Results 121 to 130 of about 709,139 (287)

Membrane composition and thermodynamic identity as boundaries of life for synthetic cell research

FEBS Letters, EarlyView.
What makes a cell a cell? The boundary of a living cell is not just a wall. Read as a Markov blanket, the membrane separates internal from external states, generating identity and non‐equilibrium order. Can this identity be rebuilt from scratch in a synthetic cell?
Caterina Presutti, Bert Poolman
wiley   +1 more source

Representing Variant Calling Format as Directed Acyclic Graphs to Enable the Use of Cloud Computing for Efficient and Cost Effective Genome Analysis

, 2017
Ever since the completion of the Human Genome Project in 2003, the human genome has been represented as a linear sequence of 3.2 billion base pairs and is referred to as the "Reference Genome".
Rizos Sakellariou, Aizad, Sanna, Anjum, Ashiq, Sakellariou, Rizos, Sanna Aizad, Ashiq Anjum   +5 more
core   +1 more source

The role of miR‐335‐5p in the redifferentiation of BRAF p.V600E thyroid cancers

Molecular Oncology, EarlyView.
The BRAF p.V600E mutation promotes thyroid cancer dedifferentiation and radioiodine resistance. Using a network approach, we identified miR‐335‐5p as a key regulator of BRAF‐mutated thyroid tumors. Restoring miR‐335‐5p increased thyroid‐specific gene expression and iodine uptake in cells and organoids.
Valeria Pecce, Simone Bini, Marialuisa Sponziello, Giorgio Grani, Giulia Fiscon, Paola Paci, Lorenzo Farina, Rosa Falcone, Valentina Maggisano, Sebastiano Filetti, Cosimo Durante, Antonella Verrienti   +11 more
wiley   +1 more source

Managing genomic variant calling workflows with Swift/T.

PLoS ONE, 2019
Bioinformatics research is frequently performed using complex workflows with multiple steps, fans, merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large ...
Azza E Ahmed, Jacob Heldenbrand, Yan Asmann, Faisal M Fadlelmola, Daniel S Katz, Katherine Kendig, Matthew C Kendzior, Tiffany Li, Yingxue Ren, Elliott Rodriguez, Matthew R Weber, Justin M Wozniak, Jennie Zermeno, Liudmila S Mainzer   +13 more
doaj   +1 more source

Circular RNA expression landscapes in myelodysplastic neoplasms: Associations with mutational signatures and disease progression

Molecular Oncology, EarlyView.
In this explorative study, the abundance of circular RNA molecules in bone marrow stem cells was found to be elevated in patients with high‐risk myelodysplastic neoplasms, and to be associated with an increased risk of progression to acute myeloid leukemia.
Eileen Wedge, Morten Tulstrup, Gabriele Todisco, Pedro Moura, Christophe Côme, Jakob Werner Hansen, Jakob Schmidt Jespersen, Balthasar Schlotmann, Maria Creignou, Mette Dahl, Claudia Schöllkopf, Klas Raaschou‐Jensen, Krister Wennerberg, Bo Porse, Joachim Weischenfeldt, Eva Hellström‐Lindberg, Lasse Sommer Kristensen, Kirsten Grønbæk   +17 more
wiley   +1 more source

IMPDH inhibition enhances cytarabine efficacy in SAMHD1‐expressing leukaemia cells via guanine nucleotide depletion

Molecular Oncology, EarlyView.
Cytarabine is a key therapy for acute myeloid leukaemia (AML), but its efficacy is limited by the dNTPase SAMHD1, which hydrolyses its active metabolite. Screening nucleotide biosynthesis inhibitors revealed that IMPDH inhibitors selectively sensitise SAMHD1‐proficient AML cells to cytarabine.
Miriam Yagüe‐Capilla, Christopher Dirks, Caroline Eiden, Sonja K. Fesenmayer, Femke M. Hormann, Yolande Klootsema, Ingrid Lilienthal, Si Min Zhang, Nikolas Herold, Sean G. Rudd   +9 more
wiley   +1 more source

Strelka2: Fast and accurate variant calling for clinical sequencing applications

, 2017
We describe Strelka2 (https://github.com/Illumina/strelka), an open-source small variant calling method for clinical germline and somatic sequencing applications.
Eunho Noh, Sangtae Kim, Christopher T Saunders, Mitchell A Bekritsky, Peter Krusche, Aaron L Halpern, Xiaoyu Chen, Konrad Scheffler, Morten Källberg, Doruk Beyter   +9 more
core   +1 more source

Developmental programmes drive cellular plasticity, disease progression and therapy resistance in lung adenocarcinoma

Molecular Oncology, EarlyView.
This study shows that lung adenocarcinomas exploit developmental branching morphogenesis to acquire a therapy resistant basal‐like tumour cell state. This process was found to be regulated by combined TP53 loss‐of‐function and type‐I interferon signalling, identifying a novel axis for biomarker and therapeutic target discovery.
Kamila J Bienkowska, Stephany Gallardo, Nur S. Zainal, Leena Arora, Matthew Ellis, Maria‐Antoinette Lopez, Judith Austine, Sai Pittla, Serena J Chee, Aiman Alzetani, Emily C Shaw, Christian H Ottensmeier, Gareth J Thomas, Christopher J Hanley   +13 more
wiley   +1 more source

Overview of the variant calling pipeline (steps marked by dashed frames are only performed in case of the variant calling pipeline with GLM).

, 2017
Overview of the variant calling pipeline (steps marked by dashed frames are only performed in case of the variant calling pipeline with GLM).
Sarah Sandmann (3768940), Bert A. van der Reijden (3768937), Martin Dugas (793), Aniek O. de Graaf (3768931), Joop H. Jansen (3768934)   +4 more
core   +1 more source

dv-trio: a family-based variant calling pipeline using DeepVariant

, 2020
Motivation: In 2018, Google published an innovative variant caller, DeepVariant, which converts pileups of sequence reads into images and uses a deep neural network to identify single-nucleotide variants and small insertion/deletions from next ...
Ho, JWK, Ip, EKK, Hadinata, C, Giannoulatou, E   +3 more
core   +1 more source