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Preprint ARTICLE | doi:10.20944/preprints202301.0123.v1

Towards Understanding the Key Signature Pathways Associated from Differentially Expressed Gene Analysis in an Indian Prostate Cancer Cohort

Nidhi Shukla, Bhumandeep Kour, Devendra Sharma, Maneesh Vijayvargiya, T C Sadasukhi, Krishna Mohan Medicherla, Babita Malik, Bhawana Bissa, Sugunakar Vuree, Nirmal Kumar Lohiya, Prashanth Suravajhala

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Prostate cancer; Systems genomics; Functional genomics; Pathways; biomarkers

Online: 6 January 2023 (09:58:26 CET)

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Prostate cancer (PCa) is one of the most prevalent cancers among men in India. Although studies on PCa have dealt with the genetics, genomics, and the environmental influence in causality of PCa, not many studies employing the next generation sequencing (NGS) approaches of PCa have been carried out. In our previous study, we have identified some causal genes and mutations specific to Indian PCa using Whole-Exome Sequencing (WES). In the recent past, with the help of different cancer consortiums such as The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), along with differentially expressed genes (DEGs), many cancer-associated novel non-coding RNAs have been identified as biomarkers. In this work, we attempt to identify DEGs as well as long non-coding RNAs (lncRNAs) associated with signature pathways from an Indian PCa cohort using RNA-sequencing (RNA-seq) approach. From a cohort of 60, we screened 6 patients who underwent prostatectomy; we performed a whole transcriptome shotgun sequencing (WTSS)/RNA-sequencing to decipher the DEGs. We further normalized the read counts using fragments per kilobase of transcript per million mapped reads (FPKM) and analyzed the DEGs using a cohort of downstream regulatory tools, viz. GeneMANIA Stringdb, Cytoscape-Cytohubba, cbioportal to map the inherent signatures associated with PCa. By comparing the RNA-seq data obtained from the pairs of normal and PCa tissue samples using our benchmarked in-house cuffdiff pipeline, we observed some important genes specific to PCa such as STEAP2, APP, PMEPA1, PABPC1, NFE2L2, HN1L and some other important genes known to be involved in different cancer pathways such as, COL6A1, DOK5, STX6, BCAS1, BACE1, BACE2, LMOD1, SNX9, CTNND1 etc. We also identified a few novel lncRNAs such as LINC01440, SOX2OT, ENSG00000232855, and ENST00000647843.1 that need to be characterized further. Deregulation of SOX2OT is observed in various tumors, including lung cancer, gastric cancer, esophageal cancer, breast cancer, hepatocellular carcinoma, ovarian cancer, pancreatic, laryngeal squamous cell carcinoma, osteosarcoma, nasopharyngeal carcinoma, and glioblastoma. It would be interesting to characterize its function in PCa as well. In comparison with publicly available datasets, we have identified characteristic DEGs and novel lncRNAs implicated in signature PCa pathways in an Indian PCa cohort which have perhaps not been reported. As a pilot study, this has set a precedent for us to validate further experimentally, and we firmly believe this will pave a way towards discovery of biomarkers and development of novel therapies.

Preprint ARTICLE | doi:10.20944/preprints201905.0182.v1

Rediscovering the Ethical Priority of the Most Actionable System of Biomolecules—The Metabolome

Cecil M. Lewis, Laura-Isobel McCall, Richard Sharp, Paul G. Spicer

Subject: Biology And Life Sciences, Endocrinology And Metabolism Keywords: metabolomics; genomics; ethics

Online: 15 May 2019 (10:09:48 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202309.1740.v1

Histone H3K36 and H3K27 Modifiers and Readers as Prognostic Factors in Patients with Cancer—A Pancancer Analysis

Chidiebube Ugwu, Pauline Lin, George Laliotis

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Histone Modifiers; cancer; Genomics;

Online: 26 September 2023 (07:15:04 CEST)

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Preprint REVIEW | doi:10.20944/preprints202307.0870.v1

Investigating Cryptosporidium spp. Using Genomic and Proteomic Techniques: Current Progress and Future Directions

Joanna Dąbrowska, Jacek Sroka, Tomasz Cencek

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Cryptosporidium spp.; genomics; proteomics

Online: 13 July 2023 (10:03:56 CEST)

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Preprint REVIEW | doi:10.20944/preprints202011.0501.v1

Genome Sequencing Guide: An Introductory Toolbox to Whole-Genome Analysis Methods

Alexis Burian, Wufan Zhao, Te-Wen Lo, Deborah Thurtle-Schmidt

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genomics; sequencing; ethics; bioinformatics

Online: 19 November 2020 (10:41:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints202105.0750.v1

Origin, Phylogeny, Variability and Epitope Conservation of SARS-CoV-2 Worldwide

Filipa F Vale, Jorge M.B. Vítor, Andreia T. Marques, José Miguel Azevedo-Pereira, Elsa Anes, João Gonçalves

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS-CoV-2 genomics; spike protein; epitope prediction; coronavirus comparative genomics

Online: 31 May 2021 (11:36:29 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0046.v1

The Future of Newborn Genomic Screening

JOHN David LANTOS

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: ethics; genomics; neonates; outcomes; economics

Online: 1 June 2023 (07:23:07 CEST)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202203.0069.v1

Could a Focus on the “Why” of Taxonomy Help Taxonomy Better Respond to the Needs of Science and Society?

Leighton Pritchard, C. Titus Brown, Bailey Harrington, Lenwood S. Heath, N. Tessa Pierce-Ward, Boris A. Vinatzer

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: prokaryotic taxonomy; classification; identification; genomics

Online: 3 March 2022 (17:18:57 CET)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202107.0546.v1

Bacterial Nomenclature in the Era of Genomics

Mark John Pallen

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Bacterial nomenclature; taxonomy; microbial genomics

Online: 23 July 2021 (14:22:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201912.0183.v2

Investigating the Influence of the Comprehensive mRNA Expression Levels of Prognostic Genes on Patient Survival in Every Type of Cancer

Minhyeong Lee

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Bioinformatics, Genomics, TCGA, Cox Model.

Online: 21 August 2020 (11:26:33 CEST)

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Preprint TECHNICAL NOTE | doi:10.20944/preprints202007.0179.v1

UCSCXenaShiny: An R Package for Exploring and Analyzing UCSC Xena Public Datasets in Web Browser

Shixiang Wang, Yi Xiong, Kai Gu, Longfei Zhao, Yin Li, Fei Zhao, Xuejun Li, Xue-Song Liu

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: UCSC Xena, cancer genomics, TCGA

Online: 9 July 2020 (07:59:18 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202003.0392.v1

In silico Comparative Genomics of the Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19) and Designing of a Cost-effective RFLP-PCR Based Mass Screening Diagnostic Protocol

Aditya Singh, Prateek Bhatia

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; diagnosis; comparative genomics

Online: 26 March 2020 (14:58:35 CET)

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SARS-CoV 2 also known as COVID-19 is a fast spreading coronavirus related disease that emerged from China in December 2019 and is currently attained the status of a pandemic. There are currently no drugs/ vaccines against the same and moreover limited diagnostic tests to identify the infection. Additionally, these tests are expensive and hence are exclusive for very highly suspected cases of the disease especially in developing countries. This is causing an under-diagnosis which is an alarming state of affairs, as even a single missed SARS-CoV 2 case would spread the disease exponentially and keep it in the community. Through this entirely in silico study, we have developed a cheaper and faster diagnostic method based on simple PCR and restriction enzyme digestion, commonly used in restriction fragment length polymorphism (RFLP) tests. Through comparative genomics, we found the closest neighbours of SARS-CoV 2 then found the highly conserved regions of the genome which were absent in SARS-CoV 1, its closest neighbour. Then we found restriction sites for various enzymes followed by designing of PCR primers flanking those sites. We have found the primer pair to produce a 401 bp amplicon and when digested by SwaI enzyme, it produces two fragments of lengths 216 bp and 185 bp. As an internal control, GAPDH primers are pooled with the SARS-CoV 2 primers as the patient sample will also include human RNA mixed with the viral RNA. This primer pair gives an amplicon of 131 bp and hence a negative sample should show a single band of 131 bp while a positive digested sample will give three bands of 401 bp, 216 bp and 131 bp. The primers are specific to SARS-CoV 2 only and can additionally be used for SYBR green based real time quantification of viral load. The developed tests have not yet been tested in vitro due to stressed out working hours in the only pathogenic virus handling laboratory in our institute. Nonetheless, this study works as a head start for other laboratories to rapidly test the suggested protocols in vitro and make available a cheaper alternative test for SARS-CoV 2 which would especially be beneficial for the lower to middle income countries.

