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Working Paper REVIEW

Sequencing Enabling Design and Learning in Synthetic Biology

Pierre-Aurelien Gilliot, Thomas E. Gorochowski

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: sequencing; omics; synthetic biology; systems biology; machine learning; biological design

Online: 23 April 2020 (03:47:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0280.v1

Early Diagnosis of Oral Cancer and Lesions in Fanconi Anemia Patients: A Prospective and Longitudinal Study Using Saliva and Plasma

Ricardo Errazquin, Estela Carrasco, Sonia Del Marro, Anna Suñol, Jorge Peral, Jessica Ortiz, Juan C. Rubio, Carmen Segrelles, Marta Dueñas, Alicia Garrido-Aranda, Martina Álvarez, Cristina Belendez, Judith Balmaña, Ramon Garcia-Escudero

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Fanconi anemia; oral cancer; oral potentially malignant lesion; liquid biopsy; saliva; oral rinse; plasma; next generation sequencing; cancer gene panel; early diagnosis; diagnostic test; deep sequencing

Online: 16 January 2023 (09:10:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints202308.1048.v1

Identification and Characterization of Alfalfa lncRNAs Based on PacBio Sequencing

Yue Li, Chu Wang, Huiting Cui, Kai Zhu, Fang Jia, Chengze Ma, Junmei Kang, Yan Sun

Subject: Biology And Life Sciences, Plant Sciences Keywords: lncRNA; alfalfa; full-length transcriptome sequencing; sequence conservation; small ORF

Online: 15 August 2023 (02:49:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201805.0244.v1

Evolutionary History of the GH3 Family Based on 48 Sequenced Plants and Identification of Jasmonic Acid-Relate GH3 Genes in Solanum tuberosum

Chao Zhang, Leilei Zhang, Dongdong Wang, Haoli Ma, Bailin Liu, Zheng Shi, Xiaohui Ma, Yue Chen, Qin Chen

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: GH3 family; sequencing plants; potato; jasmonic acids; tissues; biotic

Online: 17 May 2018 (12:01:00 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202208.0025.v1

Next-Generation Sequencing Comparative Analysis of DNA Mutations between Blood-derived Extracellular Vesicles and Matched Cancer Tissue in Patients with IV Grade Glioblastoma

Paolo Rosa, Elena De Falco, Luca Pacini, Amedeo Piazza, Paolo Ciracì, Luca Ricciardi, Francesco Fiorentino, Sokol Trungu, Massimo Miscusi, Antonino Raco, Antonella Calogero

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: glioblastoma; extracellular vesicles; Next Generation Sequencing; pathogenic mutations; NF1

Online: 1 August 2022 (15:07:04 CEST)

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Preprint REVIEW | doi:10.20944/preprints202307.1110.v1

Next Generation Sequencing in Diagnosis of Multiple Myeloma

Ikram El Fazazi, Hajar Ihlal, Meriame Abbassi, Mohamed Ahakoud, Samira Nmer, Laila Bouguenouch, Rhizlane Berrady, Karim Ouldim, Mohammed El-Azami El-Idrissi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: multiple myeloma; next generation sequencing; whole genome sequencing; whole exome se-quencing; myTYPE panel; minimal residual disease.

Online: 17 July 2023 (15:06:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0363.v1

Changes on Bacterial and Fungal Soil Communities in Long-Term Organic Cropping Systems

Jessica Cuartero, Onurcan Özbolat, Virginia Sánchez-Navarro, Marcos Egea-Cortines, Raúl Zornoza, Loredana Canfora, Luigi Orrù, José Antonio Pascual, Juana-María Vivo, Margarita Ros

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: compost; high-throughput sequencing; sheep manure; soil properties; crop yield

Online: 14 April 2021 (08:06:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202401.2076.v1

Increase of Prominent Probiotics Represents the Major Change in the Gut Microbiota in Female Morbid Obese Patients upon Bariatric Surgery and Are Accompanied with a Switch of Enterotypes

Ann-Kathrin Kissmann, Frederike Paß, Hans-Maximilian Ruzicka, Isabel Dorst, Kai R. Stieger, Tanja Weil, Adrian Gihring, Leonard Elad, Uwe Knippschild, Frank Rosenau

Subject: Medicine And Pharmacology, Dietetics And Nutrition Keywords: gut microbiome; 16S rRNA sequencing; obesity; bariatric surgery; enterotypes

Online: 30 January 2024 (05:26:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202212.0401.v1

Involvement of the Small ncRNAome in Fresh Peripheral Blood Mononuclear Cells of Human T-cell Leukemia Virus Type I- Associated Myelopathy/Tropical Spastic Paraparesis Patients and Viral Carriers

Daniela R. V. Souza, Rodrigo Pessôa, Youko Nukui, Juliana Pereira, Rosa Nascimento Marcusso, Augusto César Penalva de Oliveira, Jorge Casseb, Alberto José da Silva Duarte, Patricia Bianca Clissa, Sabri Saeed Sanabani

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: small RNA; HTLV-1; HAM/ TSP; massive parallel sequencing

Online: 21 December 2022 (11:46:09 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.1959.v1

Analysis of LncRNA and mRNA Expression Profiles in Skin Tissues of Super Merino Sheep and Small-Tailed Han Sheep

Jiaqi Fu, Anqi Hao, Xinyu Zhang, Dan Wang, Wenqing Liu, Caihong Zhang, Dazhuo Zhao, Zhongli Zhao, Lichun Zhang, Fuliang Sun

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: anagen; lncRNA; super merino sheep; small-tailed han sheep; RNA sequencing

Online: 30 November 2023 (08:27:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.1894.v1

Deciphering the Dose-Dependent Effects of Thymoquinone on Transcriptomic Changes and Cellular Proliferation in Glioblastoma

Rachana Pandey, Purushothaman Natarajan, Umesh K Reddy, Wei Du, Cristian Sirbu, Moussa Sissoko, Gerald R Hankins

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Glioblastoma; Thymoquinone; RNA-Sequencing; Gene Expression; Pathway Analysis; A172 Cells

Online: 26 January 2024 (08:41:19 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.1646.v1

Whole Exome Sequencing and Analysis of T Cell Receptor β & γ Repertoires in Rheumatoid Arthritis

Jooyoung Cho, Juwon Kim, Ju Sun Song, Young Uh, Jong-Han Lee, Hyang Sun Lee

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: whole exome sequencing; T cell receptor repertoire; diversity; rheumatoid arthritis

Online: 23 January 2024 (06:46:19 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.1565.v1

Exploring Genetic Diversity in Romanian Lycium Species: A Comparative Study of Wild and Cultivated Genotypes

Roxana Ciceoi, Adrian Asănică, Vasilica Luchian, Mihaela Iordăchescu

Subject: Biology And Life Sciences, Horticulture Keywords: goji berry; breeding; plant resistance; Whole Genome Sequencing; BODYGUARD genes.

