Junyan Lu
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View article: msBayesImpute: A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data
msBayesImpute: A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data Open
Advancements in mass spectrometry (MS) technologies have significantly improved the ability to quantify proteins and analyse their modifications. However, MS-based proteomics datasets frequently encounter missing values due to a complex in…
View article: SputOMICs identifies common and distinct markers in cystic fibrosis and chronic obstructive pulmonary disease
SputOMICs identifies common and distinct markers in cystic fibrosis and chronic obstructive pulmonary disease Open
Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are muco-obstructive lung diseases. Knowledge of molecular processes has much improved therapeutic options in CF, whereas much less is known for COPD, a disease affectin…
View article: Disease-specific U1 spliceosomal RNA mutations in mature B-cell neoplasms
Disease-specific U1 spliceosomal RNA mutations in mature B-cell neoplasms Open
View article: Advanced RPL19-TRAPKI-seq method reveals mechanism of action of bioactive compounds
Advanced RPL19-TRAPKI-seq method reveals mechanism of action of bioactive compounds Open
Natural products play a crucial role in new drug development, but their druggability is often limited by uncertain molecular targets and insufficient research on mechanisms of action. In this study, we developed a new RPL19-TRAP KI -seq me…
View article: BCL-2 dependence is a favorable predictive marker of response to therapy for chronic lymphocytic leukemia
BCL-2 dependence is a favorable predictive marker of response to therapy for chronic lymphocytic leukemia Open
View article: Detect influential points of feature rankings
Detect influential points of feature rankings Open
IPs significantly impact feature rankings and subsequent analyses; routine IP detection is necessary yet underutilized. Our method is available in the R package findIPs.
View article: SLC-RF: Improving Random Forest Performance on High-Dimensional Data via Supervised Linear Combinations
SLC-RF: Improving Random Forest Performance on High-Dimensional Data via Supervised Linear Combinations Open
View article: Epidemiological characteristics of acute viral and mycoplasma respiratory infections in Yongzhou, China: a retrospective descriptive study.
Epidemiological characteristics of acute viral and mycoplasma respiratory infections in Yongzhou, China: a retrospective descriptive study. Open
This study revealed distinct age-dependent and seasonal distribution patterns of respiratory pathogens in Yongzhou, China. The significant changes in pathogen circulation dynamics before, during, and after the COVID-19 pandemic highlight t…
View article: Aggressive Lymphoma after CD19 CAR T-Cell Therapy
Aggressive Lymphoma after CD19 CAR T-Cell Therapy Open
The development of a fatal, clonal, autonomously proliferating CD4-CD8- chimeric antigen receptor (CAR)+ peripheral T-cell lymphoma (PTCL) occurred 1 month after a patient received treatment with tisagenlecleucel for relapsed primary centr…
View article: Construct prognostic models of multiple myeloma with pathway information incorporated
Construct prognostic models of multiple myeloma with pathway information incorporated Open
Multiple myeloma (MM) is a hematological disease exhibiting aberrant clonal expansion of cancerous plasma cells in the bone marrow. The effects of treatments for MM vary between patients, highlighting the importance of developing prognosti…
View article: Concurrent inhibition of ALK and SRC kinases disrupts the ALK lung tumor cell proteome
Concurrent inhibition of ALK and SRC kinases disrupts the ALK lung tumor cell proteome Open
Precision oncology has revolutionized the treatment of ALK-positive lung cancer with targeted therapies. However, an unmet clinical need still to address is the treatment of refractory tumors that contain drug-induced resistant mutations i…
View article: Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma
Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma Open
Despite the immense success of immune checkpoint blockade (ICB) in cancer treatment, many tumors, including melanoma, exhibit innate or adaptive resistance. Tumor-intrinsic T-cell deficiency and T-cell dysfunction have been identified as e…
View article: Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma
Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma Open
Despite the immense success of immune checkpoint blockade (ICB) in cancer treatment, many tumors, including melanoma, exhibit innate or adaptive resistance. Tumor-intrinsic T-cell deficiency and T-cell dysfunction have been identified as e…
View article: Supplementary Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma
Supplementary Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma Open
This file includes all supplemental data with figure legends.
View article: Supplementary Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma
Supplementary Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma Open
This file includes supplementary methods and reagents used in this study.
View article: Supplementary Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma
Supplementary Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma Open
This file includes supplementary methods and reagents used in this study.
