UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline

Authors: Jordana Lindner, Bareket Dassa, Noa Wigoda, Gil Stelzer, Ester Feldmesser, Jaime Prilusky, Dena Leshkowitz

Source: BMC Bioinformatics, Vol 26, Iss 1, Pp 1-12 (2025)

Subject Terms: NGS (next-generation sequencing), RNA-seq, ATAC-seq, ChIP-seq, Ribo-Seq, Differential gene expression, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/1500a5a058344f78857a2735e0f5f8da

Transcriptomic signatures of severe acute mountain sickness during rapid ascent to 4,300 m

Authors: Ruoting Yang, Aarti Gautam, Rasha Hammamieh, Robert C. Roach, Beth A. Beidleman

Source: Frontiers in Physiology, Vol 15 (2025)

Subject Terms: NGS - next generation sequencing, acute mountain sickness, biomarker, machine learning, high altitude, Physiology, QP1-981

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fphys.2024.1477070/full; https://doaj.org/toc/1664-042X

Access URL: https://doaj.org/article/0adb6795ef76442bba0ef44879714e8a

Exploring the recent advancements and future prospects of personalized medicine in type 2 diabetes

Authors: Shahrzad Manavi Nameghi

Source: Endocrine and Metabolic Science, Vol 16, Iss , Pp 100193- (2024)

Subject Terms: Type 2 diabetes (T2D), Single nucleotide polymorphism (SNP), NGS (next generation sequencing), Genome-wide association studies (GWAS), Diseases of the endocrine glands. Clinical endocrinology, RC648-665

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666396124000372; https://doaj.org/toc/2666-3961

Access URL: https://doaj.org/article/d2cb188547304539a8ca15e3ccb4f6a8

16S rRNA amplicon sequencing and antimicrobial resistance profile of intensive care units environment in 41 Brazilian hospitals

Authors: Daniela Carolina de Bastiani, Claudia Vallone Silva, Ana Paula Christoff, Giuliano Netto Flores Cruz, Leonardo Daniel Tavares, Luana Silva Rodrigues de Araújo, Bruno Martins Tomazini, Beatriz Arns, Filipe Teixeira Piastrelli, Alexandre Biasi Cavalcanti, Luiz Felipe Valter de Oliveira, Adriano Jose Pereira

Source: Frontiers in Public Health, Vol 12 (2024)

Subject Terms: microbiome, bacteria, antimicrobial resistance (AMR) gene, NGS—next generation sequencing, hospital surfaces, 16S rRNA amplicon, Public aspects of medicine, RA1-1270

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Relation: https://www.frontiersin.org/articles/10.3389/fpubh.2024.1378413/full; https://doaj.org/toc/2296-2565

Access URL: https://doaj.org/article/61f8ed5d5e5c47d2863c1c95eee02dee

Novel missense variants in brain morphogenic genes associated with depression and schizophrenia

Authors: Maxim Karagyaur, Alexandra Primak, Kirill Bozov, Dmitriy Sheleg, Mikhail Arbatsky, Stalik Dzhauari, Maria Illarionova, Ekaterina Semina, Larisa Samokhodskaya, Polina Klimovich, Arkadiy Velichko, Mikhail Drach, Ekaterina Sotskaya, Vladimir Popov, Kseniya Rubina, Mariia Parfenenko, Julia Makus, Boris Tsygankov, Vsevolod Tkachuk, Elena Neyfeld

Source: Frontiers in Psychiatry, Vol 15 (2024)

Subject Terms: paranoid schizophrenia, major depressive disorder, brain morphogenesis, neurotrophines, guidance molecules, NGS (next generation sequencing), Psychiatry, RC435-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fpsyt.2024.1338168/full; https://doaj.org/toc/1664-0640

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Human mutations in SLITRK3 implicated in GABAergic synapse development in mice

Authors: Stephanie Efthymiou, Wenyan Han, Muhammad Ilyas, Jun Li, Yichao Yu, Marcello Scala, Nancy T. Malintan, Nikoleta Vavouraki, Kshitij Mankad, Reza Maroofian, Clarissa Rocca, Vincenzo Salpietro, Shenela Lakhani, Eric J. Mallack, Timothy Blake Palculict, Hong Li, Guojun Zhang, Faisal Zafar, Nuzhat Rana, Noriko Takashima, Hayato Matsunaga, Claudia Manzoni, Pasquale Striano, Mark F. Lythgoe, Jun Aruga, Wei Lu, Henry Houlden

Source: Frontiers in Molecular Neuroscience, Vol 17 (2024)

Subject Terms: SLITRK3, GABAergic synapse development, epilepsy, global developmental delay, inhibitory synaptic transmission, NGS - next generation sequencing, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

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Relation: https://www.frontiersin.org/articles/10.3389/fnmol.2024.1222935/full; https://doaj.org/toc/1662-5099

Access URL: https://doaj.org/article/4c9fba0e92c64e6881b4e82760b9b3c3

Case report: From sequence to solution: tailoring treatment for transformed follicular lymphoma (DLBCL) through next generation sequencing study

