Ecosyste.ms: Papers

10.12688/f1000research.9501.2

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Cited by: 693
Author(s): Aaron T. L. Lun, Davis J. McCarthy, John C. Marioni
Software Mentions: 12
Published: over 7 years ago

10.1186/s12864-021-07493-6

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
Cited by: 19
Author(s): Richard Edwards, Matthew A. Field, James M. Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D. Rosen, Gary S. Johnson, Edward S. Rice, La Deanna Hillier, Jillian M. Hammond, Samuel G. Towarnicki, Arina D. Omer, Ruqayya Khan, Ksenia Skvortsova, Ozren Bogdanović, Robert A. Zammit, E Aiden, Wesley C. Warren, J. William O. Ballard
Software Mentions: 10
Published: about 3 years ago

10.1093/gigascience/giz146

Systematic processing of ribosomal RNA gene amplicon sequencing data
Cited by: 45
Author(s): Julien Tremblay, Étienne Yergeau
Software Mentions: 10
Published: over 4 years ago

10.3389/fmicb.2020.01536

Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations
Cited by: 13
Author(s): Elias Broman, Xiaole Sun, Christian Stranne, Marco Salgado, Stefano Bonaglia, M. C. Geibel, Martin Jakobsson, Alf Norkko, Christoph Humborg, Francisco J. A. Nascimento
Software Mentions: 9
Published: almost 4 years ago

10.1038/s41598-020-68665-0

MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse
Cited by: 15
Author(s): Nicolas Bonhoure, Viviane Praz, Robyn D. Moir, Gilles Willemin, François Mange, Catherine Moret, Ian M. Willis, Nouria Hernandez
Software Mentions: 8
Published: almost 4 years ago

10.7717/peerj.8522

Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells
Cited by: 8
Author(s): Phongsakorn Chuammitri, Soulasack Vannamahaxay, Benjaporn Sornpet, Kidsadagon Pringproa, Prapas Patchanee
Software Mentions: 8
Published: over 4 years ago

10.3389/fonc.2021.630905

Identification of a Metabolism-Related Signature for the Prediction of Survival in Endometrial Cancer Patients
Cited by: 14
Author(s): Fan Yuan, Xingchen Li, Li Tian, Jianliu Wang
Software Mentions: 8
Published: about 3 years ago

10.3389/fnins.2021.689188

Identification of the Potential Gene Regulatory Networks and Therapeutics in Aged Mice With Postoperative Neurocognitive Disorder
Cited by: 9
Author(s): Wensi Wu, Yongbo Peng, Jiaxin Zhou, Xiaojun Zhang, Lin Cao, Wei-Jye Lin, Yanan Lu, Jing Wen, Zhi Wang
Software Mentions: 8
Published: almost 3 years ago

10.1042/BSR20203336

Comprehensive analysis of tumor mutation burden and immune microenvironment in gastric cancer
Cited by: 17
Author(s): Jie Yu, QianYun Zhang, Mengchuan Wang, Shi-Dong Liang, Hongyun Huang, Lang Xie, Chunhui Cui
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.ppat.1009418

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity
Cited by: 10
Author(s): Cédric Lood, Charlotte Peeters, Quentin Lamy-Besnier, Jeroen Wagemans, Daniël De Vos, Marijke Proesmans, Jean‐Paul Pirnay, Fedoua Echahidi, Denis Piérard, M Thimmesch, Anca Boeras, Katrien Lagrou, Evelien De Canck, Elke De Wachter, Vera van Noort, Rob Lavigne, Peter Vandamme
Software Mentions: 7
Published: about 3 years ago

10.1371/journal.pcbi.1004925

PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies
Cited by: 23
Author(s): Wenchao Zhang, Xinbin Dai, Qishan Wang, Shizhong Xu, Patrick Xuechun Zhao
Software Mentions: 7
Published: almost 8 years ago

10.1038/s41598-021-88694-7

Tumor mutation burden (TMB)-associated signature constructed to predict survival of lung squamous cell carcinoma patients
Cited by: 13
Author(s): Yan Duan, Yi Chen
Software Mentions: 7
Published: about 3 years ago