Online: 26 November 2023 (05:17:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0517.v1

Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence

Giselle C. Martin-Hernandez, Bettina Müller, Christian Brandt, Martin Hölzer, Adrian Viehweger, Volkmar Passoth

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Rhodotorula babjevae; de-novo hybrid assembly; Nanopore sequencing; genome divergence

Online: 29 November 2021 (07:57:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints202003.0424.v1

Role of GUCA1C in Primary Congenital Glaucoma and in the Retina: Functional Evaluation in Zebrafish

Samuel Morales-Cámara, Susana Alexandre-Moreno, Juan-Manuel Bonet-Fernández, Raquel Atienzar-Aroca, José-Daniel Aroca-Aguilar, Jesús-José Ferre-Fernández, Carmen-Dora Méndez, Laura Morales, Laura Fernández-Sánchez, Nicolás Cuenca, Miguel Coca-Prados, José-María Martínez-de-la-Casa, Julián Garcia-Feijoo, Julio Escribano

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: primary congenital glaucoma; exome sequencing; GUCA1C; GCAP3; zebrafish; CRISPR/Cas9

Online: 29 March 2020 (06:33:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0275.v1

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

Benjamin Istace, Caroline Belser, Cyril Falentin, Karine Labadie, Franz Boideau, Gwenaëlle Deniot, Loeiz Maillet, Corinne Cruaud, Laurie Bertrand, Anne-Marie Chèvre, Patrick Wincker, Mathieu Rousseau-Gueutin, Jean-Marc Aury

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Genome sequencing; de novo Assembly; Scaffolding; Chromosome-scale; Nanopore sequencing; Long reads; Optical maps; Bionano Genomics; Hi-C; Omni-C; Pore-C; Plant genomes

Online: 12 July 2021 (22:55:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202211.0228.v1

Genomic Diversity and Chromosomal Rearrangements in Neisseria Gonorrhoeae and Neisseria Meningitidis

Boris Shaskolskiy, Dmitry Kravtsov, Ilya Kandinov, Ekaterina Dementieva, Dmitry Gryadunov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Neisseria gonorrhoeae; Neisseria meningitidis; whole genome sequencing; chromosomal rearrange-ments; mobile elements

Online: 14 November 2022 (02:11:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.1836.v1

Using NGS Technology and Association Mapping to Identify Candidate Genes Associated with Fusarium stalk rot Resistance

Jan Bocianowski

Subject: Biology And Life Sciences, Plant Sciences Keywords: maize; next generation sequencing; SNP markers; SilicoDArT markers; stalk rot

Online: 25 December 2023 (09:20:45 CET)

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Preprint REVIEW | doi:10.20944/preprints202005.0376.v1

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, René Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria J. Martin, Roman Martin, Julian Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric Nawrocki, Áine Niamh O'Toole, Nancy Palacios-Ontiveros, Anton I. Petrov, Guillermo Rangel-Piñeros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz

Subject: Biology And Life Sciences, Virology Keywords: virus bioinformatics; SARS-CoV-2; sequencing; epidemiology; drug design; tools

Online: 23 May 2020 (11:01:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0123.v1

Identification and Characterization of microRNAs during Retinoic Acid-Induced Regeneration of a Molluscan Central Nervous System

Sarah E. Walker, Gaynor E. Spencer, Aleksandar Necakov, Robert L. Carlone

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: retinoic acid; microRNA; RNA sequencing; neuronal regeneration; growth cone; Lymnaea

Online: 7 September 2018 (03:13:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.0910.v1

Conjunctive Analyses of BSA-Seq and BSR-Seq to Identify Candidate Genes Controlling the Black Lemma and Pericarp Trait in Barley

Yajie Liu, Pengzheng Chen, Wenshuo Li, Xinchun Liu, Guowu Yu, Hui Zhao, Shuhua Zeng, Mao Li, Genlou Sun, Zongyun Feng

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: allomelanin; high throughput sequencing; bulk segregation analysis; benzoic acids derivates; barley

Online: 25 April 2023 (09:40:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.1830.v1

Reanalysis of Trio Whole Genome Sequencing Data Doubles the Yield in Autism Spectrum Disorder: De Novo Variants Present in Half

Omri Bar, Elizabeth Vahey, Mark Mintz, Richard E Frye, Richard G Boles

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Autism; diagnostic yield; DNA sequencing; novel disorders

Online: 27 December 2023 (05:40:13 CET)

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Preprint REVIEW | doi:10.20944/preprints202306.0960.v1

Autism spectrum disorder pathogenesis – a cross-sectional literature review

Agata Horecka-Lewitowicz, Olga Adamczyk-Gruszka, Dorota Kozieł, Hyebin Lim, Wojciech Lewitowicz, Piotr Lewitowicz

Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: keyword ASD, autism, Asperger syndrome, molecular sequencing

Online: 13 June 2023 (16:51:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1104.v1

Elucidating the Role of Immune Cell Dysregulation in Atypical Hemolytic Uremic Syndrome: A Comprehensive Single-Cell Sequencing Analysis

I-Ru Chen, Chiu-Ching Huang, Siang‑Jyun Tu, Guei-Jane Wang, Ping-Chin Lai, Ya-Ting Lee, Ju-Chen Yen, Ya-Sian Chang, Jan‑Gowth Chang

Subject: Medicine And Pharmacology, Urology And Nephrology Keywords: hemolytic uremic syndrome; complement; single cell sequencing

Online: 16 May 2023 (05:36:09 CEST)

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Working Paper ARTICLE

Chip-Based Digital Pcr Improves the Detection of Low-Rate pik3ca Mutations in Breast Cancer Patients

Stefano Giannoni-Luza, Oscar Acosta Conchucos, Alexis Germán Murillo Carrasco, Pierina Danos, José Manuel Cotrina Concha, Henry Guerra Miller, Joseph A. Pinto, Alfredo Aguilar Cartagena, Jhajaira M. Araujo, Ricardo Fujita, José Luis Buleje Sono

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Breast cancer; PIK3CA; digital PCR; Sanger sequencing

