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: perl

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

Perl as a Python package
2 versions
Latest release: about 5 years ago
1 dependent package
6,426 downloads last month

Papers Mentioning perl 604

10.1038/s41396-019-0450-8
Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches
Cited by: 20
Author(s): Szymon P. Szafrański, Mogens Kilian, Ines Yang, Gesa Bei der Wieden, Andreas Winkel, Jan Hegermann, Meike Stiesch
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-020-77723-6
Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order
Cited by: 13
Author(s): Sonam Gaba, Abha Kumari, Marnix H. Medema, Rajeev Kaushik
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-018-34243-8
The evolutionary dynamics of microRNAs in domestic mammals
Cited by: 17
Author(s): Luca Penso-Dolfin, Simon Moxon, Wilfried Haerty, Federica Di Palma
Software Mentions: 3
Published: about 6 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: over 9 years ago
10.1038/s41598-018-23860-y
Systemic and specific effects of antihypertensive and lipid-lowering medication on plasma protein biomarkers for cardiovascular diseases
Cited by: 30
Author(s): Stefan Enroth, Varun Maturi, Malin Berggrund, Sofia Bosdotter Enroth, Aristidis Moustakas, Åsa Johansson, Ulf Gyllensten
Software Mentions: 3
Published: over 6 years ago
10.1038/s41598-020-61857-8
De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance
Cited by: 18
Author(s): Soumya Shree Nayak, Seema Pradhan, Dinabandhu Sahoo, Ajay Parida
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-017-14617-0
KIXBASE: A comprehensive web resource for identification and exploration of KIX domains
Cited by: 6
Author(s): Archana Yadav, Jyoti Thakur, Gitanjali Yadav
Software Mentions: 3
Published: about 7 years ago
10.1371/journal.pone.0117210
Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms
Cited by: 31
Author(s): J. Michael Day, Brian B. Oakley, Bruce S. Seal, László Zsák
Software Mentions: 3
Published: almost 10 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: over 12 years ago
10.3390/ijms22031252
Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean
Cited by: 7
Author(s): Jamie A. O’Rourke, Michelle A. Graham
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-017-18128-w
Differential miRNA expression in the three-spined stickleback, response to environmental changes
Cited by: 12
Author(s): С. М. Расторгуев, Artem Nedoluzhko, Natalia Gruzdeva, Eugenia Boulygina, Fedor Sharko, Amina S. Ibragimova, Svetlana Tsygankova, Artemov Av, K. G. Skryabin, Egor Prokhortchouk
Software Mentions: 3
Published: almost 7 years ago
10.1186/1471-2105-9-311
Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge
Cited by: 5
Author(s): Don Armstrong, Chaim O. Jacob, Raphael Zidovetzki
Software Mentions: 3
Published: over 16 years ago
10.1038/s41598-017-00100-3
RNA-Sequencing data supports the existence of novel VEGFA splicing events but not of VEGFAxxxb isoforms
Cited by: 14
Author(s): Stephen Bridgett, Margaret Dellett, David Simpson
Software Mentions: 3
Published: over 7 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: over 8 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: almost 5 years ago
10.1186/1471-2164-14-371
Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor
Cited by: 34
Author(s): Franc Llorens, Manuela Hummel, Lorena Pantano, Xavier Pastor, Ana Vivancos, Ester Castillo, Heidi Mattlin, Anna Ferrer, Matthew Ingham, María Noguera, Robert Kofler, Juliane C. Dohm, Raquel Pluvinet, Mònica Bayés, Heinz Himmelbauer, José Antonio del Río, Eulàlia Martı́, Lauro Sumoy