10.3389/fpls.2021.684192

Agrobacterium VirE2 Protein Modulates Plant Gene Expression and Mediates Transformation From Its Location Outside the Nucleus
Cited by: 7
Author(s): Rachelle A. Lapham, Lan‐Ying Lee, Eder Xhako, Esteban Gañán Gómez, V. M. Nivya, Stanton B. Gelvin
Software Mentions: 7
Published: almost 3 years ago

10.1371/journal.pone.0204076

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly
Cited by: 62
Author(s): Kris A. Christensen, Eric B. Rondeau, David R. Minkley, Jong S. Leong, Cameron M. Nugent, Roy G. Danzmann, Moira M. Ferguson, Agnieszka Stadnik, Robert H. Devlin, Robin Muzzerall, Michael G. Edwards, William S. Davidson, Ben F. Koop
Software Mentions: 7
Published: over 5 years ago

10.1038/srep30794

Genome-wide Identification and Structural, Functional and Evolutionary Analysis of WRKY Components of Mulberry
Cited by: 33
Author(s): Vinay Kumar Baranwal, Nisha Negi, Paramjit Khurana
Software Mentions: 7
Published: almost 8 years ago

10.1186/s13059-021-02265-7

ReSeq simulates realistic Illumina high-throughput sequencing data
Cited by: 7
Author(s): Stephan Schmeing, Mark D. Robinson
Software Mentions: 7
Published: about 3 years ago

10.3389/fgene.2019.01372

4See: A Flexible Browser to Explore 4C Data
Cited by: 12
Author(s): Yousra Ben Zouari, Angeliki Platania, Anne Molitor, Tom Sexton
Software Mentions: 7
Published: over 4 years ago

10.7717/peerj.644

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
Cited by: 73
Author(s): Olga Golosova, Ross Henderson, Yuriy Vaskin, Andrei Gabrielian, German Grekhov, Vijayaraj Nagarajan, Andrew J. Oler, Mariam Quiñones, Darrell E. Hurt, Mikhail Fursov, Yentram Huyen
Software Mentions: 7
Published: over 9 years ago

10.1371/journal.pcbi.1008645

Ten simple rules for getting started with command-line bioinformatics
Cited by: 7
Author(s): Parice A. Brandies, Carolyn J. Hogg
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-015-1270-5

Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages
Cited by: 43
Author(s): Aiping Mao, Jun Shen, Zhixiang Zuo
Software Mentions: 7
Published: over 9 years ago

10.1002/ece3.3234

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen <i>Pseudogymnoascus destructans</i>
Cited by: 21
Author(s): Christina M. Davy, Michael E. Donaldson, Craig K. R. Willis, Barry J. Saville, L. McGuire, Heather W. Mayberry, Alana Wilcox, Gudrun Wibbelt, Vikram Misra, Trent K. Bollinger, Christopher J. Kyle
Software Mentions: 7
Published: almost 7 years ago

10.1093/gbe/evu133

Settling Down: The Genome of Serratia symbiotica from the Aphid Cinara tujafilina Zooms in on the Process of Accommodation to a Cooperative Intracellular Life
Cited by: 77
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 6
Published: almost 10 years ago

10.7554/eLife.01256

Chromatin signature of widespread monoallelic expression
Cited by: 74
Author(s): Anwesha Nag, Virginia Savova, Ho Lim Fung, Alexander Miron, Guo Cheng Yuan, Kun Zhang, Alexander A. Gimelbrant
Software Mentions: 6
Published: over 10 years ago

10.1186/s12870-014-0315-2

The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes
Cited by: 8
Author(s): Gopal Misra, Piyush Priya, Nitesh Bandhiwal, Neha Bareja, Mukesh Jain, Sabhyata Bhatia, Debasis Chattopadhyay, Akhilesh K. Tyagi, Gitanjali Yadav
Software Mentions: 6
Published: over 9 years ago

10.1099/vir.0.045351-0

Evolution of the hepatitis E virus hypervariable region
Cited by: 34
Author(s): Donald B. Smith, Jeff Vanek, Sandeep Ramalingam, Ingólfur Johannessen, Kate Templeton, Peter Simmonds
Software Mentions: 6
Published: over 11 years ago

