RNA sequencing: new technologies and applications in cancer research

M Hong, S Tao, L Zhang, LT Diao, X Huang… - Journal of hematology & …, 2020 - Springer
Over the past few decades, RNA sequencing has significantly progressed, becoming a
paramount approach for transcriptome profiling. The revolution from bulk RNA sequencing …

Advances and challenges in metatranscriptomic analysis

M Shakya, CC Lo, PSG Chain - Frontiers in genetics, 2019 - frontiersin.org
Sequencing-based analyses of microbiomes have traditionally focused on addressing the
question of community membership and profiling taxonomic abundance through amplicon …

Failure of human rhombic lip differentiation underlies medulloblastoma formation

LD Hendrikse, P Haldipur, O Saulnier, J Millman… - Nature, 2022 - nature.com
Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal
neoplasms of the hindbrain with strong links to early development of the hindbrain 1, 2, 3, 4 …

Comprehensive molecular characterization of muscle-invasive bladder cancer

AG Robertson, J Kim, H Al-Ahmadie, J Bellmunt, G Guo… - Cell, 2017 - cell.com
We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized
by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the …

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

E Bushmanova, D Antipov, A Lapidus… - GigaScience, 2019 - academic.oup.com
Background The possibility of generating large RNA-sequencing datasets has led to
development of various reference-based and de novo transcriptome assemblers with their …

Comprehensive and integrative genomic characterization of hepatocellular carcinoma

A Ally, M Balasundaram, R Carlsen, E Chuah, A Clarke… - Cell, 2017 - cell.com
Liver cancer has the second highest worldwide cancer mortality rate and has limited
therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole …

Integrative analysis identifies four molecular and clinical subsets in uveal melanoma

AG Robertson, J Shih, C Yau, EA Gibb, J Oba… - Cancer cell, 2017 - cell.com
Comprehensive multiplatform analysis of 80 uveal melanomas (UM) identifies four
molecularly distinct, clinically relevant subtypes: two associated with poor-prognosis …

A comprehensive pan-cancer molecular study of gynecologic and breast cancers

AC Berger, A Korkut, RS Kanchi, AM Hegde, W Lenoir… - Cancer cell, 2018 - cell.com
We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of
four gynecological types plus breast. Our aims were to identify shared and unique molecular …

The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions

H Bolouri, JE Farrar, T Triche Jr, RE Ries, EL Lim… - Nature medicine, 2018 - nature.com
We present the molecular landscape of pediatric acute myeloid leukemia (AML) and
characterize nearly 1,000 participants in Children's Oncology Group (COG) AML trials. The …

A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors

DM Bryant, K Johnson, T DiTommaso, T Tickle… - Cell reports, 2017 - cell.com
Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly
regenerative and can replace entire limbs. The mechanisms underlying limb regeneration …