Ecosyste.ms: Papers

10.18632/oncotarget.27188

Encyclopedic tumor analysis for guiding treatment of advanced, broadly refractory cancers: results from the RESILIENT trial
Cited by: 12
Author(s): Rajnish Nagarkar, Darshana Patil, Timothy Crook, Vineet Datta, Sagar Bhalerao, Sonal Dhande, Vijay Palwe, Sirshendu Roy, Prakash Pandit, Ashwini Ghaisas, Raymond Page, Harjeetsingh Kathuria, Ajay Srinivasan, Dadasaheb Akolkar
Software Mentions: 1
Published: about 5 years ago

10.1002/path.4729

EGFR inhibitors identified as a potential treatment for chordoma in a focused compound screen
Cited by: 71
Author(s): Susanne Scheipl, Michelle Barnard, Lucia Cottone, Mette Jørgensen, David H. Drewry, William J. Zuercher, Fabrice Turlais, Hongtao Ye, Ana Paula Leite, James Smith, Andreas Leithner, Peter Møller, Silke Brüderlein, Naomi Guppy, Fernanda Amary, Roberto Tirabosco, Sandra J. Strauss, Nischalan Pillay, Adrienne M. Flanagan
Software Mentions: 1
Published: over 8 years ago

10.1002/cjp2.80

Application of a multi‐gene next‐generation sequencing panel to a non‐invasive oesophageal cell‐sampling device to diagnose dysplastic Barrett's oesophagus
Cited by: 8
Author(s): Annalise Katz-Summercorn, Shubha Anand, Sophie Ingledew, Yuanxue Huang, Thomas M. Roberts, Núria Galeano-Dalmau, Maria O’Donovan, Hongxiang Liu, Rebecca C. Fitzgerald
Software Mentions: 1
Published: over 7 years ago

10.3390/jpm9030034

Adaptive, Iterative, Long-Term Personalized Therapy Management in a Case of Stage IV Refractory NSCLC
Cited by: 4
Author(s): Anantbhushan Ranade, Darshana Patil, Amit Bhatt, Rucha Dhasare, Vineet Datta, Rajan Datar, Dadasaheb Akolkar
Software Mentions: 1
Published: over 5 years ago

10.1186/s12967-021-02912-4

SARS-CoV-2 complete genome sequencing from the Italian Campania region using a highly automated next generation sequencing system
Cited by: 12
Author(s): Anna Maria Rachiglio, Luca De Sabato, Cristin Roma, Michele Cennamo, Mariano Fiorenza, Daniela Terracciano, Raffaella Pasquale, Francesca Bergantino, Ernesta Cavalcanti, Gerardo Botti, Gabriele Vaccari, Giuseppe Portella, Nicola Normanno
Software Mentions: 1
Published: over 3 years ago

10.4102/ajlm.v9i1.1340

Will long-read sequencing technologies replace short-read sequencing technologies in the next 10 years?
Cited by: 20
Author(s): Boluwatife Adeleye Adewale
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12967-020-02391-z

A comprehensive custom panel evaluation for routine hereditary cancer testing: improving the yield of germline mutation detection
Cited by: 11
Author(s): Carolina Velázquez, Enrique Lastra, Francisco Avila Cobos, Luis E. Abella, Virginia de la Cruz, Blanca Hernando, Lara Hernández, Noemí Martínez, Mar Infante, Mercedes Durán
Software Mentions: 1
Published: over 4 years ago

10.1007/s00216-020-02540-9

New trends in single-molecule bioanalytical detection
Cited by: 32
Author(s): Eleonora Macchia, Kyriaki Manoli, Cincia Di Franco, Gaetano Scamarcio, Luisa Torsi
Software Mentions: 1
Published: over 4 years ago

10.1155/2019/5108012

Community Structure and Abundance of Archaea in a <i>Zostera marina</i> Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites
Cited by: 12
Author(s): Pengfei Zheng, Chuantao Wang, Xiaoli Zhang, Jun Gong
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-15-302

SAGE: String-overlap Assembly of GEnomes
Cited by: 8
Author(s): Lucian Ilie, Bahlul Haider, Michael Molnar, Roberto Solis-Oba
Software Mentions: 1
Published: about 10 years ago

10.1186/s12859-016-1344-7

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
Cited by: 8
Author(s): Diego Mariano, Felipe Luiz Pereira, Edgar Lacerda de Aguiar, Letícia de Castro Oliveira, Leandro de Jesus Benevides, Luís Carlos Guimarães, Edson Luiz Folador, Thiago J. Sousa, Preetam Ghosh, Debmalya Barh, Henrique César Pereira Figueiredo, Artur M. S. Silva, Rui A. R. Ramos, Vasco Azevedo
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-15-254

ELM: enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset
Cited by: 6
Author(s): Koji Ueno, Akihiro Ishii, Kimihito Ito
Software Mentions: 1
Published: over 10 years ago

10.1186/s12885-018-4321-x

The first case of SMARCB1 (INI1) - deficient squamous cell carcinoma of the pleura: a case report
Cited by: 11
Author(s): Keisuke Yoshida, Yutaka Fujiwara, Yasushi Goto, Takashi Kohno, Akihiko Yoshida, Koji Tsuta, Yuichiro Ohe
Software Mentions: 1
Published: over 6 years ago