10.7554/eLife.16797

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians
Cited by: 46
Author(s): Jordi Solana, Manuel Irimia, Salah Ayoub, Marta Rodriguez Orejuela, Vera Zywitza, Marvin Jens, Javier Tapial, Debashish Ray, Quaid Morris, Timothy R. Hughes, Benjamin J. Blencowe, Nikolaus Rajewsky
Software Mentions: 6
Published: almost 8 years ago

10.1038/srep09549

Difference in microRNA expression and editing profile of lung tissues from different pig breeds related to immune responses to HP-PRRSV
Cited by: 33
Author(s): Jia Li, Zhisheng Chen, Junlong Zhao, Liurong Fang, Rui Fang, Jiang Xiao, Xing Chen, Ao Zhou, Yingyin Zhang, Liming Ren, Xiaoxiang Hu, Yaofeng Zhao, Shujun Zhang, Ning Li
Software Mentions: 6
Published: about 9 years ago

10.1186/1471-2105-13-154

TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data
Cited by: 50
Author(s): Aaron L. Sarver, Jesse Erdman, Timothy K. Starr, David A. Largaespada, Kevin A.T. Silverstein
Software Mentions: 6
Published: almost 12 years ago

10.1111/pbi.12834

Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (<i>Triticum aestivum</i>)
Cited by: 21
Author(s): Amanda Burridge, Paul Wilkinson, Mark Winfield, Gary Barker, Alexandra M. Allen, Jane A. Coghill, Christy Waterfall, Keith J. Edwards
Software Mentions: 6
Published: over 6 years ago

10.1080/21655979.2020.1840731

Bioinformatics analysis to screen key prognostic genes in the breast cancer tumor microenvironment
Cited by: 9
Author(s): Qian Ye, Xiaofei Han, Zhengsheng Wu
Software Mentions: 6
Published: over 4 years ago

10.1111/pbi.13210

The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley
Cited by: 39
Author(s): Miao Liu, Yan Li, Yanling Ma, Qiang Zhao, Jiri Stiller, Qi Feng, Qifeng Tian, Dengcai Liu, Bin Han, Chunji Liu
Software Mentions: 6
Published: almost 5 years ago

10.3389/fcell.2021.682002

Identification of CDK2-Related Immune Forecast Model and ceRNA in Lung Adenocarcinoma, a Pan-Cancer Analysis
Cited by: 34
Author(s): Tingting Liu, Rui Li, Huo Chen, Jianping Li, Jie Yao, Xiu-Li Ji, Yi-Qing Qu
Software Mentions: 6
Published: almost 3 years ago

10.1534/g3.116.027045

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite <i>Tolypocladium ophioglossoides</i>
Cited by: 20
Author(s): C. Alisha Quandt, Yanming Di, Justin Elser, Pankaj Jaiswal, Joseph W. Spatafora
Software Mentions: 6
Published: about 8 years ago

10.1186/s12917-014-0282-8

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives
Cited by: 115
Author(s): Brian B. Oakley, R. J. Buhr, Casey W. Ritz, Brian H. Kiepper, M. E. Berrang, Bruce S. Seal, N. A. Cox
Software Mentions: 6
Published: over 9 years ago

10.3389/fonc.2020.00809

Identification of Potential Key Genes for Pathogenesis and Prognosis in Prostate Cancer by Integrated Analysis of Gene Expression Profiles and the Cancer Genome Atlas
Cited by: 31
Author(s): Shuang Liu, Wenxin Wang, Yan Zhao, Kai-Ge Liang, Yaojiang Huang
Software Mentions: 6
Published: almost 4 years ago

10.1093/database/bay014

TransAtlasDB: an integrated database connecting expression data, metadata and variants
Cited by: 2
Author(s): Modupeore O. Adetunji, Susan J. Lamont, Carl J. Schmidt
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0102610

Potential Therapeutic Targets for Oral Cancer: ADM, TP53, EGFR, LYN, CTLA4, SKIL, CTGF, CD70
Cited by: 28
Author(s): Saurabh Bundela, Anjana Sharma, Prakash S. Bisen
Software Mentions: 6
Published: almost 10 years ago

10.1371/journal.pone.0121760

medplot: A Web Application for Dynamic Summary and Analysis of Longitudinal Medical Data Based on R
Cited by: 5
Author(s): Črt Ahlin, Daša Stupica, Franc Strle, Lara Lusa
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pbio.3000799

