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: MAST

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

MAterials Simulation Toolkit
23 versions
Latest release: almost 7 years ago
43 downloads last month

Papers Mentioning MAST 668

10.1371/journal.pgen.0030181
Genome-Wide Profiling of DNA Methylation Reveals a Class of Normally Methylated CpG Island Promoters
Cited by: 327
Author(s): Lanlan Shen, Yutaka Kondo, Yi Guo, Jiexin Zhang, Li Zhang, Saira Ahmed, Jingmin Shu, Han Y. H. Chen, Robert A. Waterland, Jean–Pierre J. Issa
Software Mentions: 2
Published: about 17 years ago
10.1371/journal.pgen.1002155
Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites
Cited by: 110
Author(s): Lars B. Scharff, Liam Childs, Dirk Walther, Ralph Bock
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pgen.0030075
Being Pathogenic, Plastic, and Sexual while Living with a Nearly Minimal Bacterial Genome
Cited by: 162
Author(s): Pascal Sirand‐Pugnet, Carole Lartigue, Marc S. Marenda, Daniel Jacob, Aurélien Barré, Valérie Barbe, Chantal Schenowitz, Sophie Mangenot, Arnaud Couloux, Béatrice Segurens, Antoine de Daruvar, Alain Blanchard, Christine Citti
Software Mentions: 2
Published: over 17 years ago
10.1371/journal.pgen.1006133
DLK-1, SEK-3 and PMK-3 Are Required for the Life Extension Induced by Mitochondrial Bioenergetic Disruption in C. elegans
Cited by: 52
Author(s): Erin Munkácsy, Maruf Khan, Rebecca Lane, Megan B. Borror, Jae H. Park, Alex Bokov, Alfred L. Fisher, Christopher D. Link, Shane L. Rea
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pgen.1000848
Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response
Cited by: 160
Author(s): Mingkang Zhong, Wei Niu, Zhi John Lu, Mihail Sarov, John I. Murray, Judith Janette, Debasish Raha, Karyn L. Sheaffer, Hugo Y. K. Lam, Elicia Preston, C. Slightham, LaDeana W. Hillier, Trisha Brock, Ashish Agarwal, Raymond K. Auerbach, Anthony A. Hyman, Mark Gerstein, Susan E. Mango, Stuart K. Kim, Robert H. Waterston, V Reinke, M Snyder
Software Mentions: 2
Published: almost 15 years ago
10.7554/eLife.12188
Inference of gene regulation functions from dynamic transcriptome data
Cited by: 13
Author(s): Patrick Hillenbrand, Kerstin Maier, Patrick Cramer, Ulrich Gerland
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pgen.1005962
Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions
Cited by: 147
Author(s): Ulrike Mäder, Pierre Nicolas, Maren Depke, Jan Pané‐Farré, Michel Débarbouillé, Magdalena M. van der Kooi-Pol, Cyprien Guérin, Sandra Dèrozier, Aurélia Hiron, Hanne Østergaard Jarmer, Aurélie Leduc, Stephan Michalik, Ewoud Reilman, Marc Schaffer, Frank Schmidt, Philippe Bessières, Philippe Naveilhan, Michael Hecker, Tarek Msadek, Uwe Völker, Jan Maarten van Dijl
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0027693
Atlantic Bluefin Tuna: A Novel Multistock Spatial Model for Assessing Population Biomass
Cited by: 96
Author(s): Nathan Taylor, Murdoch K. McAllister, Gareth L. Lawson, Tom Carruthers, Barbara A. Block
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0115149
Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in Salvia miltiorrhiza
Cited by: 44
Author(s): Haimei Chen, Bin Wu, David R. Nelson, Kai Wu, Chang Liu
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.pone.0059357
Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force
Cited by: 19
Author(s): Michael Wyrebek, Michael Bidochka
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0137184
The LysE Superfamily of Transport Proteins Involved in Cell Physiology and Pathogenesis
Cited by: 24
Author(s): Brian V Tsu, Milton H. Saier
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pone.0192851
Bioinformatic characterization of the Anoctamin Superfamily of Ca2+-activated ion channels and lipid scramblases
Cited by: 47
Author(s): Arturo Medrano-Soto, Gabriel Moreno‐Hagelsieb, Daniel F. McLaughlin, Zachary S. Ye, Kevin J. Hendargo, Milton H. Saier
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0120400
Multigene Assessment of the Species Boundaries and Sexual Status of the Basidiomycetous Yeasts Cryptococcus flavescens and C. terrestris (Tremellales)
Cited by: 36
Author(s): Andrey Yurkov, Marco Alexandre Guerreiro, Latika Sharma, Cláudia Carvalho, Álvaro Fonseca
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0148243
Gene Structures, Evolution and Transcriptional Profiling of the WRKY Gene Family in Castor Bean (Ricinus communis L.)