10.1186/s12885-016-2272-7

Radical nephrectomy and regional lymph node dissection for locally advanced type 2 papillary renal cell carcinoma in an at-risk individual from a family with hereditary leiomyomatosis and renal cell cancer: a case report
Cited by: 16
Author(s): Takao Kamai, Hideyuki Abe, Kyoko Arai, Satoshi Murakami, Setsu Sakamoto, Yuichi Kaji, Keisuke Yoshida
Software Mentions: 1
Published: over 8 years ago

10.1186/s12885-016-2720-4

Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples
Cited by: 28
Author(s): Silvia Bonfiglio, Irene Vanni, Valeria Rossella, Anna Truini, Dejan Lazarevic, Maria Giovanna Dal Bello, Angela Alama, Marco Mora, Erika Rijavec, Carlo Genova, Davide Cittaro, Francesco Grossi, Simona Coco
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2164-15-986

Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation
Cited by: 20
Author(s): Hivana Dall'Agnol, Rafael Azevedo Baraúna, Pablo Henrique Caracciolo Gomes de Sá, Rommel Thiago Jucá Ramos, Felipe Nóbrega, Catarina Nunes, Diego Assis das Graças, Adriana Ribeiro Carneiro, Daniel Moreira dos Santos, Adriano M.C. Pimenta, Marta S. P. Carepo, Vasco Azevedo, Vivian H. Pellizari, Maria Paula Cruz Schneider, Artur M. S. Silva
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-017-3885-1

The transcriptome of a “sleeping” invader: de novo assembly and annotation of the transcriptome of aestivating Cornu aspersum
Cited by: 17
Author(s): Aristeidis Parmakelis, Panayiota Kotsakiozi, Christos K. Kontos, Panagiotis G. Adamopoulos, Andreas Scorilas
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-015-2004-4

Characterizing Benzo[a]pyrene-induced lacZ mutation spectrum in transgenic mice using next-generation sequencing
Cited by: 32
Author(s): Marc A. Beal, Remi Gagné, Andrew Williams, Francesco Marchetti, Carole L. Yauk
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-14-574

Genomic characterization of JG068, a novel virulent podovirus active against Burkholderia cenocepacia
Cited by: 20
Author(s): Karlene H. Lynch, Ashraf H Abdu, Max Schobert, Jonathan J. Dennis
Software Mentions: 1
Published: about 11 years ago

10.1186/s12879-017-2727-8

Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study
Cited by: 53
Author(s): Lalanika M. Abayasekara, Jennifer Perera, Vishvanath Chandrasekharan, Vaz S. Gnanam, Nisala A. Udunuwara, D.S. Liyanage, Nuwani E. Bulathsinhala, Subhashanie Adikary, Janith V. S. Aluthmuhandiram, Chrishanthi S. Thanaseelan, D. Portia Tharmakulasingam, Tharaga Karunakaran, Janahan Ilango
Software Mentions: 1
Published: about 7 years ago

10.1186/s12881-016-0329-8

Utilization of amplicon-based targeted sequencing panel for the massively parallel sequencing of sporadic hearing impairment patients from Saudi Arabia
Cited by: 9
Author(s): Ashraf Dallol, Kamal J. Daghistani, Aisha Elaimi, Wissam A Alwazani, Afaf Bamanie, Malek Safiah, Samira Sagaty, Layla Taha, Rawabi Zahed, Osama S. Bajouh, Adeel G. Chaudhary, Mamdooh Gari, Rola Turki, Mohammed Hussein Al-Qahtani, Adel M. Abuzenadah
Software Mentions: 1
Published: about 8 years ago

10.1186/s12881-017-0489-1

Characterization of a novel splicing mutation in UNC13D gene through amplicon sequencing: a case report on HLH
Cited by: 5
Author(s): Dongling Liu, Xi‐Jiang Hu, Xiaoqian Jiang, Bo Gao, Cheng Wan, Changying Chen
Software Mentions: 1
Published: about 7 years ago

10.1186/s12881-018-0714-6

Targeted gene panel for genetic testing of south Indian children with steroid resistant nephrotic syndrome
Cited by: 12
Author(s): Annes Siji, K. N. Karthik, V. C. Pardeshi, Pankaj Hari, Anil Vasudevan
Software Mentions: 1
Published: about 6 years ago

10.1186/s12881-016-0322-2

Nonsynonymous variants in MYH9 and ABCA4 are the most frequent risk loci associated with nonsyndromic orofacial cleft in Taiwanese population
Cited by: 14
Author(s): Hsiu Huei Peng, Nai Chung Chang, Kuo Ting Chen, Jang Jih Lu, Pi Yueh Chang, Shih Cheng Chang, Yah Huei Wu-Chou, Yi Ting Chou, Wanni Phang, Po Jen Cheng
Software Mentions: 1
Published: over 8 years ago

