COGNATE: comparative gene annotation characterizer by Jeanne Wilbrandt, Bernhard Misof, Oliver Niehuis

“…COGNATE is written in Perl and freely available at the ZFMK homepage ( https://www.zfmk.de/en/COGNATE ) and on github ( https://github.com/ZFMK/COGNATE ). …”
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Micronization of zeolite in vibration mill by Andrić Ljubiša, Trumić Milan, Trumić Maja, Nikolić Vladimir

“…For the production of powders - particles of micron dimensions, the mechano-actuators are used and all micronizers - disintegrators, colloidal (perl mills), vibratory, planetary, ultra-centrifugal mill, Jet-current mills and others operate on the principle of impact, shock and friction. …”
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The distribution characteristics of global blaOXA-carrying Klebsiella pneumoniae by Lingning Meng, Ziyao Liu, Chang Liu, Chuchu Li, Han Shen, Xiaoli Cao

“…The MLST (multi-locus sequence type) website and blastn tools were utilized to determine the sequence types (STs) of these blaOXA-carrying strains. and sample resource, isolation country, date and host were extracted by perl program for analyzing the characteristics of these strains. …”
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API Driven On-Demand Participant ID Pseudonymization in Heterogeneous Multi-Study Research by Shorabuddin Syed, Mahanazuddin Syed, Hafsa Bareen Syeda, Maryam Garza, William Bennett, Jonathan Bona, Salma Begum, Ahmad Baghal, Meredith Zozus, Fred Prior

“…This paper presents a novel tool that pseudonymizes participant identifiers (PIDs) using a researcher-driven automated process that takes advantage of application-programming interface (API) and the Perl Open-Source Digital Imaging and Communications in Medicine Archive (POSDA) to further de-identify PIDs. …”
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Iron accumulation induced by hepcidin1 knockout accelerates the progression of aging osteoporosis by Lu-lin Liu, Zhong-rui Liu, Lu-jun Cao, Jun Wang, San-ming Huang, Shui-gen Hu, Yi-zhong Yang, Dong-sheng Li, Wei-wei Cao, Qing-bao Zeng, Sheng Huang, Qiong Wu, Jian-hua Xiao, Wu-yang Liu, Yao-sheng Xiao

“…Methods Iron accumulation in hepcidin1 knockout aging mice was assessed by atomic absorption spectroscopy and Perl’s staining. Bone microarchitecture was observed using Micro-CT. …”
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Exploration of the Immune-Related Signatures and Immune Infiltration Analysis in Melanoma by Ai-lan Li, Yong-mei Zhu, Lai-qiang Gao, Shu-yue Wei, Ming-tao Wang, Qiang Ma, You-you Zheng, Jian-hua Li, Qing-feng Wang

“…After merging the genome expression data using Perl, the limma package was used for data normalization. …”
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Construction and validation of an RNA-binding protein-associated prognostic model for colorectal cancer by Yandong Miao, Hongling Zhang, Bin Su, Jiangtao Wang, Wuxia Quan, Qiutian Li, Denghai Mi

“…Gene expression profiles were analyzed to identify differentially expressed RBPs using R and Perl software. Hub RBPs were filtered out using univariate Cox and multivariate Cox regression analysis. …”
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Effects of physical therapy modalities for motor function, functional recovery, and post-stroke complications in patients with severe stroke: a systematic review update by Katrin Roesner, Bettina Scheffler, Martina Kaehler, Bianca Schmidt-Maciejewski, Tabea Boettger, Susanne Saal

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Automatic extraction of candidate nomenclature terms using the doublet method by Berman Jules J

“…An implementation of the algorithm, in the Perl programming language, is provided with this article.…”
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Sequence variation of PfEMP1-DBLα in association with rosette formation in <it>Plasmodium falciparum </it>isolates causing severe and uncomplicated malaria by Craig Alister, Kalambaheti Thareerat, Horata Natharinee, Khusmith Srisin

“…</p> <p>Methods</p> <p>Two hundred and ninety five PfEMP1-DBLα sequences from Thai clinical isolates causing severe and uncomplicated malaria were evaluated by sequencing and direct comparison using the specific text string analysis functions in Microsoft Excel and Perl. The relationships between the PfEMP1-DBLα sequences were also analysed by network analysis. …”
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UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study by Peng Qi, Davis Gimode, Dipnarayan Saha, Stephan Schröder, Debkanta Chakraborty, Xuewen Wang, Mathews M. Dida, Russell L. Malmberg, Katrien M. Devos