Online: 5 July 2021 (14:00:22 CEST)

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Working Paper ARTICLE

An Amplicon-Based Approach for the Whole Genome Sequencing of Human Metapneumovirus

Rachel Tulloch, Jen Kok, Ian Carter, Dominic Dwyer, John-Sebastian Eden

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: human metapneumovirus; whole genome sequencing; genomic epidemiology

Online: 3 February 2021 (10:08:44 CET)

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Preprint ARTICLE | doi:10.20944/preprints202002.0192.v1

Microbial Patterns in Rumen Are Associated with Gain of Weight in Beef Cattle

Anderson Freitas, Diego David, Beatriz Takagaki, Luiz Fernando Wurdig Roesch

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: bacteria; fungi; livestock; microbiome; next generation sequencing

Online: 14 February 2020 (10:32:54 CET)

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Preprint ESSAY | doi:10.20944/preprints201912.0141.v1

Global Stewardship of Recombinant Plasmid Sequences

Michael Parker, Michelle Murti, Robert Emerson Tuttle

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Biosecurity; Dual-use; Plasmids; Sequencing; Science Policy

Online: 10 December 2019 (16:07:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints201906.0117.v1

Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Yun Gyeong Lee, Sang Chul Choi, Yuna Kang, Kyeong Min Kim, Chon-Sik Kang, Changsoo Kim

Subject: Biology And Life Sciences, Plant Sciences Keywords: sorghum; Canu; Miniasm; MinION; long-read sequencing

Online: 13 June 2019 (09:26:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0138.v2

Whole Genome Sequencing Reveals Identification of New Acinetobacter spp. (maqsudiensis) from Cow Fecal Sample Collected from Dhaka, Bangladesh

Muhammad Maqsud Hossain, Abdus Sadique, Aura Rahman, Tahmina Tabassum, Arman Hossain, Tasnuva Avzun, Abdul Mueed Ibne Momen, Mrinmoy Sarker, Abdul Khaleque, Gias U. Ahsan

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Acinetobacter; ANI; Bangladesh; next-generation sequencing; ATCC

Online: 21 November 2018 (07:07:54 CET)

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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/preprints202310.1276.v1

Genomic analysis and tracking of SARS-CoV-2 variants in Gwangju, South Korea from 2020 to 2022

Yeong-Un Lee, Kwangho Lee, Hongsu Lee, Jung wook Park, Sun-Ju Cho, Ji-Su Park, Jeongeun Mun, Sujung Park, Cheong-mi Lee, Juhye Lee, Mihee Seo, Eunju Kim, Jinjong Seo, Yonghwan Kim, Sun-Hee Kim, Yoon-Seok Chung

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; whole-genome sequencing; variants; lineages

Online: 19 October 2023 (11:25:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0612.v1

Novel RNA-Seq Signatures Post-Methamphetamine and Oxycodone Use in a Model of HIV-Associated Neurocognitive Disorders

Pranavi Athota, Nghi M Nguyen, Victoria L Schaal, Sankarasubramanian Jagadesan, Chittibabu Guda, Sowmya V Yelamanchili, Gurudutt Pendyala

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Polysubstance use; methamphetamine; oxycodone; HIV; transgenic rat; RNA-sequencing, bioinformatics

Online: 10 July 2023 (11:34:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0350.v1

Diversity and Distribution of β-lactamase Genes Circulating in Indian Isolates of Multi-drug Resistant Klebsiella pneumoniae

Suraj Shukla, Siddhi Desai, Ashutosh Bagchi, Pushpendra Singh, Madhvi Joshi, Chaitanya Joshi, Jyoti Patankar, Geeti Maheshwari, Ekadashi Rajni, Manali Shah, Devarshi Gajjar

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: whole genome sequencing; β-lactamases; MLST; plasmid replicons; Klebsiella pneumoniae

Online: 19 January 2023 (09:06:46 CET)

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Preprint ARTICLE | doi:10.20944/preprints202404.1209.v1

Genetic Characterization and Population Structure of Drug Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing

Leonardo Souza Esteves, Lia Lima Gomes, Daniela Brites, Fátima Cristina Onofre Fandinho, Marcela Bhering, Márcia Aparecida da Silva Pereira, Emilyn Costa Conceição Sharma, Richard Salvato, Bianca Porphirio da Costa, Reginalda Ferreira de Melo Medeiros, Paulo Cesar de Souza Caldas, Paulo Redner, Margareth Pretti Dalcolmo, Vegard Eldholm, Sebastien Gagneux, Maria Lucia Rossetti, Afrânio Lineu Kritski, Philip Noel Suffys

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Mycobacterium tuberculosis; Drug Resistance; Whole Genome Sequencing; Genetic Diversity; Brazil; Novel Mutations

Online: 18 April 2024 (07:51:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.0530.v1

Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling

Leticia Sandoval, Wazim Mohammed Ismail, Amelia Mazzone, Mihai Dumbrava, Jenna Fernandez, Amik Munankarmy, Terra Lasho, Mortiz Binder, Vernadette Simon, Kwan Hyun Kim, Nicholas Chia, Jeong Heon Lee, S. John Weroha, Mrinal M. Patnaik, Alexandre Gaspar-Maia

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: single-cell sequencing; epigenomic profiling; snATAC-seq; snRNA-seq; nuclei preparation

Online: 8 May 2023 (11:00:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0231.v1

Broadening the Chrysoviridae Horizons: A New Geographical Area and Potential Arthropod Vector for the Xanthi Chryso-Like Virus

Marko Jankovic, Valentina Ćirković, Maja Stanojević, Gorana Stamenković, Ana Lončar, Marina Šiljić

Subject: Biology And Life Sciences, Virology Keywords: Mosquito; arthropod-borne; vector; RNA virus; mycovirus; Chrysoviridae; sequencing; Serbia

Online: 15 July 2022 (11:44:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0480.v1

An Evaluation of Avian Influenza Virus Whole Genome Sequencing Approaches Using Nanopore Technology

Hon S. Ip, Sarah Uhm, Mary Lea Killian, Mia K. Torchetti

Subject: Biology And Life Sciences, Virology Keywords: avian influenza; highly pathogenic avian influenza; next generation sequencing; whole genome sequencing; nanopore technology; methods comparison; clinical validation

Online: 26 January 2023 (15:19:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202008.0285.v1

Sequence Analysis of Egyptian Foot-And-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus

Sahar Abd El Rahman, Bernd Hoffmann, Reham Karam, Mohamed El-Beskawy, Mohammed F. Hamed, Leonie F. Forth, Dirk Höper, Michael Eschbaumer

Subject: Biology And Life Sciences, Virology Keywords: FMDV; Egypt; full-genome sequencing; interserotypic recombination; vaccine composition analysis; frozen evolution

Online: 12 August 2020 (11:56:33 CEST)

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Preprint REVIEW | doi:10.20944/preprints202012.0738.v1

Utility of Whole-Exome Sequencing in Pediatric and Medical Diagnosis

Mohd Fareed, Varun Sharma, Hemender Singh

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Next generation sequencing; Genetic disorders; Genomic medicine; Genetic counseling; Rare diseases

Online: 29 December 2020 (16:47:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints201912.0354.v1

Whole-Genome Sequencing of Lactobacillus Helveticus D75 and D76 Confirms Safety and Probiotic Potential

Vyacheslav Toropov, Elena Demyanova, Olga Shalaeva, Stanislav Sitkin, Timur Vakhitov

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Lactobacillus helveticus; probiotics; whole genome sequencing; PacBio; probiotic genes; bacteriocins; gene expression

Online: 26 December 2019 (10:56:44 CET)

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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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Working Paper ARTICLE

Different Responses of Bacterial and Archaeal Communities in River Sediments to Water Transfer and Seasonal Changes

Jiali Lv, Ruiqiang Yuan, Shiqin Wang

Subject: Environmental And Earth Sciences, Environmental Science Keywords: archaea; bacteria; 16SrRNA high-throughput sequencing; water transfer; seasonal changes; river sediments

Online: 18 August 2020 (04:36:46 CEST)

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Preprint SHORT NOTE | doi:10.20944/preprints201911.0318.v4

Single Molecule Protein Sequencing Based on the Superspecificity of tRNA Synthetases

G Sampath

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: protein sequencing; single molecule; nanopore; tRNA; amino acyl tRNA synthetase; codon; optical tag

Online: 18 February 2020 (11:50:29 CET)

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Preprint REVIEW | doi:10.20944/preprints202011.0034.v1

A Roadmap to Immunotherapy: Lesson from the Hallmarks and Signaling Pathways of Cancer

Afshin Derakhshani, Zeinab Rostami, Hossein Safarpour, Sina Taefehshokr, Neda Jalili Tabrizi, Mahdi Abdoli Shadbad, Omid Kooshkaki, Reza Vaezi Astamal, Antonella Argentiero, Pankaj K. Singh, Nima Taefehshokr, Nazila Alizadeh, Nicola Silvestris, Behzad Baradaran

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: cell signaling; signaling pathways; single-cell sequencing; immunotherapy; hallmarks cancer; cancer

Online: 2 November 2020 (11:28:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202207.0038.v1

Progeria and Aging - Omics Based Comparative Analysis

Aylin Caliskan, Samantha Agnetz Wilhelmine Crouch, Sara Giddins, Thomas Dandekar, Seema Dangwal

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: progeria; aging; omics; RNA Sequencing; bioinformatics; sun exposure; HGPS; IGFBP2; ACKR4; WNT

Online: 4 July 2022 (08:10:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.1431.v1

Increasing the number of contributors identified by SNP panels

Darrell Ricke

Subject: Biology And Life Sciences, Other Keywords: DNA mixture; single nucleotide polymorphism; mixture analysis; high throughput sequencing; massively parallel sequencing; SNP panels

Online: 26 February 2024 (10:54:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0249.v1

Physiological and Transcriptomic Analysis Reveals the Melatonin Alleviates Aluminum Toxicity in Alfalfa (Medicago sativa L.)

Congge Liu, Haijing Cheng, Shuwei Wang, Dashi Yu, Yunmin Wei

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Al toxicity; Melatonin; Redox homeostasis; RNA sequencing; Cell wall; Carbon metabolism

Online: 3 November 2023 (11:25:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0232.v1

The microRNAs in the Antennae of Apolygus lucorum (Hemiptera: Miridae): Expression Properties and Targets Prediction

Adel Khashaveh, Xingkui An, Shuang Shan, Xiaoqian Pang, Yan Li, Xiaowei Fu, Yongjun Zhang

Subject: Biology And Life Sciences, Insect Science Keywords: Small RNA sequencing; miRNAs; Target prediction; Chemosensory-associated genes; Apolygus lucorum

Online: 18 February 2022 (10:01:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints201705.0206.v1

Genome Characterization of a Novel Binary Toxin-Positive Strain of Clostridium difficile and Comparison with the Epidemic 027 and 078 Strains

Zhong Peng, Sidi Liu, Xiujuan Meng, Wan Liang, Biao Tang, Yuanguo Wang, Juping Duan, Chenchao Fu, Bin Wu, Anhua Wu, Chunhui Li

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Clostridium difficile; ST201; binary toxin-positive; whole genome sequencing; comparative genomic analysis

Online: 30 May 2017 (06:15:11 CEST)

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A novel binary toxin-positive non-027, non-078 Clostridium difficile strain designated LC693 whose sequence type was ST201 was isolated from the fecal sample of a patient with severe diarrhea in China. To understand the pathogenesis basis of C. difficile ST201, this recently recovered isolate LC693 was then chosen for whole genome sequencing. The project finally generated an estimated genome size of approximately 4.07 Mbp. The genome sequence was then analyzed together with the other two ST201 strains VL-0104 and VL-0391 and compared to the epidemic 027/ST1 and 078/ST11 strains. Phylogenetic analysis demonstrated that the ST201 strains belonged to clade 3. Genome size of the three ST201 strains ranged from 4.07 Mb~4.16 Mb, with an average GC content between 28.5%~28.9%. The ST201 genomes contained more than 40 antibiotic resistance genes and 15 of them were predicted to be associated with vancomycin-resistance, suggesting that they may have a strong antibiotic resistance. The ST201 strains contained a typical clade 3 specific PaLoc with a Tn6218 element inserted, and those genes harbored on their PaLoc that participated in the toxin expression and regulation were highly homologues to the epidemic 027 and 078 strains, with the exception of tcdC. A truncated TcdC was found in the ST201 strains, which is suggestive to have a contribution to the toxin production of the ST201 strains. In addition, the ST201 strains contained intact binary toxin coding and regulation genes, which is also proposed to contribute to the virulence. Genome comparison of the ST201 strains with the epidemic 027 and 078 strain identified 641 genes specific for the C. difficile ST201, and a number of them were predicted as fitness and virulence associated genes. The identification of those genes also contributes to the pathogenesis of the ST201 strain. To our knowledge, this is the first study that the genome sequence of C. difficile ST201 was discussed in detail, and the present study would have a contribution to understanding the pathogenesis basis of C. difficile ST201.