10.1186/s12920-019-0636-y

Comparison of somatic variant detection algorithms using Ion Torrent targeted deep sequencing data
Cited by: 8
Author(s): Qing Wang, Vassiliki Kotoula, Pei-Chen Hsu, Kyriaki Papadopoulou, Joshua W. K. Ho, George Fountzilas, Eleni Giannoulatou
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12920-015-0092-2

New recurrent BRCA1/2 mutations in Polish patients with familial breast/ovarian cancer detected by next generation sequencing
Cited by: 31
Author(s): Anna Kluska, Aneta Bałabas, Agnieszka Paziewska, Maria Kulecka, Dorota Nowakowska, Michał Mikula, Jerzy Ostrowski
Software Mentions: 1
Published: over 9 years ago

10.1186/s12866-017-1148-6

Whole genome analysis of hypervirulent Klebsiella pneumoniae isolates from community and hospital acquired bloodstream infection
Cited by: 59
Author(s): Chaitra Shankar, Balaji Veeraraghavan, Laura Nabarro, Raji Ravi, Naveen Kumar Devanga Ragupathi, Priscilla Rupali
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-016-0968-0

EcoTILLING by sequencing reveals polymorphisms in genes encoding starch synthases that are associated with low glycemic response in rice
Cited by: 22
Author(s): Ramadoss Bharathi Raja, Somanath Agasimani, Sarita Jaiswal, T. Venkatesan, S. Robin, Ravindra N. Chibbar, Sundaram Ganesh Ram
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13104-015-1530-0

Targeted amplification for enhanced detection of biothreat agents by next-generation sequencing
Cited by: 21
Author(s): Shea N. Gardner, K. G. Frey, C. L. Redden, James B. Thissen, Jonathan Allen, Adam F. Allred, Matthew D. Dyer, Vishwesh Mokashi, Tom Slezak
Software Mentions: 1
Published: about 9 years ago

10.1186/1756-0500-7-805

Molecular characterization of serous ovarian carcinoma using a multigene next generation sequencing cancer panel approach
Cited by: 14
Author(s): Nurul Syakima Ab Mutalib, Saiful Effendi Syafruddin, Reena Rahayu Md Zain, Ahmad Zailani Hatta Mohd Dali, Ryia Illani Mohd Yunos, Sazuita Saidin, Rahman Jamal, Norfilza Mohd Mokhtar
Software Mentions: 1
Published: about 10 years ago

10.1186/s13104-018-3872-x

Validation of differentially methylated microRNAs identified from an epigenome-wide association study; Sanger and next generation sequencing approaches
Cited by: 10
Author(s): Laura Smyth, Alexander P. Maxwell, Katherine Benson, Jill Kilner, Gareth J. McKay, Amy Jayne McKnight
Software Mentions: 1
Published: about 6 years ago

10.1186/s13104-017-2664-z

Design and implementation of a custom next generation sequencing panel for selected vitamin D associated genes
Cited by: 2
Author(s): Katherine Benson, Sourabh Chand, Alexander P. Maxwell, Laura Smyth, Jill Kilner, Richard Borrows, Amy Jayne McKnight
Software Mentions: 1
Published: over 7 years ago

10.1186/s12917-017-1280-4

Whole genome sequence and a phylogenetic analysis of the G8P[14] group A rotavirus strain from roe deer
Cited by: 10
Author(s): Urška Jamnikar-Ciglenečki, Urška Kuhar, Andrej Steyer, Andrej Kirbiš
Software Mentions: 1
Published: almost 7 years ago

10.3390/biology1030495

Genome Walking by Next Generation Sequencing Approaches
Cited by: 21
Author(s): Mariateresa Volpicella, Claudia Leoni, Alessandra Costanza, Immacolata Fanizza, Antonio Placido, Luigi R. Ceci
Software Mentions: 1
Published: about 12 years ago

10.1155/2017/2370927

Food Waste to Energy: An Overview of Sustainable Approaches for Food Waste Management and Nutrient Recycling
Cited by: 310
Author(s): Kunwar Paritosh, Sandeep Kushwaha, Monika Yadav, Nidhi Pareek, Aakash Chawade, Vivekanand Vivekanand
Software Mentions: 1
Published: almost 8 years ago

10.1155/2016/6341870

Unravelling the Complexity of Inherited Retinal Dystrophies Molecular Testing: Added Value of Targeted Next-Generation Sequencing
Cited by: 37
Author(s): Isabella Bernardis, Laura Chiesi, Elena Tenedini, Lucia Artuso, Antonio Percesepe, Valentina Artusi, Maria Luisa Simone, Rossella Manfredini, Monica Camparini, Chiara Rinaldi, Antonio P. Ciardella, Claudio Graziano, Nicole Balducci, Antonia Tranchina, Gian Maria Cavallini, Antonello Pietrangelo, Valeria Marigo, Enrico Tagliafico
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13068-018-1283-9

Determinants of selection in yeast evolved by genome shuffling
Cited by: 8
Author(s): Damien Biot-Pelletier, Dominic Pinel, Kane Larue, Vincent J. J. Martin
Software Mentions: 1
Published: about 6 years ago

