Search Publications
2025 Publications
. 2025.
TMPO promotes cellular dissemination and metastasis in circulating tumor cells..
bioRxiv : the preprint server for biology.
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. 2025.
TMPO promotes cellular dissemination and metastasis in circulating tumor cells..
bioRxiv : the preprint server for biology.
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. 2025.
Lipidomic changes in persister cancer cells drive enhanced ferroptosis sensitivity..
Ferroptosis and oxidative stress.
1
(1)
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. 2025.
Primate-specific adaptation of Ku protects transcriptomic integrity by suppressing Alu-mediated alternative splicing..
bioRxiv : the preprint server for biology.
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. 2025.
A neuron type-specific microexon in /ankyrin-G modulates calcium activity and neuronal excitability..
bioRxiv : the preprint server for biology.
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. 2025.
Determinants of sensitivity to HER2-targeted antibody drug conjugates in urothelial cancer..
Nature communications.
17
(1)
:919
▶ Go to Pubmed
. 2025.
Comparative metagenomics using pan-metagenomic graphs..
bioRxiv : the preprint server for biology.
▶ Go to Pubmed
. 2025.
MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data..
Microbiome.
14
(1)
:28
▶ Go to Pubmed
. 2025.
A generalizable cross-continent prediction of esophageal squamous cell carcinoma using the oral microbiome..
bioRxiv : the preprint server for biology.
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. 2025.
selectively governs hematopoietic stem cell self-renewal by regulating proteostasis..
Science advances.
11
(49)
:eaea7451
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. 2025.
Towards Clinical Translation: Establishing Optimal Dose and Dose-Rate Parameters for the FLASH Skin-Sparing Effect..
Dose-response : a publication of International Hormesis Society.
23
(4)
:15593258251401947
▶ Go to Pubmed
. 2025.
Deciphering the role of complement system genes in pancreatic cancer susceptibility and prognosis..
Nature communications.
16
(1)
:10769
▶ Go to Pubmed
. 2025.
Distributional bias compromises leave-one-out cross-validation..
Science advances.
11
(48)
:eadx6976
▶ Go to Pubmed
. 2025.
Colibactin-producing promote carcinogenesis of gastroesophageal adenocarcinoma and simultaneously induce autophagy and differentiation..
bioRxiv : the preprint server for biology.
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. 2025.
Macroecological Laws Can Naturally Arise from Chaotic Internal Species Dynamics..
bioRxiv : the preprint server for biology.
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. 2025.
MotifAE Reveals Functional Sequence Patterns from Protein Language Model: Unsupervised Discovery and Interpretability Analysis..
bioRxiv : the preprint server for biology.
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. 2025.
Molecular Systems Biology at 20: reflecting on the past, envisioning the future..
Molecular systems biology.
21
(12)
:1667-1673
▶ Go to Pubmed
. 2025.
Combinatorial protein engineering identifies potent CRISPR activators with reduced toxicity..
Nature communications.
16
(1)
:11114
▶ Go to Pubmed
. 2025.
Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut..
Nature biotechnology.
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. 2025.
Engineered probiotic restores GLP-1 signaling to ameliorate fiber-deficiency exacerbated colitis..
Science advances.
11
(45)
:eadx6869
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. 2025.
TDP-43-dependent mis-splicing of KCNQ2 triggers intrinsic neuronal hyperexcitability in ALS/FTD..
Nature neuroscience.
28
(12)
:2476-2492
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. 2025.
Accurate affinity models for SH2 domains from peptide binding assays and free-energy regression..
Protein science : a publication of the Protein Society.
34
(11)
:e70317
▶ Go to Pubmed
. 2025.
Mitochondrial Lon Peptidase 1 Controls Diaphragm and Lung Development in a Context-Dependent Manner..
Journal of respiratory biology and translational medicine.
2
(3)
▶ Go to Pubmed
. 2025.
Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability..
bioRxiv : the preprint server for biology.
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. 2025.
Convection-enhanced delivery of dexamethasone in glioma suppresses myeloid inflammation while avoiding systemic toxicities..
bioRxiv : the preprint server for biology.
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. 2025.
Developments and Opportunities in Temperature-Responsive Thermal Smart Materials..
Advanced materials (Deerfield Beach, Fla.).
:e09337
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. 2025.
Identification of Sample Processing Errors in Microbiome Studies Using Host Genetic Profiles..
bioRxiv : the preprint server for biology.
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. 2025.
Factors Influencing Bile Leakage and Incisional Infection Post Choledocholithotomy: An Analysis Based on 621 Patients..
European surgical research. Europaische chirurgische Forschung. Recherches chirurgicales europeennes.
:1-20
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. 2025.
The Role of Recruited Adipose Stromal Cells and Their Fibroblastic Differentiation in Cancer..
Frontiers in bioscience (Landmark edition).
30
(8)
:36559
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. 2025.
Morphogenesis and regeneration share a conserved core transition cell state program that controls lung epithelial cell fate..
Developmental cell.
60
(18)
:2533
▶ Go to Pubmed
. 2025.
A Simple data-driven dietary pattern associated with lower risk for adverse pregnancy outcomes..