Preprint ESSAY | doi:10.20944/preprints202001.0107.v1

Ten Recommendations for Supporting Open Pathogen Genomic Analysis in Public Health Settings

Allison Black, Duncan R. MacCannell, Thomas R. Sibley, Trevor Bedford

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: pathogen genomics; public health; bioinformatics

Online: 11 January 2020 (11:30:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints201905.0113.v1

Introducing DNA Sequencing to the Next Generation on a Research Vessel Sailing the Bering Sea Through a Storm

Anne-Lise Ducluzeau, Rachel M. Lekanoff, Noah S. Khalsa, Hillary H. Smith, Devin M. Drown

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: education; genomics; nanopore; oceanography; fieldwork

Online: 9 May 2019 (12:57:09 CEST)

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Experiential learning in the field is an opportunity for students to enter the heart of a scientific discipline. Through such experience, they can extract conceptual clues and discover motivational stepping stones that will potentially influence the rest of their education and career choice. Unfortunately, in Biology, the inescapable topic of Next-Generation Sequencing represents a challenge when it comes to create an educational curriculum that aims to provide students with hands-on experience on sequencers. It is an even more difficult task to accomplish if one’s purpose was to set such curriculum in a field situation. However, in recent years, educators have seen possibility to bring Next-Generation Sequencing to the reach of students more easily, with the Oxford Nanopore MinION, a low-budget, user-friendly, hand-held sequencer. Academic researchers have illustrated the performances of this device in the field and are inspirational for curricula aiming to take the next generation of scientists in the outdoors. We designed a modular 5-day workshop, with nanopore sequencing to be performed in field conditions. Here we describe the material and methods that lead the students and instructors from sample collection, DNA extraction and preparation for nanopore sequencing with MinION to real-time analysis of the data collected. This curriculum was implemented for the first-time aboard Research Vessel Sikuliaq during a transit organized by the STEMSEAS program at Columbia University in collaboration with the University of Alaska BLaST program. The line of investigation formulated for the workshop was an open-ended question that led the students to establish a proof of concept in terms of technology deployment at sea: what will show metagenomic results from DNA obtained from sea water and sequenced with Oxford Nanopore MinION? The workshop took place in October 2018 while Research Vessel Sikuliaq sailed the Alaskans seas for 7 days. Students successfully used nanopore sequencing for multiple metagenomic seawater samples. Their introductory analysis was consistent with environmental conditions and they were able to present their results by the end of the workshop.

Preprint ARTICLE | doi:10.20944/preprints201807.0618.v1

Mountains and Chasms - Surveying the Oncogenomic Publication Landscape

Paula Carrio Cordo, Michael Baudis

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Cancer genomics; CNA; CGH; bioinformatics

Online: 31 July 2018 (10:21:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1797.v1

The Genome Assembly of the King Ratsnake Elaphe carinata, Helps Reveal Its Biological Characteristics

Jiale Fan, Ruyi Huang, Diancheng Yang, Yanan Gong, Zhangbo Cui, Xinge Wang, Zicheng Su, Jing Yu, Yi Zhang, Tierui Zhang, Zhihao Jiang, Tianming Lan, He Wang, Song Huang

Subject: Biology And Life Sciences, Life Sciences Keywords: Genetics and Genomics; Zoology; Animal Genetics

Online: 25 August 2023 (09:35:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1451.v1

The Genome Assembly and Annotation of the Oriental Ratsnake Ptyas mucosa

Jiangang Wang, Shiqing Wang, Song Huang, Qing Wang, Tianming Lan, Ming Jiang, Haitao Wu, Yuxiang Yuan

Subject: Biology And Life Sciences, Other Keywords: Genetics and Genomics; Evolutionary Biology; Zoology

Online: 22 August 2023 (03:43:10 CEST)

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Preprint DATA DESCRIPTOR | doi:10.20944/preprints202306.0658.v1

The Genome Assembly and Annotation of the Bungarus multicinctus

Boyang Liu, Liangyu Cui, Zhangwen Deng, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Tianming Lan, Shuhui Yang, Song Huang

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Genetics and Genomics; Evolutionary Biology; Zoology

Online: 9 June 2023 (03:30:56 CEST)

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Preprint REVIEW | doi:10.20944/preprints202303.0336.v1

Plankton Genes and Extracellular Organic Substances in the Ocean

Ian R. Jenkinson

Subject: Biology And Life Sciences, Aging Keywords: ocean; phytoplankton; bacteria; biogeochemistry; rheology; genomics

Online: 20 March 2023 (03:07:57 CET)

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Preprint REVIEW | doi:10.20944/preprints202209.0050.v1

An Overview of the Infectious Cycle of Bunyaviruses

Hani Boshra

Subject: Biology And Life Sciences, Virology Keywords: bunyavirus; structure; genomics; immune response; review

Online: 5 September 2022 (07:49:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0337.v1

Mitochondrial Control Region Variants Related to Breast Cancer

Luis Enrique Hernández, Jorge Hermilo Vega Avalos, Laura Yareni Zuñiga, Maria Guadalupe Sánchez-Parada, Ana Elizabeth González Santiago, Luis Miguel Román Pintos, Rolando Castañeda Arellano, Luis Daniel Hernández Ortega, Arieh Roldan Mercado Sesma, Felipe de Jesús Orozco-Luna, Raul C. Baptista-Rosas

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: breast cancer; polymorphism; mitochondrial genomics; D310

Online: 18 August 2022 (10:17:28 CEST)

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Preprint REVIEW | doi:10.20944/preprints202204.0149.v1

Visiting Sweet Potato from a Breeding Perspective: An Update

Shankar AB, Prashant Kaushik

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: sweet potato; breeding; genetics; genomics; health

Online: 15 April 2022 (14:58:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0112.v1

Phthalate Esters Metabolic Strain Gordonia sp. GZ-YC7, A Potential Soil Degrader for High Concentration Di-(2-ethylhexyl) Phthalate

Tong Hu, Chen Yang, Zhengyu Hou, Tengfei Liu, Xiaotong Mei, Lianbao Zheng, Weihong Zhong

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: PAEs; Comparative genomics analysis; DEHP; Bioremediation

Online: 8 March 2022 (01:58:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0533.v1

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

Carla L. Saldaña, Pedro Rodriguez-Grados, Julio C. Chávez-Galarza, Shefferson Feijoo, Juan Carlos Guerrero Abad, Héctor V. Vásquez, Jorge L. Maicelo, Jorge H. Jhoncon, Carlos I. Arbizu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chloroplast; genetic resources; genomics capirona; phylogenomics

Online: 29 November 2021 (12:32:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints202001.0064.v1

Measuring the Microscopic Structures of Human Dental Enamel Can Predict Caries Experience

Ariana M. Kelly, Anna Kaliskova, Erika C. Küchler, Helena F. Romanos, Andrea Lips, Marcelo C. Costa, Adriana Modesto, Alexandre R. Vieira

Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: dental enamel; dental caries; genomics; odontogenesis

Online: 8 January 2020 (06:35:12 CET)