Cited by: 29
Author(s): Zhi Zou, Lei Yang, Danhua Wang, Qixing Huang, MO Yeyong, Guishui Xie
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pone.0023934
Diversity in the Architecture of ATLs, a Family of Plant Ubiquitin-Ligases, Leads to Recognition and Targeting of Substrates in Different Cellular Environments
Cited by: 42
Author(s): Víctor Aguilar-Hernández, Laura Aguilar-Henonin, Plinio Guzmán
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0089334
Carbohydrate Availability Regulates Virulence Gene Expression in Streptococcus suis
Cited by: 45
Author(s): Maria Laura Ferrando, Peter van Baarlen, Germano Orrù, Rosaria Piga, Roger S. Bongers, Michiel Wels, Astrid de Greeff, Hilde E. Smith, Jerry M. Wells
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0195023
Bacteriophage cocktail for biocontrol of Escherichia coli O157:H7: Stability and potential allergenicity study
Cited by: 51
Author(s): Karina Ramírez, Carmina Cazarez-Montoya, Héctor Samuel López-Moreno, Nohelia Castro‐del Campo
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0013935
The Arabidopsis ABA-Activated Kinase OST1 Phosphorylates the bZIP Transcription Factor ABF3 and Creates a 14-3-3 Binding Site Involved in Its Turnover
Cited by: 176
Author(s): Caroline Sirichandra, Marlène Davanture, Benjamin E. Turk, Michel Zivy, Benoı̂t Valot, Jeffrey Leung, Sylvain Merlot
Software Mentions: 2
Published: about 14 years ago
10.1186/1748-7188-7-31
Gene tree correction for reconciliation and species tree inference
Cited by: 18
Author(s): Krister M. Swenson, Andrea Doroftei, Nadia El-Mabrouk
Software Mentions: 2
Published: about 12 years ago
10.1371/journal.pone.0050171
Global Identification of Multiple OsGH9 Family Members and Their Involvement in Cellulose Crystallinity Modification in Rice
Cited by: 54
Author(s): Guosheng Xie, Bo Yang, Zhengdan Xu, Fengcheng Li, Kai Guo, Mingliang Zhang, Lingqiang Wang, Weihua Zou, Yanting Wang, Liangcai Peng
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0006473
A Novel Putative miRNA Target Enhancer Signal
Cited by: 8
Author(s): Thorsten Schmidt, Hans‐Werner Mewes, Volker Stümpflen
Software Mentions: 2
Published: over 15 years ago
10.1371/journal.pone.0017121
Characterization of the Contradictory Chromatin Signatures at the 3′ Exons of Zinc Finger Genes
Cited by: 62
Author(s): Kimberly R. Blahnik, Lei Dou, Lorigail Echipare, Sushma Iyengar, Henriette O’Geen, Erica Sanchez, Yongjun Zhao, Marco A. Marra, Martin Hirst, J Costello, Ian F Korf, Peggy J. Farnham
Software Mentions: 2
Published: almost 14 years ago
10.1371/journal.pone.0121893
Genome-Wide Comparative Analysis Reveals Similar Types of NBS Genes in Hybrid Citrus sinensis Genome and Original Citrus clementine Genome and Provides New Insights into Non-TIR NBS Genes
Cited by: 9
Author(s): Yunsheng Wang, Lijuan Zhou, Dazhi Li, Liangying Dai, Amy Lawton‐Rauh, Pradip K. Srimani, Yongping Duan, Feng Luo
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0167068
Iron-Regulated Phospholipase C Activity Contributes to the Cytolytic Activity and Virulence of Acinetobacter baumannii
Cited by: 51
Author(s): Steven E. Fiester, Brock A. Arivett, Robert E. Schmidt, Amber C. Beckett, Tomislav Ticak, Mary V. Carrier, R. K. Ghosh, Emily J. Ohneck, Maeva Metz, Marlo K. Sellin Jeffries, Luis A. Actis
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0182469
Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice
Cited by: 34
Author(s): Showkat Ahmad Ganie, Dipti Ranjan Pani, Tapan Kumar Mondal
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.pone.0186084
Expression patterns and promoter analyses of aluminum-responsive NAC genes suggest a possible growth regulation of rice mediated by aluminum, hormones and NAC transcription factors
Cited by: 16