Software Mentions: 3
Published: over 11 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: over 13 years ago
10.1371/journal.ppat.1005943
Cathelicidin Insufficiency in Patients with Fatal Leptospirosis
Cited by: 21
Author(s): Janet C. Lindow, Elsio A. Wunder, Stephen J. Popper, Jinsoo Min, Praveen Mannam, Anup Srivastava, Yi Yao, Kathryn P. Hacker, Khadir Raddassi, Patty J Lee, Ruth R. Montgomery, Albert C. Shaw, José E. Hagan, Guilherme C. Araújo, Nívison Nery, David A. Relman, Charles C. Kim, Mitermayer Galvão dos Reis, Albert I. Ko
Software Mentions: 3
Published: about 8 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: over 12 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
10.1038/srep15786
Genome-wide analysis correlates Ayurveda Prakriti
Cited by: 73
Author(s): Periyasamy Govindaraj, Sheikh Nizamuddin, Sharath Anugula, Vuskamalla Jyothi, Harish Rotti, Ritu Raval, Jayakrishna Nayak, Balakrishna K Bhat, B V Prasanna, Pooja Shintre, Mayura Sule, Kalpana Joshi, Amrish P Dedge, Ramachandra Bharadwaj, G G Gangadharan, Sreekumaran Nair, P. M. Gopinath, Bhushan Patwardhan, Paturu Kondaiah, Kapaettu Satyamoorthy, Marthanda Varma Sankaran Valiathan, Kumarasamy Thangaraj
Software Mentions: 3
Published: about 9 years ago
10.1186/1471-2164-9-390
Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays
Cited by: 100
Author(s): Alexandra B. Graf, Brigitte Gasser, Martin Dragosits, Michael Sauer, Germán Leparc, Thomas Tüchler, David P. Kreil, Diethard Mattanovich
Software Mentions: 3
Published: over 16 years ago
10.1186/1471-2105-9-S2-S15
SWS: accessing SRS sites contents through Web Services
Cited by: 4
Author(s): Paolo Romano, Domenico Marra
Software Mentions: 3
Published: over 16 years ago
10.1186/s12886-020-01365-5
Identification of lncRNA–miRNA–mRNA regulatory network associated with primary open angle glaucoma
Cited by: 24
Author(s): Minwen Zhou, Bing Lu, Wei Tan, Mingshui Fu
Software Mentions: 3
Published: over 4 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
10.1371/journal.pntd.0008234
Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes
Cited by: 20
Author(s): Anthony M. Ford, Daniel Kepple, Beka Raya Abagero, Jordan Connors, Richard D. Pearson, Sarah Auburn, Sisay Getachew, Colby T. Ford, Karthigayan Gunalan, Louis H. Miller, Daniel Janies, Julian C. Rayner, Guiyun Yan, Delenasaw Yewhalaw, Eugenia Lo
Software Mentions: 3
Published: about 4 years ago
10.3389/fvets.2016.00011
Spatial and Temporal Changes in the Broiler Chicken Cecal and Fecal Microbiomes and Correlations of Bacterial Taxa with Cytokine Gene Expression
Cited by: 148
Author(s): Brian B. Oakley, Michael H. Kogut
Software Mentions: 3
Published: almost 9 years ago
10.1371/journal.pgen.1003496
The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster
Cited by: 130
Author(s): Kathryn E. Bushley, Rajani Raja, Pankaj Jaiswal, Jason S. Cumbie, Mariko Nonogaki, Alexander Boyd, C. Alisha Owensby, Brian J. Knaus, Justin Elser, Daniel Miller, Yanming Di, Kerry L. McPhail, Joseph W. Spatafora
Software Mentions: 3
Published: over 11 years ago
10.1186/s12859-020-3408-y
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species
Cited by: 16
Author(s): Zhenmin Du, Qi Hu, Xinxing Liu, Kai Zou, Emmanuel Konadu Sarkodie, Xueduan Liu, Fei Gao
Software Mentions: 3
Published: over 4 years ago
10.1186/1471-2164-10-S3-S13
MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads
Cited by: 13
Author(s): Hua Bao, Yuanyan Xiong, Hui Guo, Renchao Zhou, Xuemei Lu, Zhen Yang, Yang Zhong, Suhua Shi
