Results 81 to 90 of about 184,715 (310)

Intact DNA purified from flow-sorted nuclei unlocks the potential of next-generation genome mapping and assembly in Solanum species

MethodsX, 2018
Next-generation genome mapping through nanochannels (Bionano optical mapping) of plant genomes brings genome assemblies to the ‘nearly-finished’ level for reliable and detailed gene annotations and assessment of structural variations.
Paola Gaiero, Hana Šimková, Jan Vrána, Federico F. Santiñaque, Beatriz López-Carro, Gustavo A. Folle, José van de Belt, Sander A. Peters, Jaroslav Doležel, Hans de Jong   +9 more
doaj   +1 more source

Bridging the gap: Multi‐stakeholder perspectives of molecular diagnostics in oncology

Molecular Oncology, EarlyView.
Although molecular diagnostics is transforming cancer care, implementing novel technologies remains challenging. This study identifies unmet needs and technology requirements through a two‐step stakeholder involvement. Liquid biopsies for monitoring applications and predictive biomarker testing emerge as key unmet needs. Technology requirements vary by
Jorine Arnouts, Senada Koljenović, Elise Daems, Karolien De Wael, Marc Peeters, Léon C. van Kempen, Greetje Vanhoutte, Karen Zwaenepoel, Timon Vandamme   +8 more
wiley   +1 more source

De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space [PDF]

, 2017
Sequencing technologies allow for an in-depth analysis of biological species but the size of the generated datasets introduce a number of analytical challenges.
Robertson, David L., Tapinos, Avraam
core   +1 more source

Investigating the cell of origin and novel molecular targets in Merkel cell carcinoma: a historic misnomer

Molecular Oncology, EarlyView.
This study indicates that Merkel cell carcinoma (MCC) does not originate from Merkel cells, and identifies gene, protein & cellular expression of immune‐linked and neuroendocrine markers in primary and metastatic Merkel cell carcinoma (MCC) tumor samples, linked to Merkel cell polyomavirus (MCPyV) status, with enrichment of B‐cell and other immune cell
Richie Jeremian, Sriraam Sivachandran, Melissa Galati, Brandon Ramchatesingh, Hibo Rijal, Johnny Hanna, Elena Netchiporouk, May Chergui, Margaret Redpath, Samy Abou Setah, Ivan V. Litvinov   +10 more
wiley   +1 more source

Optical Genome Mapping Reveals Genomic Alterations upon Gene Editing in hiPSCs: Implications for Neural Tissue Differentiation and Brain Organoid Research

Cells
Genome editing, notably CRISPR (cluster regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), has revolutionized genetic engineering allowing for precise targeted modifications.
Lucia Gallego Villarejo, Wanda M. Gerding, Lisa Bachmann, Luzie H. I. Hardt, Stefan Bormann, Huu Phuc Nguyen, Thorsten Müller   +6 more
doaj   +1 more source

Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity. [PDF]

PLoS ONE, 2015
Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V ...
Carol Chapman, Matthew Henry, Kimberly A Bishop-Lilly, Joy Awosika, Adam Briska, Ryan N Ptashkin, Trevor Wagner, Chythanya Rajanna, Hsinyi Tsang, Shannon L Johnson, Vishwesh P Mokashi, Patrick S G Chain, Shanmuga Sozhamannan   +12 more
doaj   +1 more source

REAPR: a universal tool for genome assembly evaluation. [PDF]

, 2013
Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked.
Berriman, Matthew, Hunt, Martin, Kikuchi, Taisei, Newbold, Chris, Otto, Thomas D, Sanders, Mandy   +5 more
core   +2 more sources

Utility of Optical Genome Mapping in Repeat Disorders

Clinical Genetics
ABSTRACT Genomic repeat sequences are patterns of nucleic acids that exist in multiple copies throughout the genome. More than 60 Mendelian disorders are caused by the expansion or contraction of these repeats. Various specific methods for determining tandem repeat variations have been developed.
Mehmet Burak Mutlu, Taner Karakaya, Hamide Betül Gerik Çelebi, Fahrettin Duymuş, Serhat Seyhan, Sanem Yılmaz, Uluç Yiş, Tahir Atik, Mehmet Fatih Yetkin, Hakan Gümüş   +9 more
openaire   +6 more sources

BiSCoT: Improving large eukaryotic genome assemblies with optical maps

PeerJ, 2019
ABSTRACTMotivationLong read sequencing and Bionano Genomics optical maps are two techniques that, when used together, make it possible to reconstruct entire chromosome or chromosome arms structure. However, the existing tools are often too conservative and organization of contigs into scaffolds is not always optimal.ResultsWe developed BiSCoT (Bionano ...
Istace, Benjamin, Belser, Caroline, Aury, Jean-Marc   +2 more
openaire   +3 more sources

Modeling hepatic fibrosis in TP53 knockout iPSC‐derived human liver organoids

Molecular Oncology, EarlyView.
This study developed iPSC‐derived human liver organoids with TP53 gene knockout to model human liver fibrosis. These organoids showed elevated myofibroblast activation, early disease markers, and advanced fibrotic hallmarks. The use of profibrotic differentiation medium further amplified the fibrotic signature seen in the organoids.
Mustafa Karabicici, Soheil Akbari, Ceyda Caliskan, Canan Celiker, Ozden Oz, Leman Binokay, Gökhan Karakulah, Serif Senturk, Esra Erdal   +8 more
wiley   +1 more source