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Objectives: The hierarchical structure of enamel gives insight on the properties of enamel and can influence its strength and ultimately caries experience. Presently, past caries experience is quantified using the decayed, missing, filled teeth/decayed, missing, filled surface (DMFT/DMFS for permanent teeth; dmft/dmfs for primary teeth) or international caries detection and assessment system (ICDAS) scores. By analyzing the structure of enamel, a new measurement can be utilized clinically to predict susceptibility to future caries experience based on a patient’s individual’s biomarkers. The purpose of this study was to test the hypothesis that number of prisms by square millimeter in enamel and average gap distance between prisms and interprismatic areas, influence caries experience through genetic variation of the genes involved in enamel formation. Materials and Methods: Scanning electron microscopy (SEM) images of enamel from primary teeth were used to measure number of prisms by square millimeter and interprismatic spaces, prism density and gap distances between prisms in the enamel samples. The measurements were tested to explore a genetic association with variants of selected genes and correlations with caries experience based on the individual’s DMFT+ dmft score and enamel microhardness at baseline, after an artificial lesion was created and after the artificial lesion was treated with fluoride. Results: Associations were found between variants of genes including ameloblastin, amelogenin, enamelin, tuftelin, tuftelin interactive protein 11, beta defensin 1, matrix metallopeptidase 20 and enamel structure variables measured. Significant correlations were found between caries experience and microhardness and enamel structure. Negative correlations were found between number of prisms by square millimeter and high caries experience (r value= -0.71), gap distance between prisms and the enamel microhardness after an artificial lesion was created (r value= -0.70), and gap distance between prisms and the enamel microhardness after an artificial lesion was created and then treated with fluoride (r value= -0.81). There was a positive correlation between number of prisms by square millimeter and prism density of the enamel (r value= 0.82). Conclusions: our data support that genetic variation may impact enamel formation, and therefore influence susceptibility to dental decay and future caries experience. Clinical Relevance: The evaluation of enamel structure that may impact caries experience allows for hypothesizing that the identification of individuals at higher risk for dental caries and implementation of personalized preventative treatments may one day become a reality.

Preprint ARTICLE | doi:10.20944/preprints201808.0423.v1

mitoMaker: A Pipeline for Automatic Assembly and Annotation of Animal Mitochondria Using Raw NGS Data

Alex Schomaker-Bastos, Francisco Prosdocimi

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: mitochondrial DNA; mitochondrial genome; genome assembly; genome annotation; next generation sequencing; animal genomics; partial genomics; bioinformatics

Online: 24 August 2018 (03:24:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0775.v1

Genome Assembly and Annotation of the Sharp-Nosed Pit Viper Deinagkistrodon acutus Based on Next-Generation Sequencing Data

Xinyu Wang, Lirong Liu, Wenbiao Zhu, Shiqing Wang, Minhui Shi, Shuhui Yang, Haorong Lu, Jun Cao

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Genetics and Genomics; Animal Genetics; Evolutionary Biology

Online: 9 August 2023 (10:51:51 CEST)

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Preprint REVIEW | doi:10.20944/preprints202302.0405.v1

The Promise of Explainable Deep Learning for Omics Data Analysis: Adding New Discovery Tools to AI

Mariangela Santorsola, Francesco Lescai

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Explainability; Deep Learning; Artificial Intelligence; Genomics; Transcriptomics

Online: 23 February 2023 (09:32:09 CET)

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Preprint ARTICLE | doi:10.20944/preprints202301.0345.v1

Genetic Diversity and Population Structure of the Peruvian Andean Legume, tarwi (Lupinus mutabilis), With High Quality SNPs

Amelia Huaringa-Joaquin, Carla L. Saldaña, David Saravia, Sady García-Bendezú, Pedro Rodriguez-Grados, Wilian Salazar, Felix Camarena, Pedro Injante, Carlos I. Arbizu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Fabaceae; bioinformatics; molecular markers; neglected crop; genomics

Online: 19 January 2023 (03:57:25 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202109.0485.v2

The Case for Standardising Gene Nomenclature Across Vertebrates

Fiona M. McCarthy, Tamsin E.M. Jones, Anne E. Kwitek, Cynthia L. Smith, Peter D. Vize, Monte Westerfield, Elspeth A. Bruford

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: gene nomenclature; vertebrate genomics; oxytocin; arginine vasopressin

Online: 29 April 2022 (08:09:45 CEST)

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Preprint REVIEW | doi:10.20944/preprints202101.0521.v1

Approaches to Integrating Metabolomics and Multi-Omics Data: A Primer

Takoua Jendoubi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Data integration; multi-omics; integration strategies; genomics

Online: 25 January 2021 (16:19:31 CET)

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Preprint REVIEW | doi:10.20944/preprints202010.0118.v1

From FAANG to Fork: Application of Highly Annotated Genomes to Improve Farmed Animal Production

Emily L Clark, Alan L Archibald, Hans D Daetwyler, Martien AM Groenen, Peter W Harrison, Ross D Houston, Christa Kuehn, Sigbjorn Lien, Daniel J Macqueen, James M Reecy, Diego Robledo, Mick Watson, Christopher K Tuggle, Elisabetta Giuffra

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: FAANG; farmed animal; genomics; genotype-to-phenotype

Online: 6 October 2020 (10:53:17 CEST)

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Preprint REVIEW | doi:10.20944/preprints202009.0073.v1

Genetics and Genomics of Pediatric Pulmonary Arterial Hypertension

Carrie L. Welch, Wendy K. Chung

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: genomics; pediatrics; lung disease; pulmonary arterial hypertension

Online: 3 September 2020 (15:29:36 CEST)

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Working Paper ARTICLE

Bringing Onco-innovation to Europe's Healthcare Systems: The Potential of Biomarker Testing, Real World Evidence, Tumour Agnostic Therapies to Empower Personalised Medicine

Denis Horgan, Gennaro Ciliberto, Pierfranco Conte, Giuseppe Curigliano, Luis Seijo, Luis M. Montuenga, Marina Garassino, Frederique Penault-Llorca, Fabrizia Galli, Isabelle Ray-Coquard, Denis Querleu, Peter Riegman, Keith Kerr, Hendrik Van Poppel, Anders Bjartell, Giovanni Codacci-Pisanelli, Benedikt Westphalen, Jasmina Koeva-Balabanova, Angelo Paradiso, Zorana Maravic, Vassiliki Fotaki, Nuria Malats, Chiara Bernini, Simonetta Buglioni, Alastair Kent, Elisabetta Munzone, Ivica Belina, Jan Van Meerbeeck, Michael Duffy, Beata Jagielska, Ettore Capoluongo

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: cancer biomarkers; BRCA1/2; genomics; European recommendation

Online: 18 August 2020 (16:30:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0307.v1

Bringing onco-innovation to Europe’s healthcare systems: the unexploited potential of biomarker testing, real world evidence and the potential of Tumour Agnostics. The lesson from BRCA1/2 genetic testing

Denis Horgan, Gennaro CILIBERTO, Pierfranco Conte, Giuseppe CURIGLIANO, Luis Seijo, Luis M. Montuenga, Luis Paz-Ares, Marina Chiara Garassino, Penault-Llorca Frederique, Fabrizia GALLI, Isabelle Ray-Coquard, Denis Querleu, David R. Baldwin, Susana Banerjee, Peter H.J. Riegman, Keith Kerr, Benjamin Horbach, Reinhard Büttner, Hendrik Van Poppel, Anders Bjartell, Giovanni Codacci-Pisanelli, Westphalen Christoph Benedikt, Fabien CALVO, Jasmina Koeva-Balabanova, Stephen Hall, Angelo Virgilio Paradiso, Dipak. Kalra, Christa M. Cobbaert, Rocio Varea Mendez, Zorana Maravic, Vassiliki Fotaki, Jaafar Bennouna, Estelle Cauchin, Núria Malats, Iñaki Gutiérrez-Ibarluzea, Benjamin Gannon, Ken Mastris, Chiara Benini, William M. Gallagher, Simonetta Buglioni, Alastair Kent, Elisabetta Munzone, Ivica Belina, Jan P. van Meerbeeck, Michael Joe Duffy, Elzbieta. Sarnowska, Beata Jagielska, Sarah Mee, Ettore Domenico Capoluongo