10.1038/s41416-018-0345-x

Molecular characterisation of aromatase inhibitor-resistant advanced breast cancer: the phenotypic effect of ESR1 mutations
Cited by: 13
Author(s): Elena López-Knowles, Alex Pearson, Eugene F. Schuster, Pascal Gellert, Ricardo Ribas, Belinda Yeo, Ros Cutts, Richard Buus, Isaac García-Murillas, Ben P. Haynes, Lesley-Ann Martin, Ian Smith, Nicholas C. Turner, Mitch Dowsett
Software Mentions: 1
Published: almost 6 years ago

10.20892/j.issn.2095-3941.2019.0295

Identification of novel Lynch syndrome mutations in Chinese patients with endometriod endometrial cancer
Cited by: 3
Author(s): Caixia Ren, Yan Liu, Yuxiang Wang, Yan Tang, Yawei Wei, Congrong Liu, Hongquan Zhang
Software Mentions: 1
Published: almost 5 years ago

10.1002/cam4.542

Molecular profiles of high‐grade and low‐grade pseudomyxoma peritonei
Cited by: 55
Author(s): Rei Noguchi, Hideaki Yano, Yoshimasa Gohda, Ryuichiro Suda, Toru Igari, Yasunori Ohta, Naohide Yamashita, Kiyoshi Yamaguchi, Yumi Terakado, Tsuneo Ikenoue, Yoichi Furukawa
Software Mentions: 1
Published: about 9 years ago

10.1155/2020/8462659

Fecal Microbial Transplantation for the Treatment of Persistent Multidrug-Resistant K<i>lebsiella pneumoniae</i> Infection in a Critically Ill Patient
Cited by: 7
Author(s): Veronica Ueckermann, Ebrahim Hoosien, Nico de Villiers, J. Geldenhuys
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41375-019-0496-7

Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study
Cited by: 154
Author(s): Monika Brüggemann, Michaela Kotrová, Henrik Knecht, Jack Bartram, Myriam Boudjogrha, Vojtěch Bystrý, Grazia Fazio, Eva Froňková, Mathieu Giraud, Andrea Grioni, Jeremy Hancock, Doris Herrmann, Cristina Jiménez, Adam Krejčí, John Moppett, Tomáš Reigl, Mikaël Salson, Blanca Scheijen, Martin Schwarz, Simona Songia, Michael Svatoň, Jacques J.M. van Dongen, Patrick Villarèse, Stephanie Wakeman, Gary Wright, Giovanni Cazzaniga, Frédéric Davi, Ramón García‐Sanz, David González, Patricia J.T.A. Groenen, Michael Hummel, Elizabeth Macintyre, Kostas Stamatopoulos, Christiane Pott, Jan Trka, Nikos Darzentas, Anton W. Langerak
Software Mentions: 1
Published: over 5 years ago

10.3390/life11070654

Genetic Investigation of Inverse Psoriasis
Cited by: 3
Author(s): Anikó Göblös, Emese Varga, Katalin Farkas, Kristóf Árvai, Lajos Kemény
Software Mentions: 1
Published: over 3 years ago

10.3390/md14040078

Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products
Cited by: 95
Author(s): Juan Pablo Gomez-Escribano, Silke Alt, Mervyn J. Bibb
Software Mentions: 1
Published: over 8 years ago

10.1097/MD.0000000000000298

Genomic Profiling of Patient-Derived Colon Cancer Xenograft Models
Cited by: 17
Author(s): Won Suk Lee, Hye-Youn Kim, Jae Yeon Seok, Ho Hee Jang, Yeon Ho Park, Soyoung Kim, Dong Bok Shin, Seok Pyo Hong
Software Mentions: 1
Published: almost 10 years ago

10.1016/j.mex.2014.06.001

Determining methylation status of methylguanine DNA methyl transferase (MGMT) from formalin-fixed, paraffin embedded tumor tissue
Cited by: 2
Author(s): Francine B. de Abreu, Torrey L. Gallagher, Emmeline Z. Liu, Gregory J. Tsongalis
Software Mentions: 1
Published: almost 11 years ago

10.1016/j.mex.2015.11.008

NGS-based deep bisulfite sequencing
Cited by: 3
Author(s): Suman Lee, Joomyeong Kim
Software Mentions: 1
Published: almost 9 years ago

10.3390/microarrays5020012

Advantages of Array-Based Technologies for Pre-Emptive Pharmacogenomics Testing
Cited by: 10
Author(s): Ali Shahandeh, Daniel M. Johnstone, Joshua Atkins, Jean‐Marie Sontag, Mohsen Heidari, Nilofar Daneshi, Elvis Freeman-Acquah, Elizabeth A. Milward
Software Mentions: 1
Published: over 8 years ago

10.1128/MRA.00924-18

Draft Whole-Genome Sequence of Leishmania (Viannia) braziliensis Presenting Leishmania RNA Virus 1, from Western Amazon, Brazil
Cited by: 0
Author(s): Andonai Krauze, Raul Maia Falcão, Márlon Grégori Flores Custódio, Iasmin Ferreira Pimentel, Lilian Motta Cantanhêde, Gabriel Eduardo Melim Ferreira, Elisa Cupolillo, Ricardo de Godoi Mattos Ferreira
Software Mentions: 1
Published: about 6 years ago

