21 Result(s)
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Chih Long Liu
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Open AccessQuantification of cerebrospinal fluid tumor DNA in lung cancer patients with suspected leptomeningeal carcinomatosis
Cerebrospinal fluid tumor-derived DNA (CSF-tDNA) analysis is a promising approach for monitoring the neoplastic processes of the central nervous system. We applied a lung cancer-specific sequencing panel (CAPP...
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Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling
The scarcity of malignant Hodgkin and Reed–Sternberg cells hampers tissue-based comprehensive genomic profiling of classic Hodgkin lymphoma (cHL). By contrast, liquid biopsies show promise for molecular profil...
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Inferring gene expression from cell-free DNA fragmentation profiles
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles fr...
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Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA
Circulating tumor-derived DNA (ctDNA) is an emerging biomarker for many cancers, but the limited sensitivity of current detection methods reduces its utility for diagnosing minimal residual disease. Here we de...
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Integrating genomic features for non-invasive early lung cancer detection
Radiologic screening of high-risk adults reduces lung-cancer-related mortality1,2; however, a small minority of eligible individuals undergo such screening in the United States3,4. The availability of blood-based...
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Predicting HLA class II antigen presentation through integrated deep learning
Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II molecules would be valuable for vaccine development and cancer immunotherapies. Current computational methods trained on in...
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Determining cell type abundance and expression from bulk tissues with digital cytometry
Single-cell RNA-sequencing has emerged as a powerful technique for characterizing cellular heterogeneity, but it is currently impractical on large sample cohorts and cannot be applied to fixed specimens collec...
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Open AccessData normalization considerations for digital tumor dissection
In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The...
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Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens
Evidence for the abundant presentation of class II neoantigens by a human B-cell lymphoma.
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Integrated digital error suppression for improved detection of circulating tumor DNA
Circulating tumor DNA is detected with high sensitivity and specificity using molecular barcoding and in silico error correction.
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The prognostic landscape of genes and infiltrating immune cells across human cancers
A searchable pan-cancer resource generated using data from nearly 18,000 human tumors reveals links between tumor infiltration by particular leukocyte subsets, tumor expression of particular gene signatures, a...
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Robust enumeration of cell subsets from tissue expression profiles
A computational method to identify cell types within a complex tissue, based on analysis of gene expression profiles, is described in this paper.
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Transient expression of Bcl6 is sufficient for oncogenic function and induction of mature B-cell lymphoma
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma and can be separated into two subtypes based upon molecular features with similarities to germinal centre B-cells (GCB-like) or activated B-cel...
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An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage
Aaron Newman and his colleagues introduce a next-generation sequencing–based approach for the cost-effective detection and quantitation of tumor-derived circulating DNA in both early- and advanced-stage tumors...
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On silico peptide microarrays for high-resolution map** of antibody epitopes and diverse protein-protein interactions
Using the semiconductor synthesis technology of maskless photolithography on microprocessor-grade silicon wafers, Jordan Price and colleagues synthesized microarrays containing every possible overlap** pepti...
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Open AccessSpecific post-translational histone modifications of neutrophil extracellular traps as immunogens and potential targets of lupus autoantibodies
Autoreactivity to histones is a pervasive feature of several human autoimmune disorders, including systemic lupus erythematosus (SLE). Specific post-translational modifications (PTMs) of histones within neutro...
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Open AccessA proteomic approach for the identification of novel lysine methyltransferase substrates
Signaling via protein lysine methylation has been proposed to play a central role in the regulation of many physiologic and pathologic programs. In contrast to other post-translational modifications such as ph...
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Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling
Binding of the transcription factor NF-κB subunit RelA activates proinflammatory gene expression. Gozani and colleagues show that basal expression of RelA target genes is suppressed by methylation of RelA by S...
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Open AccessRNA polymerase map** during stress responses reveals widespread nonproductive transcription in yeast
The use of genome-wide RNA abundance profiling by microarrays and deep sequencing has spurred a revolution in our understanding of transcriptional control. However, changes in mRNA abundance reflect the combin...
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Open AccessGlobal nucleosome occupancy in yeast
Although eukaryotic genomes are generally thought to be entirely chromatin-associated, the activated PHO5 promoter in yeast is largely devoid of nucleosomes. We systematically evaluated nucleosome occupancy in ye...