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: cancer biomarkers, BRCA1/2, genomics; European recommendation

Online: 14 August 2020 (04:27:45 CEST)

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Preprint REVIEW | doi:10.20944/preprints201810.0708.v1

Overview of Genomic Tools for Circular Visualization in next-Generation Genomic Sequencing Era

Alisha Parveen, Sukank Khurana, Abhishek Kumar

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: circular visualization; circos; genomics; next-generation sequencing

Online: 30 October 2018 (07:06:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints201809.0388.v1

The Emerging Landscape of Epidemiological Research Based on Biobanks Linked to Electronic Health Records: Existing Resources, Analytic Challenges and Potential Opportunities

Lauren Beesley, Maxwell Salvatore, Lars Fritsche, Anita Pandit, Arvind Rao, Chad Brummett, Cristen J. Willer, Lynda D. Lisabeth, Bhramar Mukherjee

Subject: Medicine And Pharmacology, Other Keywords: biobanks, electronic health records, Michigan Genomics Initiative

Online: 19 September 2018 (14:57:30 CEST)

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Biobanks linked to electronic health records provide a rich data resource for health-related research. With the establishment of large-scale infrastructure, the availability and utility of data from biobanks has dramatically increased over time. As more researchers become interested in using biobank data to explore a diverse spectrum of scientific questions, resources guiding the data access, design, and analysis of biobank-based studies will be crucial. The first aim of this review is to characterize the types of biobanks that are discussed in the recent literature and provide detailed descriptions of specific biobanks including their location, size, data access, data linkages and more. The development and accessibility of large-scale biorepositories provide the opportunity to accelerate agnostic searches, new discoveries, and hypothesis-generating studies of disease-treatment, disease-exposure and disease-gene associations. Rather than spending time and money designing and implementing a single study with pre-defined objectives, researchers can use biobanks’ existing data-rich resources to answer scientific questions as quickly as they can analyze them. While the data are becoming increasingly available, additional thought is needed to address issues related to the design of such studies and analysis of these data. In the second aim of this review, we discuss statistical issues related to biobank research in general including study design, sampling strategy, phenotype identification, and missing data. These issues are illustrated using data from the Michigan Genomics Initiative, UK Biobank, and Genes for Good. We summarize the current body of statistical literature aimed at addressing some of these challenges and discuss some of the standing open problems in this area. This work serves to complement and extend recent reviews about biobank-based research and aims to provide a resource catalog with statistical and practical guidance to researchers pursuing biobank-based research.

Preprint REVIEW | doi:10.20944/preprints201806.0191.v1

Recent Developments in Using Drosophila as a Model for Human Genetic Disease

Christine Oriel, Paul Lasko

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: rare disease; functional genomics; genetic variant validation

Online: 12 June 2018 (12:36:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201612.0098.v1

Adenovirus with DNA Packaging Gene Mutations Increased Virus Release

Stephen L. Wechman, Xiao-Mei Rao, Kelly M. McMasters, Heshan Sam Zhou

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: lung cancer; adenovirus; E1b; UV-irradiation; genomics

Online: 19 December 2016 (09:33:20 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202309.0079.v1

Data Literacy in Genome Research

Katharina Wolff, Ronja Friedhoff, Friderieke Schwarzer, Boas Pucker

Subject: Biology And Life Sciences, Life Sciences Keywords: computational biology; genomics; sequencing; data literacy; bioinformatics; education

Online: 4 September 2023 (04:32:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0696.v1

Comparison of Two Bacterial Characterization Techniques for the Genomic Analysis of River Microbiome

Roberto Bonnelly, Victor V. Calderon, Irene Ortiz, Argenys Ovando, Confesora Pinales, Willy Lara, Santo Emilio Mateo-Perez, Oscar Victor Cardenas-Alegría, Rommel Thiago Jucá Ramos, Yaset Rodríguez-Rodríguez, Luis Orlando Maroto Martín, Edian Franklin Franco De Los Santos

Subject: Biology And Life Sciences, Life Sciences Keywords: MALDI-TOF; enviromental; Rivers; Genomics method; Dominican Republic

Online: 11 July 2023 (09:30:41 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.0805.v1

Comparative Phylogeography of Three Marine Species with Different PLD Modes Reveals Two Genetic Breaks Across the Southern Caribbean Sea

Juan Carlos Narváez-Barandica, Julián Quintero-Galvis, Juan Carlos Aguirre-Pabon, Lyda R. Castro, Ricardo Betancur-R., Arturo Acero P.

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: biogeographic barrier; phylogeographic break; conservation genomics; Caribbean Sea

Online: 11 May 2023 (05:42:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202210.0470.v1

Temporal Dissection of Altered Pathways during the Evolution of Cancer

Johanne Ahrenfeldt, Ditte S. Christensen, Mateo Sokač, Judit Kisistók, Nicholas McGranahan, Nicolai J. Birkbak

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: metastasis; cancer evolution; bioinformatics; cancer biology; cancer genomics

Online: 31 October 2022 (07:06:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202209.0248.v1

Analysis of the Genetic Variation of the Fruitless Gene within the An. gambiae (Diptera: Culicidae) Complex Populations in Africa

Mahamadi Kientega, Nace Kranjc, Nouhoun Traoré, Honorine Kaboré, Morianou Ioanna, Dieudonné Diloma Soma, Adrien Marie Gaston Belem, Moussa Namountougou, Abdoulaye Diabaté

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Fruitless; genomics; An. gambiae s.l; vector control; Africa

Online: 16 September 2022 (11:33:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0224.v1

The Complete Mitochondrial Genome of a Neglected Breed, the Peruvian Creole Cattle (Bos taurus), and Its Phylogenetic Analysis

Carlos I. Arbizu, Rubén D. Ferro-Mauricio, Julio C. Chávez-Galarza, Héctor V. Vásquez, Jorge L. Maicelo, Carlos Poemape, Jhony Gonzales, Carlos Quilcate, Flor-Anita Corredor

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: zoogenetic resources; organelle; genomics; NGS; cattle; Bos taurus

Online: 16 March 2022 (07:36:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202110.0367.v1

Agrococcus massiliensis sp. nov., a Novel Bacterial Species Isolated from Human Healthy Skin

Manon Boxberger, Sibylle Magnien, Angeline Antezack, Clara Rolland, Marine Makoa Meng, Bernard La Scola, Nadim Cassir

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Bacteria; culturomics; genome; species; sp. nov.,; taxono-genomics

Online: 25 October 2021 (15:47:32 CEST)

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Working Paper REVIEW

Current Genetic and Epigenetic Targeting Therapy for Pediatric Acute Lymphoblastic Leukemia

Huan Xu, Hui Yu, Runming Jin, Xiaoyan Wu, Hongbo Chen

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Pediatric Acute Lymphoblastic Leukemia; Genomics; Epigenetics; Targeted Therapy

Online: 1 October 2021 (12:23:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0281.v1

Clinical Application of Next Generation Sequencing in Recurrent Glioblastoma

Daniel Zeitouni, Michael Catalino, Jordan Wise, Sean McCabe, Kathryn Pietrosimone, Naim Rashid, Simon Khagi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Glioblastoma; Precision Medicine; Targeted Therapy; Genomics; Neuro-Oncology

Online: 13 July 2021 (09:28:35 CEST)

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Preprint CASE REPORT | doi:10.20944/preprints202009.0543.v1

Identification and Characterization of a Novel clcn7 Variant Associated With Osteopetrosis

Dmitrii S. Bug, Ildar M. Barkhatov, Yana V. Gudozhnikova, Artem V. Tishkov, Natalia V. Petukhova, Igor B. Zhulin