Author(s): Hugo Fernando Escobar-Sepúlveda, Libia Iris Trejo-Téllez, Soledad García Morales, Fernando Carlos Gómez-Meriño
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.pone.0150227
Personality, Executive Control, and Neurobiological Characteristics Associated with Different Forms of Risky Driving
Cited by: 63
Author(s): Thomas G. Brown, Marie Claude Ouimet, Manal Eldeb, Jacques Tremblay, Evelyn Vingilis, Louise Nadeau, Jens C. Pruessner, Antoine Bechara
Software Mentions: 2
Published: over 8 years ago
10.1186/s12864-015-1696-9
Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions
Cited by: 42
Author(s): Ricardo Balhana, Ashima Singla, Mahmudul Hasan Sikder, Mike Withers, Sharon L. Kendall
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0203218
In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations
Cited by: 10
Author(s): Louis A. Clark, Danielle Leatherby, Elizabeth Krilich, Alexander J. Ropelewski, John Perozich
Software Mentions: 2
Published: about 6 years ago
10.1016/j.celrep.2020.03.059
Enhancing WNT Signaling Restores Cortical Neuronal Spine Maturation and Synaptogenesis in Tbr1 Mutants
Cited by: 27
Author(s): Siavash Fazel Darbandi, Sarah E. Robinson Schwartz, Emily Ling-Lin Pai, Amanda Everitt, Marc Turner, Benjamin N.R. Cheyette, A. Jeremy Willsey, Matthew W. State, Vikaas S. Sohal, John L.R. Rubenstein
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2164-9-587
Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns
Cited by: 31
Author(s): Guénola Ricard, R.M. de Graaf, Bas E. Dutilh, Isabel Margarida Duarte, Theo A. van Alen, Angela Ham van Hoek, Brigitte Boxma, G.W.M. van der Staay, S.Y. Moon-van der Staay, Wei‐Jen Chang, Laura F. Landweber, J.H.P. Hackstein, Martijn A. Huynen
Software Mentions: 2
Published: almost 16 years ago
10.1186/s12864-018-4543-y
Divergence and evolution of cotton bHLH proteins from diploid to allotetraploid
Cited by: 3
Author(s): Bingliang Liu, Xueying Guan, Wan Liang, Jiedan Chen, Lei Fang, Yan Hu, Wangzhen Guo, Junkang Rong, Guohua Xu, Tianzhen Zhang
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2164-9-145
A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1
Cited by: 47
Author(s): Christof Francke, Robert Kerkhoven, Michiel Wels, Roland J. Siezen
Software Mentions: 2
Published: almost 17 years ago
10.1039/c4sc03885a
Discovery of a novel ligand that modulates the protein–protein interactions of the AAA+ superfamily oncoprotein reptin
Cited by: 10
Author(s): Alan R. Healy, Douglas R. Houston, Lucy Remnant, Anne-Sophie Huart, Veronika Brychtová, Magdalena M. Maslon, Olivia Meers, Petr Müller, Adam Krejčí, Elizabeth A. Blackburn, Borek Vojtesek, Lenka Hernychová, Malcolm D. Walkinshaw, Nicholas J. Westwood, Ted R. Hupp
Software Mentions: 2
Published: almost 10 years ago
10.1038/s42003-019-0529-9
Spatially conserved motifs in complement control protein domains determine functionality in regulators of complement activation-family proteins
Cited by: 10
Author(s): Hina Ojha, Payel Ghosh, Hemendra Singh Panwar, Rajashri Shende, Aishwarya Gondane, Shekhar C. Mande, Arvind Sahu
Software Mentions: 2
Published: over 5 years ago
10.1155/2019/7308197
Mathematical Models for Possible Roles of Oxytocin and Oxytocin Receptors in Autism
Cited by: 2
Author(s): Mark M. Gottlieb
Software Mentions: 2
Published: about 5 years ago
10.1186/1471-2164-15-213
Secretome weaponries of Cochliobolus lunatus interacting with potato leaf at different temperature regimes reveal a CL[xxxx]LHM - motif
Cited by: 12
Author(s): Bengyella Louis, Sayanika Devi Waikhom, Pranab Roy, Pardeep Kumar Bhardwaj, Mohendro Wakambam Singh, Sailendra Goyari, Chandradev Sharma, Narayan Chandra Talukdar
Software Mentions: 2
Published: almost 11 years ago
10.1093/dnares/dst060
Genome-Wide Evolutionary Characterization and Expression Analyses of WRKY Family Genes in Brachypodium distachyon
