Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty

C Badowski, B He, LX Garmire - NPJ precision oncology, 2022 - nature.com
Cancer ranks as one of the deadliest diseases worldwide. The high mortality rate associated
with cancer is partially due to the lack of reliable early detection methods and/or inaccurate …

Chromatin-state discovery and genome annotation with ChromHMM

J Ernst, M Kellis - Nature protocols, 2017 - nature.com
Noncoding DNA regions have central roles in human biology, evolution, and disease.
ChromHMM helps to annotate the noncoding genome using epigenomic information across …

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

Y Ji, Z Zhou, H Liu, RV Davuluri - Bioinformatics, 2021 - academic.oup.com
Motivation Deciphering the language of non-coding DNA is one of the fundamental
problems in genome research. Gene regulatory code is highly complex due to the existence …

The UCSC genome browser database: 2021 update

J Navarro Gonzalez, AS Zweig, ML Speir… - Nucleic acids …, 2021 - academic.oup.com
For more than two decades, the UCSC Genome Browser database (https://genome. ucsc.
edu) has provided high-quality genomics data visualization and genome annotations to the …

Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus

DJ Downes, AR Cross, P Hua, N Roberts… - Nature …, 2021 - nature.com
The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) disease (COVID-19)
pandemic has caused millions of deaths worldwide. Genome-wide association studies …

Cancer SLC43A2 alters T cell methionine metabolism and histone methylation

Y Bian, W Li, DM Kremer, P Sajjakulnukit, S Li… - Nature, 2020 - nature.com
Abnormal epigenetic patterns correlate with effector T cell malfunction in tumours,,–, but the
cause of this link is unknown. Here we show that tumour cells disrupt methionine …

A fluid biomarker reveals loss of TDP-43 splicing repression in presymptomatic ALS–FTD

KE Irwin, P Jasin, KE Braunstein, IR Sinha, MA Garret… - Nature medicine, 2024 - nature.com
Although loss of TAR DNA-binding protein 43 kDa (TDP-43) splicing repression is well
documented in postmortem tissues of amyotrophic lateral sclerosis (ALS) and frontotemporal …

The UCSC genome browser database: 2019 update

M Haeussler, AS Zweig, C Tyner, ML Speir… - Nucleic acids …, 2019 - academic.oup.com
Abstract The UCSC Genome Browser (https://genome. ucsc. edu) is a graphical viewer for
exploring genome annotations. For almost two decades, the Browser has provided …

Pharmacological blockade of TEAD–YAP reveals its therapeutic limitation in cancer cells

Y Sun, L Hu, Z Tao, GK Jarugumilli, H Erb… - Nature …, 2022 - nature.com
Targeting TEAD autopalmitoylation has been proposed as a therapeutic approach for YAP-
dependent cancers. Here we show that TEAD palmitoylation inhibitor MGH-CP1 and …

DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load

H Jung, HS Kim, JY Kim, JM Sun, JS Ahn… - Nature …, 2019 - nature.com
Mitotic cell division increases tumour mutation burden and copy number load, predictive
markers of the clinical benefit of immunotherapy. Cell division correlates also with genomic …