10.1186/2049-2618-1-10

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform
Cited by: 128
Author(s): Erin B. Fichot, R. Sean Norman
Software Mentions: 1
Published: over 11 years ago

10.1186/s40168-016-0212-z

Transmission of viruses via our microbiomes
Cited by: 40
Author(s): Melissa Ly, Marcus B. Jones, Shira R. Abeles, Tasha M. Santiago-Rodríguez, Jonathan Gao, Ivan C. Chan, Chandrabali Ghose, David T. Pride
Software Mentions: 1
Published: almost 8 years ago

10.1186/s40168-016-0187-9

Microbial diversity in individuals and their household contacts following typical antibiotic courses
Cited by: 115
Author(s): Shira R. Abeles, Marcus B. Jones, Tasha M. Santiago-Rodríguez, Melissa Ly, Niels Klitgord, Shibu Yooseph, Karen E. Nelson, David T. Pride
Software Mentions: 1
Published: over 8 years ago

10.3390/microorganisms8020305

Pathogenicity and Virulence Factors of Fusarium graminearum Including Factors Discovered Using Next Generation Sequencing Technologies and Proteomics
Cited by: 29
Author(s): Molemi Evelyn Rauwane, Udoka Vitus Ogugua, Chimdi Mang Kalu, Lesiba Klaas Ledwaba, Adugna Abdi Woldesemayat, Khayalethu Ntushelo
Software Mentions: 1
Published: almost 5 years ago

10.1007/s11033-020-05527-y

SNP marker development in Pinus sylvestris L. in stress-responsive genes characterized from Pinus cembra L. transcriptomes
Cited by: 0
Author(s): Zoltán Attila Köbölkuti, Endre György Tóth, Daniela Jahn, Berthold Heinze, Mária Höhn
Software Mentions: 1
Published: over 4 years ago

10.1186/s13039-015-0190-z

Prenatal diagnosis of complete maternal uniparental isodisomy of chromosome 4 in a fetus without congenital abnormality or inherited disease-associated variations
Cited by: 5
Author(s): Weiqiang Liu, Huimin Zhang, Jian Wang, Guojiu Yu, Wenjun Qiu, Zhihua Li, Min Chen, Kwong Wai Choy, Xiaofang Sun
Software Mentions: 1
Published: about 9 years ago

10.1002/mgg3.500

Mitochondrial and nuclear disease panel (Mito-aND-Panel): Combined sequencing of mitochondrial and nuclear DNA by a cost-effective and sensitive NGS-based method
Cited by: 20
Author(s): Benedikt Schöser, Florentine Scharf, Stephanie Kleinle, Ulrike Schön, Elke Holinski‐Feder, Rita Horvath, Anna Benet‐Pagès, Isabel Diebold
Software Mentions: 1
Published: about 6 years ago

10.1002/1878-0261.12537

Liquid biopsy in pancreatic ductal adenocarcinoma: current status of circulating tumor cells and circulating tumor<scp>DNA</scp>
Cited by: 59
Author(s): Hyukmin Lee, Sung Sup Park, Young Kyung Lee, Jeffrey A. Norton, Stefanie S. Jeffrey
Software Mentions: 1
Published: over 5 years ago

10.1186/s13567-015-0225-9

Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection
Cited by: 12
Author(s): Bernardo Bello-Ortí, Kate J. Howell, Alexander W. Tucker, Duncan J. Maskell, Virginia Aragón
Software Mentions: 1
Published: about 9 years ago

10.1007/s00428-018-2411-4

Validation of the Oncomine™ focus panel for next-generation sequencing of clinical tumour samples
Cited by: 64
Author(s): Hannah L. Williams, Kathy Walsh, Austin G. Diamond, Anca Oniscu, Zandra C. Deans
Software Mentions: 1
Published: over 6 years ago

10.1186/s12985-017-0907-1

Detection and full genome characterization of two beta CoV viruses related to Middle East respiratory syndrome from bats in Italy
Cited by: 51
Author(s): Ana Moreno, Davide Lelli, Luca De Sabato, Guendalina Zaccaria, Arianna Boni, Enrica Sozzi, Alice Prosperi, Antonio Llombart‐Bosch, Eleonora Cella, Maria Rita Castrucci, Massimo Ciccozzi, Gabriele Vaccari
Software Mentions: 1
Published: almost 7 years ago

10.3390/v12080859

A CRISPR/Cas9 Generated Bovine CD46-knockout Cell Line—A Tool to Elucidate the Adaptability of Bovine Viral Diarrhea Viruses (BVDV)
Cited by: 12
Author(s): Kevin P. Szillat, Susanne Koethe, Kerstin Wernike, Dirk W. Höper, Martin Beer
Software Mentions: 1
Published: over 4 years ago

10.3390/v13050899

Symptomatic SARS-CoV-2 Reinfection in a Healthy Healthcare Worker in Italy Confirmed by Whole-Genome Sequencing
Cited by: 7
Author(s): Daniela Loconsole, Anna Sallustio, Marisa Accogli, Francesca Centrone, Daniele Casulli, Andrea Madaro, Ersilia Tedeschi, Antonio Parisi, Maria Chironna
Software Mentions: 1
Published: over 3 years ago