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetics； comparative genomics； phylogenetic analysis； osteopetrosis； CLCN7 gene

Online: 23 September 2020 (07:56:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0220.v1

The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology

Emma J. Griffiths, Ruth E. Timme, Andrew J. Page, Nabil-Fareed Alikhan, Dan Fornika, Finlay Maguire, Catarina Inês Mendes, Simon H. Tausch, Allison Black, Thomas R. Connor, Gregory H. Tyson, David M. Aanensen, Brian Alcock, Josefina Campos, Alan Christoffels, Anders Gonçalves da Silva, Emma Hodcroft, William W.L. Hsiao, Lee S. Katz, Samuel M. Nicholls, Paul E. Oluniyi, Idowu B. Olawoye, Amogelang R. Raphenya, Ana Tereza R. Vasconcelos, Adam A. Witney, Duncan R. MacCannell

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: genomics; metadata; SARS-CoV-2; bioinformatics; data standards

Online: 9 August 2020 (15:53:58 CEST)

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Working Paper ARTICLE

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

Daniele Mercatelli, Federico Manuel Giorgi

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; genomics coronavirus; COVID-19 evolution

Online: 3 July 2020 (09:45:43 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202005.0428.v1

Speciation in Stickleback Facilitated by Admixture – Where is the Evidence?

Daniel Berner

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: evolutionary genomics; Gasterosteus aculeatus; gene flow; hybridization; phylogeny

Online: 26 May 2020 (08:44:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201906.0293.v1

Molecular Characterization of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

John McCallum, William Laing, Sean Bulley, Susan Thomson, Andrew Catanach, Martin Shaw, Mareike Kanebel, Jibran Tahir, Simon Deroles, Gail Timmerman-Vaughan, Ross Crowhurst, Elena Hilario, Matthew Chisnall, Robyn Lee, Richard Macknight, Alan Seal

Subject: Biology And Life Sciences, Plant Sciences Keywords: kiwifruit; genomics; polyploidy; breeding; ascorbic acid; vitamin C

Online: 28 June 2019 (08:09:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0135.v1

Estimating Algorithmic Information using Quantum Computing for Genomics Applications

Aritra Sarkar, Zaid Al-Ars, Koen Bertels

Subject: Computer Science And Mathematics, Applied Mathematics Keywords: algorithmic information theory; universal distribution; Kolmogorov complexity; quantum algorithms; quantum circuit model; quantum Turing machine; genomics; viral genomics; meta-biology

Online: 4 February 2021 (12:04:02 CET)

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Preprint REVIEW | doi:10.20944/preprints202309.0496.v1

Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies

Simone Papalini, Valerio Di Vittori, Alice Pieri, Marina Allegrezza, Giulia Frascarelli, Laura Nanni, Elena Bitocchi, Elisa Bellucci, Tania Gioia, Luis Guasch, Karolina Susek, Maud Irène Tenaillon, Kerstin Neumann, Roberto Papa

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: plant genetic resources; population genomics; crop evolution; food legumes

Online: 7 September 2023 (09:23:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0398.v1

Nephrotoxicity Development of a Clinical Decision Support System Based on Tree-Based Machine Learning Methods to Detect Diagnostic Biomarkers from Genomic Data in Methotrexate Induced Rats

Ipek Balikci Cicek, Cemil Colak, Saim Yologlu, Zeynep Kucukakcali, Onural Ozhan, Elif Taslidere, Nefsun Danis, Ahmet Koc, Hakan Parlakpinar, Sami Akbulut

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Nephrotoxicity; Methotrexate; Genomics; Machine Learning; Explainable Artificial Intelligence; Biomarker

Online: 6 July 2023 (08:41:31 CEST)

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Background: The purpose of this study is to carry out bioinformatic analysis of lncRNA data obtained as a result of genomic analysis of kidney tissue samples taken from rats with nephrotoxicity induced by methotrexate (MTX) and from rats without pathology and modeling with tree-based machine learning method. Another aim of the study is to identify potential biomarkers for the diagnosis of nephrotoxicity and to provide a better understanding of the nephrotoxicity formation process by providing the interpretability of the model with explainable artificial intelligence methods as a result of the modeling. Methods: To identify potential indicators of drug-induced nephrotoxicity, 20 female Wistar Albino rats were separated into two groups: nephrotoxicity and control. Kidney tissue samples were collected from the rats, and genomic, histological, and immunohistochemical analyses were performed. The data set obtained as a result of genomic analysis was modeled with Random Forest (RF), one of the tree-based methods. Modeling results were evaluated with sensitivity (Se), specificity (Sp), balanced accuracy (B-Acc), negative predictive value (Npv), accuracy (Acc), positive predictive value (Ppv), and F1-score performance metrics. The Local Interpretable Model-Agnostic Annotations (LIME) method was used to determine the lncRNAs that could be biomarkers for nephrotoxicity by providing the interpretability of the RF model. Results: The outcomes of the histological and immunohistochemical analyses done in the study supported the conclusion that MTX use caused kidney injury. According to the results of the bioinformatics analysis, 52 lncRNAs showed different expression in the groups. As a result of modeling with RF for lncRNAs selected with Boruta variable selection, the B-Acc, Acc, Sp, Se, Npv, Ppv, and F1-score were 88.9%, 90%, 90.9%, 88.9%, 90.9%, 88.9% and 88.9%. respectively. lncRNAs with id rnaXR_591534.3 rnaXR_005503408.1, rnaXR_005495645.1, rnaXR_001839007.2, rnaXR_005492056.1 and rna_XR_005492522.1 the lncRNAs with the highest variable importance values produced from RF modeling can be used as nephroxicity biomarker candidates. Also, according to the LIME results, the high level of lncRNAs with id rnaXR_591534.3 and rnaXR_005503408.1 especially increased the possibility of nephrotoxicity. Conclusions: With the possible biomarkers obtained as a result of the analyses made within the scope of this study, it can be ensured that the procedures for the diagnosis of drug-induced nephrotoxicity can be carried out easily, quickly and effectively.

Preprint COMMUNICATION | doi:10.20944/preprints202211.0440.v1

Exome Sequencing reveals characteristic KMT2C mutations in the Indian Phenotype of Cervical Cancer

Santosh Kumari Duppala, Bhumandeep Kour, Nidhi Shukla, Maruti A Dhakane, Ashwani Kumar Mishra, Raghunadharao Digumarti, Smita C Pawar, Prashanth N Suravajhala, Sugunakar Vuree

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Cervical cancer; Functional genomics; Bioinformatics; Next Generation Sequencing; Exome

Online: 23 November 2022 (07:42:19 CET)

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Preprint ARTICLE | doi:10.20944/preprints202208.0191.v1

Snakemake Workflows for Long-read Bacterial Genome Assembly and Evaluation

Peter Menzel

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bacterial genomics; de novo assembly; Oxford Nanopore Technologies; Snakemake

Online: 10 August 2022 (04:37:01 CEST)

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Preprint REVIEW | doi:10.20944/preprints202111.0203.v1

From Single Cells to Flowers – Biological Complexity Driving Plant Reproductive Development

Isabel Schwarz, Manuel Neumann, Rosario Vega, Xiaocai Xu, Letizia Cornaro, Lucia Colombo, Teva Vernoux, Jian Xu, Sebastian Marquardt, Kerstin Kaufmann

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: flower development; epigenetics; RNA biology; Genomics; single cell biology

Online: 10 November 2021 (11:00:03 CET)

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Preprint REVIEW | doi:10.20944/preprints202108.0514.v1

Advances and Milestones of Radish Breeding: An Update

Anand Kumar, Prashant Kaushik

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: radish; breeding; interspecific hybridization; molecular breeding; genomics; genetic engineering

Online: 26 August 2021 (16:46:36 CEST)

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Preprint REVIEW | doi:10.20944/preprints202010.0149.v1

Advances in Melon Breeding (Cucumis melo L.): An Update

Hari Kesh, Prashant Kaushik

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: breeding; diversity; genetic engineering; genomics; male sterility; melon; QTLs

