B cells and tertiary lymphoid structures promote immunotherapy response

…, J Blando, G Han, V Gopalakrishnan, Y Xi… - Nature, 2020 - nature.com
Abstract Treatment with immune checkpoint blockade (ICB) has revolutionized cancer therapy.
Until now, predictive biomarkers 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 – 10 and strategies to augment …

Dnmt3a is essential for hematopoietic stem cell differentiation

…, JS Berg, C Bock, A Vasanthakumar, H Gu, Y Xi… - Nature …, 2012 - nature.com
Loss of the de novo DNA methyltransferases Dnmt3a and Dnmt3b in embryonic stem cells
obstructs differentiation; however, the role of these enzymes in somatic stem cells is largely …

[HTML][HTML] BSMAP: whole genome bisulfite sequence MAPping program

Y Xi, W Li - BMC bioinformatics, 2009 - Springer
Background Bisulfite sequencing is a powerful technique to study DNA cytosine methylation.
Bisulfite treatment followed by PCR amplification specifically converts unmethylated …

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

…, L Echipare, H O'geen, R Lister, M Pelizzola, Y Xi… - Nature …, 2010 - nature.com
Abstract Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling
methods. The four most frequently used sequencing-based technologies are the bisulfite…

[HTML][HTML] Neoadjuvant chemotherapy plus nivolumab with or without ipilimumab in operable non-small cell lung cancer: the phase 2 platform NEOSTAR trial

…, MCB Godoy, H Feldman, WN William Jr, Y Xi… - Nature medicine, 2023 - nature.com
Neoadjuvant ipilimumab + nivolumab (Ipi+Nivo) and nivolumab + chemotherapy (Nivo+CT)
induce greater pathologic response rates than CT alone in patients with operable non-small …

SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation

MF Barber, E Michishita-Kioi, Y Xi, L Tasselli, M Kioi… - Nature, 2012 - nature.com
Sirtuin proteins regulate diverse cellular pathways that influence genomic stability, metabolism
and ageing 1 , 2 . SIRT7 is a mammalian sirtuin whose biochemical activity, molecular …

[PDF][PDF] Patterns of transcription factor programs and immune pathway activation define four major subtypes of SCLC with distinct therapeutic vulnerabilities

…, S Heeke, BY Nabet, J Fujimoto, LM Solis, W Lu, Y Xi… - Cancer cell, 2021 - cell.com
Despite molecular and clinical heterogeneity, small cell lung cancer (SCLC) is treated as a
single entity with predictably poor results. Using tumor expression data and non-negative …

[PDF][PDF] NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming

…, P Cheung, K Chen, BM Zee, M Kioi, J Lauring, Y Xi… - Molecular cell, 2011 - cell.com
The histone lysine methyltransferase NSD2 (MMSET/WHSC1) is implicated in diverse
diseases and commonly overexpressed in multiple myeloma due to a recurrent t(4;14) …

DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing

K Chen, Y Xi, X Pan, Z Li, K Kaestner, J Tyler… - Genome …, 2013 - genome.cshlp.org
Recent developments in next-generation sequencing have enabled whole-genome profiling
of nucleosome organizations. Although several algorithms for inferring nucleosome position …

[PDF][PDF] AF9 YEATS domain links histone acetylation to DOT1L-mediated H3K79 methylation

Y Li, H Wen, Y Xi, K Tanaka, H Wang, D Peng, Y Ren… - Cell, 2014 - cell.com
The recognition of modified histones by "reader" proteins constitutes a key mechanism
regulating gene expression in the chromatin context. Compared with the great variety of readers …