10.1016/j.pvr.2015.05.004

Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection
Cited by: 73
Author(s): Michael Cullen, Joseph F. Boland, Mark Schiffman, Xijun Zhang, Nicolas Wentzensen, Qi Yang, Zigui Chen, Kai Yu, Jason Mitchell, David A. Roberson, Sara Bass, Laurie Burdette, Moara Machado, Sarangan Ravichandran, Brian T. Luke, Mitchell J. Machiela, Mark Andersen, M. F. Osentoski, Michael W. Laptewicz, Sholom Wacholder, Ashlie Feldman, Tina Raine‐Bennett, Thomas Lorey, Philip E. Castle, Meredith Yeager, Robert D. Burk, Lisa Mirabello
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13071-018-3225-6

Polyomic tools for an emerging livestock parasite, the rumen fluke Calicophoron daubneyi; identifying shifts in rumen functionality
Cited by: 10
Author(s): Kathryn M. Huson, Russell M. Morphew, Nathan R. Allen, Matthew J. Hegarty, Hillary J. Worgan, Susan Elizabeth Girdwood, Eleanor Jones, Helen Phillips, Martin Vickers, Martin Swain, Daniel R. Smith, Alison H. Kingston‐Smith, Peter M. Brophy
Software Mentions: 1
Published: almost 6 years ago

10.3390/pathogens3020437

WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare?
Cited by: 46
Author(s): Kelly L. Wyres, Thomas Conway, Saurabh Garg, Carlos Queiroz, Matthias Reumann, Kathryn E. Holt, Laura-Cristina Rusu
Software Mentions: 1
Published: over 10 years ago

10.3390/pathogens9050335

Genotyping, Assessment of Virulence and Antibacterial Resistance of the Rostov Strain of Mycobacterium tuberculosis Attributed to the Central Asia Outbreak Clade
Cited by: 4
Author(s): Mikhail V. Fursov, Egor Shitikov, Julia Bespyatykh, А. Г. Богун, Angelina A. Kislichkina, Т. И. Комбарова, Tatiana I. Rudnitskaya, Natalia S. Grishenko, Elena Ganina, Л. В. Домотенко, Nadezhda K. Fursova, В. Д. Потапов, I. A. Dyatlov
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.421

BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU
Cited by: 19
Author(s): Ruibang Luo, Yiu-Lun Wong, Wai-Chun Law, Lap-Kei Lee, Jeanno Cheung, Chi-Man Liu, Tak Wah Lam
Software Mentions: 1
Published: over 10 years ago

10.7717/peerj.6661

Next-generation sequencing of <i>BRCA1</i> and <i>BRCA2</i> genes for rapid detection of germline mutations in hereditary breast/ovarian cancer
Cited by: 13
Author(s): Arianna Nicolussi, Francesca Belardinilli, Yasaman Mahdavian, Valeria Colicchia, Sonia D’Inzeo, Marialaura Petroni, Massimo Zani, Sergio Ferraro, Virginia Valentini, Laura Ottini, Giuseppe Giannini, Carlo Capalbo, Anna Coppa
Software Mentions: 1
Published: over 5 years ago

10.1186/s13007-015-0062-x

Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome
Cited by: 18
Author(s): Leonardo Galindo‐González, David Pinzón-Latorre, Erik A Bergen, Dustin C Jensen, Michael K. Deyholos
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pmed.1002230

Clinical applicability and cost of a 46-gene panel for genomic analysis of solid tumours: Retrospective validation and prospective audit in the UK National Health Service
Cited by: 58
Author(s): Angela Hamblin, Sarah Wordsworth, Jilles M Fermont, Suzanne Page, Kulvinder Kaur, Carlos Camps, Pamela J. Kaisaki, Avinash Gupta, Denis Talbot, Mark R. Middleton, Shirley Henderson, Anthony Cutts, Dimitrios V Vavoulis, Nick Housby, Ian Tomlinson, Jenny C. Taylor, Anna Schuh
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pntd.0003681

Whole Genome Comparisons Suggest Random Distribution of Mycobacterium ulcerans Genotypes in a Buruli Ulcer Endemic Region of Ghana
Cited by: 21
Author(s): Anthony Ablordey, Koen Vandelannoote, Isaac A. Frimpong, Evans K. Ahortor, Nana Ama Amissah, Miriam Eddyani, Lies Durnez, Françoise Portaels, Bouke C. de Jong, Herwig Leirs, Jessica L. Porter, Kirstie M. Mangas, Margaret M C Lam, Andrew H. Buultjens, Torsten Seemann, Nicholas J. Tobias, Timothy P. Stinear
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0107703

Guava Leaf Extract Inhibits Quorum-Sensing and Chromobacterium violaceum Induced Lysis of Human Hepatoma Cells: Whole Transcriptome Analysis Reveals Differential Gene Expression
Cited by: 41
Author(s): Rajib Ghosh, Bipransh Kumar Tiwary, Anoop Kumar, Ranadhir Chakraborty
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0064084