Online: 7 October 2020 (09:22:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0413.v1

Characterization of Nucleocapsid (N) Protein from Novel Coronavirus SARS-CoV-2

Abhishek Kumar, Alisha Parveen, Narendra Kumar, Sneha Bairy, Vibha Kaushik, Chetan Chandola, Jyoti Sharma, Phulwanti Sharma, Akhil Agarwal, Akhilesh Pandey, Pankaj Goyal, Muniasamy Neerathilingam

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; nucleocapsid (N); genomics; coronavirus; Wuhan; Pandemic

Online: 25 May 2020 (17:45:40 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0005.v1

SARS-CoV-2/COVID-19: Viral Genomics, Epidemiology, Vaccines, and Therapeutic Interventions

Mohammed Uddin, Farah Mustafa, Tahir A. Rizvi, Tom Loney, Hanan Al Suwaidi, Ahmad Al Marzouqi, Afaf Kamal Eldin, Nabeel Alsabeeha, Thomas E. Adrian, Cesare Stefanini, Norbert Nowotny, Alawi Alsheikh-Ali, Abiola C. Senok

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Coronavirus; Pandemic; Viral Genomics

Online: 1 April 2020 (09:22:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0336.v1

Complete Genome Sequence of a Distinct Isolate of Cassava common mosaic virus (CsCMV) Infecting Cassava in Hainan, China

Nai-tong Yu, Yi Yang, Jun-hua Li, Wei-li Li, Zhi-xin Liu

Subject: Biology And Life Sciences, Virology Keywords: Manihot esculenta Crantz; potexvirus; Cassava common mosaic virus; genomics

Online: 23 March 2020 (05:46:35 CET)

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Preprint REVIEW | doi:10.20944/preprints201612.0061.v1

Conducting Wine Symphonics with the Aid of Yeast Genomics

Isak Pretorius

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: alcohol; aroma; bioengineering; flavour; synthetic genomics; taste; wine; yeast

Online: 10 December 2016 (09:09:54 CET)

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A perfectly balanced wine can be said to create a symphony in the mouth. To achieve the sublime, both in wine and music, requires imagination and skilled orchestration of artistic craftmanship. For wine, inventiveness starts in the vineyard. Similar to a composer of music, the grapegrower produces grapes through a multitude of specifications to achieve a quality result. Different Vitis vinifera grape varieties allow the creation of wine of different genres. Akin to a conductor of music, the winemaker decides what genre to create and considers resources required to realise the grape’s potential. A primary consideration is the yeast: inoculate the grape juice or leave it ‘wild’; which specific or combined Saccharomyces strain(s) should be used; or proceed with a non-Saccharomyces species? Whilst the various Saccharomyces and non-Saccharomyces yeasts perform their role during fermentation, the performance is not over until the ‘fat lady’ (S. cerevisiae) has sung (i.e. the grape sugar has been fermented to specified dryness and alcoholic fermentation is complete). Is the wine harmonious or discordant? Will the consumer demand an encore and make a repeat purchase? Understanding consumer needs lets winemakers orchestrate different symphonies (i.e. wine styles) using single- or multi-species ferments. Some consumers will choose the sounds of a philharmonic orchestra comprising a great range of diverse instrumentalists (as is the case with wine created from spontaneous fermentation); some will prefer to listen to a smaller ensemble (analogous to wine produced by a selected group of non-Saccharomyces and Saccharomyces yeast); and others will favour the well-known and reliable superstar soprano (i.e. S. cerevisiae). But what if a digital music synthesiser ‒ such as a synthetic yeast ‒ becomes available that can produce any music genre with the purest of sounds by the touch of a few buttons? Will synthesisers spoil the character of the music and lead to the loss of the much-lauded romantic mystique? Or will music synthesisers support composers and conductors to create novel compositions and even higher quality performances that will thrill audiences? This article explores these and other relevant questions in the context of winemaking and the role that yeast and its genomics play in the betterment of wine quality.

Preprint REVIEW | doi:10.20944/preprints202304.0798.v1

Attempts to Understand Oral Mucositis in Head and Neck Cancer Patients Through Omics Studies

Cielito C. Reyes-Gibby, Erin Marie D. San Valentin, Sai-ching J Yeung

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Head and neck cancer; oral mucositis; pain; genomics; transcriptomics; microbiomics

Online: 23 April 2023 (12:29:17 CEST)

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Preprint REVIEW | doi:10.20944/preprints202201.0084.v1

Yeast Hybrids in Brewing

Matthew J. Winans

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: hybrid; lager; yeast; introgression; interspecific; domestication; phylogeny; brewing; molecular; genomics

Online: 6 January 2022 (11:55:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0457.v1

Integrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches

Ying Chen, Nan Li, Shenxi Zhao, Chuan Zhang, Nanzhen Qiao, Hui Duan, Yue Xiao, Bowen Yan, Jianxin Zhao, Fengwei Tian, Qixiao Zhai, Leilei Yu, Wei Chen

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Latilactobacillus sakei; comparative genomics; carbohydrate utilization; antibiotic tolerance; CRISPR-Cas

Online: 20 July 2021 (15:02:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0060.v1

Experimental Evolution of Magnetite Nanoparticle Resistance in Escherichia coli

Akamu Ewunkem, LaShunta Rodgers, Daisha Campbell, Constance Staley, Kiran Subedi, Sada Boyd, Joseph L. Graves Jr

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Escherichia coli; magnetite nanoparticles; metals; antibiotics; genomics; pleiotropy; cell morphology

Online: 1 February 2021 (15:58:10 CET)

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Preprint REVIEW | doi:10.20944/preprints202008.0133.v1

A Review on Viral Data Sources and Integration Methods for COVID-19 Mitigation

Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Pietro Pinoli, Stefano Ceri

Subject: Biology And Life Sciences, Virology Keywords: epidemic; viral sequences; genomics; metadata; data harmonization; integration and search

Online: 5 August 2020 (10:58:27 CEST)

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Preprint REVIEW | doi:10.20944/preprints201811.0571.v2

Revisiting Prostate Cancer in India: A Genomic View

Prameesha Perera, Ayam Gupta, Nidhi Shukla, Mamta Nehra, Mukesh Sharma, Sneha Mishra, Vikram Singh Chauhan, Maneesh Kumar Vijay, Suresh Kumar Jatawa, Archana Tiwari, Krishna Mohan Medicherla, Praveen Mathur, Devendra Sharma, Prashanth Suravajhala

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: prostate cancer; prostate-specific antigen; incidence; genomics; next generation sequencing

Online: 3 April 2019 (10:15:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0071.v1

Resolution of Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics

Dingxuan He, Andrew W. Gichira, Zhizhong Li, John M. Nzei, Youhao Guo, Qingfeng Wang, Jinming Chen

Subject: Biology And Life Sciences, Plant Sciences Keywords: basal angiosperms; chloroplast; comparative genomics; Nymphaeales; Nymphaeaceae; phylogenomics; water lily

Online: 2 November 2018 (16:20:31 CET)

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Preprint REVIEW | doi:10.20944/preprints202203.0388.v1

Evolutionary Ecology of Fixed Alternative Male Mating Strategies in the Ruff (Calidris pugnax)

Michel Baguette, Baptiste Bataille, Virginie M. Stevens

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: phenotypic polymorphism; structural genomics; chromosomal inversion; supergene; functional genomics; hormonal plasticity; frequency-dependent selection; cryptic female choice of sperm; sexual selection; eco-evolutionary dynamics

Online: 30 March 2022 (10:15:55 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.1641.v1

Exploring Pan-Genomes of Crops: Genomic Resources and Tools for Unraveling Gene Evolution, Function, and Adaptation

Sushma Naithani, Cecilia H. Deng, Sunil Kumar Sahu, Pankaj Jaiswal

Subject: Biology And Life Sciences, Plant Sciences Keywords: pan-genomes; comparative genomics; plant pathways; genomic databases; gravitropism; Gene Ontology