Cited by: 79
Author(s): Feng Wen, Hong Zhu, Peng Li, Min Jiang, Wenqing Mao, Chermaine Ong
Software Mentions: 2
Published: almost 11 years ago
10.1186/1471-2164-9-70
In silico discovery of transcription regulatory elements in Plasmodium falciparum
Cited by: 111
Author(s): Jason A. Young, J. R. Johnson, Chris Benner, S. Frank Yan, Kaisheng Chen, Karine G. Le Roch, Yingyao Zhou, Elizabeth A. Winzeler
Software Mentions: 2
Published: almost 17 years ago
10.1242/dev.134510
The human PRD-like homeobox gene <i>LEUTX</i> has a central role in embryo genome activation
Cited by: 39
Author(s): Eeva-Mari Jouhilahti, Elo Madissoon, Liselotte Vesterlund, Virpi Töhönen, Kaarel Krjutškov, Álvaro Plaza Reyes, Sophie Petropoulos, Robert Månsson, Sten Linnarsson, Thomas R. Bürglin, Fredrik Lanner, Outi Hovatta, Shintaro Katayama, Juha Kere
Software Mentions: 2
Published: almost 9 years ago
10.1080/10717544.2017.1359863
Biomimetic synthesis of proline-derivative templated mesoporous silica for increasing the brain distribution of diazepam and improving the pharmacodynamics of nimesulide
Cited by: 8
Author(s): Heran Li, Jianxin Wang, Jialiang Cong, Wei Chen, Jing Li, Hongzhuo Liu, Sanming Li, Mingshi Yang
Software Mentions: 2
Published: almost 8 years ago
10.3390/e22010053
Explanation of Experimentally Observed Phenomena in Hot Tokamak Plasmas from the Nonequilibrium Thermodynamics Position
Cited by: 3
Author(s): K. A. Razumova, В. В. Андреев, N. V. Kasyanova, С. Е. Лысенко
Software Mentions: 2
Published: almost 5 years ago
10.1007/s00267-020-01267-8
Factors Controlling Calanoid Copepod Biomass and Distribution in the Upper San Francisco Estuary and Implications for Managing the Imperiled Delta Smelt (Hypomesus transpacificus)
Cited by: 2
Author(s): Scott Hamilton, Steve Bartell, James J. Pierson, Dennis D. Murphy
Software Mentions: 2
Published: over 4 years ago
10.1007/s00267-018-1014-9
Analysis of Limiting Factors Across the Life Cycle of Delta Smelt (Hypomesus transpacificus)
Cited by: 14
Author(s): Scott Hamilton, Dennis D. Murphy
Software Mentions: 2
Published: over 6 years ago
10.1017/S095026881900150X
Epidemiology, molecular characterisation and antimicrobial susceptibility of<i>Neisseria gonorrhoeae</i>isolates in Madrid, Spain, in 2016
Cited by: 6
Author(s): María Dolores Guerrero-Torres, M. B. Menéndez, C. S. Guerras, Esther Villarreal Tello, Joan Ballesteros, Petunia Clavo, Teresa Puerta, Martínez Vera, Oskar Ayerdi, Jaume Carrió, I. Mozo, Jorge del Romero, Julio Vázquez, Raquel Abad
Software Mentions: 2
Published: almost 6 years ago
10.1007/s10096-014-2297-2
Analysis of Bordetella pertussis clinical isolates circulating in European countries during the period 1998–2012
Cited by: 75
Author(s): Marjolein van Gent, C.J. Heuvelman, H. G. van der Heide, Hans O. Hallander, Abdolreza Advani, Nicole Guiso, Carl Heinz Wirsing von König, Didrik Frimann Vestrheim, Tine Dalby, Norman K. Fry, Denis Piérard, Liselot Detemmerman, Jana Zavadilová, Kateřina Fabiánová, Catriona Logan, Adele Habington, Margaret M. Byrne, Anna Lutyńska, Ewa Mosiej, Carmen Peláz, Kirsi Gröndahl-Yli-Hannuksela, Alex‐Mikael Barkoff, Jussi Mertsola, A. Economopoulou, Qiushui He, Frits R. Mooi
Software Mentions: 2
Published: almost 10 years ago
10.2807/1560-7917.ES.2020.25.41.1900648
Molecular epidemiological typing of Neisseria gonorrhoeae isolates identifies a novel association between genogroup G10557 (G7072) and decreased susceptibility to cefixime, Germany, 2014 to 2017
Cited by: 3
Author(s): Sebastian Banhart, Klaus Jansen, Susanne Buder, Thalea Tamminga, Sébastien Calvignac‐Spencer, Tanja Pilz, Andréa Martini, Sandra Dudareva, Sergejs Nikisins, Kerstin Dehmel, Gabriele Zuelsdorf, Eva Guhl, Ingeborg Graeber, Peter K. Kohl, Magnus Unemo, Viviane Bremer, Dagmar Heuer
Software Mentions: 2