A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps
Cited by: 33
Author(s): Swee Jin Tan, Huan L. Phan, Benjamin Michael Gerry, Aléxandre Kuhn, Lewis Z. Hong, Yao Min Ong, Polly Suk Yean Poon, Marc Unger, Robert C. Jones, Stephen R. Quake, William F. Burkholder
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0110387

Direct Chloroplast Sequencing: Comparison of Sequencing Platforms and Analysis Tools for Whole Chloroplast Barcoding
Cited by: 22
Author(s): Marta Brożyńska, Agnelo Furtado, Robert J. Henry
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0227009

Genomic insights on heterogeneous resistance to vancomycin and teicoplanin in Methicillin-resistant Staphylococcus aureus: A first report from South India
Cited by: 23
Author(s): Yamuna Devi Bakthavatchalam, P G Babu, Elakkiya Munusamy, Hariharan Triplicane Dwarakanathan, Priscilla Rupali, Marcus J. Zervos, Peter John Victor, Balaji Veeraraghavan
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0255003

Fungal species in endodontic infections: A systematic review and meta-analysis
Cited by: 9
Author(s): Alice Alberti, Stefano Corbella, Silvio Taschieri, Luca Francetti, Kausar Sadia Fakhruddin, LP Samaranayake
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0101648

Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the Ammonia-Oxidizing Archaea
Cited by: 82
Author(s): Kateryna Zhalnina, Raquel Dias, Michael T. Leonard, Patrícia Dörr de Quadros, Flávio Anastácio de Oliveira Camargo, Jennifer C. Drew, William G. Farmerie, Samira H. Daroub, Eric W. Triplett
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0216179

Targeted re-sequencing of F8, F9 and VWF: Characterization of Ion Torrent data and clinical implications for mutation screening
Cited by: 5
Author(s): Eric Manderstedt, Rosanna Nilsson, Christina Lind‐Halldén, Rolf Ljung, Jan Astermark, Christer Halldén
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0185169

Identification of LAG3 high affinity aptamers by HT-SELEX and Conserved Motif Accumulation (CMA)
Cited by: 25
Author(s): Mario Martínez Soldevilla, Sandra Hervás, Helena Villanueva, Teresa Lozano, Obdulia Rabal, Julen Oyarzábal, Juan José Lasarte, Maurizio Bendandi, Susana Inogés, Ascensión López‐Díaz de Cerio, Fernando Pastor
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0185586

Advances in the analysis of complex food matrices: Species identification in surimi-based products using Next Generation Sequencing technologies
Cited by: 46
Author(s): Alice Giusti, Andrea Armani, Carmen G. Sotelo
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0119123

Challenges with Using Primer IDs to Improve Accuracy of Next Generation Sequencing
Cited by: 29
Author(s): Johanna Brodin, Charlotte Hedskog, Alexander Heddini, Emmanuel Bénard, Richard A. Neher, Mattias Mild, Jan Albert
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0173760

Risk for molecular contamination of tissue samples evaluated for targeted anti-cancer therapy
Cited by: 8
Author(s): Eyal Asor, Michael Y. Stav, Einav Simon, Ibrahim Fahoum, Edmond Sabo, Ofer Ben‐Izhak, Dov Hershkovitz
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0025531

Practical Tools to Implement Massive Parallel Pyrosequencing of PCR Products in Next Generation Molecular Diagnostics
Cited by: 42
Author(s): Kim De Leeneer, Joachim De Schrijver, Lieven Clement, Machteld Baetens, Steve Lefever, Sarah De Keulenaer, Wim Van Criekinge, Dieter Deforce, Filip Van Nieuwerburgh, Sofie Bekaert, Filip Pattyn, Bram De Wilde, Paul Coucke, Jo Vandesompele, Kathleen Claes, Jan Hellemans
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0086965

The Role of Viral and Host MicroRNAs in the Aujeszky’s Disease Virus during the Infection Process
Cited by: 21
Author(s): Timoneda Oriol, Fernando Núñez-Hernández, Ingrid Balcells, Marta Muñoz, Anna Castelló, Gonzalo Vera, Lester J. Pérez, Raquel Egea, Gisela Mir, Shaun-Paul Cordoba, Rosa Rosell, Joaquím Segalés, Tomas Axelsson, Armand Sánchez, José I. Núñez
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0135346

Microevolution of Anthrax from a Young Ancestor (M.A.Y.A.) Suggests a Soil-Borne Life Cycle of Bacillus anthracis
Cited by: 32
Author(s): Peter Braun, Gregor Grass, Angela Aceti, Luigina Serrecchia, Alessia Affuso, Leonardo Mariño, Stefania Grimaldi, Stefania Pagano, Matthias Hanczaruk, Enrico Georgi, Bernd H. Northoff, Anne Schöler, Michael Schloter, Markus Antwerpen, Antonio Fasanella
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0077963

Influence of Plasma Processing on Recovery and Analysis of Circulating Nucleic Acids
Cited by: 155
Author(s): Karen M. Page, David S. Guttery, Nathalie Zahra, Lindsay Primrose, Shona R. Elshaw, J. H. Pringle, Kevin Blighe, S Marchese, Alice Hills, Laura Woodley, Justin Stebbing, R. Charles Coombes, Jacqueline A Shaw
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0076627

