Ecosyste.ms: Papers

10.1186/s12859-017-1991-3

Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform
Cited by: 18
Author(s): Aditya Deshpande, Wenhua Liu, Tina L. McDowell, Smruthy Sivakumar, Jiexin Zhang, Jing Wang, F. Anthony San Lucas, Jerry Fowler, Humam Kadara, Paul Scheet
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-60751-7

Ancient mtDNA from the extinct Indian cheetah supports unexpectedly deep divergence from African cheetahs
Cited by: 6
Author(s): Niraj Rai, Sunil Kumar Verma, Ajay Gaur, Florin Mircea Iliescu, Mukesh Thakur, Tirupathi Rao Golla, Kailash Chandra, Satya Prakash, Wajeeda Tabasum, Sreenivas Ara, Lalji Singh, Kumarasamy Thangaraj, Guy S. Jacobs
Software Mentions: 2
Published: over 4 years ago

10.1186/s13100-020-0204-1

Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines
Cited by: 10
Author(s): Witold Tatkiewicz, James Dickie, Franchesca Bedford, Alexander Jones, Mark Atkin, Michele Kiernan, Emmanuel A. Maze, Bora Agit, Garry Farnham, Alexander Kanapin, Robert Belshaw
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0090761

Next Generation MUT-MAP, a High-Sensitivity High-Throughput Microfluidics Chip-Based Mutation Analysis Panel
Cited by: 18
Author(s): Erica Schleifman, Rachel Tam, Rajesh Patel, Alison Tsan, Teiko Sumiyoshi, Ling Fu, Rupal Desai, Nancy Schoenbrunner, Thomas W. Myers, Keith Bauer, E. J. Smith, Rajiv Raja
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0168860

Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation
Cited by: 21
Author(s): Linh D. N. Nguyen, Pieter Deschaght, Sophie Merlin, Alexandre Loywick, Christophe Audebert, S. Van Daele, Éric Viscogliosi, Mario Vaneechoutte, Laurence Delhaès
Software Mentions: 2
Published: almost 8 years ago

10.3390/life10100228

The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers
Cited by: 21
Author(s): Soyeon Kim, Joo Won Lee, Young‐Seok Park
Software Mentions: 2
Published: about 4 years ago

10.3389/fnut.2016.00026

Considerations For Optimizing Microbiome Analysis Using a Marker Gene
Cited by: 26
Author(s): Jacobo de la Cuesta-Zuluaga, Juan S. Escobar
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2016.01907

Detection of Inter-Lineage Natural Recombination in Avian Paramyxovirus Serotype 1 Using Simplified Deep Sequencing Platform
Cited by: 23
Author(s): Dilan Amila Satharasinghe, Kavitha Murulitharan, Sheau Wei Tan, Swee Keong Yeap, Muhammad Munir, Aini Ideris, Abdul Rahman Omar
Software Mentions: 2
Published: almost 8 years ago

10.1186/1756-0500-7-40

XS: a FASTQ read simulator
Cited by: 20
Author(s): Diogo Pratas, Armando J. Pinho, João M. O. S. Rodrigues
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-021-93606-w

Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress
Cited by: 13
Author(s): Laura Entrambasaguas, Miriam Ruocco, Koen Verhoeven, Gabriele Procaccini, Lázaro Marín-Guirao
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2018.03009

Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture
Cited by: 41
Author(s): Lucy Peters, Sofie Spatharis, Maria Augusta Dario, Toni Dwyer, Inaki J. T. Roca, Anna Kintner, Øyvind Kanstad-Hanssen, Martin S. Llewellyn, Kim Præbel
Software Mentions: 2
Published: almost 6 years ago

10.3389/fcimb.2021.555072

Microbiota Detection Patterns Correlate With Presence and Severity of Barrett’s Esophagus
Cited by: 4
Author(s): Ikenna Okereke, Aaron L. Miller, Daniel C. Jupiter, Catherine Hamilton, Gabriel Reep, Timothy Krill, Clark R. Andersen, Richard B. Pyles
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-98318-9

High concordance in preimplantation genetic testing for aneuploidy between automatic identification via Ion S5 and manual identification via Miseq
Cited by: 3
Author(s): Tsu-Hwang Chuang, Zih-Huei Wu, Chin-Sheng Kuan, Meng-Ju Lee, Chu‐Chin Hsieh, Huai-Lin Wang, Hsing-Hua Lai, Yu-Jen Chang, Shee–Uan Chen
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0142373

Dual Action of miR-125b As a Tumor Suppressor and OncomiR-22 Promotes Prostate Cancer Tumorigenesis
Cited by: 47
Author(s): William T. Budd, Sarah Seashols‐Williams, Gene C Clark, Danielle Weaver, Valerie Calvert, Emanuel F. Petricoin, Ema Dragoescu, Katherine O’Hanlon, Zendra E. Zehner
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2020.573972

German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing
Cited by: 10
Author(s): Laura Uelze, Maria Blettner, Markus Bönn, Erik Brinks, Carlus Deneke, Thomas Hankeln, Sylvia Kleta, Larissa Murr, Kerstin Stingl, Kathrin Szabo, Simon H. Tausch, Anne Wöhlke, Burkhard Malorny
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0185697

Indigenous species barcode database improves the identification of zooplankton
Cited by: 20
Author(s): Jianghua Yang, Xiaowei Zhang, Wanwan Zhang, Jingying Sun, Yuwei Xie, Yimin Zhang, G.A. Burton, Yu H
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0131925

Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms
Cited by: 18
Author(s): Francesca Bertolini, Concetta Scimone, Calogero Geraci, Giuseppina Schiavo, Valerio Joe Utzeri, Vincenzo Chiofalo, Luca Fontanesi
Software Mentions: 2
Published: over 9 years ago

10.15252/embr.201949248

Small‐molecule inhibition of aging‐associated chromosomal instability delays cellular senescence
Cited by: 24
Author(s): Monika Barroso-Vilares, Joana Catarina Macedo, Mário Reis, Jessica D Warren, Duane A. Compton, Elsa Logarinho
Software Mentions: 2
Published: over 4 years ago

10.1016/j.dib.2017.11.049

Complete genome sequence of native Bacillus cereus strains isolated from intestinal tract of the crab Ucides sp.
Cited by: 8
Author(s): João Costa Filho, Sérgio Jorge, Frederico Schmitt Kremer, Natasha Rodrigues de Oliveira, Vinícius Farias Campos, Luciano da Silva Pinto, Odir A. Dellagostin, Rubens Galdino Feijó, Francisca Gleire Rodrigues de Menezes, Oscarina Viana de Sousa, Rodrigo Maggioni, Luís Fernando Marins
Software Mentions: 2
Published: almost 7 years ago

10.1128/mSystems.00580-20

Metabolic Interactions between <i>Brachypodium</i> and Pseudomonas fluorescens under Controlled Iron-Limited Conditions
Cited by: 13
Author(s): Rene Boiteau, Lye Meng Markillie, David Hoyt, Dehong Hu, Rosalie K. Chu, Hugh D. Mitchell, Ljiljana Paša‐Tolić, Janet K. Jansson, Christer Jansson
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0051263

Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes
Cited by: 14
Author(s): Agnès Dettaı̈, Cyril Gallut, Sophie Brouillet, Joël Pothier, Guillaume Lecointre, Régis Debruyne
Software Mentions: 2
Published: almost 12 years ago

10.3389/fmicb.2017.01382

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies
Cited by: 25
Author(s): Chandni Sidhu, Surendra Vikram, Anil Kumar Pinnaka
Software Mentions: 2
Published: over 7 years ago

10.1186/s13000-020-01011-0

The decisive role of molecular pathology in presumed somatic metastases of type II testicular germ cell tumors: report of 2 cases
Cited by: 3
Author(s): Mariëtte E.G. Kranendonk, Wenzel M. Hackeng, G. Johan A. Offerhaus, Folkert H.M. Morsink, G. N. Jonges, Gerard Groenewegen, Pieter-Jaap Krijtenburg, Heinz‐Josef Klümpen, Wendy W.J. de Leng, Leendert Looijenga, Lodewijk A.A. Brosens
Software Mentions: 2
Published: over 4 years ago

10.1111/1751-7915.12020

Ion Torrent-based transcriptional assessment of a<i>Corynebacterium pseudotuberculosis</i>equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method
Cited by: 12
Author(s): Thiago Luiz de Paula Castro, Núbia Seyffert, Rommel Thiago Jucá Ramos, Silvanira Barbosa, Rodrigo Coelho de Carvalho, Anne Cybelle Pinto, Adriana Ribeiro Carneiro, Wanderson Marques Silva, Luis Gustavo Carvalho Pacheco, Christopher G. Downson, Maria Paula Cruz Schneider, Anderson Miyoshi, Vasco Azevedo, Artur da Costa da Luiz Silva
Software Mentions: 2
Published: almost 12 years ago

10.3389/fmicb.2015.00944

Geriatric Respondents and Non-Respondents to Probiotic Intervention Can be Differentiated by Inherent Gut Microbiome Composition
Cited by: 18
Author(s): Suja Senan, J. B. Prajapati, Chaitanya G. Joshi, V. Sreeja, Manisha Kalpesh Gohel, Sunil Trivedi, Rupal Patel, Himanshu Pandya, Udaybir Singh, Ajay Phatak, Hasmukh A. Patel
Software Mentions: 2
Published: about 9 years ago

10.1186/s40246-016-0092-0

A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease
Cited by: 24
Author(s): Elisa Napolitano Ferreira, Bruna Durães de Figueiredo Barros, Jorge E. de Souza, Renan Valieris Bueno de Almeida, Giovana Tardin Torrezan, Sheila Garcia, Ana Cristina Victorino Krepischi, Celso Abdon Lopes de Mello, Isabela Werneck da Cunha, Clóvis Antônio Lopes Pinto, Fernando Augusto Soares, Emmanuel Dias‐Neto, Ademar Lopes, Sandro J. de Souza
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2020.544162

Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance
Cited by: 37
Author(s): Aquillah M. Kanzi, James Emmanuel San, Benjamin Chimukangara, Eduan Wilkinson, Maryam Fish, Veron Ramsuran, Túlio de Oliveira
Software Mentions: 2
Published: about 4 years ago

10.1002/mbo3.584

Microbial dynamics during harmful dinoflagellate<i>Ostreopsis</i>cf.<i>ovata</i>growth: Bacterial succession and viral abundance pattern
Cited by: 14
Author(s): Flavio Guidi, Laura Pezzolesi, Silvana Vanucci
Software Mentions: 2
Published: over 6 years ago