American journal of obstetrics & gynecology MFM.
7
(11)
:101773
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. 2025.
Predicting the DNA binding specificity of transcription factor mutants using family-level biophysically interpretable machine learning..
Nucleic acids research.
53
(16)
▶ Go to Pubmed
. 2025.
Multimodal learning decodes the global binding landscape of chromatin-associated proteins..
bioRxiv : the preprint server for biology.
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. 2025.
Redefining druggable targets with artificial intelligence..
Nature biotechnology.
43
(9)
:1416-1418
▶ Go to Pubmed
. 2025.
Alpha-synuclein abundance and localization are regulated by the RNA-binding protein PUMILIO1..
Cell reports.
44
(8)
:116145
▶ Go to Pubmed
. 2025.
Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age..
Nature immunology.
26
(9)
:1612-1625
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. 2025.
Noise-driven morphogenesis independent of transcriptional regulatory programs..
bioRxiv : the preprint server for biology.
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. 2025.
Transcriptome sequencing of Hodgkin lymphoma Hodgkin and Reed-Sternberg cells reveals escape from NK cell recognition and an unfolded protein response..
bioRxiv : the preprint server for biology.
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. 2025.
Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas..
The Journal of clinical investigation.
135
(20)
▶ Go to Pubmed
. 2025.
Understanding Language Model Scaling on Protein Fitness Prediction..
bioRxiv : the preprint server for biology.
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. 2025.
PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context..
Nature communications.
16
(1)
:7189
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. 2025.
The spatial landscape of glial pathology and T cell response in Parkinson's disease substantia nigra..
Nature communications.
16
(1)
:7146
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. 2025.
Aberrant pace of cortical neuron development in brain organoids from patients with 22q11.2 deletion syndrome-associated schizophrenia..
Nature communications.
16
(1)
:6986
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. 2025.
Protocol for automated graph-based clustering of single-cell RNA-seq data with application in mouse intestinal stem cells..
STAR protocols.
6
(3)
:104000
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. 2025.
Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord..
Acta neuropathologica.
150
(1)
:10
▶ Go to Pubmed
. 2025.
Precise virulence inactivation using a CRISPR-associated transposase for combating Enterobacteriaceae gut pathogens..
Nature biomedical engineering.
9
(12)
:2017-2027
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. 2025.
Differential Predictability of Preterm Birth Types: Strong Signals for Indicated Cases versus Limited Success in Spontaneous Preterm Birth..
medRxiv : the preprint server for health sciences.
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. 2025.
Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs..
Nucleic acids research.
53
(13)
▶ Go to Pubmed
. 2025.
Integrating structural homology with deep learning to achieve highly accurate protein-protein interface prediction for the human interactome..
bioRxiv : the preprint server for biology.
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. 2025.
Adaptation by stochastic tuning of gene expression in mammalian cells..
bioRxiv : the preprint server for biology.
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. 2025.
G2VTCR: predicting antigen binding specificity by Weisfeiler-Lehman graph embedding of T cell receptor sequences..
bioRxiv : the preprint server for biology.
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. 2025.
A computational framework for mapping isoform landscape and regulatory mechanisms from spatial transcriptomics data..
bioRxiv : the preprint server for biology.
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. 2025.
Genome sequencing is critical for forecasting outcomes following congenital cardiac surgery..
Nature communications.
16
(1)
:6365
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. 2025.
ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets..
Nature communications.
16
(1)
:5852
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. 2025.
Genomic landscape of virus-associated cancers..
Nature communications.
16
(1)
:5887
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. 2025.
A Spectral Interpretable Bearing Fault Diagnosis Framework Powered by Large Language Models..
Sensors (Basel, Switzerland).
25
(12)
▶ Go to Pubmed
. 2025.
Reverse engineering neuron-type-specific and type-orthogonal splicing-regulatory networks using diverse cellular transcriptomes..
Cell reports.
44
(7)
:115898
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. 2025.
Reverse engineering neuron-type-specific and type-orthogonal splicing-regulatory networks using diverse cellular transcriptomes..
Cell reports.
44
(7)
:115898
▶ Go to Pubmed
. 2025.
Systematic identification and targeting of master regulator checkpoints (MRC) governing tumor microenvironment-mediated immune evasion..
Journal for immunotherapy of cancer.
13
(6)
▶ Go to Pubmed
. 2025.
Guidelines for preventing and reporting contamination in low-biomass microbiome studies..
Nature microbiology.
10
(7)
:1570-1580
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. 2025.
Tissue signatures of human macrophages during homeostasis and activation..
bioRxiv : the preprint server for biology.
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. 2025.
Quantitative molecular cartography of emergency myelopoiesis reveals conserved modules of hematopoietic activation..
bioRxiv : the preprint server for biology.
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. 2025.
Combination regimen of intravesical docetaxel, gemcitabine, and cisplatin in patients with BCG-unresponsive bladder cancer: clinical outcomes and genomic correlations..
Urologic oncology.
43
(10)
:594.e1-594.e7
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. 2025.
Combining structural modeling and deep learning to calculate the protein interactome and functional networks..
bioRxiv : the preprint server for biology.