Authors: Antonin Bouroumeau, Sarah Perdikis-Prati, Noémie Lang

Source: Frontiers in Oncology, Vol 14 (2024)

Subject Terms: follicular lymphoma, aggressive transformation, NGS - next generation sequencing, PD-1 inhibitor, tumor mutational burden (TMB), Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2024.1308492/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/5bfc0f433de5436196b17ad772ffc159

Corrigendum: Personalized monitoring of circulating tumor DNA with a specific signature of trackable mutations after chimeric antigen receptor T-cell therapy in follicular lymphoma patients

Authors: Ana Jiménez-Ubieto, Alejandro Martín-Muñoz, María Poza, Sara Dorado, Almudena García-Ortiz, Enrique Revilla, Pilar Sarandeses, Yanira Ruiz-Heredia, Tycho Baumann, Antonia Rodríguez, María Calbacho, Pilar Martínez Sánchez, José María Sánchez Pina, Alejandro Martín García-Sancho, Gloria Figaredo, Daniel Gil-Alós, Laura Rufián, Margarita Rodríguez, Laura Carneros, Carolina Martínez-Laperche, Mariana Bastos-Oreiro, Chongwu Wang, María-Teresa Cedena, Inmaculada Rapado, Paula de Toledo, Miguel Gallardo, Antonio Valeri, Rosa Ayala, Joaquín Martínez-López, Santiago Barrio

Source: Frontiers in Immunology, Vol 14 (2024)

Subject Terms: follicular lymphoma, ctDNA (circulating tumor DNA), NGS (Next-Generation Sequencing), minimal residual disease, monitoring, PET/CT 18F-FDG, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1349296/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/6180b4e41d7e48c3aa85430dc0d50bae

Erratum: Approaching hemophagocytic lymphohistiocytosis

Authors: Frontiers Production Office

Source: Frontiers in Immunology, Vol 15 (2024)

Subject Terms: HLH - hemophagocytic lymphohistiocytosis, FHL – familial hemophagocytic lymphohistiocytosis, perforin, degranulation, flow cytometric assay, NGS - next generation sequencing, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1369687/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/f1941019d2414e97be8565c5de19db52

Outcomes of fertility preservation treatments in patients with endometrial cancer with different molecular classifications based on an NGS panel

Authors: Yan Xu, Mingming Zhao, Li Zhang, Tianyou Wang, Bo Wang, Yu Xue, Zhiying Xu, Wenyu Shao, Xiaojun Chen, Chao Wang

Source: Frontiers in Oncology, Vol 13 (2023)

Subject Terms: endometrial cancer, NGS - next generation sequencing, fertility preservation treatment, molecular classifcation, molecular features, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2023.1282356/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/526ad8325bfd4d13a3bce7e9db556791

Editorial: Molecular genetic testing and emerging targeted therapies for non-small cell lung cancer

Authors: Carlos Gil Ferreira, Marina Xavier Reis, Gilson Gabriel Viana Veloso

Source: Frontiers in Oncology, Vol 13 (2023)

Subject Terms: NSCLC - lung adenocarcinoma - EGFR - ALK - BRAF - KRAS - RET - MET - PD-L1 - ROS1, NGS - next generation sequencing, molecular profiling, liquid biopsy, driver mutations, target therapy, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2023.1308525/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/f877df3f574d48bfb56ab3e342332fd8

Novel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity

Authors: Anastasia O. Smirnova, Anna M. Miroshnichenkova, Laima D. Belyaeva, Ilya V. Kelmanson, Yuri B. Lebedev, Ilgar Z. Mamedov, Dmitriy M. Chudakov, Alexander Y. Komkov

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: TRB repertoire, VDJ recombination, NGS - next generation sequencing, T cell, Thymus, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1245175/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/7c744d23d4c24f8fa70e56c8a7bd5e3e

The novel EGFR mutations (p.E746_S752delinsI, p.T751_I759delinsG, p.L747_S752delinsAA) in patients with non-small cell lung cancer and the clinical treatment strategy: three case reports

Authors: Yamin Meng, Xiaodong Li, Lei Zhang, Minhua Ye

Source: Frontiers in Oncology, Vol 13 (2023)

Subject Terms: NSCLC (non-small cell lung cancer), EGFR (epidermal growth factor receptor), mutation, icotinib, NGS (next-generation sequencing), Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2023.1129629/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/e2771ad19aef4f69ae8931e7a58efddb

Corrigendum: Personalized monitoring of circulating tumor DNA with a specific signature of trackable mutations after chimeric antigen receptor T-cell therapy in follicular lymphoma patients

Authors: Ana Jiménez-Ubieto, Alejandro Martín-Muñoz, María Poza, Sara Dorado, Almudena García-Ortiz, Enrique Revilla, Pilar Sarandeses, Yanira Ruiz-Heredia, Tycho Baumann, Antonia Rodríguez, María Calbacho, Pilar Martínez Sánchez, José María Sánchez Pina, Alejandro Martín García-Sancho, Gloria Figaredo, Laura Rufián, Margarita Rodríguez, Laura Carneros, Carolina Martínez-Laperche, Mariana Bastos-Oreiro, Chongwu Wang, María-Teresa Cedena, Inmaculada Rapado, Paula de Toledo, Miguel Gallardo, Antonio Valeri, Rosa Ayala, Joaquín Martínez-López, Santiago Barrio