Online: 23 August 2023 (09:29:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0526.v1

Effects of Forest Fragmentation on Connectivity and Genetic Diversity in an Endemic and an Invasive Rodent in Northwestern Madagascar

Malcolm S. Ramsay, Gabriele Sgarlata, Christopher D. Barratt, Jordi Salmona, Bertrand Andriatsitohaina, Frederik Kiene, Sophie Manzi, Miarisoa L. Ramilison, Romule Rakotondravony, Lounés Chikhi, Shawn M. Lehman, Ute Radespiel

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Dispersal; Connectivity; Movement; Conservation Genomics; Madagascar; Habitat Loss and Fragmentation; Rodents

Online: 7 June 2023 (09:30:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0105.v1

Virulent Phages Isolated from A Smear-Ripened Cheese are Also Detected in Reservoirs of the Cheese Factory

Thomas Paillet, Julien Lossouarn, Clarisse Figueroa, Cédric Midoux, Olivier Rué, Marie-Agnès Petit, Eric Dugat-Bony

Subject: Biology And Life Sciences, Virology Keywords: Smear-ripened cheese; virulent phages; rind bacteria; phage reservoirs; viral genomics

Online: 7 June 2022 (10:37:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0070.v1

Taxonomic Re-Evaluation and Genomic Comparison of Novel Extracellular Electron Uptake-Capable Rhodovulum visakhapatnamense and Rhodovulum sulfidophilum isolates

Emily J Davenport, Arpita Bose

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: phototrophic bacteria; phototrophic extracellular electron uptake; comparative genomics; transcriptomics; environmental microbiology

Online: 6 May 2022 (09:35:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0102.v1

Genome-wide Investigation and Expression Profiles of Heat Shock Transcription Factor (HSF) Gene Family in Maize (Zea mays L.) under Different Growth Stages and Abiotic Stress Conditions

Saqlain Haider, Shazia Rehman, Yumna Ahmad, Ali Raza, Javaria Tabassum, Talha Javed, Hany S. Osman, Tariq Mahmood

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: abiotic stress; HSFs; genomics; gene ontology; maize breeding; protein 3D structures

Online: 6 September 2021 (13:57:37 CEST)

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Heat shock transcription factors (HSFs) participate in regulating many environmental stress responses and biological processes in plants. Maize (Zea mays L.) is a major cash crop that is grown worldwide. However, the growth and yield of maize are affected by several adverse environmental inputs. Therefore, investigating the factors that regulate maize growth and development and resistance to abiotic stress is an essential task for developing stress-resilient maize varieties. Thus, a comprehensive genome-wide identification analysis was performed to identify HSFs in the maize genome. The current study identified 25 ZmHSFs, randomly distributed throughout the maize genome. Phylogenetic analysis revealed that ZmHSFs are divided into three classes and 13 sub-classes. Gene structure and protein motif analysis supported the results obtained through the phylogenetic analysis. Domain analysis showed the DNA-binding domain to be the most conserved region of ZmHSFs. Segmental duplication is shown to be responsible for the expansion of ZmHSFs. Most of the ZmHSFs are localized inside the nucleus, and the ZmHSFs which belong to the same group show similar physio-chemical properties. The 3D structures revealed comparable conserved ZmHSFs protein structures. RNA-seq analysis revealed a major role of class A HSFs including, ZmHSFA-1a and ZmHSFA-2a in all the maize growth stages, i.e., seed, vegetative, and reproductive development. Furthermore, ZmHSFs displayed an obvious spatiotemporal expression. Under abiotic stress conditions (heat, drought, cold, UV, and salinity), members of class A and B ZmHSFs are induced. Gene ontology (GO) annotation analysis indicated a major role of ZmHSFs in resistance to environmental stress and regulation of primary metabolism. Further, the protein-protein interaction analysis showed that ZmHSFs interact with several molecular chaperons and major stress-responsive proteins. To summarize, this study provides novel insights for functional studies on the ZmHSFs in maize breeding programs.

Preprint ARTICLE | doi:10.20944/preprints202103.0103.v1

Automated Capture-Based NGS Workflow: One Thousand Patients Experience in a Clinical Routine Framework

Elena Tenedini, Fabio Celestini, Pierluigi Iapicca, Marco Marino, Sara Castellano, Lucia Artuso, Fiammetta Biagiarelli, Laura Cortesi, Angela Toss, Elena Barbieri, Luca Roncucci, Monica Pedroni, Rossella Manfredini, Mario Luppi, Tommaso Trenti, Enrico Tagliafico

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Next Generation Sequencing; Laboratory automation; Hereditary Cancer; Genetic Testing; Clinical Genomics.

Online: 2 March 2021 (16:00:24 CET)

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Preprint REVIEW | doi:10.20944/preprints202010.0301.v1

The Genetic Basis of Obesity and Related Metabolic Diseases in Humans and Companion Animals

Natalie Wallis, Eleanor Raffan

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Obesity; Genetics; Companion Animals; Metabolic Disease; Comparative Genomics; Dogs; Cats; Horses

Online: 14 October 2020 (10:51:29 CEST)

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Preprint REVIEW | doi:10.20944/preprints202005.0448.v1

Betacoronavirus Genomes: How Genomic Information Has Been Used to Deal with past Outbreaks and the COVID-19 Pandemic

Alejandro Llanes, Carlos M. Restrepo, Zuleima Caballero, Sreekumari Rajeev, Melissa A. Kennedy, Ricardo Lleonart

Subject: Biology And Life Sciences, Virology Keywords: betacoronaviruses; genomics; SARS-CoV; MERS-CoV; SARS-CoV-2; COVID-19

Online: 27 May 2020 (08:50:46 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0333.v1

Visiting Bitter Gourd (Momordica charantia) from a Breeding Perspective: A Review

Hari Kesh, Prashant Kaushik

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bitter gourd; breeding; genetic diversity; genomics; heterosis; molecular breeding; mutation breeding

Online: 19 April 2020 (06:00:00 CEST)

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Preprint REVIEW | doi:10.20944/preprints201912.0316.v1

Past, Present and Future Perspectives on Groundnut Breeding in Burkina Faso

Moumouni Konate, Jacob Sanou, Amos Miningou, David Kalule Okello, Haile Desmae, Janila Pasupuleti, Rita H. Mumm

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Peanut; plant breeding; research; funding; genomics; INERA; cultivar; selection; Arachis hypogaea

Online: 24 December 2019 (11:07:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints201812.0026.v2

Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus Plantarum - A Novel Lineage of Lactobacillus Phages Comprising Five New Members

Ifigeneia Kyrkou, Alexander Byth Carstens, Lea Ellegaard-Jensen, Witold Kot, Athanasios Zervas

Subject: Biology And Life Sciences, Virology Keywords: Lactobacillus plantarum; phage; new genus; annotation; comparative genomics; phylogenetics; isolation; diversity

Online: 11 June 2019 (09:54:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201905.0284.v1

Proprietary Algorithms for Polygenic Risk: Protecting Scientific Innovation or Hiding the Lack of It?