Software Mentions: 3
Published: almost 15 years ago
10.1371/journal.pgen.1002053
Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules
Cited by: 82
Author(s): Bin He, Alisha K. Holloway, Sebastian J. Maerkl, Martin Kreitman
Software Mentions: 3
Published: over 13 years ago
10.3389/fpls.2017.00969
Identification and Characterization of miRNA Transcriptome in Asiatic Cotton (Gossypium arboreum) Using High Throughput Sequencing
Cited by: 14
Author(s): Muhammad Farooq, Shahid Mansoor, Hui Guo, Imran Amin, Peng W. Chee, M. Kamran Azim, Andrew H. Paterson
Software Mentions: 3
Published: over 7 years ago
10.1186/gb-2009-10-4-r39
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
Cited by: 64
Author(s): Jessica Severin, Andrew Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J. Balwierz, Michiel de Hoon, David Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O. Daub, Alistair R.R. Forrest
Software Mentions: 3
Published: almost 16 years ago
10.1186/s12864-015-1724-9
Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes
Cited by: 21
Author(s): Vikas Kumar, Verena E. Kutschera, Maria A. Nilsson, Axel Janke
Software Mentions: 3
Published: over 9 years ago
10.1186/1471-2164-14-340
Insights into organ-specific pathogen defense responses in plants: RNA-seq analysis of potato tuber-Phytophthora infestans interactions
Cited by: 98
Author(s): Liangliang Gao, Zheng Jin Tu, Benjamin P. Millett, James M. Bradeen
Software Mentions: 3
Published: over 11 years ago
10.1371/journal.pgen.1004223
Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species
Cited by: 87
Author(s): Kohta Yoshida, Takashi Makino, Katsushi Yamaguchi, Shuji Shigenobu, Mitsuyasu Hasebe, Masakado Kawata, Manabu Kume, Seiichi Mori, Catherine L. Peichel, Atsushi Toyoda, Asao Fujiyama, Jun Kitano
Software Mentions: 3
Published: over 10 years ago
10.1186/s12864-019-6202-3
The neurogenomic transition from territory establishment to parenting in a territorial female songbird
Cited by: 9
Author(s): Alexandra B. Bentz, Douglas B. Rusch, Aaron Buechlein, Kimberly A. Rosvall
Software Mentions: 3
Published: about 5 years ago
10.3389/fmicb.2015.00197
The transcriptional response of microbial communities in thawing Alaskan permafrost soils
Cited by: 111
Author(s): Marco J. L. Coolen, William D. Orsi
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pgen.0040014
Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules
Cited by: 481
Author(s): Todd P. Michael, Todd C. Mockler, Ghislaı̀n Breton, Connor McEntee, Amanda Byer, Jonathan D. Trout, Samuel P. Hazen, Rongkun Shen, Henry D. Priest, Christopher Sullivan, Scott A. Givan, Marcelo J. Yanovsky, Fangxin Hong, Steve A. Kay, Joanne Chory
Software Mentions: 3
Published: almost 17 years ago
10.3389/fimmu.2021.684807
The Regulatory Network and Potential Role of LINC00973-miRNA-mRNA ceRNA in the Progression of Non-Small-Cell Lung Cancer
Cited by: 14
Author(s): Qiang Guo, Dan Li, Xiangyu Luo, Yuan Yao, Li Tian, Huasong Liu, Xinju Wang
Software Mentions: 3
Published: over 3 years ago
10.1038/srep32590
Snapshots of a shrinking partner: Genome reduction in Serratia symbiotica
Cited by: 61
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 3
Published: about 8 years ago
10.3390/plants9040527
Paternity Assignment in White Guinea Yam (Dioscorea Rotundata) Half-Sib Progenies from Polycross Mating Design Using SNP Markers
Cited by: 7
Author(s): Prince E. Norman, Paterne A. Agre, Agyemang Danquah, Pangirayi Tongoona, Eric Danquah, David De Koeyer, Ugochukwu N. Ikeogu, Robert Asiedu, Asrat Asfaw
Software Mentions: 3