View article: Supplementary Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma
Supplementary Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma Open
This file includes all supplemental data with figure legends.
View article: The changing career paths of PhDs and postdocs trained at EMBL
The changing career paths of PhDs and postdocs trained at EMBL Open
Individuals with PhDs and postdoctoral experience in the life sciences can pursue a variety of career paths. Many PhD students and postdocs aspire to a permanent research position at a university or research institute, but competition for …
View article: Ex vivo drug response profiling for response and outcome prediction in hematologic malignancies: the prospective non-interventional SMARTrial
Ex vivo drug response profiling for response and outcome prediction in hematologic malignancies: the prospective non-interventional SMARTrial Open
View article: Negative feedback regulation of MAPK signaling is an important driver of chronic lymphocytic leukemia progression
Negative feedback regulation of MAPK signaling is an important driver of chronic lymphocytic leukemia progression Open
Despite available targeted treatments for the disease, drug-resistant chronic lymphocytic leukemia (CLL) poses a clinical challenge. The objective of this study is to examine whether the dual-specific phosphatases DUSP1 and DUSP6 are requi…
View article: Author response: The changing career paths of PhDs and postdocs trained at EMBL
Author response: The changing career paths of PhDs and postdocs trained at EMBL Open
View article: <i>BCL3</i> rearrangements in B-cell lymphoid neoplasms occur in two breakpoint clusters associated with different diseases
<i>BCL3</i> rearrangements in B-cell lymphoid neoplasms occur in two breakpoint clusters associated with different diseases Open
The t(14;19)(q32;q13) often juxtaposes BCL3 with immunoglobulin heavy chain (IGH) resulting in overexpression of the gene. In contrast to other oncogenic translocations, BCL3 rearrangement (BCL3-R) has been associated with a broad spectrum…
View article: IGLV3-21R110 mutation has prognostic value in patients with treatment-naive chronic lymphocytic leukemia
IGLV3-21R110 mutation has prognostic value in patients with treatment-naive chronic lymphocytic leukemia Open
Chronic lymphocytic leukemia (CLL) has high biological and clinical heterogeneity.1,2 A few prognostic factors are used in clinical practice, including immunoglobulin heavy-chain variable (IGHV) gene somatic hypermutation (SHM) status, chr…
View article: Comparing the value of mono- vs coculture for high-throughput compound screening in hematological malignancies
Comparing the value of mono- vs coculture for high-throughput compound screening in hematological malignancies Open
Large-scale compound screens are a powerful model system for understanding variability of treatment response and discovering druggable tumor vulnerabilities of hematological malignancies. However, as mostly performed in a monoculture of tu…
View article: Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia
Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia Open
Understanding the molecular and phenotypic heterogeneity of cancer is a prerequisite for effective treatment. For chronic lymphocytic leukemia (CLL), recurrent genetic driver events have been extensively cataloged, but this does not suffic…
View article: Negative feedback regulation of MAPK signaling is an important driver of CLL progression
Negative feedback regulation of MAPK signaling is an important driver of CLL progression Open
Despite several potent targeted treatments for chronic lymphocytic leukemia (CLL), the clinical challenge of treating drug-resistant disease is emerging. In this study, we discovered that the dual-specific phosphatases DUSP1 and DUSP6 are …
View article: Viral transduction of primary human lymphoma B cells reveals mechanisms of NOTCH-mediated immune escape
Viral transduction of primary human lymphoma B cells reveals mechanisms of NOTCH-mediated immune escape Open
View article: Proteogenomics refines the molecular classification of chronic lymphocytic leukemia
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia Open
Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic-based diagnostics. The relevance of proteomics for disease classifications rem…
View article: Inferring tumor-specific cancer dependencies through integrating ex vivo drug response assays and drug-protein profiling
Inferring tumor-specific cancer dependencies through integrating ex vivo drug response assays and drug-protein profiling Open
The development of cancer therapies may be improved by the discovery of tumor-specific molecular dependencies. The requisite tools include genetic and chemical perturbations, each with its strengths and limitations. Chemical perturbations …
View article: A gene expression assay based on chronic lymphocytic leukemia activation in the microenvironment to predict progression
A gene expression assay based on chronic lymphocytic leukemia activation in the microenvironment to predict progression Open
Several gene expression profiles with a strong correlation with patient outcomes have been previously described in chronic lymphocytic leukemia (CLL), although their applicability as biomarkers in clinical practice has been particularly li…