A. Cecile J.W. Janssens

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: personal genomics, DNA, polygenic, risk, regulation, discrimination, calibration, prediction, transparency, autonomy

Online: 23 May 2019 (16:23:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201803.0145.v1

Structural and Functional Analysis of Transposable Elements Focusing on B Chromosomes of the Cichlid Fish Astatotilapia latifasciata

Rafael Coan, Cesar Martins

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: repetitive elements; RNA-Seq; genomics; evolution; cytogenetics; supernumerary elements; extra chromosomes

Online: 19 March 2018 (08:33:48 CET)

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Preprint REVIEW | doi:10.20944/preprints201612.0113.v1

Breast Cancer Brain Metastases: Clonal Evolution in Clinical Context

Jodi M. Saunus, Amy E. McCart Reed, Zhun Leong Lim, Sunil R. Lakhani

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: breast cancer; brain metastases; clonal evolution; precision medicine; genomics; tumour microenvironment

Online: 22 December 2016 (09:57:33 CET)

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Preprint REVIEW | doi:10.20944/preprints202308.1703.v1

The Role of Uric Acid in Human Health: Insights from the Uricase Gene

Youssef M Roman

Subject: Biology And Life Sciences, Life Sciences Keywords: neurodegenerative diseases; cardiovascular diseases; fructose metabolism; adaptation; evolutionary biology; genomics; gout; hyperuricemia

Online: 24 August 2023 (03:53:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1828.v1

Genomic Surveillance of Rabies Virus in Georgian Canines

Celeste Huaman, Adrian C. Paskey, Caitlyn Clouse, Austin Feasley, Madeline Rader, Gregory K Rice, Andrea E Luquette, Maren C Fitzpatrick, Hannah M Drumm, Regina Z Cer, Marina Donduashvili, Tamar Buchukuri, Anna Nanava, Christine E Hulseberg, Michael A Washington, Eric D Laing, Francisco Malagon, Kimberly A Bishop-Lilly, Christopher C Broder, Brian C Schaefer

Subject: Biology And Life Sciences, Virology Keywords: Rabies; lyssaviruses; RABV; dog; jackal; canine; neutralization; genomics; next-generation sequencing; phylogeny

Online: 26 June 2023 (14:44:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0280.v1

Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase

Colbie Reed, Geoffrey Hutinet, Valérie de Crécy-Lagard

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: comparative genomics; metabolic reconstruction; bioinformatics; conserved unknowns; function prediction; functional annotation; orthology

Online: 13 July 2021 (08:58:31 CEST)

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Working Paper REVIEW

Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain by Omics Technologies

Paola Zanfardino, Stefano Doccini, Filippo Maria Santorelli, Vittoria Petruzzella

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: mitochondria; mitochondrial DNA; nervous tissue, OxPhos complexes; bioenergetics; genomics; proteomics; mitochondrial diseases

Online: 17 June 2021 (15:12:01 CEST)

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Preprint REVIEW | doi:10.20944/preprints202106.0363.v1

Linking Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified Foods and Sustainable Food Security

Ajay Kumar, Anju T, Sushil Kumar, Sushil Satish Chhapekar, Sajana Sreedharan, Sonam Singh, Nirala Ramchiary, Su Ryun Choi, Yong Pyo Lim

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Traditional food crops; Climate change; Food security; Omics; Translational genomics; Gene editing

Online: 14 June 2021 (13:02:24 CEST)

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The indigenous communities across the globe especially in the rural areas consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many of the traditional food plants are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. TFPs are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in times of pandemics and other situations like COVID-19. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realising the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of traditional food plants for their improvements, further cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in few TFPs. This suggests that there is ample scope of integrated use of modern omics and editing tools/techniques for improvement of TFPs and their use for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

Preprint ARTICLE | doi:10.20944/preprints202106.0214.v1

Understanding the Molecular Bases of the Endophytic/Pathogenic Behavior of Fusarium Oxysporum Interacting With Vanilla Planifolia

Marco Tulio Solano De la Cruz, Esteban Elías Elías Escobar – Hernández, Jorge Arturo Arciniega – González, Rocío del Pilar Rueda – Zozaya, Jacel Adame – García, Edel Pérez-López, Mauricio Luna – Rodríguez

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: formae speciales; horizontal gene transfer; endophytic; pathogenic; Fusarium; RNAseq; comparative genomics; vanilla

Online: 8 June 2021 (11:37:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0387.v1

iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification

Sara Castellano, Federica Cestari, Giovanni Faglioni, Elena Tenedini, Marco Marino, Lucia Artuso, Rossella Manfredini, Mario Luppi, Tommaso Trenti, Enrico Tagliafico

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: next-generation sequencing; database; variant annotation; variant classification; data management; clinical genomics

Online: 15 December 2020 (13:14:21 CET)

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Preprint REVIEW | doi:10.20944/preprints202011.0060.v1

Trajectories of Cotton Fiber Initiation: A Regulatory Perspective

Pravin Prakash, Rakesh Srivastava, Priti Prasad, Vipin Kumar Tiwari, Ajay Kumar, Shatrujeet Pandey, Samir V. Sawant

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Cotton; Fiber initiation; Genomics; Epigenomics; Phytohormones; Transcription factors; MicroRNAs; Gene expression regulation

Online: 2 November 2020 (15:50:39 CET)

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Working Paper REVIEW

The Reuse of Public Datasets in the Life Sciences: Potential Risks and Rewards

Katharina Sielemann, Alenka Hafner, Boas Pucker

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: data science; reuse; sequencing data; genomics; bioinformatics; databases; computational biology; open science

Online: 16 July 2020 (12:39:43 CEST)

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Preprint REVIEW | doi:10.20944/preprints201911.0300.v1

Next Generation Biological Control: The Need for Integrating Genetics and Evolution

Kelley Leung, Erica Ras, Kim Ferguson, Simone Ariëns, Dirk Babendreier, Piter Bijma, Kostas Bourtzis, Jacques Brodeur, Margreet Bruins, Alejandra Centurión, Sophie Chattington, Milena Chinchilla-Ramírez, Marcel Dicke, Nina Fatouros, Joel González Cabrera, Thomas Groot, Tim Haye, Markus Knapp, Panagioata Koskinioti, Sophie Le Hesran, Manolis Lirakis, Angeliki Paspati, Meritxell Pérez-Hedo, Wouter Plouvier, Christian Schlötterer, Judith Stahl, Andra Thiel, Alberto Urbaneja, Louis van de Zande, Eveline Verhulst, Louise Vet, Sander Visser, John Werren, Shuwen Xia, Bas Zwaan, Sara Magalhães, Leo Beukeboom, Bart Pannebakker

Subject: Biology And Life Sciences, Insect Science Keywords: artificial selection; biological control; genetics; genome assembly; genomics; insect breeding; microbiome; modelling

Online: 24 November 2019 (17:10:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints201809.0169.v1

“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome and Nutrigenomics of the European Sardine, Sardina pilchardus

André M. Machado, Ole K. Tørresen, Naoki Kabeya, Alvarina Couto, Bent Petersen, Mónica Felício, Paula F. Campos, Elza Fonseca, Narcisa Bandarra, Mónica Lopes-Marques, Renato Ferraz, Raquel Ruivo, Miguel M. Fonseca, Sissel Jentoft, Óscar Monroig, Rute Da Fonseca, L. Filipe C. Castro

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: European sardine; draft genome; teleosts; comparative genomics; long chain polyunsaturated fatty acids

Online: 10 September 2018 (12:37:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201805.0471.v1

Harmonizing Outcomes for Genomic Medicine: Comparison of eMERGE Outcomes to ClinGen Outcome/Intervention Pairs

Janet L. Williams, Wendy K. Chung, Alex Fedotov, Krzysztof Kiryluk, Chunhua Weng, John J. Connolly, Margaret Harr, Hakon Hakonarson, Kathleen A. Leppig, Eric B. Larson, Gail P. Jarvik, David L. Veenstra, Christin Hoell, Maureen E. Smith, Ingrid A. Holm, Josh F. Peterson, Marc S. Williams

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: genomics; genomic medicine; health outcomes; evidence; standards; eMERGE; ClinGen; precision public health

Online: 31 May 2018 (11:27:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201803.0009.v1

Transitions from Single- to Multi-locus Processes during Speciation

Martin P. Schilling, Sean P. Mullen, Marcus Kronforst, Rebecca J. Safran, Patrik Nosil, Jeffrey L. Feder, Zachariah Gompert, Samuel M. Flaxman

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: gene flow; sympatry; parapatry; simulation model; population genomics; Heliconius; coupling; nonlinear transitions

Online: 1 March 2018 (15:23:13 CET)

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