Preprint REVIEW | doi:10.20944/preprints202401.0451.v1

Harnessing the Transcriptional Signatures of Car-T Cells and Leukemia/Lymphoma Using Single-Cell Sequencing Technologies

Yu-Mei Liao, Shih-Hsien Hsu, Shyh-Shin Chiou

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Single-cell sequencing technologies; CAR-T therapy; Tumor microenvironment; Transcriptional complexity

Online: 5 January 2024 (10:37:47 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0947.v1

Expression of FAD and SAD Genes in Developing Seeds of Flax Varieties under Different Growth Conditions

Elena N. Pushkova, Liubov V. Povkhova, Ekaterina M. Dvorianinova, Roman O. Novakovskiy, Tatiana A. Rozhmina, Aleksey A. Gryzunov, Elizaveta A. Sigova, Daiana A. Zhernova, Elena V. Borkhert, Anastasia A. Turba, Arthur G. Yablokov, Nadezhda L. Bolsheva, Alexey A. Dmitriev, Nataliya V. Melnikova

Subject: Biology And Life Sciences, Plant Sciences Keywords: Linum usitatissimum; flax; fatty acids; SAD; FAD; gene expression; transcriptome sequencing

Online: 13 December 2023 (05:20:29 CET)

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Preprint ARTICLE | doi:10.20944/preprints202305.1165.v1

A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi

Matthew Harrison, V. Alex Sotola, Alexander Zalmat, Kyle T. Sullivan, Bradley M. Littrell, Timothy Bonner, Noland H. Martin

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: non-destructive DNA sampling; DNA collection methods; Louisiana Pigtoe; visceral swabbing; freshwater mussels; Fusconaia askewi; genotyping-by-sequencing; population genetic structure; genomic coverage; sequencing depth

Online: 16 May 2023 (14:15:33 CEST)

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Preprint REVIEW | doi:10.20944/preprints202102.0230.v1

Astrocytes in Alzheimer´s Disease: Pathological Significance and Molecular Pathways

Pranav Preman, Maria Alfonso-Triguero, Elena Alberdi, Alexej Verkhratsky, Amaia M Arranz

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Astrocyte, Alzheimer´s disease, neurodegeneration, transcriptomics, RNA sequencing (RNA-seq), cellular states.

Online: 9 February 2021 (10:04:24 CET)

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Preprint REVIEW | doi:10.20944/preprints202403.0443.v1

Barcoding of Atropa Belladonna’s DNA: A Systemic Review

Mohammad Odah

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: DNA, Atropa belladonna, Barcoding, Adulteration, Sequencing.

Online: 7 March 2024 (10:47:04 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/preprints202308.0649.v1

Genetic Diversity of Type A Influenza Viruses Found in Swine Herds in Northwestern Poland from 2017 to 2019. The One Health Perspective

Lukasz Rabalski, Maciej Kosinski, Piotr Cybulski, Tomasz Stadejek, Krzysztof Lepek

Subject: Biology And Life Sciences, Virology Keywords: zoonosis; emerging diseases; influenza; epidemiology; NGS sequencing; surveillance

Online: 8 August 2023 (09:29:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0473.v1

Genes Involved by Dexamethasone in Prevention of Long-Term Memory Impairment Caused by Lipopolysaccharide-Induced Neuroinflammation

Galina T. Shishkina, Tatiana S Kalinina, Dmitry A. Lanshakov, Veta V. Bulygina, Natalia P. Komysheva, Anita V. Bannova, Uliana S. Drozd, Nikolay N. Dygalo

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: lipopolysaccharide; dexamethasone; hippocampus; RNA- sequencing; memory; inflammation; glutamate

Online: 7 August 2023 (03:38:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0808.v1

Canine Somatic Mutations from Whole Exome Sequencing of B-Cell Lymphomas in Six Canine Breeds

Sungryong Kim, Namphil Kim, Hyo-Min Kang, Hye-Jin Jang, Ki-Jeong Na

Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: Canine lymphoma; Whole-exome sequencing; B-cell; PARR

Online: 12 July 2023 (09:38:44 CEST)

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Preprint CASE REPORT | doi:10.20944/preprints202305.0609.v1

Encephalopathy Caused by Human Parvovirus B19 Genotype 1 Associated With Haemophilus influenzae Meningitis in a Newborn

Noely E. Ferreira, Antonio Charlys Da Costa, Esper Kallas, Cassia G.T. Silveira, Ana Carolina Soares, Layla Honorato, Heuder Gustavo Oliveira Paiao, Silvia Helena Lima, Dewton M. Vasconcelos, Marina F. Côrtes, Silvia Figueiredo Costa, Tania Regina Tozetto-Mendoza, Hélio Rodrigues Gomes, Steven S. Witkin, Maria Cassia Mendes-Correa

Subject: Biology And Life Sciences, Virology Keywords: Human parvovirus B19; Encephalopathy; Metagenomic next-generation sequencing.

Online: 9 May 2023 (08:41:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0290.v1

Exploring the Microbiome of Marmara Sea Mucilage: A Shotgun Metagenomics Study

Aycan Gundogdu, Özkan Ufuk Nalbantoğlu, Gizem Karis, Ilknur Sarikaya, Meryem Nisa Erdogan, Mehmet Hora, Herdem Aslan

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Mucilage microbiome; Shotgun-metagenome sequencing; Comparative marine microbiome

Online: 15 March 2023 (15:24:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202212.0457.v1

Residual Humidity in Paraffin Embedded Tissue Reduces Nucleic Acid Stability

Peter M. Abuja, Daniela Pabst, Benjamin Bourgeois, Martina Loibner, Christine Ulz, Iris Kufferath, Ulrike Fackelmann, Conny Stumptner, Rainer Kraemer, Tobias Madl, Kurt Zatloukal

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: fixed tissue; nucleic acid quality; next-generation sequencing,

Online: 23 December 2022 (09:04:08 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0218.v1

Lactobacillus on Recovering of Immune-Damage by Chemotherapy (Cancer Treatment)

Shousong Yue, Zhenzhong Zhang, Fei Bian, Yan Zhang, Gao Chen, Jun Li, Jean-François Picimbon

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Illumina MiSeq sequencing; gut microflora; Lactobacilli; immunostimulant; anticancer