5-Formylcytosine landscapes of human preimplantation embryos at single-cell resolution
Cited by: 5
Author(s): Yun Gao, Lin Li, Peng Yuan, Fan Zhai, Yixuan Ren, Liying Yan, Rong Li, Ying Lian, Xiaohui Zhu, Xinglong Wu, Kehkooi Kee, Lu Wen, Jie Qiao, Fuchou Tang
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0072238

Effect of Doxorubicin/Pluronic SP1049C on Tumorigenicity, Aggressiveness, DNA Methylation and Stem Cell Markers in Murine Leukemia
Cited by: 73
Author(s): Daria Y. Alakhova, Yi Zhao, Shu Li, Alexander V. Kabanov
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12870-016-0860-y

CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors
Cited by: 16
Author(s): Saurabh Gayali, Shankar Acharya, Nilesh Vikram Lande, Ashish Pandey, Subhra Chakraborty, Niranjan Chakraborty
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.55792

An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes
Cited by: 56
Author(s): Nathan D. Lawson, Rui Li, Masahiro Shin, Ann S. Grosse, Onur Yukselen, Oliver A. Stone, Alper Küçükural, Lihua Julie Zhu
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.21476

Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated
Cited by: 67
Author(s): Ximena Ibarra-Soria, Thiago S. Nakahara, Jingtao Lilue, Yue Jiang, Casey Trimmer, Mateus A.A. Souza, Paulo H.M. Netto, Kentaro Ikegami, Nicolle R. Murphy, Mairi Kusma, Andrea Kirton, Luís R. Saraiva, Thomas Keane, Hiroaki Matsunami, Joel D. Mainland, Fábio Papes, Darren W. Logan
Software Mentions: 5
Published: about 7 years ago

10.3389/fonc.2021.566539

Prognostic Significance of Autophagy-Relevant Gene Markers in Colorectal Cancer
Cited by: 6
Author(s): Qinglian He, Ziqi Li, Jun Yin, Yuling Li, Yuting Yin, Lijun Xue, Wei Zhu
Software Mentions: 5
Published: about 3 years ago

10.1186/s40168-016-0164-3

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants
Cited by: 52
Author(s): Colin Hill, Jillian R. Brown, Denise B. Lynch, Ian B. Jeffery, C. Anthony Ryan, R. Paul Ross, Catherine Stanton, Paul W. O’Toole
Software Mentions: 5
Published: about 8 years ago

10.1186/s12864-018-5271-z

Genomic insights into virulence mechanisms of Leishmania donovani: evidence from an atypical strain
Cited by: 23
Author(s): Sumudu R. Samarasinghe, Nilakshi Samaranayake, Udeshika Kariyawasam, Yamuna Deepani Siriwardana, Hideo Imamura, Nadira D. Karunaweera
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-12-S3-S6

ApicoAlign: an alignment and sequence search tool for apicomplexan proteins
Cited by: 5
Author(s): Jamshaid Ali, Umadevi Paila, Akash Ranjan
Software Mentions: 5
Published: over 12 years ago

10.1186/1752-0509-1-27

Non-linear dimensionality reduction of signaling networks
Cited by: 18
Author(s): Sergii Ivakhno, J. Douglas Armstrong
Software Mentions: 5
Published: almost 17 years ago

10.1038/s42003-020-01382-6

Adaptation by copy number variation increases insecticide resistance in the fall armyworm
Cited by: 40
Author(s): Sylvie Gimenez, Heba Abdelgaffar, Gaëlle Le Goff, Frédérique Hilliou, Carlos A. Blanco, Sabine Hänniger, Anthony Bretaudeau, Fabrice Legeai, Nicolas Nègre, Juan Luís Jurat-Fuentes, Emmanuelle d’Alençon, Kiwoong Nam
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-015-2040-0

Plasmodium parasites mount an arrest response to dihydroartemisinin, as revealed by whole transcriptome shotgun sequencing (RNA-seq) and microarray study
Cited by: 27
Author(s): Philip Shaw, Sastra Chaotheing, Pavita Kaewprommal, Jittima Piriyapongsa, Chayaphat Wongsombat, Nattida Suwannakitti, Pongpisid Koonyosying, Chairat Uthaipibull, Yongyuth Yuthavong, Sumalee Kamchonwongpaisan
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0233808