Published: over 4 years ago
10.1111/pbi.13305
Cytokinin dehydrogenase: a genetic target for yield improvement in wheat
Cited by: 84
Author(s): Lei Chen, Jingjing Zhao, Jiancheng Song, Paula E. Jameson
Software Mentions: 3
Published: almost 5 years ago
10.3389/fgene.2021.671650
A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi)
Cited by: 7
Author(s): Weidong Ding, Xinhui Zhang, Xiaomeng Zhao, Jing Wu, Zhen Cao, Jia Li, Yu Huang, Xinxin You, Min Wang, Qiong Shi, Xuwen Bing
Software Mentions: 3
Published: over 3 years ago
10.7717/peerj.356
The complex hybrid origins of the root knot nematodes revealed through comparative genomics
Cited by: 85
Author(s): David H. Lunt, Sujai Kumar, Georgios Koutsovoulos, Mark Blaxter
Software Mentions: 3
Published: over 10 years ago
10.1186/1471-2164-15-53
MafFilter: a highly flexible and extensible multiple genome alignment files processor
Cited by: 61
Author(s): Julien Dutheil, Sylvain Gaillard, Eva H. Stukenbrock
Software Mentions: 3
Published: almost 11 years ago
10.3389/fgene.2018.00291
Transcriptome Analyses Reveal Adult Metabolic Syndrome With Intrauterine Growth Restriction in Pig Models
Cited by: 21
Author(s): Linyuan Shen, Mailin Gan, Shunhua Zhang, Jideng Ma, Guoqing Tang, Yanzhi Jiang, Mingzhou Li, Jinyong Wang, Xuewei Li, Lianqiang Che, Li Zhu
Software Mentions: 3
Published: over 6 years ago
10.1186/1471-2164-14-895
Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation
Cited by: 52
Author(s): Adam B. Olson, Heather Kent, Christopher D. Sibley, Margot E. Grinwis, Philip Mabon, Claude Ouellette, Shari Tyson, Morag Graham, Shaun Tyler, Gary Van Domselaar, Michael G. Surette, Cindi R. Corbett
Software Mentions: 3
Published: almost 11 years ago
10.1186/1471-2164-12-99
De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum
Cited by: 106
Author(s): Joshua P. Der, Michael S. Barker, Norman J. Wickett, Claude W. dePamphilis, Paul G. Wolf
Software Mentions: 3
Published: almost 14 years ago
10.7717/peerj.9424
An updated genetic marker for detection of Lake Sinai Virus and metagenetic applications
Cited by: 5
Author(s): Deborah D. Iwanowicz, Judy Wu‐Smart, Tuğçe Olgun, Matthew Smart, Clint R. V. Otto, Dawn Lopez, Jay D. Evans, Robert S. Cornman
Software Mentions: 3
Published: over 4 years ago
10.7717/peerj.8088
Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge<i>Isodictya</i>sp.
Cited by: 11
Author(s): Marcelo González-Aravena, Nathan J. Kenny, Magdalena Osorio, Alejandro Font, Ana Riesgo, César Cárdenas
Software Mentions: 3
Published: almost 5 years ago
10.4161/epi.26017
DNA methylation analysis of murine hematopoietic side population cells during aging
Cited by: 42
Author(s): Oluwatosin Taiwo, Gareth A. Wilson, Warren Emmett, Tiffany Morris, Dominique Bonnet, Eugene F. Schuster, Tomas Adejumo, Stephan Beck, Daniel J. Pearce
Software Mentions: 3
Published: about 11 years ago
10.1111/eva.13194
Standing genetic variation in laboratory populations of insecticide‐susceptible <i>Phlebotomus papatasi</i> and <i>Lutzomyia longipalpis</i> (Diptera: Psychodidae: Phlebotominae) for the evolution of resistance
Cited by: 2
Author(s): David S. Denlinger, Spencer B. Hudson, Nadya S. Keweshan, Zachariah Gompert, Scott A. Bernhardt
Software Mentions: 3
Published: almost 4 years ago
10.1186/1471-2164-5-60
POSA: Perl Objects for DNA Sequencing Data Analysis
Cited by: 5
Author(s): Jan Aerts, B.J. Jungerius, Martien A. M. Groenen
Software Mentions: 3
Published: about 20 years ago
10.7717/peerj.5443
Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (<i>Morus alba</i>L.)