Online: 17 February 2022 (17:31:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0333.v1

Creating Variant Features to Enhance Covid-19 Predictions with Machine Learning Ensemble

Justin Wood, Wenjia Wang

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Covid-19; Ensemble; Genome sequencing; Machine learning; Variant

Online: 21 January 2022 (15:17:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202103.0374.v1

Dynamics of Specific cfDNA Fragments in Plasma of Full Marathon Participants

Takehito Sugasawa, Shin-ichiro Fujita, Tomoaki Kuji, Noriyo Ishibashi, Kenshirou Tamai, Yasushi Kawakami, Kazuhiro Takekoshi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: cfDNA; next generation sequencing; full marathon; exercise; physiology

Online: 15 March 2021 (11:52:33 CET)

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Preprint CASE REPORT | doi:10.20944/preprints202103.0108.v1

Prenatal Identification of a Novel Mutation in the MCPH1 Gene Associated with Autosomal Recessive Primary Microcephaly (MCPH) using Next Generation Sequencing (NGS)

Ioannis Papoulidis, Makarios Eleftheriades, Emmanouil Manolakos, Simoni Maria Liapi, Anastasia Konstantinidou, Maria Papamichail, Vasileios Papadipoulos, Antonios Garas, Sotirios Sotiriou, Ioannis Papastefanou, Georgios Daskalakis, Aleksandar Ristic

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: microcephalin gene, homozygous, next generation sequencing, microcephaly. MCPH1

Online: 2 March 2021 (16:22:48 CET)

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Preprint ARTICLE | doi:10.20944/preprints202012.0547.v1

The Potential Effect of Oral Bacterial Community in Melanophryniscus Admirabilis (Admirable Red-Belly Toads) Conservation

Michele Bertoni Mann, Janira Prischula, Ícaro Maia Santos de Castro, Juliana Mello Severo, Michelle Abadie, Thayná Mendes De Freitas Lima, Valentina Z. Caorsi, Márcio Borges-Martins, Jeverson Frazzon, Ana Paula Guedes Frazzon

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: high throughput sequencing; amphibian; bacteria; xenobiotic; anthropogenic action

Online: 22 December 2020 (09:54:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints201912.0183.v1

Investigating Strength that Comprehensive mRNA Expression Level of Prognostic Genes Influences on Patient Survival for Every Cancer Type

Minhyeong Lee

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Bioinformatics, Cancer, Genomics, Computational Biology, RNA sequencing, TCGA

Online: 13 December 2019 (10:57:29 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.1035.v1

Integrating Single-Cell RNA-Seq and Bulk RNA-Seq to Explore the Key Role of Fatty Acid Metabolism in Breast Cancer

Yongxing Chen, Chenxin Jin, Jiaxue Cui, Yizhuo Diao, Ruiqi Wang, Rongxuan Xu, Zhihan Yao, Wei Wu, Xiaofeng Li

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Fatty Acid Metabolism; Immunotherapy; Breast cancer; Tumor microenvironment; Single-cell sequencing

Online: 14 June 2023 (09:40:33 CEST)

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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 ARTICLE | doi:10.20944/preprints201902.0020.v1

Moraxella nonliquefaciens and M. osloensis are Important Moraxella Species that Cause Ocular Infections

Samantha LaCroce, Mollie N. Wilson, John E. Romanowski, Jeffrey D. Newman, Vishal Jhanji, Robert M.Q. Shanks, Regis P. Kowalski

Subject: Medicine And Pharmacology, Ophthalmology Keywords: Moraxella; keratitis; conjunctivitis; endophthalmitis; DNA sequencing; MALDI TOF MS; Biolog ID system

Online: 6 February 2019 (06:27:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.0601.v1

Virological and Clinical Outcomes in Adults Treated with Ribavirin Aerosol for COVID-19 Pneumonia

Emanuela Messina, Giulia Morsica, Sabrina Bagaglio, Laura Galli, Riccardo Lolatto, Michela Sampaolo, Maxime Barakat, Robert J Israel, Antonella Castagna, Nicola Clementi

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: COVID-19; pneumonia; ribavirin aerosol; treatment; outcome; viral load; whole genome sequencing

Online: 10 July 2023 (10:16:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201911.0353.v1

Unbiased High-Resolution Composition Analysis of an Inactivated Polyvalent Foot-and-Mouth Disease Vaccine

Leonie Forth, Dirk Höper, Martin Beer, Michael Eschbaumer

Subject: Biology And Life Sciences, Virology Keywords: inactivated vaccine; vaccine matching; composition; deep sequencing; degraded RNA; FMDV; whole genome

Online: 28 November 2019 (04:03:46 CET)

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Preprint ARTICLE | doi:10.20944/preprints201809.0428.v1

Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing

Zhihui Yang, Mark Mammel, Chris A. Whitehouse, Diana Ngo, Michael Kulka

Subject: Biology And Life Sciences, Virology Keywords: inter- and intra-host nucleotide variations; Hepatitis A virus; next-generation sequencing; pyrosequencing

Online: 21 September 2018 (04:59:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0218.v1

Temporal and Cultivar-Specific Effects on Potato Root- and Rhizosphere Fungal Diversity

Kaire Loit, Liina Soonvald, Alar Astover, Eve Runno-Paurson, Maarja Öpik, Leho Tedersoo

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Solanum tuberosum; agroecosystems; high-throughput sequencing; fungal guild, fungal diversity; host specificity; potato cultivars

Online: 11 July 2020 (02:02:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202110.0287.v1

Identification and Comparison of Colletotrichum Secreted Effector Candidates Reveal Two Independent Lineages Pathogenic to Soybean

Thaís Regina Boufleur, Nelson Sidnei Massola Júnior, Ísis Tikami, Serenella Ana Sukno, Michael Ronald Thon, Riccardo Baroncelli

Subject: Biology And Life Sciences, Plant Sciences Keywords: anthracnose; genome sequencing; pathogenicity factors; Colletotrichum truncatum; Colletotrichum orchidearum; Glomerella; Glycine max

Online: 20 October 2021 (10:11:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201803.0149.v1

Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production

Patrick D. Slaine, Cara MacRae, Mariel Kleer, Emily Lamoureux, Sarah McAlpine, Michelle Warhuus, André M. Comeau, Craig McCormick, Todd Hatchette, Denys A. Khaperskyy

Subject: Biology And Life Sciences, Virology Keywords: influenza; H1N1; mouse adaptation; deep sequencing; polymerase; PA; PB1; defective viral genomes