10.1186/1756-0500-7-488

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers
Cited by: 27
Author(s): Shorash Amin, Peter J. Prentis, Edward K. Gilding, Ana Pavasovic
Software Mentions: 2
Published: over 10 years ago

10.3390/cancers10040088

Use of the Ion PGM and the GeneReader NGS Systems in Daily Routine Practice for Advanced Lung Adenocarcinoma Patients: A Practical Point of View Reporting a Comparative Study and Assessment of 90 Patients
Cited by: 12
Author(s): Simon Heeke, Paul Hofman, Élodie Long-Mira, Virginie Lespinet, Salomé Lalvée, Olivier Bordone, Camille Ribeyre, Virginie Tanga, Jonathan Benzaquen, Sylvie Leroy, Charlotte Cohen, Jérôme Mouroux, Charles Hugo Marquette
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-S10-S5

TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads
Cited by: 40
Author(s): Naoki Nariai, Kazuyuki Kojima, Tsuneyo Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki
Software Mentions: 2
Published: almost 10 years ago

10.3390/cancers11070998

BRAF Mutation Status in Circulating Tumor DNA from Patients with Metastatic Colorectal Cancer: Extended Mutation Analysis from the AGEO RASANC Study
Cited by: 19
Author(s): Léo Mas, Jean‐Baptiste Bachet, Valérie Taly, Olivier Bouché, Julien Taieb, Romain Cohen, Aurélia Meurisse, Claudine Normand, Jean–Marc Gornet, Pascal Artru, Samy Louafi, Anne Thirot-Bidault, Isabelle Baumgaertner, Romain Coriat, David Tougeron, Thierry Lecomte, Florence Mary, Thomas Aparicio, Lysiane Marthey, Hélène Blons, Déwi Vernerey, Pierre Laurent‐Puig
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.48591

Maternal spindle transfer overcomes embryo developmental arrest caused by ooplasmic defects in mice
Cited by: 19
Author(s): Nuno Costa-Borges, K Spath, Irene Miguel-Escalada, Enric Mestres, Rosa Balmaseda, Anna Serafín, M. G. García-Jiménez, Ivette Vanrell, J. González, Klaus Rink, Dagan Wells, Gloria Calderón
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms161226129

Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGM™ Platform
Cited by: 33
Author(s): Irene Vanni, Simona Coco, Anna Truini, Marta Rusmini, Maria Giovanna Dal Bello, Angela Alama, Barbara Banelli, Marco Mora, Erika Rijavec, Giulia Barletta, Carlo Genova, Federica Biello, C. Maggioni, Francesco Grossi
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms17091416

Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients
Cited by: 12
Author(s): Nadia Marascio, Grazia Pavia, Alessio Strazzulla, Tim Dierckx, Lize Cuypers, Bram Vrancken, Giorgio Settimo Barreca, Teresa Mirante, Donatella Malanga, Duarte Mendes Oliveira, Anne‐Mieke Vandamme, Carlo Torti, Maria Carla Liberto, Alfredo Focà
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-15-S5-S7

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data
Cited by: 16
Author(s): Serghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Ion Măndoiu, Alexander Zelikovsky
Software Mentions: 2
Published: over 10 years ago

10.3390/cancers12092490

Single-Cell NGS-Based Analysis of Copy Number Alterations Reveals New Insights in Circulating Tumor Cells Persistence in Early-Stage Breast Cancer
Cited by: 25
Author(s): Tania Rossi, Giulia Gallerani, Davide Angeli, Claudia Cocchi, Erika Bandini, Pietro Fici, Michele Gaudio, Giovanni Martinelli, Andrea Rocca, Roberta Maltoni, Francesco Fabbri
Software Mentions: 2
Published: about 4 years ago

10.1128/genomeA.01232-15

Genome Sequence of the Mosquitocidal Bacillus thuringiensis Strain BR58, a Biopesticide Product Effective against the Coffee Berry Borer ( Hypothenemus hampei )
Cited by: 4
Author(s): Janaína Zorzetti, Ana Paula Scaramal Ricietto, Carlos R. M. da Silva, Ivan Rodrigo Wolf, Gislayne Trindade Vilas-Bôas, Pedro Manuel Oliveira Janeiro Neves, Ana M. Meneguim, Laurival A. Vilas-Bôas
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0224847

Ion torrent high throughput mitochondrial genome sequencing (HTMGS)
Cited by: 11
Author(s): Nicholas R. Harvey, Cassie L. Albury, Shani Stuart, Miles C. Benton, David Eccles, Jasmine Connell, Heidi G. Sutherland, Richard Allcock, Rodney Arthur Lea, Larisa M. Haupt, Lyn R. Griffiths
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms21228807

Currently Applied Molecular Assays for Identifying ESR1 Mutations in Patients with Advanced Breast Cancer
Cited by: 5
Author(s): Nuri Lee, Min-Jeong Park, Wonkeun Song, Kibum Jeon, Seri Jeong
Software Mentions: 2
Published: about 4 years ago

10.1186/s13059-015-0736-8

Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions
Cited by: 83
Author(s): Elena M. Pugacheva, Samuel Rivero-Hinojosa, Celso A. Espinoza, Claudia Fabiola Méndez-Catalá, Sungyun Kang, Tomohiko Suzuki, Natsuki Kosaka-Suzuki, Susan Robinson, Vijayaraj Nagarajan, Zhen Ye, Abdelhalim Boukaba, John E.J. Rasko, Alexander Strunnikov, Dmitri Loukinov, Bing Ren, Victor Lobanenkov
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0022751

Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology
Cited by: 692
Author(s): Alexander Mellmann, Dag Harmsen, Craig Cummings, Emily B. Zentz, Shana R. Leopold, Alain Rico, Karola Prior, Rafael Szczepanowski, Yongmei Ji, Wenlan Zhang, Stephen McLaughlin, John Henkhaus, Benjamin Leopold, Martina Bielaszewska, Rita Prager, Pius Brzoska, Richard Moore, Simone M Guenther, Jonathan M. Rothberg, Helge Karch
Software Mentions: 2
Published: over 13 years ago

10.1186/s13073-016-0313-0

Development and clinical application of an integrative genomic approach to personalized cancer therapy
Cited by: 70
Author(s): Andrew Uzilov, Wei Ding, Marc Y. Fink, Yevgeniy Antipin, Andrew S. Brohl, Claire Davis, Chun Yee Lau, Chetanya Pandya, Hardik Shah, Yumi Kasai, James Powell, Mark Micchelli, Rafael Castellanos, Zhongyang Zhang, Michael D. Linderman, Yayoi Kinoshita, Micol Zweig, Katie Raustad, Kakit Cheung, Diane T. Castillo, Melissa Wooten, Imane Bourzgui, Leah Newman, Gintaras Deikus, Bino Mathew, Jun Zhu, Benjamin S. Glicksberg, Aye S. Moe, Jun Liao, Lisa Edelmann, Joel T. Dudley, Robert G. Maki, Andrew Kasarskis, Randall F. Holcombe, Milind Mahajan, Ke Hao, Boris Reva, Janina A. Longtine, Daniela Starcevic, Robert Sebra, Michael Donovan, Shuyu Li, Eric E. Schadt, Rong Chen
Software Mentions: 2
Published: over 8 years ago

10.1016/j.virusres.2014.10.004

Beyond the whole genome consensus: Unravelling of PRRSV phylogenomics using next generation sequencing technologies
Cited by: 10
Author(s): Zen H. Lu, Alan Archibald, Tahar Aït-Ali
Software Mentions: 2
Published: almost 10 years ago

10.3390/v10080436

Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies
Cited by: 89
Author(s): Varvara I. Maliogka, A. Minafra, P. Saldarelli, Ana Belén Ruiz-García, Miroslav Glasa, N. I. Katis, Antonio Olmos
Software Mentions: 2
Published: over 6 years ago

10.1186/s13742-015-0088-z

Addressing health disparities in Hispanic breast cancer: accurate and inexpensive sequencing of BRCA1 and BRCA2
Cited by: 39
Author(s): Michael Dean, Joseph F. Boland, Meredith Yeager, Kate M. Im, L. H. Garland, Maria Rodríguez-Herrera, M. del Rosarion Pérez, Jason Mitchell, David A. Roberson, Kristine Jones, Hyo‐Jung Lee, Rebecca Eggebeen, Julie Sawitzke, Sara Bass, Xijun Zhang, Vivian Robles, Celia Hollis, Claudia Barajas, Edna Rath, Candy Arentz, José A. Figueroa, Diane Nguyen, Zeina Nahleh
Software Mentions: 2
Published: about 9 years ago

10.1128/genomeA.01169-14

Exploring the Genome of a Butyric Acid Producer, Clostridium butyricum INCQS635
Cited by: 1
Author(s): Thiago Bruce, Fernanda Gomes Leite, Diogo A. Tschoeke, Mauro Sayão de Miranda, Nei Pereira, Rogério Valle, Cristiane C. Thompson, Fabiano L. Thompson
Software Mentions: 2
Published: almost 10 years ago

10.3389/fimmu.2018.02294

Reference Grade Characterization of Polymorphisms in Full-Length HLA Class I and II Genes With Short-Read Sequencing on the ION PGM System and Long-Reads Generated by Single Molecule, Real-Time Sequencing on the PacBio Platform
Cited by: 29
Author(s): Shingo Suzuki, Swati Ranade, Ken Osaki, Sayaka Ito, Atsuko Shigenari, Yuko Ohnuki, Akira Oka, Anri Masuya, John Harting, Primo Baybayan, Miwako Kitazume, Junichi Sunaga, Satoko Morishima, Yasuo Morishima, Hidetoshi Inoko, Jerzy K. Kulski, Takashi Shiina
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0081718

Ion Torrent PGM as Tool for Fungal Community Analysis: A Case Study of Endophytes in Eucalyptus grandis Reveals High Taxonomic Diversity
Cited by: 74
Author(s): Martin Kemler, Jeffrey R. Garnas, Michael J. Wingfield, Marieka Gryzenhout, Kerry-Anne Pillay, Bernard Slippers
Software Mentions: 2
Published: almost 11 years ago

10.3390/jcm9010132

Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics
Cited by: 102
Author(s): Rute Pereira, Jorge Oliveira, Mário Sousa
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0092192

Performance Comparison between Rapid Sequencing Platforms for Ultra-Low Coverage Sequencing Strategy
Cited by: 25
Author(s): Sheng‐Pei Chen, Sheng Li, Wen Xie, Xuchao Li, Chunlei Zhang, Hanyang Jiang, Jing Zheng, Xiaoyu Pan, Hancheng Zheng, Jia Sophie Liu, Yongqiang Deng, Fang Chen, Hui Jiang
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-15-699

Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes
Cited by: 81
Author(s): Mari Miyamoto, Daisuke Motooka, Kazuyoshi Gotoh, Takeshi Imai, Kazutoshi Yoshitake, Naohisa Goto, Tetsuya Iida, Teruo Yasunaga, Toshihiro Horii, Kazuharu Arakawa, Masahiro Kasahara, Shota Nakamura
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.7391

Characterization of novel low passage primary and metastatic colorectal cancer cell lines
Cited by: 11
Author(s): Arnoud Boot, Jaap van Eendenburg, Stijn Crobach, Dina Ruano, Frank M. Speetjens, J.J. Calame, Jan Oosting, Hans Morreau, Tom van Wezel
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.ppat.1004447

Programmed Ribosomal Frameshift Alters Expression of West Nile Virus Genes and Facilitates Virus Replication in Birds and Mosquitoes
Cited by: 30
Author(s): Ezequiel Balmori Melian, Sonja Hall‐Mendelin, Du Fangyao, Nick S. Owens, Angela M. Bosco‐Lauth, Tomoko Nagasaki, Stephen Rudd, Aaron C. Brault, Richard A. Bowen, Roy A. Hall, Andrew F. van den Hurk, Alexander A. Khromykh
Software Mentions: 2
Published: about 10 years ago

10.1186/s12859-019-2918-y

Viral coinfection analysis using a MinHash toolkit
Cited by: 3
Author(s): Eric T. Dawson, Sarah Wagner, David A. Roberson, Meredith Yeager, Joseph F. Boland, Erik Garrison, Stephen J. Chanock, Mark Schiffman, Tina Raine‐Bennett, Thomas Lorey, Phillip E. Castle, Lisa Mirabello, Richard Durbin
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-15-264

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data
Cited by: 80
Author(s): Ségolène Caboche, Christophe Audebert, Yves Lemoine, David Hot
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12931-018-0736-9

Impaired diversity of the lung microbiome predicts progression of idiopathic pulmonary fibrosis
Cited by: 44
Author(s): Youhei Takahashi, Atsushi Saito, Hirofumi Chiba, Koji Kuronuma, Kimiyuki Ikeda, Tomofumi Kobayashi, Shigeru Ariki, Motoko Takahashi, Yasushi Sasaki, Hiroki Takahashi
Software Mentions: 2
Published: over 6 years ago

10.1186/s12931-019-1203-y

Unique patterns of lower respiratory tract microbiota are associated with inflammation and hospital mortality in acute respiratory distress syndrome
Cited by: 41
Author(s): Michihito Kyo, Keisuke Nishioka, Takaaki Nakaya, Yoshiko Kida, Yuko Tanabe, Shinichiro Ohshimo, Nobuaki Shime
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0075793

Massively Parallel DNA Sequencing Successfully Identifies New Causative Mutations in Deafness Genes in Patients with Cochlear Implantation and EAS
Cited by: 81
Author(s): Maiko Miyagawa, Shin‐ya Nishio, Takuo Ikeda, Kunihiro Fukushima, Shin‐ichi Usami
Software Mentions: 2
Published: about 11 years ago

10.3390/cancers11121895

Identification of Circulating Genomic and Metabolic Biomarkers in Intrahepatic Cholangiocarcinoma
Cited by: 16
Author(s): H Winter, Pamela J. Kaisaki, Joe Harvey, Edoardo Giacopuzzi, Matteo P. Ferla, Melissa M Pentony, Samantha J. L. Knight, Ricky A. Sharma, Jenny C. Taylor, James McCullagh
Software Mentions: 2
Published: almost 5 years ago

10.1002/mgg3.406

Identification of novel mutations causing pediatric cataract in Bhutan, Cambodia, and Sri Lanka
Cited by: 13
Author(s): Shahrbanou Javadiyan, Sionne E. M. Lucas, Dechen Wangmo, Meng Ning, Kapila Edussuriya, Jamie E Craig, Adam K Rudkin, Robert J. Casson, Dinesh Selva, Shilpi Sharma, Karen M. Lower, James Meucke, Kathryn P. Burdon
Software Mentions: 2
Published: over 6 years ago

10.1038/srep18568

PSIP1/LEDGF: a new gene likely involved in sensorineural progressive hearing loss
Cited by: 6
Author(s): Giorgia Girotto, Déborah I. Scheffer, Anna Morgan, Diego Vozzi, Elisa Rubinato, Mariateresa Di Stazio, Enrico Muzzi, Stefano Pensiero, Anne B.S. Giersch, David P. Corey, Paolo Gasparini
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep36948

Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano
Cited by: 51
Author(s): Sunil Banskar, Shrikant Bhute, Mangesh V. Suryavanshi, Sachin A. Punekar, Yogesh S. Shouche
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-017-01170-z

Enhancing the throughput and multiplexing capabilities of next generation sequencing for efficient implementation of pooled shRNA and CRISPR screens
Cited by: 3
Author(s): Md. Fahmid Islam, Atsushi Watanabe, Lai Hong Wong, Conor Lazarou, Frederick S. Vizeacoumar, Omar Abuhussein, Wayne Hill, Maruti Uppalapati, C. Ronald Geyer
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-12866-7