Cited by: 20
Author(s): Dujun Wang, Li Zhao, Dan Wang, Jia Liu, Xin Yu, Yuan Wei, Zhen Ouyang
Software Mentions: 3
Published: about 6 years ago
10.12688/f1000research.12302.1
BAT: Bisulfite Analysis Toolkit
Cited by: 12
Author(s): Helene Kretzmer, Christian Otto, Steve Hoffmann
Software Mentions: 3
Published: over 7 years ago
10.1186/s40168-018-0476-6
Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota
Cited by: 57
Author(s): Ruairi C. Robertson, Kanakaraju Kaliannan, Conall Strain, R. Paul Ross, Catherine Stanton, Jing Kang
Software Mentions: 3
Published: over 6 years ago
10.1186/1746-4811-8-12
Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis
Cited by: 18
Author(s): Kun-Hsiang Liu, Matthew McCormack, Jenq-Yunn Sheen
Software Mentions: 3
Published: almost 13 years ago
10.1111/1755-0998.12959
High‐throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations
Cited by: 84
Author(s): Leho Tedersoo, Rein Drenkhan, Sten Anslan, Carmen Morales‐Rodríguez, Michelle Cleary
Software Mentions: 3
Published: almost 6 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: about 4 years ago
10.1016/j.cels.2017.07.007
Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes
Cited by: 8
Author(s): Christoph N. Schlaffner, Georg J. Pirklbauer, Andreas Bender, Jyoti S. Choudhary
Software Mentions: 3
Published: over 7 years ago
10.3390/v11050397
RNAseq Analysis Reveals Virus Diversity within Hawaiian Apiary Insect Communities
Cited by: 24
Author(s): Laura E. Brettell, Declan C. Schroeder, Stephen J. Martin
Software Mentions: 3
Published: over 5 years ago
10.1186/1471-2164-13-721
Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice
Cited by: 75
Author(s): Tingting Lu, Chuanrang Zhu, Lu Gui, Yunli Guo, Yan Zhou, Zhiyong Zhang, Yan Zhao, Wenjun Li, Ying Lu, Weihua Tang, Qi Feng, Bin Han
Software Mentions: 3
Published: almost 13 years ago
10.1002/ece3.305
Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities
Cited by: 78
Author(s): Lara Danielsen, Andrea Thürmer, Peter Meinicke, Marc Buée, Emmanuelle Morin, Francis Martin, Gilles Pilate, Rolf Daniel, Andrea Polle, M. Reich
Software Mentions: 3
Published: over 12 years ago
10.3390/v11070607
Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-Infection Estimation towards Enhanced Vaccine Efficacy Assessment
Cited by: 11
Author(s): Raabya Rossenkhan, Morgane Rolland, Jan Phillipus Lourens Labuschagne, Roux-Cil Ferreira, Craig A. Magaret, Lindsay N. Carpp, F. A. Matsen, Yunda Huang, Erika Rudnicki, Yuanyuan Zhang, Nonkululeko Ndabambi, Murray Logan, Ted Holzman, Melissa-Rose Abrahams, Colin Anthony, Sodsai Tovanabutra, Christopher Warth, G. Botha, David Matten, Sorachai Nitayaphan, Hannah Kibuuka, Fred Sawe, Denis Chopera, Leigh Anne Eller, Simon Travers, Merlin L. Robb, Carolyn Williamson, Peter B. Gilbert, Paul T. Edlefsen
Software Mentions: 3
Published: over 5 years ago
10.1186/1752-0509-8-34
Network and matrix analysis of the respiratory disease interactome
Cited by: 3
Author(s): Benjamin J. Garcia, Gargi Datta, Gregory P. Cosgrove, Michael Strong
Software Mentions: 3
Published: over 10 years ago
10.1186/s12917-017-1093-5
Whole genome sequencing of an ExPEC that caused fatal pneumonia at a pig farm in Changchun, China
Cited by: 9
Author(s): Lingcong Kong, Xulin Guo, Zi Wang, Yunhang Gao, Boyin Jia, Shuming Liu, Huiqin Ma
Software Mentions: 3
Published: over 7 years ago
10.1186/1471-2164-12-73
Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies
Cited by: 33
Author(s): Minxiao Wang, Song Sun, Chaolun Li, Xin Shen
Software Mentions: 3
Published: almost 14 years ago
10.18632/aging.202989
Integrated analysis of long noncoding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in early stage of post-peripheral nerve injury in Sprague-Dawley rats
Cited by: 3
Author(s): Yujing Zhang, Zhaowei Zhu, Xiangxia Liu, Shuqia Xu, Yi Zhang, Yangbin Xu, Bo He
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2350-7-18
Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions
Cited by: 24
Author(s): Raihan K. Uddin, Yang Zhang, Victoria Mok Siu, Yao Shan Fan, Richard O’Reilly, Jay Rao, Shiva M. Singh
Software Mentions: 3
Published: over 18 years ago
10.1186/1754-6834-6-72
Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation
Cited by: 79
Author(s): Tao Xiang, Yang Fang, Yao Xiao, Yanling Jin, Xinrong Ma, Yun Zhao, Kai He, Hai Zhao, Haiyan Wang
Software Mentions: 3
Published: over 11 years ago
10.1038/srep40301
Evolution of protein N-glycosylation process in Golgi apparatus which shapes diversity of protein N-glycan structures in plants, animals and fungi
Cited by: 25
Author(s): Peng Wang, Hong Wang, Jiangtao Gai, Xiaoli Tian, Xiaoxiao Zhang, Yongzhi Lv, Yi Jiang
Software Mentions: 3
Published: almost 8 years ago
10.3389/fpls.2018.00500
Molecular Mechanisms of Acclimatization to Phosphorus Starvation and Recovery Underlying Full-Length Transcriptome Profiling in Barley (Hordeum vulgare L.)