Published: about 4 years ago
10.1186/s12864-016-2684-4
The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression
Cited by: 93
Author(s): Albor Dobón, Daniel C. E. Bunting, Luis Enrique Cabrera-Quio, Cristóbal Uauy, Diane G. O. Saunders
Software Mentions: 2
Published: over 8 years ago
10.1186/1471-2164-13-75
Identification and localisation of the NB-LRR gene family within the potato genome
Cited by: 253
Author(s): Florian Jupe, Leighton Pritchard, Graham J. Etherington, Katrin MacKenzie, Peter J. A. Cock, Frank Wright, Sanjeev Sharma, Dan Bolser, Glenn J. Bryan, Jonathan D. G. Jones, Ingo Hein
Software Mentions: 2
Published: almost 13 years ago
10.1111/1574-6968.12196
<i>bkaR</i>is a TetR-type repressor that controls an operon associated with branched-chain keto-acid metabolism in<i>Mycobacteria</i>
Cited by: 14
Author(s): Ricardo Balhana, Sade N. Swanston, S. B. Coade, Mike Withers, Mahmudul Hasan Sikder, Neil G. Stoker, Sharon L. Kendall
Software Mentions: 2
Published: over 11 years ago
10.3389/fbioe.2020.645520
prPred: A Predictor to Identify Plant Resistance Proteins by Incorporating k-Spaced Amino Acid (Group) Pairs
Cited by: 6
Author(s): Yansu Wang, Pingping Wang, Yingjie Guo, Shan Huang, Yu Chen, Lei Xu
Software Mentions: 2
Published: almost 4 years ago
10.7554/eLife.08445
Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo
Cited by: 40
Author(s): Rupinder Sayal, Jacqueline M. Dresch, Irina Pushel, Benjamin Taylor, David N. Arnosti
Software Mentions: 2
Published: over 8 years ago
10.3389/fcimb.2018.00401
Iron and Virulence in Stenotrophomonas Maltophilia: All We Know So Far
Cited by: 25
Author(s): Viveka Kalidasan, Narcisse Joseph, Suresh Kumar, Rukman Awang Hamat, Vasantha Kumari Neela
Software Mentions: 2
Published: about 6 years ago
10.1186/s12864-020-07306-2
Transcriptome analysis reveals modulation of the STAT family in PEDV-infected IPEC-J2 cells
Cited by: 11
Author(s): Zhengzheng Hu, Yuchen Li, Huarui Du, Jingyao Ren, Xianrui Zheng, Kejian Wei, Jianfeng Liu
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12864-019-5780-4
Genome-wide comparison reveals divergence of cassava and rubber aquaporin family genes after the recent whole-genome duplication
Cited by: 15
Author(s): Zhi Zou, Jianghua Yang
Software Mentions: 2
Published: over 5 years ago
10.1186/s12864-016-2635-0
TNL genes in peach: insights into the post-LRR domain
Cited by: 27
Author(s): Cyril Van Ghelder, Daniel Esmenjaud
Software Mentions: 2
Published: over 8 years ago
10.7554/eLife.37912
An NAD+-dependent novel transcription factor controls stage conversion in Entamoeba
Cited by: 19
Author(s): Dipak Manna, Christian S. Lentz, Gretchen Ehrenkaufer, Susmitha Suresh, Amrita Bhat, Upinder Singh
Software Mentions: 2
Published: about 6 years ago
10.3389/fgene.2020.00469
Wheat Encodes Small, Secreted Proteins That Contribute to Resistance to Septoria Tritici Blotch
Cited by: 11
Author(s): Binbin Zhou, Harriet R. Benbow, Ciarán J. Brennan, Chanemougasoundharam Arunachalam, Sujit Jung Karki, Ewen Mullins, Angela Feechan, John R. Burke, Fiona M. Doohan
Software Mentions: 2
Published: over 4 years ago
10.7554/eLife.62293
Mouse aging cell atlas analysis reveals global and cell type-specific aging signatures
Cited by: 48
Author(s): Martin Jinye Zhang, Angela Oliveira Pisco, Spyros Darmanis, James Zou
Software Mentions: 2
Published: over 3 years ago
10.3389/fnhum.2018.00513
Disrupted Brain Network Efficiency and Decreased Functional Connectivity in Multi-sensory Modality Regions in Male Patients With Alcohol Use Disorder
Cited by: 23
Author(s): Yaqi Wang, Yilin Zhao, Hanxiang Nie, Changsheng Liu, Jun Chen
Software Mentions: 2
Published: almost 6 years ago
10.3389/fnhum.2019.00370
Increased Awakenings From Non-rapid Eye Movement Sleep Explain Differences in Dream Recall Frequency in Healthy Individuals