Safety assessment of antibiotic and probiotic feed additives for Gallus gallus domesticus
Cited by: 25
Author(s): Deon P. Neveling, Liesel van Emmenes, Jayesh J. Ahire, E. Pieterse, Carine Smith, Leon M. T. Dicks
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-019-40843-9

Convergent Evolution of Copy Number Alterations in Multi-Centric Hepatocellular Carcinoma
Cited by: 2
Author(s): Carolin Lackner, Luca Quagliata, William Cross, Sebastian Ribi, Karl Heinimann, Viola Paradiso, Cristina Quintavalle, Monika Kováčová, Daniel Baumhoer, Salvatore Piscuoglio, Luigi Terracciano, Michal Kováč
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-53449-y

A simple method for sequencing the whole human mitochondrial genome directly from samples and its application to genetic testing
Cited by: 16
Author(s): Yao Ya, Motoi Nishimura, Kei Murayama, Naomi Kuranobu, Satomi Tojo, Minako Beppu, Takayuki Ishige, Sakae Itoga, Sachio Tsuchida, Masayuki Mori, Masaki Takayanagi, Masataka Yokoyama, Kunio Yamagata, Yoshihito Kishita, Yasushi Okazaki, Fumio Nomura, Hiroshi Matsushita, Tomoaki Tanaka
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-55282-9

High polymorphism detected by massively parallel sequencing of autosomal STRs using old blood samples from a Chinese Han population
Cited by: 2
Author(s): Wenshen Dai, Ya-Jiao Pan, Xiaochen Sun, Riga Wu, Li Luo, Dongming Yang
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-71516-7

Generation and characterization of CRISPR/Cas9-mediated MEN1 knockout BON1 cells: a human pancreatic neuroendocrine cell line
Cited by: 5
Author(s): Azita Monazzam, Su-Chen Li, Hanna Wargelius, Masoud Razmara, Dragan Bajic, Jia Mi, Jonas Bergquist, Joakim Crona, Britt Skogseid
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-021-81065-2

Molecular analysis of cyst fluids improves the diagnostic accuracy of pre-operative assessment of pancreatic cystic lesions
Cited by: 16
Author(s): Lena Haeberle, Martin Schramm, Wolfgang Goering, Lisa Frohn, Caroline Driescher, Werner Hartwig, Hubert-Karl Preissinger-Heinzel, Torsten Beyna, Horst Neuhaus, Katharina Fuchs, Verena Keitel-Anselmino, Wolfram Trudo Knoefel, Irene Espósito
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-88724-4

Carnitine/organic cation transporter 1 precipitates the progression of interstitial fibrosis through oxidative stress in diabetic nephropathy in mice
Cited by: 4
Author(s): Shohei Makiishi, Kengo Furuichi, Yuta Yamamura, Keisuke Sako, Yukiko Shinozaki, Tadashi Toyama, Shinji Kitajima, Yasunori Iwata, Norihiko Sakai, Miho Shimizu, Tomoko Hirose-Sugiura, Shuichi Kaneko, Yukio Kato, Takashi Wada
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-90139-0

Distribution of genetic alterations in high-risk early-stage cervical cancer patients treated with postoperative radiation therapy
Cited by: 6
Author(s): Naoya Murakami, Yuka Asami, Hiroshi Yoshida, Daisuke Takayanagi, Sou Hirose, Ikumi Kuno, Kazuaki Takahashi, Maiko Matsuda, Yôko Shimada, Shotaro Yamano, Kuniko Sunami, Takayuki Honda, Tomomi Nakahara, Tomoko Watanabe, Kae Okuma, Takafumi Kuroda, Takashi Kohno, Tomoyasu Kato, Kouya Shiraishi, Jun Itami
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-94739-8

DNA methylation of Vesicular Glutamate Transporters in the mesocorticolimbic brain following early-life stress and adult ethanol exposure—an explorative study
Cited by: 2
Author(s): Maria Vrettou, Liying Yan, Kent W. Nilsson, Åsa Wallén-Mackenzie, Ingrid Nylander, Erika Comasco
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-98527-2

TP53 mutants and non-HPV16/18 genotypes are poor prognostic factors for concurrent chemoradiotherapy in locally advanced cervical cancer
Cited by: 13
Author(s): Ikumi Kuno, Daisuke Takayanagi, Yuka Asami, Naoya Murakami, Maiko Matsuda, Yôko Shimada, Sou Hirose, Mayumi Kobayashi Kato, Masaaki Komatsu, Ryuji Hamamoto, Kae Okuma, Takashi Kohno, Jun Itami, Hiroshi Yoshida, Kouya Shiraishi, Tomoyasu Kato
Software Mentions: 1
Published: about 3 years ago

10.1111/1759-7714.13460

Targeted RNA sequencing with touch imprint cytology samples for non‐small cell lung cancer patients
Cited by: 2
Author(s): Katsutoshi Seto, Katsuhiro Masago, Shiro Fujita, Masataka Haneda, Yoshitsugu Horio, Toyoaki Hida, Hiroaki Kuroda, Waki Hosoda, Kan Okubo
Software Mentions: 1
Published: over 4 years ago

10.3390/toxins10110433

Current Status and Future Opportunities of Omics Tools in Mycotoxin Research
Cited by: 40
Author(s): Manal Eshelli, Mallique Qader, Ebtihaj J. Jambi, Andrew Hursthouse, Mostafa E. Rateb
Software Mentions: 1
Published: about 6 years ago

