Author details

Full Name

Jian Ma

Affiliation

ORCID

Career Start Year

2005

Papers

107

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37163136	UNADON: Transformer-based model to predict genome-wide chromosome spatial position.		2023
37845234	Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.	Nat Commun	2023
37873233	PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning.		2023
37961445	Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types.	bioRxiv	2023
37387176	UNADON: transformer-based model to predict genome-wide chromosome spatial position.		2023
36871158	Compartmentalization with nuclear landmarks yields random, yet precise, genome organization.		2023
36624346	SPICEMIX enables integrative single-cell spatial modeling of cell identity.		2023
37238637	CVAM: CNA Profile Inference of the Spatial Transcriptome Based on the VGAE and HMM.		2023
37292994	scGHOST: Identifying single-cell 3D genome subcompartments.		2023
37546900	Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells.		2023
37419111	Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.	Mol Cell	2023
34635838	Multiscale and integrative single-cell Hi-C analysis with Higashi.	Nature Biotechnology	2022
35962045	Author Correction: Comparative and demographic analysis of orang-utan genomes.	Nature	2022
35686465	Feeding activates FGF15-SHP-TFEB-mediated lipophagy in the gut.	EMBO Journal	2022
35486737	Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription.	Sci Adv	2022
35864167	Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome.	Nat Methods	2022
36265466	Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi.		2022
35241841	Author Correction: Multiscale and integrative single-cell Hi-C analysis with Higashi.	Nature Biotechnology	2022
34465168	The 3D Genome Structure of Single Cells.		2021
33446254	SPIN reveals genome-wide landscape of nuclear compartmentalization.	Genome Biol	2021
33711014	Assessing the contribution of tumor mutational phenotypes to cancer progression risk.	PLoS Computational Biology	2021
33355299	TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes.	Genome Research	2021
31549733	MicroRNA-210 Promotes Bile Acid-Induced Cholestatic Liver Injury by Targeting Mixed-Lineage Leukemia-4 Methyltransferase in Mice.	Hepatology	2020
31647422	A Multi-Organ Nucleus Segmentation Challenge.	IEEE Trans Med Imaging	2020
31907193	MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome.	Genome Research	2020
31690584	LncRNA-mediated regulation of expression in basal subtype breast cancer cells.	RNA	2020
32550271	MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning.		2020
32541958	CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity.	Nat Biotechnol	2020
33235221	Intestinal FGF15/19 physiologically repress hepatic lipogenesisÂ in the late fed-state by activating SHP and DNMT3A.	Nature Communications	2020
32962144	COL2A1 Is a Novel Biomarker of Melanoma Tumor Repopulating Cells.	Biomedicines	2020
33013452	Neural Network Deconvolution Method for Resolving Pathway-Level Progression of Tumor Clonal Expression Programs With Application to Breast Cancer Brain Metastases.	Frontiers in Physiology	2020
32675111	Antagonism between splicing and microprocessor complex dictates the serum-induced processing of lnc-<i>MIRHG</i> for efficient cell cycle reentry.	RNA	2020
32657413	Cancer mutational signatures representation by large-scale context embedding.		2020
32657393	Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis.		2020
31367745	An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi).	Gigascience	2019
31699985	Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions.	Nature Communications	2019
34113473	Predicting enhancer-promoter interaction from genomic sequence with deep neural networks.	Quantitative Biology	2019
30649288	A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert.	Gigascience	2019
31510662	Rotation equivariant and invariant neural networks for microscopy image analysis.		2019
30760546	Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.	Genome Res	2019
31229558	Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.	Cell Syst	2019
30735630	Replication Timing Becomes Intertwined with 3D Genome Organization.	Cell	2019
30792192	Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, <i>Apis mellifera</i>.	G3 (Bethesda)	2019
29416063	AhR and SHP regulate phosphatidylcholine and S-adenosylmethionine levels in the one-carbon cycle.	Nature Communications	2018
29936186	Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.	Cell Systems	2018
30154186	Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler.	J Cell Biol	2018
30496290	A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability.	PLoS Genetics	2018
29912475	CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci.	Nucleic Acids Research	2018
29911994	Fasting-induced JMJD3 histone demethylase epigenetically activates mitochondrial fatty acid Î²-oxidation.	Journal of Clinical Investigation	2018
29949986	Predicting CTCF-mediated chromatin loops using CTCF-MP.		2018