Cited by: 24
Author(s): Mariza van Wyk, Mark Solms, Gosia Lipinska
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0045097
Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1
Cited by: 12
Author(s): Tilman Todt, Michiel Wels, Roger S. Bongers, Roland S. Siezen, Sacha A. F. T. van Hijum, Michiel Kleerebezem
Software Mentions: 2
Published: about 12 years ago
10.1186/1471-2164-12-S2-S10
Correlating CpG islands, motifs, and sequence variants in human chromosome 21
Cited by: 6
Author(s): Leah Spontaneo, Nick Cercone
Software Mentions: 2
Published: almost 14 years ago
10.1371/journal.pone.0147144
Identification and Comparison of Candidate Olfactory Genes in the Olfactory and Non-Olfactory Organs of Elm Pest Ambrostoma quadriimpressum (Coleoptera: Chrysomelidae) Based on Transcriptome Analysis
Cited by: 27
Author(s): Yinliang Wang, Qi Chen, Hanbo Zhao, Bingzhong Ren
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pone.0087156
Genome-Wide Analysis of Soybean HD-Zip Gene Family and Expression Profiling under Salinity and Drought Treatments
Cited by: 97
Author(s): Xue Chen, Zhu Chen, Hualin Zhao, Yang Zhao, Beijiu Cheng, Yan Xiang
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0140110
Towards a Supertree of Arthropoda: A Species-Level Supertree of the Spiny, Slipper and Coral Lobsters (Decapoda: Achelata)
Cited by: 10
Author(s): Katie E. Davis, Thomas W. Hesketh, Cyrille Delmer, Matthew A. Wills
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pone.0020340
SNP-Based Typing: A Useful Tool to Study Bordetella pertussis Populations
Cited by: 37
Author(s): Marjolein van Gent, Marieke J. Bart, Han G. J. van der Heide, Kees Heuvelman, Teemu Kallonen, Qiushui He, Jussi Mertsola, Abdolreza Advani, Hans O. Hallander, Koen Janssens, Peter W. M. Hermans, Frits R. Mooi
Software Mentions: 2
Published: over 13 years ago
10.1186/1471-2164-14-659
Male-specific Fruitless isoforms have different regulatory roles conferred by distinct zinc finger DNA binding domains
Cited by: 59
Author(s): Justin E. Dalton, Justin M. Fear, Simon Knott, Bruce S. Baker, Lauren M. McIntyre, Michelle N. Arbeitman
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0026999
Evolutionary History of the Vertebrate Mitogen Activated Protein Kinases Family
Cited by: 53
Author(s): Meng Li, Jun Li, Chiyu Zhang
Software Mentions: 2
Published: about 13 years ago
10.1371/journal.pone.0072729
Expansion and Diversification of BTL Ring-H2 Ubiquitin Ligases in Angiosperms: Putative Rabring7/BCA2 Orthologs
Cited by: 11
Author(s): Víctor Aguilar-Hernández, Juliana Medina, Laura Aguilar-Henonin, Plinio Guzmán
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0171725
Survey of the rubber tree genome reveals a high number of cysteine protease-encoding genes homologous to Arabidopsis SAG12
Cited by: 13
Author(s): Zhi Zou, Jianting Liu, Lei Yang, Guishui Xie
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0037463
The R2R3-MYB Transcription Factor Gene Family in Maize
Cited by: 236
Author(s): Hongwu Du, Bo-Run Feng, Sisi Yang, Yubi Huang, Yixiong Tang
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0012536
The Distribution of GYR- and YLP-Like Motifs in Drosophila Suggests a General Role in Cuticle Assembly and Other Protein-Protein Interactions
Cited by: 17
Author(s): Robert S. Cornman
Software Mentions: 2
Published: about 14 years ago
10.1371/journal.pone.0204545
Tele-expertise for diagnosis of skin lesions is cost-effective in a prison setting: A retrospective cohort study of 450 patients
Cited by: 17
Author(s): Kevin Zarca, Nathanaël Charrier, E. Mahé, F. Guibal, B. Carton, F. Moreau, Isabelle Durand‐Zaleski
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0132051
Genome-Wide Survey and Expression Profile Analysis of the Mitogen-Activated Protein Kinase (MAPK) Gene Family in Brassica rapa