Mitochondrial Sequence Variation in African-American Primary Open-Angle Glaucoma Patients
Cited by: 19
Author(s): David W. Collins, Harini V. Gudiseva, Benjamin Trachtman, Matthew Jerrehian, Thomasine Gorry, William T. Merritt, Allison Rhodes, Prithvi S. Sankar, Meredith Regina, Eydie Miller-Ellis, Joan M. O’Brien
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0166288

Technical Evaluation: Identification of Pathogenic Mutations in PKD1 and PKD2 in Patients with Autosomal Dominant Polycystic Kidney Disease by Next-Generation Sequencing and Use of a Comprehensive New Classification System
Cited by: 25
Author(s): Moritoshi Kinoshita, Eiji Higashihara, Haruna Kawano, Ryo Higashiyama, Daisuke Koga, Takafumi Fukui, Nobuhisa Gondo, Takehiko Oka, Kozo Kawahara, Krisztina Rigó, Tim Hague, Kiyonori Katsuragi, Kimiyoshi Sudo, Masahiko Takeshi, Shigeo Horie, Kikuo Nutahara
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0168910

High-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Time
Cited by: 10
Author(s): Tiffany M. Jamann, Shilpa Sood, Randall J. Wisser, James B. Holland
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0094100

Mutation Spectrum of Six Genes in Chinese Phenylketonuria Patients Obtained through Next-Generation Sequencing
Cited by: 21
Author(s): Ying Gu, Kangmo Lu, Guanghui Yang, Zhong Cen, Li Yu, Lin Lin, Jun Hao, Zhigang Yang, J Peng, Shu-Jian Cui, Jian Huang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0198980

Novel RNA aptamers targeting gastrointestinal cancer biomarkers CEA, CA50 and CA72-4 with superior affinity and specificity
Cited by: 18
Author(s): Qing Pan, Carmen O. K. Law, Mingo M. H. Yung, Ki-Cheol Han, Yuen L. Pon, Terrence Chi-Kong Lau
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0049239

BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data
Cited by: 42
Author(s): Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Eduardo Pareja, Raquel Tobes
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0130219

Validation of an Ion Torrent Sequencing Platform for the Detection of Gene Mutations in Biopsy Specimens from Patients with Non-Small-Cell Lung Cancer
Cited by: 4
Author(s): Shiro Fujita, Katsuhiro Masago, Jumpei Takeshita, Chiyuki Okuda, Kyoko Otsuka, Akito Hata, Ryuji Kaji, Nobuyuki Katakami, Yukio Hirata
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0211261

Mutation screening in non-syndromic hearing loss patients with cochlear implantation by massive parallel sequencing in Taiwan
Cited by: 21
Author(s): Wei‐Hsiu Liu, Pi-Yueh Chang, Shih-Cheng Chang, Jang-Jih Lu, Che-Ming Wu
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0104984

Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms
Cited by: 569
Author(s): Rolf Sommer Kaas, Pimlapas Leekitcharoenphon, Frank Møller Aarestrup, Ole Lund
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0084971

Unusual Large-Scale Chromosomal Rearrangements in Mycobacterium tuberculosis Beijing B0/W148 Cluster Isolates
Cited by: 18
Author(s): Egor Shitikov, Julia Bespyatykh, Dimitry D Ischenko, Dmitry Alexeev, Irina Y. Karpova, Elena S. Kostryukova, Yulia D Isaeva, Elena Nosova, Igor Mokrousov, Anna Vyazovaya, Olga Narvskaya, Boris Vishnevsky, Tatiana Otten, Viacheslav Zhuravlev, Piotr Yablonsky, Elena N. Ilina, Vadim M. Govorun
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0112950

A Bumpy Ride on the Diagnostic Bench of Massive Parallel Sequencing, the Case of the Mitochondrial Genome
Cited by: 11
Author(s): Kim Vancampenhout, Ben Caljon, Claudia Spits, Katrien Stouffs, An I. Jonckheere, Linda De Meırleır, Willy Lissens, Arnaud Vanlander, Joél Smet, Boél De Paepe, Rudy Van Coster, Sara Seneca
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0128122

Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches
Cited by: 147
Author(s): Stefan J. Green, Raghavee Venkatramanan, Ankur Naqib
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0136257

Isolation of Tibet orbivirus, TIBOV, from Culicoides Collected in Yunnan, China
Cited by: 19
Author(s): Wenwen Lei, Xin Guo, Shihong Fu, Yue Feng, Kai Nie, Jingdong Song, Yang Li, Xuejun Ma, Guodong Liang, Hongning Zhou
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0144811

Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance
Cited by: 39
Author(s): Gabriel Minárik, Gabriela Repiská, Michaela Hýblová, Emília Nagyová, Katarína Šoltýs, Jaroslav Budiš, František Ďuriš, Rastislav Sysak, Maria Gerykova Bujalkova, Barbora Vlková-Izrael, Orsolya Bíró, Bálint Nagy, Tomáš Szemeš
Software Mentions: 1
Published: almost 9 years ago