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: follicular lymphoma, ctDNA (circulating tumor DNA), NGS (Next-Generation Sequencing), minimal residual disease, monitoring, PET/CT 18F-FDG, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1243241/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/85d6ea9ac18848589608d5c77dbb5343

Editorial: Methods and applications in molecular diagnostics

Authors: Naina Arora, Anubha Chaudhary, Amit Prasad

Source: Frontiers in Molecular Biosciences, Vol 10 (2023)

Subject Terms: diagnosis, molecular biology, PCR, NGS—next generation sequencing, cancer, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2023.1239005/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/bf77b2f09c694abd9425f85ecfe39d7a

Resolution on the results of Advisory Board 'Searching the effective methods of testing and treating patients with NSCLC caused by NTRK gene fusions'

Authors: E. V. Artamonova, V. V. Breder, L. Yu. Vladimirova, I. A. Demidova, E. N. Imyanitov, К. К. Laktionov, M. P. Matrosova, S. V. Orlov, E. О. Rodionov, D. D. Sakaeva, M. I. Sekacheva, A. V. Smolin, N. V. Fadeeva, M. L. Filipenko

Source: Медицинский совет, Vol 0, Iss 9, Pp 50-56 (2022)

Subject Terms: ntrk gene fusions, larotrectinib, ngs (next generation sequencing), trk inhibitors, non-small cell lung cancer, Medicine

File Description: electronic resource

Relation: https://www.med-sovet.pro/jour/article/view/6916; https://doaj.org/toc/2079-701X; https://doaj.org/toc/2658-5790

Access URL: https://doaj.org/article/186fbc488e5c4c5dbd4fa32b6b40705e

Personalized monitoring of circulating tumor DNA with a specific signature of trackable mutations after chimeric antigen receptor T-cell therapy in follicular lymphoma patients

Authors: Ana Jiménez-Ubieto, Alejandro Martín-Muñoz, María Poza, Sara Dorado, Almudena García-Ortiz, Enrique Revilla, Pilar Sarandeses, Yanira Ruiz-Heredia, Tycho Baumann, Antonia Rodríguez, María Calbacho, Pilar Martínez Sánchez, José María Sánchez Pina, Alejandro Martín García-Sancho, Gloria Figaredo, Daniel Gil-Alós, Laura Rufián, Margarita Rodríguez, Laura Carneros, Carolina Martínez-Laperche, Mariana Bastos-Oreiro, Chongwu Wang, María-Teresa Cedena, Inmaculada Rapado, Paula de Toledo, Miguel Gallardo, Antonio Valeri, Rosa Ayala, Joaquín Martínez-López, Santiago Barrio

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: follicular lymphoma, ctDNA (circulating tumor DNA), NGS (Next-Generation Sequencing), minimal residual disease, monitoring, PET/CT 18F-FDG, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1188818/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/1d554d9f1fd5420eabc9eb1cd0499e0c

Approaching hemophagocytic lymphohistiocytosis

Authors: Aurora Chinnici, Linda Beneforti, Francesco Pegoraro, Irene Trambusti, Annalisa Tondo, Claudio Favre, Maria Luisa Coniglio, Elena Sieni

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: HLH - hemophagocytic lymphohistiocytosis, FHL – familial hemophagocytic lymphohistiocytosis, perforin, degranulation, flow cytometric assay, NGS - next generation sequencing, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1210041/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/e5416618a7cb4444a24e60c4681541a3

Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls

Authors: Caine Lucas Grandt, Lara Kim Brackmann, Alicia Poplawski, Heike Schwarz, Federico Marini, Thomas Hankeln, Danuta Galetzka, Sebastian Zahnreich, Johanna Mirsch, Claudia Spix, Maria Blettner, Heinz Schmidberger, Manuela Marron

Source: Frontiers in Oncology, Vol 13 (2023)

Subject Terms: weighted co-expression network analysis (WGCNA), differential gene expression analysis, RNA-Seq, radiation experiments, NGS - next generation sequencing, radiation response, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2023.1158176/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/b0bdc83a02bf48d1aef2fa53dae0bee1

Decoding the microbial universe with metagenomics: a brief insight

Authors: Hiral G. Chaudhari, Shobha Prajapati, Zuhour Hussein Wardah, Gopal Raol, Vimalkumar Prajapati, Rajesh Patel, Ali A. Shati, Mohammad Y. Alfaifi, Serag Eldin I. Elbehairi, R. Z. Sayyed

Source: Frontiers in Genetics, Vol 14 (2023)

Subject Terms: NGS, next-generation sequencing, metagenomics, microbial diversity, microbiome, shotgun sequencing, amplicon sequencing, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2023.1119740/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/c693b850016542c1a7dd9f7766db366b