Cited by: 54
Author(s): Ping Ren, Yali Meng, Baochun Li, Xiao Ma, Erjing Si, Yong Lai, Juncheng Wang, Lirong Yao, Ke Yang, Xianwen Shang, Huajun Wang
Software Mentions: 3
Published: over 6 years ago
10.1186/1471-2164-15-848
Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites
Cited by: 10
Author(s): Karen Russell, Chia-Ho Cheng, Jeffrey W. Bizzaro, Nadia Ponts, Richard D. Emes, Karine G. Le Roch, Kenneth A. Marx, Paul Horrocks
Software Mentions: 2
Published: about 10 years ago
10.1186/1471-2148-11-291
Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling
Cited by: 61
Author(s): David Gerard, H. Lisle Gibbs, Laura Kubatko
Software Mentions: 2
Published: about 13 years ago
10.1371/journal.pone.0083383
New rRNA Gene-Based Phylogenies of the Alphaproteobacteria Provide Perspective on Major Groups, Mitochondrial Ancestry and Phylogenetic Instability
Cited by: 99
Author(s): Matteo P. Ferla, J. Cameron Thrash, Stephen J. Giovannoni, Wayne M. Patrick
Software Mentions: 2
Published: almost 11 years ago
10.1186/s12864-016-2932-7
Computational characterization of Iron metabolism in the Tsetse disease vector, Glossina morsitans: IRE stem-loops
Cited by: 2
Author(s): Zahra Jalali Sefid Dashti, Junaid Gamieldien, Alan Christoffels
Software Mentions: 2
Published: over 8 years ago
10.1186/1471-2148-8-316
Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster
Cited by: 29
Author(s): Andrew C. Doxey, Michael Lynch, Kirsten M. Müller, Elizabeth M. Meiering, Brendan J. McConkey
Software Mentions: 2
Published: about 16 years ago
10.1186/1471-2105-11-609
RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes
Cited by: 6
Author(s): Vipin Kumar Singh, Rakesh K. Mishra
Software Mentions: 2
Published: almost 14 years ago
10.1371/journal.pone.0180135
Reversible perturbations of gene regulation after genome editing in Drosophila cells
Cited by: 5
Author(s): Stefan Kunzelmann, Klaus Förstemann
Software Mentions: 2
Published: over 7 years ago
10.1186/1471-2164-12-267
Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: Role of the LINE-encoded endonuclease
Cited by: 13
Author(s): Vandana Kumari, Rahul Sharma, Vijay Pal Yadav, Abhishek Kumar Gupta, Alok Bhattacharya, Sudha Bhattacharya
Software Mentions: 2
Published: over 13 years ago
10.1186/1471-2105-6-S4-S19
High performance workflow implementation for protein surface characterization using grid technology
Cited by: 5
Author(s): Ivan Merelli, Giulia Morra, Daniele D’Agostino, Andrea Clematis, Luciano Milanesi
Software Mentions: 2
Published: almost 19 years ago
10.1186/1471-2105-6-145
Satellog: A database for the identification and prioritization of satellite repeats in disease association studies
Cited by: 15
Author(s): Perseus I. Missirlis, Carri-Lyn Mead, Stefanie Butland, B. F. Francis Ouellette, Rebecca S. Devon, Blair R. Leavitt, Robert A. Holt
Software Mentions: 2
Published: over 19 years ago
10.1186/1471-2164-14-573
Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis)
Cited by: 160
Author(s): Xiaoming Song, Ying Liu, Xilin Hou
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0006447
Mining Biological Pathways Using WikiPathways Web Services
Cited by: 107
Author(s): Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Martijn P. van Iersel, Chris T. Evelo, Bruce R. Conklin
Software Mentions: 2
Published: over 15 years ago
10.1371/journal.pone.0125989
Dicer-Dependent Biogenesis of Small RNAs and Evidence for MicroRNA-Like RNAs in the Penicillin Producing Fungus Penicillium chrysogenum
Cited by: 33
Author(s): Tim A. Dahlmann, Ulrich Kück
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2164-12-142
Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis
Cited by: 13
Author(s): Zhixi Tian, Yong Yu, Feng Lin, Yeisoo Yu, Phillip SanMiguel, Rod A. Wing, Susan R. McCouch, Jianxin Ma, Scott A. Jackson