Online: 19 March 2018 (08:59:26 CET)

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Preprint ARTICLE | doi:10.20944/preprints202211.0375.v1

Effects pf Cr Stress on Bacterial Community Structure and Composition in Rhizosphere Soils of Iris Tectorum

Zhao Wei, Gu Baojing, Yang Xiuqing, Xia Guodong, Wang Baichun, Zhu Sixi

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Cr stress; rhizosphere bacterial community; Iris tectorum; 16S rRNA sequencing technology; Phytoremediation

Online: 21 November 2022 (06:27:02 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0020.v1

Molecular Biology and Pathological Process of an Infectious Bronchitis Virus With Enteric Tropism in Commercial Broilers

Ana Paula da Silva, Ruediger Hauck, Sabrina R.C. Nociti, Colin Kern, H.L. Shivaprasad, Huaijun Zhou, Rodrigo A. Gallardo

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: IBV; infectious bronchitis; variants; whole-genome sequencing, enteric tropism; runting-stunting syndrome

Online: 1 July 2021 (11:25:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0040.v1

Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer

Diamanto Skopelitou, Beiping Miao, Aayushi Srivastava, Abhishek Kumar, Magdalena Kuświk, Dagmara Dymerska, Nagarajan Paramasivam, Matthias Schlesner, Jan Lubiński, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: APCDD1; HDAC5; germline variants; familial colorectal cancer; whole exome sequencing; promoter activity

Online: 1 February 2021 (14:04:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0150.v1

Lentil Landrace Seed Origin and Genotype Affects Rhizosphere Microbiome

Anthoula Gleridou, Georgios Giannopoulos, Alexios N. Polidoros, Photini V. Mylona

Subject: Biology And Life Sciences, Plant Sciences Keywords: organic-; conventional-farming; next-generation sequencing; metagenomics; microbial diversity; N2-fixing bacteria; archaea

Online: 2 November 2023 (10:53:27 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.2147.v1

Effects of Chronic Heat Stress on Lung and Growth Performance in Cherry-Valley Ducks under Different Ambient Temperatures

Min Tang, Yi Liu, Dongyue Sun, Congcong Xu, Kongdong Li, Hantao Zhang, Jie Gu, Chaofan Shan, Shijia Ying

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: chronic heat stress; duck rearing; environmental temperature; next-generation sequencing; carcass traits

Online: 1 August 2023 (05:35:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202112.0049.v1

Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy Against the Phytopathogen Ralstonia solanacearum

Elena G. Biosca, José F. Català-Senent, Àngela Figàs-Segura, Edson Bertolini, María M. López, Belén Álvarez

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: bacterial wilt; biological control; phage; microscopy; sequencing; molecular characterization; genomic characterization; depolymerase

Online: 3 December 2021 (10:36:47 CET)

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Preprint ARTICLE | doi:10.20944/preprints202305.1290.v1

Is Cutaneous T-Cell Lymphoma Caused by Ultraviolet Radiation? Comparison of UV Mutational Signatures Between Malignant Melanoma and Mycosis Fungoides.

Robert Gniadecki, Sandra O’Keefe, Dylan Hennessey, Aishwarya Iyer

Subject: Medicine And Pharmacology, Dermatology Keywords: cutaneous T-cell lymphoma; ultraviolet; mutation signatures; malignant melanoma, whole exome sequencing

Online: 18 May 2023 (07:36:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0154.v1

Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways

Aayushi Srivastava, Abhishek Kumar, Sara Giangiobbe, Elena Bonora, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: papillary thyroid cancer; germline mutations; whole genome sequencing; predisposition markers; pathway analysis

Online: 13 October 2019 (17:07:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0467.v1

Effects of Phage Cocktail, Probiotics and Their Combinations on Growth Performance and Gut Microbiota of Broiler Chickens

Mohd Shaufi Mohd Asrore, Chin Chin Sieo, Chong Chun Wie, Tan Geok Hun, Abdul Rahman Omar, Gan Han Ming, Yin Wan Ho

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: antibiotic growth promoter; alternative; poultry production; next-generation sequencing; 16S rRNA; gut microbial diversity

Online: 26 January 2023 (04:06:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.1603.v1

Single Cell Transcriptomic Analysis in a Mouse Model of Barth Syndrome Reveals Cell-Specific Alterations in Gene Expression and Intercellular Communication

Gayani Perera, Liam Power, Amy Larson, Christina J. Codden, Junya Awata, Rebecca Batorsky, Douglas Strathdee, Michael T. Chin

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Tafazzin; Barth Syndrome; Single-Nucleus RNA-sequencing; Cardiomyopathy; Mitochondria; Gene Expression; Metabolism

Online: 22 June 2023 (11:31:02 CEST)

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Barth Syndrome, a rare X-linked disorder affecting 1:300,000 live births, results from defects in Tafazzin, an acyltransferase that remodels cardiolipin and is essential for mitochondrial respiration. Barth Syndrome patients develop cardiomyopathy, muscular hypotonia and cyclic neutropenia during childhood, rarely surviving to middle age. At present, no effective therapy exists and downstream transcriptional effects of Tafazzin dysfunction are incompletely understood. To identify novel, cell-specific, pathological pathways that mediate heart dysfunction, we performed single-nucleus RNA-sequencing (snRNA-seq) on wild-type (WT) and Tafazzin-knockout (Taz-KO) mouse hearts. We determined differentially expressed genes (DEGs) and inferred predicted cell-cell communication networks from these data. Surprisingly, DEGs were distributed heterogeneously across the cell types, with fibroblasts, cardiomyocytes, endothelial cells, macrophages, adipocytes and pericytes exhibiting the greatest number of DEGs between genotypes. One differentially expressed gene was detected for the lymphatic endothelial and mesothelial cell types, while no significant DEGs were found in the lymphocytes. A Gene Ontology (GO) analysis of these DEGs showed cell-specific effects on biological processes such as fatty acid metabolism in adipocytes and cardiomyocytes, increased translation in cardiomyocytes, endothelial cells and fibroblasts, in addition to other cell-specific processes. Analysis of ligand-receptor pair expression, to infer intercellular communication patterns, revealed the strongest dysregulated communication involved adipocytes and cardiomyocytes. For the knockout hearts, there was a strong loss of ligand-receptor pair expression involving adipocytes, and cardiomyocyte expression of ligand-receptor pairs underwent reorganization. These findings suggest that adipocyte and cardiomyocyte mitochondria may be most sensitive to mitochondrial Tafazzin deficiency and that rescuing adipocyte mitochondrial dysfunction, in addition to cardiomyocyte mitochondrial dysfunction, may provide therapeutic benefit in Barth Syndrome patients.