Cited by: 48
Author(s): Kun Lü, Wenjin Guo, Junxing Lu, Hao Yu, Cunmin Qu, Zhongjie Tang, Jiana Li, Yourong Chai, Ying Liang
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0000044
A New Family of Giardial Cysteine-Rich Non-VSP Protein Genes and a Novel Cyst Protein
Cited by: 88
Author(s): Barbara J. Davids, David S. Reiner, Shanda R. Birkeland, Sarah P. Preheim, Michael J. Cipriano, Andrew G. McArthur, Frances D. Gillin
Software Mentions: 2
Published: almost 18 years ago
10.3390/ijms140816901
Bioinformatic Prediction of Gene Functions Regulated by Quorum Sensing in the Bioleaching Bacterium Acidithiobacillus ferrooxidans
Cited by: 23
Author(s): Alvaro Banderas, Nicolás Guiliani
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0231085
Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families
Cited by: 11
Author(s): Arturo Medrano-Soto, Faezeh Ghazi, Kevin J. Hendargo, Gabriel Moreno‐Hagelsieb, Scott J. Myers, Milton H. Saier
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms18122768
Genome-Wide Identification, Evolutionary and Expression Analyses of the GALACTINOL SYNTHASE Gene Family in Rapeseed and Tobacco
Cited by: 22
Author(s): Yonghai Fan, Mengna Yu, Miao Liu, Rui Zhang, Wei Sun, Mingchao Qian, Huichun Duan, Wei Chang, Jinqi Ma, Cunmin Qu, Kai Zhang, Bo Lei, Kun Lu
Software Mentions: 2
Published: almost 7 years ago
10.18632/aging.103574
Prognostic validation and treatment decision making of the 8th edition of the American Joint Committee on Cancer pathological staging system for elderly women with early-stage breast cancer
Cited by: 2
Author(s): San‐Gang Wu, Jimin Shi, Wen Zhang, Jun Wang, Chen-Lu Lian, Jian Lei, Hua Li, Juan Zhou, Zhen-Yu He
Software Mentions: 2
Published: over 4 years ago
10.3389/fimmu.2019.02606
Chronic Immune Activation in Systemic Lupus Erythematosus and the Autoimmune PTPN22 Trp620 Risk Allele Drive the Expansion of FOXP3+ Regulatory T Cells and PD-1 Expression
Cited by: 27
Author(s): Ricardo C. Ferreira, Xaquín Castro Dopico, João J. Oliveira, Daniel B. Rainbow, Jennie H.M. Yang, Dominik Trzupek, Sarah A. Todd, Mhairi McNeill, Maristella Steri, Valeria Orrù, Edoardo Fiorillo, Daniel J.M. Crouch, Marcin Ł. Pękalski, Francesco Cucca, Timothy Tree, Tim J. Vyse, Linda S. Wicker, John Todd
Software Mentions: 2
Published: about 5 years ago
10.3389/fimmu.2020.01784
Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches
Cited by: 114
Author(s): Rong Dong, Zhugang Chu, Fangfang Yu, Yan Zha
Software Mentions: 2
Published: over 4 years ago
10.1186/s12875-018-0814-6
Implementing telemonitoring in primary care: learning from a large qualitative dataset gathered during a series of studies
Cited by: 31
Author(s): James A. Hanley, Hilary Pinnock, Mary Paterson, Brian McKinstry
Software Mentions: 2
Published: over 6 years ago
10.3389/fmed.2020.616490
Genetic Diversity, Biochemical Properties, and Detection Methods of Minor Carbapenemases in Enterobacterales
Cited by: 26
Author(s): Rémy A. Bonnin, Agnès B Jousset, Cécile Emeraud, Saoussen Oueslati, Laurent Dortet, Thierry Naas
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2015.01069
Recovering full-length viral genomes from metagenomes
Cited by: 25
Author(s): Saskia L. Smits, Rogier Bodewes, Aritz Ruiz‐González, Wolfgang Baumgärtner, Marion Koopmans, Albert D. M. E. Osterhaus, Anita C. Schürch
Software Mentions: 2
Published: about 9 years ago
10.3389/fmicb.2018.00228
Assessment of Bona Fide sRNAs in Staphylococcus aureus
Cited by: 29
Author(s): Wenfeng Liu, Tatiana Rochat, Claire Toffano‐Nioche, Thao Nguyen Le Lam, Philippe Bouloc, Claire Morvan
Software Mentions: 2
Published: almost 7 years ago
10.3389/fmicb.2017.00798
Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing
Cited by: 19
Author(s): Abhishek Rajput, Manoj Kumar