Software Mentions: 2
Published: over 13 years ago
10.1186/1471-2148-10-282
The evolutionary trajectory of mitochondrial carrier family during metazoan evolution
Cited by: 7
Author(s): Ming Gong, Jie Li, Meng Wang, Jin Wang, Ke Zen, Chenyu Zhang
Software Mentions: 2
Published: about 14 years ago
10.1186/1471-2164-15-1126
Bovine serum albumin in saliva mediates grazing response in Leymus chinensis revealed by RNA sequencing
Cited by: 10
Author(s): Xin Huang, Xianjun Peng, Lexin Zhang, Shuangyan Chen, Long Cheng, Gongshe Liu
Software Mentions: 2
Published: almost 10 years ago
10.1186/1471-2105-9-21
LeARN: a platform for detecting, clustering and annotating non-coding RNAs
Cited by: 10
Author(s): Céline Noirot, Christine Gaspin, Thomas Schiex, Jérôme Gouzy
Software Mentions: 2
Published: almost 17 years ago
10.1186/1471-2105-12-457
A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships
Cited by: 12
Author(s): Claire Lemaitre, Aurélien Barré, Christine Citti, Florence Tardy, François Thiaucourt, Pascal Sirand‐Pugnet, Patricia Thébault
Software Mentions: 2
Published: almost 13 years ago
10.1186/1471-2148-10-123
Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach
Cited by: 52
Author(s): Ajna S. Rivera, M. Sabrina Pankey, David C. Plachetzki, Carlos Darwin Angulo Villacorta, Anna Syme, Jeanne M. Serb, Angela R. Omilian, Todd H. Oakley
Software Mentions: 2
Published: over 14 years ago
10.3390/ani10010053
Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes
Cited by: 13
Author(s): Siavash Salek Ardestani, Mehdi Aminafshar, Mohammad Bagher Zandi Baghche Maryam, Mohammad Hossein Banabazi, Mehdi Sargolzaei, Younes Miar
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0035152
Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics
Cited by: 119
Author(s): Peifeng Ji, Guiming Liu, Jian Xu, Xumin Wang, Jiong-Tang Li, Zixia Zhao, Xiaofeng Zhang, Yan Zhang, Peng Xu, Xin Sun
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0066476
The Composition of Microbiome in Larynx and the Throat Biodiversity between Laryngeal Squamous Cell Carcinoma Patients and Control Population
Cited by: 66
Author(s): Hongli Gong, Yi Shi, Liang Zhou, Chunping Wu, Pengyu Cao, Lei Tao, Chen Xu, Dongsheng Hou, Yuezhu Wang
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0255523
Finding inhibitors for PCSK9 using computational methods
Cited by: 12
Author(s): Rida Zainab, Afshan Kaleem, Michał B. Ponczek, Roheena Abdullah, Mehwish Iqtedar, Daniel C. Hoessli
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0079011
Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots
Cited by: 45
Author(s): Sunita Kumari, Doreen Ware
Software Mentions: 2
Published: about 11 years ago
10.1186/1471-2105-15-266
Natural language processing of radiology reports for the detection of thromboembolic diseases and clinically relevant incidental findings
Cited by: 80
Author(s): Anne-Dominique Pham, Aurélie Névéol, Thomas Lee, D Yasunaga, Olivier Clémеnt, Guy Meyer, Rémy Morello, Anita Burgun
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0002103
The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria
Cited by: 128
Author(s): Sara H. Thomas, Ryan D. Wagner, Adrián K. Arakaki, Jeffrey Skolnick, John R. Kirby, Lawrence J. Shimkets, Robert A. Sanford, Frank E. Löffler
Software Mentions: 2
Published: over 16 years ago
10.1371/journal.pone.0027297
Pseudomonas syringae pv. actinidiae Draft Genomes Comparison Reveal Strain-Specific Features Involved in Adaptation and Virulence to Actinidia Species
Cited by: 118
Author(s): Simone Marcelletti, Patrizia Ferrante, Milena Petriccione, Giuseppe Firrao, M. Scortichini
Software Mentions: 2
Published: almost 13 years ago