“…Results UGbS-Flex combines publicly available software with in-house python and perl scripts to efficiently call SNPs from genotyping-by-sequencing reads irrespective of the species’ ploidy level, breeding system and availability of a reference genome. …”
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Network Pharmacology and Experimental Validation to Reveal the Pharmacological Mechanisms of Chongcaoyishen Decoction Against Chronic Kidney Disease by Zhenliang Fan, Jingjing Chen, Qiaorui Yang, Jiabei He

“…We matched the active ingredients with gene targets and conducted regulatory networks through Perl5 and R 3.6.1. The network visualization analysis was performed by Cytoscape 3.7.1, which contains ClueGO plug-in for GO and KEGG analysis. …”
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Morphological Spectrum of Bone Marrow Changes in Patients of Chronic Kidney Disease: A Cross-sectional Study by Mayank Kumar Singh, Narendra Singh Sengar, Sufia Ahmad Khan, Ashish Kumar

“…The Medonic-M Series, an automated haematological analyser, performed the Complete Blood Count (CBC) with red cell indices. Perl’s staining and the Gale Grading Systems were used for assessing iron storage. …”
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Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome by Jun-Sub Kim, Jun-Hyeong Jang, Jeong-Min Kim, Yoon-Seok Chung, Cheon-Kwon Yoo, Myung-Guk Han

“…Multiple sequence alignment for phylogenetic analysis and comparative genomic approach for mutation analysis were conducted using Molecular Evolutionary Genetics Analysis (MEGA), and an in-house program based on Perl language, respectively. Results Phylogenetic analysis of SARS-CoV-2 strains indicated that there were 3 major clades including S, V, and G, and 2 subclades (G.1 and G.2). …”
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Preliminary Studies on Biodegradable Zinc Oxide Nanoparticles Doped with Fe as a Potential Form of Iron Delivery to the Living Organism by Paula Kielbik, Jarosław Kaszewski, Bartłomiej Dominiak, Magdalena Damentko, Izabela Serafińska, Julita Rosowska, Mikołaj A. Gralak, Marcin Krajewski, Bartłomiej S. Witkowski, Zdzislaw Gajewski, Marek Godlewski, Michal M. Godlewski

“…The iron concentration measured with atomic absorption spectrometry and histological staining (Perl’s method) showed a rapid distribution of iron-doped nanoparticles to tissues specifically related with iron homeostasis. …”
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Relationship between cognitive impairment and hippocampal iron overload: A quantitative susceptibility mapping study of a rat model by Xi Deng, Meiru Bu, Jiali Liang, Yihao Sun, Liyan Li, Heishu Zheng, Zisan Zeng, Muliang Jiang, Bihong T. Chen

“…The iron content in hippocampal tissue sections of the rats were assessed using diaminobenzidine (DAB)-enhanced Perl's Prussian blue (PPB) staining. Results: The rat groups with iron overload including the Group H and Group L had higher hippocampal magnetic susceptibility values than the control rat group, i.e., Group D. …”
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PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data by Ritwika Das, Vasu Arora, Sarika Jaiswal, MA Iquebal, UB Angadi, Samar Fatma, Rakesh Singh, Sandip Shil, Anil Rai, Dinesh Kumar

“…We developed the tool (PolyMorphPredict) using Perl, R, Java and launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. …”
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<it>De novo</it> assembly of the pepper transcriptome (<it>Capsicum annuum</it>): a benchmark for <it>in silico</it> discovery of SNPs, SSRs and candidate genes by Ashrafi Hamid, Hill Theresa, Stoffel Kevin, Kozik Alexander, Yao JiQiang, Chin-Wo Sebastian, Van Deynze Allen

“…BWA, SAMtools and in-house Perl scripts were used to identify SNPs among three pepper genotypes. …”
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The ARTI framework: cosmic rays atmospheric background simulations by Christian Sarmiento-Cano, Mauricio Suárez-Durán, Rolando Calderón-Ardila, Adriana Vásquez-Ramírez, Andrei Jaimes-Motta, Luis A. Núñez, Sergio Dasso, Iván Sidelnik, Hernán Asorey, For the LAGO Collaboration

“…Formulated through a sequence of codes written in C++, Fortran, Bash and Perl, it provides an easy-to-use integration of three different simulation environments: MagnetoCosmics, CORSIKA and Geant4. …”
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Quantitative detection of Vibrio alginolyticus strain XSBZ14 by a newly developed RT-PCR method by Na Zhang, Siyue Yang, Xiang Zhang, Hao Long, Xiaoni Cai, Yanan Fu, Zhenyu Xie

“…Methods At first, a low sequence identity single-copy sequence S2 was selected from the genome by in-house Perl script. Using the designed specific primers, four different types of standard curves were subsequently plotted for the accurate quantification of the strain XSBZ14 in four different samples (DNA, bacterial suspension, coral tissue, seawater). …”
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