10.1128/mBio.00429-21

Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles
Cited by: 5
Author(s): Sonu Kumar, Xue Lin, Timothy Ngo, Benjamin Shapero, Cindy Sou, Joel D. Allen, Jeffrey Copps, Lei Zhang, Gabriel Ozorowski, Linling He, Max Crispin, Andrew B. Ward, Ian A. Wilson, Jiang Zhu
Software Mentions: 1
Published: over 3 years ago

10.1007/s00439-016-1656-8

Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies
Cited by: 27
Author(s): Eufemia Damiati, Giuseppe Borsani, Edoardo Giacopuzzi
Software Mentions: 1
Published: over 8 years ago

10.1186/s40246-016-0093-z

Targeted next generation sequencing identifies novel NOTCH3 gene mutations in CADASIL diagnostics patients
Cited by: 21
Author(s): Neven Maksemous, Robert A. Smith, Larisa M. Haupt, Lyn R. Griffiths
Software Mentions: 1
Published: almost 8 years ago

10.1186/s40246-017-0110-x

Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology
Cited by: 9
Author(s): Ana Lígia Buzolin, Caroline Mônaco Moreira, Patricia Rossi Sacramento, Andre Yuji Oku, Alexandre Ricardo dos Santos Fornari, David Santos Marco Antônio, Caio Robledo Quaio, Wagner Rosa Baratela, Miguel Mitne‐Neto
Software Mentions: 1
Published: over 7 years ago

10.1002/humu.22825

Evaluation of Hybridization Capture Versus Amplicon‐Based Methods for Whole‐Exome Sequencing
Cited by: 187
Author(s): Eric Samorodnitsky, Benjamin M. Jewell, Raffi Hagopian, Jharna Miya, Michele R. Wing, E Lyon, Srinivasan Damodaran, Darshna Bhatt, Julie W. Reeser, Jharna Datta, Sukla Roychowdhury
Software Mentions: 1
Published: over 9 years ago

10.1007/s00414-020-02294-0

Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects
Cited by: 58
Author(s): David J. Ballard, Jakub Winkler-Galicki, Joanna Wesoły
Software Mentions: 1
Published: over 4 years ago

10.3892/ijmm.2012.1056

Mass spectrometry-based proteomic analysis of middle-aged vs. aged vastus lateralis reveals increased levels of carbonic anhydrase isoform 3 in senescent human skeletal muscle
Cited by: 64
Author(s): Lisa Staunton, Margit Zweyer, Dieter Swandulla, Kay Ohlendieck
Software Mentions: 1
Published: over 12 years ago

10.3390/ijns6040090

Neonatal Screening for MPS Disorders in Latin America: A Survey of Pilot Initiatives
Cited by: 5
Author(s): Francyne Kubaski, Inês Sousa, Tatiana Amorim, Danilo Florentino Pereira, Joe Trometer, Alexandre Wagner Silva de Souza, Enzo Ranieri, Giulia Polo, Alberto Burlina, Ana Carolina Brusius‐Facchin, Alice Brinckmann Oliveira Netto, Shunji Tomatsu, Roberto Giugliani
Software Mentions: 1
Published: about 4 years ago

10.1016/j.ijscr.2021.106237

Malignant pleural mesothelioma showing rare morphology indistinguishable from myxofibrosarcoma concomitant with EGFR-mutated lung adenocarcinoma: A case report
Cited by: 0
Author(s): Hiroko Onagi, Takuo Hayashi, Tsuyoshi Saito, Satsuki Kishikawa, Kazuya Takamochi, Kenji Suzuki
Software Mentions: 1
Published: over 3 years ago

10.1099/jmmcr.0.005167

Two male siblings with a novel LRBA mutation presenting with different findings of IPEX syndrome
Cited by: 16
Author(s): Sanem Eren Akarcan, Neslihan Edeer Karaca, Güzide Aksu, Ayça Aykut, Deniz Yılmaz Karapınar, Funda Çetin, Yeşim Aydınok, Elif Azarsız, Eleonora Gambineri, Özgür Çoğulu, Ezgi Ulusoy Severcan, Hüdaver Alper, Necil Kütükçüler
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms18020267

Metabolomic Fingerprinting in the Comprehensive Study of Liver Changes Associated with Onion Supplementation in Hypercholesterolemic Wistar Rats
Cited by: 30
Author(s): Diana González‐Peña, Danuta Dudzik, Antonia Garcı́a, Begoña de Ancos, Coral Barbas, Concepción Sánchez‐Moreno
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms20246227

A Novel DES L115F Mutation Identified by Whole Exome Sequencing is Associated with Inherited Cardiac Conduction Disease
Cited by: 4
Author(s): Lung‐An Hsu, Yu-Shien Ko, Yung‐Hsin Yeh, Chi-Jen Chang, Yi‐Hsin Chan, Chi‐Tai Kuo, Hsin–Yi Tsai, Gwo‐Jyh Chang
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13048-016-0242-y

Establishment and characterization of a cell line (HCH-1) originating from a human clear cell carcinoma of the ovary
Cited by: 7
Author(s): Takashi Yamada, Kengo Hattori, Hidetoshi Satomi, Tadashi Okazaki, Hiroshi Mori, Yoshinobu Hirose
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.7175