Software Mentions: 2
Published: over 7 years ago
10.3389/fmicb.2017.01121
Microbial Eukaryote Diversity and Activity in the Water Column of the South China Sea Based on DNA and RNA High Throughput Sequencing
Cited by: 50
Author(s): Dapeng Xu, Ran Li, Chen Hu, Ping Sun, Nianzhi Jiao, Alan Warren
Software Mentions: 2
Published: over 7 years ago
10.3389/fmicb.2018.01940
Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species
Cited by: 32
Author(s): Małgorzata Golanowska, Marta Potrykus, Agata Motyka-Pomagruk, Michał Kabza, Giovanni Bacci, Marco Galardini, Marco Bazzicalupo, Izabela Makałowska, Kornelia Smalla, Alessio Mengoni, Nicole Hugouvieux‐Cotte‐Pattat, Ewa Łojkowska
Software Mentions: 2
Published: about 6 years ago
10.3389/fmicb.2017.00569
Zinc-Dependent Transcriptional Regulation in Paracoccus denitrificans
Cited by: 15
Author(s): Durga Neupane, Belkis Jacquez, Anitha Sundararajan, Thiruvarangan Ramaraj, Faye Schilkey, Erik T. Yukl
Software Mentions: 2
Published: over 7 years ago
10.3389/fmicb.2015.00926
Iron is a signal for Stenotrophomonas maltophilia biofilm formation, oxidative stress response, OMPs expression, and virulence
Cited by: 55
Author(s): Carlos García, Eliana Alcaraz, Mirta Franco, Beatriz N. Passerini de Rossi
Software Mentions: 2
Published: about 9 years ago
10.3389/fmicb.2014.00714
Assembly of viral genomes from metagenomes
Cited by: 35
Author(s): Saskia L. Smits, Rogier Bodewes, Aritz Ruiz‐González, Wolfgang Baumgärtner, Marion Koopmans, Albert D. M. E. Osterhaus, Anita C. Schürch
Software Mentions: 2
Published: almost 10 years ago
10.1186/1471-2148-11-101
Evolution of light-harvesting complex proteins from Chl c-containing algae
Cited by: 40
Author(s): Gabriel E. Hoffman, M. Virginia Sánchez-Puerta, Charles F. Delwiche
Software Mentions: 2
Published: over 13 years ago
10.3390/nu12051340
Research Implications for Future Telemedicine Studies and Innovations in Diabetes and Hypertension—A Mixed Methods Study
Cited by: 14
Author(s): Patrick Timpel, Lorenz Harst
Software Mentions: 2
Published: over 4 years ago
10.3389/fnana.2019.00025
Neuron Names: A Gene- and Property-Based Name Format, With Special Reference to Cortical Neurons
Cited by: 24
Author(s): Gordon M. Shepherd, Luis N. Marenco, Michael L. Hines, Michele Migliore, Robert A. McDougal, Nicholas T. Carnevale, Adam J. H. Newton, Monique C Surles-Zeigler, Giorgio A. Ascoli
Software Mentions: 2
Published: over 5 years ago
10.1186/1471-2148-9-179
Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4
Cited by: 23
Author(s): Ke Chen, Elijah Roberts, Zaida Luthey‐Schulten
Software Mentions: 2
Published: over 15 years ago
10.3389/fnins.2021.631852
In silico Analysis of Polymorphisms in microRNAs Deregulated in Alzheimer Disease
Cited by: 4
Author(s): Mahta Moraghebi, Reza Maleki, Mohsen Ahmadi, Ahmad Agha Negahi, Hossein Abbasi, Pegah Mousavi
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2148-12-140
The mammalian PYHIN gene family: Phylogeny, evolution and expression
Cited by: 154
Author(s): Jasmyn A. Cridland, Eva Z. Curley, Michelle N. Wykes, Kate Schroder, Matthew J. Sweet, Tara L. Roberts, Mark A. Ragan, Karin S. Kassahn, Katryn J. Stacey
Software Mentions: 2
Published: over 12 years ago
10.3389/fonc.2019.00143
Noninferior Outcome After Breast-Conserving Treatment Compared to Mastectomy in Breast Cancer Patients With Four or More Positive Lymph Nodes
Cited by: 8
Author(s): Jun Wang, Jiapeng Deng, Jiayuan Sun, Yong Dong, Wen Zhang, Zhenyu He, San‐Gang Wu
Software Mentions: 2
Published: over 5 years ago
10.3389/fonc.2018.00518
Moving Breast Cancer Therapy up a Notch
Cited by: 45
Author(s): Erik Mollen, Jonathan Ient, Vivianne C. G. Tjan‐Heijnen, Liesbeth Boersma, Lucio Miele, Marjolein L. Smidt, Marc Vooijs
Software Mentions: 2
Published: about 6 years ago