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina
Cited by: 20
Author(s): Pierre Luisi, Angelina García, Juan Manuel Berros, Josefina María Brenda Motti, Darío Alfredo Demarchi, Emma Alfaro, Eliana Aquilano, Carina F. Argüelles, Sergio Alejandro Avena, Graciela Bailliet, Julieta Beltramo, Cláudio M. Bravi, Mariela Cuello, Cristina Beatriz Dejean, José Edgardo Dipierri, Laura Smeldy Jurado Medina, José Luis Lanata, Marina Muzzio, María Laura Parolin, Maia Pauro, Paula B. Paz Sepúlveda, Daniela Rodríguez Golpe, Maria Rita de Morais Chaves Santos, Marisol Schwab, Natalia Silvero, Jeremías Enrique Zubrzycki, Virgínia Ramallo, Hernán Dopazo
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0141719

Potential Compounds for Oral Cancer Treatment: Resveratrol, Nimbolide, Lovastatin, Bortezomib, Vorinostat, Berberine, Pterostilbene, Deguelin, Andrographolide, and Colchicine
Cited by: 37
Author(s): Saurabh Bundela, Anjana Sharma, Prakash S. Bisen
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0125663

Protein Structure and Evolution: Are They Constrained Globally by a Principle Derived from Information Theory?
Cited by: 5
Author(s): Les Hatton, Gregory W. Warr
Software Mentions: 4
Published: about 9 years ago

10.1186/1471-2210-9-4

residues implicated in the formation K+ and Na+ ion channels effector toxins
Cited by: 11
Author(s): Rima Soli, Belhassen Kaabi, Mourad Barhoumi, Mohamed Elayeb, Najet Srairi-Abid
Software Mentions: 4
Published: about 15 years ago

10.1371/journal.pone.0058294

Sequencing and Comparative Analysis of the Straw Mushroom (Volvariella volvacea) Genome
Cited by: 128
Author(s): Dapeng Bao, Ming Gong, Huajun Zheng, Mingjie Chen, Liang Zhang, Hong Wang, Jianping Jiang, Lin Wu, Yaping Zhu, Gang Zhu, Yan Zhou, Chuanhua Li, Shengyue Wang, Yan Zhao, Guoping Zhao, Qian Tan
Software Mentions: 4
Published: about 11 years ago

10.1186/1471-2105-14-S7-S14

Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements
Cited by: 16
Author(s): Swaraj Basu, Ferenc Müller, Remo Sanges
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pntd.0007560

Potent and selective inhibitors for M32 metallocarboxypeptidases identified from high-throughput screening of anti-kinetoplastid chemical boxes
Cited by: 3
Author(s): Emir Salas‐Sarduy, Lionel Urán Landaburu, Adriana K. Carmona, Juán José Cazzulo, Fernán Agüero, Vanina E. Álvarez, Gabriela T. Niemirowicz
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-020-75553-0

Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species
Cited by: 13
Author(s): Manosh Kumar Biswas, Mita Bagchi, Ujjal Kumar Nath, Dhiman Biswas, Sathishkumar Natarajan, Denison Michael Immanuel Jesse, Jong-In Park, Ill–Sup Nou
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0145031

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing
Cited by: 27
Author(s): Margaret Staton, Teodora Best, Sudhir Khodwekar, Sandra A. Owusu, Tao Xu, Yi Xu, Tara Jennings, Richard Cronn, Aru K. Arumuganathan, Mark V. Coggeshall, Oliver Gailing, Haiying Liang, Jeanne Romero‐Severson, Scott E. Schlarbaum, John E. Carlson
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms19010271

Integrated Analyses Reveal Overexpressed Notch1 Promoting Porcine Satellite Cells’ Proliferation through Regulating the Cell Cycle
Cited by: 21
Author(s): Yiren Jiao, Bo Huang, Yu Chen, Guang-liang Hong, Jian Xu, Chen Hu, Chong Wang
Software Mentions: 4
Published: over 6 years ago