Preprint ARTICLE | doi:10.20944/preprints202311.1514.v1

Genetic Diversity, Pathogenicity and Host Resistance of Fusarium Species from Soybean in Canada

Longfei Wu, Sheau-Fang Hwang, Stephen E. Strelkov, Rudolph Fredua-Agyeman, Sanghoen Oh, Richard R. Bélanger, Owen Wally, Yong Min Kim

Subject: Biology And Life Sciences, Plant Sciences Keywords: Fusarium spp.; genetic diversity; pathogenicity; phylogenetic analyses; resistance; root rot; Sanger sequencing; soybean

Online: 23 November 2023 (11:06:49 CET)

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Preprint ARTICLE | doi:10.20944/preprints202304.0855.v1

Global Profile of tRNA-Derived Small RNAs in Pathological Cardiac Hypertrophy Plasma and Identification of tRF-21-NB8PLML3E as a New Hypertrophy Suppressor

Jingyi Xu, Buyun Qian, Feng Wang, Ying Huang, Xinxin Yan, Ping Li, Qian Zhang, Yuan Li, Kangyun Sun

Subject: Biology And Life Sciences, Life Sciences Keywords: transfer RNA-derived small RNAs; pathological cardiac hypertrophy; small RNA sequencing; biomarkers

Online: 24 April 2023 (11:01:16 CEST)

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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/preprints202205.0083.v1

Gene Expression Profile Provides Novel Insights of Fasting-Refeeding Response in Zebrafish Skeletal Muscle

Ritsuko Komine, Takehito Sugasawa, Lev Manevich, Shinsuke Tamai, Kazuhiro Takekoshi, Yasuharu Kanki

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: fasting; refeeding; skeletal muscle; zebrafish; mRNA-sequencing; gene length

Online: 6 May 2022 (14:31:07 CEST)

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Preprint REVIEW | doi:10.20944/preprints202106.0526.v1

Towards the Forest Virome: Next-Generation-Sequencing Drastically Expands our Understanding on Virosphere in Temperate Forest Ecosystems

Artemis Rumbou, Eeva J. Vainio, Carmen Büttner

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: virome; microbiome; next generation sequencing; mycoviruses; plant pathogenic viruses

Online: 21 June 2021 (16:23:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202103.0514.v1

The Nanopore-Tweezing-Based, Targeted Detection of Nucleobases on Short Functionalized Peptide-Nucleic Acid Sequences

Isabela Dragomir, Alina Asandei, Irina Schiopu, Ioana Bucataru, Loredana Mereuta, Tudor Luchian

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: nanopore tweezer; peptide nucleic acid; sequencing; single molecule recordings

Online: 22 March 2021 (11:08:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints202103.0257.v1

Whole Exome Sequencing Identifies Novel Germline Variants of SLC15A4 Gene as Potentially Cancer Predisposing in Familial Colorectal Cancer

Diamanto Skopelitou, Aayushi Srivastava, Beiping Miao, Abhishek Kumar, Dagmara Dymerska, Nagarajan Paramasivam, Matthias Schlesner, Jan Lubiński, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SLC15A4; germline variant; familial colorectal cancer; whole exome sequencing

Online: 9 March 2021 (10:24:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints202103.0121.v1

A Novel Low-Risk Germline Variant in the SH2 Domain of the SRC Gene Affects Multiple Pathways in Familial Colorectal Cancer

Diamanto Skopelitou, Beiping Miao, Aayushi Srivastava, Abhishek Kumar, Magdalena Kuświk, Dagmara Dymerska, Nagarajan Paramasivam, Matthias Schlesner, Jan Lubiński, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Familial colorectal cancer; SRC; germline variant; whole genome sequencing

Online: 3 March 2021 (09:52:06 CET)

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Preprint CASE REPORT | doi:10.20944/preprints202012.0704.v1

Overlapping Phenotype of Cardiomyopathy in Patient With Double Mutation

Sigita Glaveckaitė, Violeta Mikštienė, Darius Palionis, Nomeda Rima Valevičienė

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: left ventricular noncompaction; apical hypertrophic cardiomyopathy; next generation sequencing

Online: 28 December 2020 (13:19:41 CET)

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Preprint ARTICLE | doi:10.20944/preprints202009.0483.v1

Enhancing the Landscape of Colorectal Cancer Using Targeted Deep Sequencing

Chul Seung Lee, In Hye Song, Ahwon Lee, Jun Kang, Yoon Suk Lee, In Kyu Lee, Young Soo Song, Sung Hak Lee

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: next-generation sequencing; colorectal cancer; ATM mutation; FBXW7 mutation

Online: 20 September 2020 (15:20:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0395.v1

Rapid Diagnosis of Capnocytophaga canimorsus Septic Shock in an Immunocompetent Individual Using Real-Time Nanopore Sequencing

Seweryn Bialasiewicz, Tania P.S. Duarte, Son H. Nguyen, Vichitra Sukumaran, Alexandra Stewart, Sally Appleton, Miranda E. Pitt, Arnold Bainomugisa, Amy V. Jennison, Rikki Graham, Lachlan J.M. Coin, Krispin Hajkowicz

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: nanopore sequencing; droplet digital PCR; Capnocytophaga canimorsus; diagnosis; sepsis

Online: 16 November 2018 (09:45:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints201802.0090.v1

High-throughput Sequencing Analysis of the Actinobacterial Apatial Diversity in Moonmilk Deposits

Marta Maciejewska, Magdalena Calusinska, Luc Cornet, Delphine Adam, Igor Pessi, Sandrine Malchair, Philippe Delfosse, Denis Baurain, Hazel Barton, Monique Carnol, Sébastien Rigali

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: antibiotics; geomicrobiology; Illumina sequencing; microbiome diversity; Streptomyces; Cave microbiology

Online: 12 February 2018 (16:30:42 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0461.v1

Common and Distinctive Intercellular Communication Patterns in Human Obstructive and Nonobstructive Hypertrophic Cardiomyopathy

Christina J. Codden, Michael T. Chin

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Hypertrophic Cardiomyopathy; Left ventricular outflow tract obstruction; single nucleus RNA-sequencing; dendritic cells; integrin-b1.

Online: 29 December 2021 (09:43:00 CET)

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