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. 2025.
Molecular dynamics simulations of intrinsically disordered protein regions enable biophysical interpretation of variant effect predictors..
bioRxiv : the preprint server for biology.
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. 2025.
HDAC inhibitors engage MITF and the disease-associated microglia signature to enhance amyloid β uptake..
Brain, behavior, and immunity.
129
:279-293
▶ Go to Pubmed
. 2025.
Astrocyte morphogenesis requires self-recognition..
Nature.
644
(8075)
:164-172
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. 2025.
Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in Xenopus trachea-esophageal morphogenesis..
Developmental cell.
60
(18)
:2487-2502.e4
▶ Go to Pubmed
. 2025.
Regulatory network analysis of Dclk1 gene expression reveals a tuft cell-ILC2 axis that inhibits pancreatic tumor progression..
Cell reports.
44
(6)
:115734
▶ Go to Pubmed
. 2025.
A probabilistic graphical model for estimating selection coefficients of nonsynonymous variants from human population sequence data..
Nature communications.
16
(1)
:4670
▶ Go to Pubmed
. 2025.
Identification and targeting of regulators of SARS-CoV-2-host interactions in the airway epithelium..
Science advances.
11
(20)
:eadu2079
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. 2025.
Identification and targeting of regulators of SARS-CoV-2-host interactions in the airway epithelium..
Science advances.
11
(20)
:eadu2079
▶ Go to Pubmed
. 2025.
Phase II Study of Pexidartinib Plus Sirolimus in Unresectable Malignant Peripheral Nerve Sheath Tumors Identifies M2 Macrophage Activation..
JCO oncology advances.
2
(1)
:e2400083
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. 2025.
mA alters ribosome dynamics to initiate mRNA degradation..
Cell.
188
(14)
:3728-3743.e20
▶ Go to Pubmed
. 2025.
Compositional transformations can reasonably introduce phenotype-associated values into sparse features..
mSystems.
10
(5)
:e0002125
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. 2025.
Compositional transformations can reasonably introduce phenotype-associated values into sparse features..
mSystems.
:e0002125
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. 2025.
Simultaneous determination of cations in nuclear power plant water by conductometric ion chromatography equipped with fluorescence detector..
Journal of chromatography. A.
1752
:465984
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. 2025.
Conserved genetic basis for microbial colonization of the gut..
Cell.
188
(10)
:2823-2824
▶ Go to Pubmed
. 2025.
Illuminating the Noncoding Genome in Cancer using Artificial Intelligence..
Cancer research.
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. 2025.
Rare mutations implicate CGE interneurons as a vulnerable axis of cognitive deficits across psychiatric disorders..
bioRxiv : the preprint server for biology.
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. 2025.
The regulatory architecture of the primed pluripotent cell state..
Nature communications.
16
(1)
:3351
▶ Go to Pubmed
. 2025.
Genetic Risk and First-Trimester Cardiovascular Health Predict Hypertensive Disorders of Pregnancy in Nulliparous Women..
Journal of the American College of Cardiology.
85
(14)
:1488-1500
▶ Go to Pubmed
. 2025.
A factor-based analysis of individual human microglia uncovers regulators of an Alzheimer-related transcriptional signature..
bioRxiv : the preprint server for biology.
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. 2025.
Conserved genetic basis for microbial colonization of the gut..
Cell.
188
(9)
:2505-2520.e22
▶ Go to Pubmed
. 2025.
Conserved genetic basis for microbial colonization of the gut..
Cell.
188
(9)
:2505-2520.e22
▶ Go to Pubmed
. 2025.
Ultrasound-MRI Agreement in Individuals Undergoing Surveillance of Fontan-associated Liver Disease..
Journal of computer assisted tomography.
49
(5)
:705-713
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. 2025.
Latest possible timing for endoscopic-assisted intervention in capsule endoscopy..
Gastroenterology report.
13
:goaf011
▶ Go to Pubmed
. 2025.
Latest possible timing for endoscopic-assisted intervention in capsule endoscopy..
Gastroenterology report.
13
:goaf011
▶ Go to Pubmed
. 2025.
Targeting Monoallelic / Mutations in Germinal Center-Derived B-Cell Lymphoma with a First-in-Class Histone Acetyltransferase Activator..
bioRxiv : the preprint server for biology.
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. 2025.
A niche driven mechanism determines response and a mutation-independent therapeutic approach for myeloid malignancies..
Cancer cell.
43
(6)
:1007-1024.e13
▶ Go to Pubmed
. 2025.
Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models..
Nature microbiology.
10
(4)
:897-911
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. 2025.
Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models..
Nature microbiology.
10
(4)
:897-911
▶ Go to Pubmed
. 2025.
A patient-derived T cell lymphoma biorepository uncovers pathogenetic mechanisms and host-related therapeutic vulnerabilities..
Cell reports. Medicine.
6
(4)
:102029
▶ Go to Pubmed
. 2025.
A patient-derived T cell lymphoma biorepository uncovers pathogenetic mechanisms and host-related therapeutic vulnerabilities..
Cell reports. Medicine.
6
(4)
:102029
▶ Go to Pubmed
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