10.1007/s13238-017-0480-9

TDP-43 regulates cancer-associated microRNAs
Cited by: 28
Author(s): Xiaowei Chen, Zhen Fan, W Ambrose McGee, Mengmeng Chen, Ruirui Kong, Pushuai Wen, Tengfei Xiao, Xiaomin Chen, Jianghong Liu, Li Zhu, Runsheng Chen, Jane Y. Wu
Software Mentions: 4
Published: over 6 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.gpb.2016.06.003

Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins
Cited by: 37
Author(s): Obed Ramírez-Sánchez, Paulino Pérez‐Rodríguez, Luis Delaye, Axel Tiessen
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-12-192

FungalRV: adhesin prediction and immunoinformatics portal for human fungal pathogens
Cited by: 64
Author(s): Rupanjali Chaudhuri, Faraz Alam Ansari, Muthukurussi Varieth Raghunandanan, Srinivasan Ramachandran
Software Mentions: 4
Published: about 13 years ago

10.1038/s41598-018-20414-0

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies
Cited by: 53
Author(s): Stefano Campanaro, Laura Treu, Panagiotis Kougias, Xinyu Zhu, Irini Angelidaki
Software Mentions: 4
Published: over 6 years ago

10.1186/gb-2011-12-8-r76

The head-regeneration transcriptome of the planarian Schmidtea mediterranea
Cited by: 110
Author(s): Thomas Sandmann, Matthias Christian Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer
Software Mentions: 4
Published: over 13 years ago

10.1186/gb-2011-12-2-r16

Genomewide characterization of non-polyadenylated RNAs
Cited by: 358
Author(s): Li Yang, Michael O. Duff, Brenton R. Graveley, Gordon G. Carmichael, Lingling Chen
Software Mentions: 4
Published: over 13 years ago

10.1186/s13059-020-02007-1

Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection
Cited by: 62
Author(s): Qiang Zhang, Jin Hu, Jia-Wu Feng, Xiaoru Hu, Wang Ting, Wenxiao Gong, Kun Huang, Yi-Xiong Guo, Zhong Zou, Xian Lin, Run Zhou, Yuqi Yuan, Anding Zhang, Hong Wei, Gang Cao, Chen Liu, Lingling Chen, Meilin Jin
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-018-5157-0

Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.)
Cited by: 39
Author(s): Rui Hu, Jie Xiao, Tao Gu, Xiao‐Lan Yu, Yang Zhang, Junli Chang, Guangxiao Yang, Guangyuan He
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-018-2446-1

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics
Cited by: 26
Author(s): Shakuntala Baichoo, Yassine Souilmi, Sumir Panji, Gerrit Botha, Ayton Meintjes, Scott Hazelhurst, Hocine Bendou, Eugene de Beste, Phelelani T. Mpangase, Oussema Souiai, Mustafa Alghali, Long Yi, Brian D. O’Connor, Michael R. Crusoe, Don Armstrong, Shaun Aron, Fourie Joubert, Azza E. Ahmed, Mamana Mbiyavanga, Peter van Heusden, Lerato E Magosi, Jennie Zermeno, Liudmila Sergeevna Mainzer, Faisal M. Fadlelmola, C V Jongeneel, Nicola Mulder
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-49446-w

De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya
Cited by: 19
Author(s): Nisha Dhiman, Nitesh Kumar Sharma, Pooja Thapa, Isha Sharma, Mohit Kumar Swarnkar, Amit Chawla, Ravi Shankar, Amita Bhattacharya
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2021.692453

Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping
Cited by: 12
Author(s): Amar Ćosić, Eva Leitner, Christian Petternel, Herbert Galler, Franz F. Reinthaler, Kathrin A. Herzog-Obereder, Elisabeth Tatscher, Sandra Raffl, Gebhard Feierl, Christoph Högenauer, Ellen L. Zechner, Sabine Kienesberger
Software Mentions: 4
Published: almost 3 years ago

10.3389/fimmu.2018.02999

Shrimp miR-1000 Functions in Antiviral Immunity by Simultaneously Triggering the Degradation of Two Viral mRNAs
Cited by: 11
Author(s): Yi Gong, Chenyu Ju, Xiaobo Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-015-0133-2

