van Turenhout, Sebastiaan M. Bossers, Stephan A. Loer, Georgios F. Giannakópoulos, Lothar A. Schwarte, Patrick Schober
Software Mentions: 2
Published: almost 5 years ago

10.1111/tme.12667

Pre‐hospital transfusion of red blood cells. Part 1: A scoping review of current practice and transfusion triggers
Cited by: 17
Author(s): Elisabeth C van Turenhout, Sebastiaan M. Bossers, Stephan A. Loer, Georgios F. Giannakópoulos, Lothar A. Schwarte, Patrick Schober
Software Mentions: 2
Published: over 4 years ago

10.1038/s41398-021-01374-y

Imaging beta-amyloid (Aβ) burden in the brains of middle-aged individuals with alcohol-use disorders: a [11C]PIB PET study
Cited by: 0
Author(s): Margaret Flanigan, Sarah K Royse, David P. Cenkner, Katelyn M. Kozinski, Clara Stoughton, Michael L. Himes, Davneet Minhas, Brian J. Lopresti, Meryl A. Butters, Rajesh Narendran
Software Mentions: 2
Published: over 3 years ago

10.1128/mBio.00737-19

Nuclear Factor Y (NF-Y) Modulates Encystation in <i>Entamoeba</i> via Stage-Specific Expression of the NF-YB and NF-YC Subunits
Cited by: 11
Author(s): Dipak Manna, Upinder Singh
Software Mentions: 2
Published: over 5 years ago