The next generation of metastatic melanoma: uncovering the genetic variants for anti-BRAF therapy response
Cited by: 6
Author(s): Rosamaria Pinto, Simona De Summa, Sabino Strippoli, Brunella Pilato, Amalia Azzariti, Gabriella Guida, Michele Guida, Stefania Tommasi
Software Mentions: 1
Published: almost 9 years ago

10.18632/oncotarget.11717

Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer
Cited by: 63
Author(s): Catherine W Bennett, Guy Berchem, Yeoun Jin Kim, Victoria El-Khoury
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.12551

Wide spetcrum mutational analysis of metastatic renal cell cancer: a retrospective next generation sequencing approach
Cited by: 18
Author(s): Michelangelo Fiorentino, Elisa Gruppioni, Francesco Massari, Francesca Giunchi, Annalisa Altimari, Chiara Ciccarese, Davide Bimbatti, Aldo Scarpa, Roberto Iacovelli, Camillo Porta, Virinder Sarhadi, Giampaolo Tortora, Walter Artibani, Riccardo Schiavina, Andrea Ardizzoni, Matteo Brunelli, Sakari Knuutila, Guido Martignoni
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.16799

Validation and optimization of the Ion Torrent S5 XL sequencer and Oncomine workflow for <i>BRCA1</i> and <i>BRCA2</i> genetic testing
Cited by: 29
Author(s): Saeam Shin, Yoonjung Kim, Seoung Chul Oh, Nae Yu, Seung Tae Lee, Jong Rak Choi, Kyung A. Lee
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.17199

Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences
Cited by: 26
Author(s): Minho Cho, Soomin Ahn, Mineui Hong, Heejin Bang, Michael Van Vrancken, Seungtae Kim, Jeeyun Lee, Se Hoon Park, Joon Oh Park, Young Suk Park, Ho Yeong Lim, Won Ki Kang, Jong Mu Sun, Se‐Hoon Lee, Myung Ju Ahn, Keunchil Park, Duk Hwan Kim, Seunggwan Lee, Woong-Yang Park, Kyoung Mee Kim
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.18359

Active evolution of memory B-cells specific to viral gH/gL/pUL128/130/131 pentameric complex in healthy subjects with silent human cytomegalovirus infection
Cited by: 26
Author(s): Xia Lin, Aimin Tang, Wenxiang Meng, Daniel C. Freed, Linling He, Dai Wang, Fengsheng Li, Leike Li, Wei Xiong, Xun Gui, Robbie D. Schultz, Hao-tai Chen, Xi He, Ryan Swoyer, Sha Ha, Yaping Liu, Charles D. Morris, Yu Zhou, I‐Ming Wang, Qinjian Zhao, Wenxin Luo, Ningshao Xia, Amy S. Espeseth, Daria J. Hazuda, Richard Rupp, Alan D.T. Barrett, Ningyan Zhang, Jiang Zhu, Tong-Ming Fu, Zhiqiang An
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.24912

Identification of copy number alterations in colon cancer from analysis of amplicon-based next generation sequencing data
Cited by: 10
Author(s): Duarte Mendes Oliveira, Gianluca Santamaria, Carmelo Laudanna, Simona Migliozzi, Pietro Zoppoli, Michael J. Quist, Catie Grasso, Chiara Mignogna, Laura Elia, Maria Concetta Faniello, Cinzia Marinaro, Rosario Sacco, Francesco Corcione, Giuseppe Viglietto, Donatella Malanga, Antonia Rizzuto
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.25810

Genomic alterations at the basis of treatment resistance in metastatic breast cancer: clinical applications
Cited by: 10
Author(s): Angela Toss, Federico Piacentini, Laura Cortesi, Lucia Artuso, Isabella Bernardis, Sandra Parenti, Elena Tenedini, Guido Ficarra, Antonino Maiorana, Anna Iannone, Claudia Omarini, Luca Moscetti, Massimo Cristofanilli, Massimo Federico, Enrico Tagliafico
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.26000

Rapid detection of copy number variations and point mutations in BRCA1/2 genes using a single workflow by ion semiconductor sequencing pipeline
Cited by: 10
Author(s): Aldo Germani, Fabio Libi, Stefano Maggi, Gianluca Stanzani, A. Lombardi, Patrizia Pellegrini, Mauro Mattei, Laura De Marchis, C. Amanti, Antonio Pizzuti, Maria Rosaria Torrisi, Maria Piane
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.26343

Monitoring BRAF and NRAS mutations with cell-free circulating tumor DNA from metastatic melanoma patients
Cited by: 26
Author(s): Élodie Long-Mira, Marius Ilié, Emmanuel Chamorey, Florence Leduff-Blanc, Henri Montaudié, Virginie Tanga, Maryline Allégra, Virginie Lespinet‐Fabre, Olivier Bordone, Christelle Bonnetaud, Renaud Schiappa, Catherine Butori, Coraline Bence, Jean‐Philippe Lacour, Paul Hofman
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.26511

Can we predict long-term survival in resectable pancreatic ductal adenocarcinoma?
Cited by: 5
Author(s): Tamara Gall, Gareth Gerrard, Adam E. Frampton, Leandro Castellano, Raida Ahmad, Nagy Habib, Duncan Spalding, Madhava Pai, Letizia Foroni, Long R. Jiao
Software Mentions: 1
Published: almost 6 years ago