The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles
Cited by: 64
Author(s): Yasir Tarabichi, K. Li, Shishan Hu, Cam Nguyen, X. Wang, David Elashoff, Kazima Saira, Bryan Frank, Monika Bihan, Elodie Ghedin, Barbara A. Methé, Jane C. Deng
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2014.00576

In vivo function and comparative genomic analyses of the Drosophila gut microbiota identify candidate symbiosis factors
Cited by: 65
Author(s): Peter D. Newell, John M. Chaston, Yiping Wang, Nathan J. Winans, David R. Sannino, Adam C. N. Wong, A. Dobson, Jeanne Kagle, Angela E. Douglas
Software Mentions: 4
Published: over 9 years ago

10.3389/fninf.2013.00039

Explicit B-spline regularization in diffeomorphic image registration
Cited by: 173
Author(s): Nicholas J. Tustison, Brian B. Avants
Software Mentions: 4
Published: over 11 years ago

10.1186/s12935-019-0975-y

Identification of differentially expressed circRNAs and a novel hsa_circ_0000144 that promote tumor growth in gastric cancer
Cited by: 27
Author(s): Jianming Wei, Jinmiao Wang, Xibo Gao, Feng Qi
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2017.00052

Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs
Cited by: 25
Author(s): Andrew D. L. Nelson, Upendra Kumar Devisetty, Kyle Palos, Asher Haug-Baltzell, Eric Lyons, Mark A. Beilstein
Software Mentions: 4
Published: about 7 years ago

10.3762/bjnano.2.48

Towards a scalable and accurate quantum approach for describing vibrations of molecule–metal interfaces
Cited by: 18
Author(s): David M. Benoit, Bruno Madebène, Inga S. Ulusoy, Luis Mancera, Yohann Scribano, Sergey K. Chulkov
Software Mentions: 4
Published: almost 13 years ago

10.1186/1471-2164-15-341

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics
Cited by: 34
Author(s): Ghanasyam Rallapalli, Eric Kemen, Alexandre Robert-Seilaniantz, Cécile Segonzac, Graham J. Etherington, Kee Hoon Sohn, Dan MacLean, Jonathan D. G. Jones
Software Mentions: 4
Published: about 10 years ago

10.1002/ece3.7322

Local environment‐driven adaptive evolution in a marine invasive ascidian (<i>Molgula manhattensis</i>)
Cited by: 10
Author(s): Yiyong Chen, Yangchun Gao, Xuena Huang, Shiguo Li, Aibin Zhan
Software Mentions: 4
Published: about 3 years ago

10.1186/1756-0500-5-85

Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes
Cited by: 84
Author(s): Axel Tiessen, Paulino Pérez‐Rodríguez, Luis Delaye
Software Mentions: 4
Published: over 12 years ago

10.1186/1471-2105-9-537

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
Cited by: 28
Author(s): Fan Mo, Hong Xu, Feng Gao, Lin Du, Jun Wang, Gilbert S. Omenn, Biaoyang Lin
Software Mentions: 4
Published: over 15 years ago

10.1186/s12864-015-1624-z

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens
Cited by: 132
Author(s): Abraham Morales‐Cruz, Katherine C. H. Amrine, Bárbara Blanco-Ulate, Daniel P. Lawrence, Renaud Travadon, Philippe E. Rolshausen, Kendra Baumgartner, Dario Cantu
Software Mentions: 4
Published: almost 9 years ago

10.1186/s13148-021-01050-4

Epigenetic evidence of an Ac/Dc axis by VPA and SAHA
Cited by: 10
Author(s): Sebastian Lunke, Scott Maxwell, Ishant Khurana, K N Harikrishnan, Jun Okabe, Keith Al-Hasani, Assam El‐Osta
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0228964

Genetic characteristics of Jiaji Duck by whole genome re-sequencing
Cited by: 7
Author(s): Lihong Gu, Wang Feng, Zhemin Lin, Tieshan Xu, Dajie Lin, Manping Xing, Shuo Yang, Zhe Chao, Baoguo Ye, Licong Peng, Chunhui Hui, Lizhi Liu, Shuisheng Hou
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2229-11-63

OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics
Cited by: 62
Author(s): Mohamed Helmy, Masaru Tomita, Yasushi Ishihama
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pone.0129422

Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties
Cited by: 45
Author(s): Nagaraja Reddy Rama Reddy, Rucha Harishbhai Mehta, Palak Harendrabhai Soni, Jayanti Makasana, Narendra Gajbhiye, P. Manivel, Jitendra Kumar
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0218938

Genome-wide comparative analysis of RNA-binding Glycine-rich protein family genes between Gossypium arboreum and Gossypium raimondii
Cited by: 11
Author(s): Yang Wei, Min Yu, Changsong Zou, Changming Lu, Daoqian Yu, Hongyan Cheng, Pengfei Jiang, Feng Xu, Youping Zhang, Qiaolian Wang, Hong Zhang, Guoli Song, Zhuqing Zhou
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0120410

High-Density Genetic Linkage Mapping in Turbot (Scophthalmus maximus L.) Based on SNP Markers and Major Sex- and Growth-Related Regions Detection
Cited by: 43
Author(s): Weiji Wang, Yulong Hu, Yu Ma, Liyong Xu, Jiantao Guan, Jie Kong
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0143193

Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome
Cited by: 10
Author(s): Elena Hilario, Lorna Barron, Cecilia Deng, Paul M. Datson, Nihal De Silva, Marcus Davy, Roy Storey
Software Mentions: 3
Published: over 8 years ago

10.1186/s12862-016-0659-3

Bayesian species delimitation in Pleophylla chafers (Coleoptera) – the importance of prior choice and morphology
Cited by: 29
Author(s): Jonas Eberle, Rachel C. M. Warnock, Dirk Ahrens
Software Mentions: 3
Published: about 8 years ago

10.1186/1471-2105-6-69

Cited by: 37
Author(s): Fenglin Tang, Ching Lian Chua, Liang-Yoong Ho, Yun Ping Lim, Praveen Issac, Arun V. Krishnan
Software Mentions: 3
Published: over 19 years ago

10.1371/journal.pone.0034225

Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology
Cited by: 60
Author(s): Yixing Wang, Xin Zeng, Niranjani J. Iyer, Douglas W. Bryant, Todd C. Mockler, Ramamurthy Mahalingam
Software Mentions: 3
Published: about 12 years ago

10.1016/j.celrep.2020.108401

Atypical UV Photoproducts Induce Non-canonical Mutation Classes Associated with Driver Mutations in Melanoma
Cited by: 12
Author(s): Marian F. Laughery, Alexander Brown, Kaitlynne A. Bohm, Smitha Sivapragasam, Haley S. Morris, Mila Tchmola, Angelica D. Washington, Debra Mitchell, Stephen J. Mather, Ewa Malc, Piotr A. Mieczkowski, Steven A. Roberts, John J. Wyrick
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0040194

Microarray-Based Sketches of the HERV Transcriptome Landscape
Cited by: 46
Author(s): Philippe Pérot, Nathalie Mugnier, Cécile Montgiraud, Juliette Gimenez, Magali Jaillard, Bertrand Bonnaud, François Mallet
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12898-015-0051-y

Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach
Cited by: 161
Author(s): Wiebke Sickel, Markus J. Ankenbrand, Gudrun Grimmer, Andrea Holzschuh, Stephan Härtel, Jonathan Lanzen, Ingolf Steffan‐Dewenter, Alexander Keller
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2407-5-86

Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression
Cited by: 63
Author(s): Asa Oudes, Jared C. Roach, Laura S Walashek, Lillian J. Eichner, Lawrence D. True, Robert L. Vessella, Alvin Y. Liu
Software Mentions: 3
Published: almost 19 years ago

10.1186/s12911-019-0983-9

Proof-of-concept study: Homomorphically encrypted data can support real-time learning in personalized cancer medicine
Cited by: 8
Author(s): Silvia Paddock, Hamed Abedtash, Jacqueline Zummo, Samuel Thomas
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2407-14-880

Deep Sequencing the microRNA profile in rhabdomyosarcoma reveals down-regulation of miR-378 family members
Cited by: 55
Author(s): Francesca Megiorni, Samantha Cialfi, Heather P. McDowell, Armando Felsani, Simona Camero, Alessandro Guffanti, Barry Pizer, Aldo Clerico, Alessandra De Grazia, Antonio Pizzuti, Anna Moles, Carlo Dominici
Software Mentions: 3
Published: over 9 years ago