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List of works by Jian Ma

A Rewritable, Random-Access DNA-Based Storage System

scientific article

A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability

article

A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert

scientific article published on 01 February 2019

A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression

scientific article published on 04 February 2014

A new correlation clustering method for cancer mutation analysis

scientific article published on 18 August 2016

A postprandial FGF19-SHP-LSD1 regulatory axis mediates epigenetic repression of hepatic autophagy

scientific article published on 26 April 2017

ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins

scientific article

AhR and SHP regulate phosphatidylcholine and S-adenosylmethionine levels in the one-carbon cycle

scientific article published on 7 February 2018

Alignathon: a competitive assessment of whole-genome alignment methods

scientific article

Allele-Specific Quantification of Structural Variations in Cancer Genomes.

scientific article published on 20 July 2016

An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)

scientific article published on 01 August 2019

Analyses of pig genomes provide insight into porcine demography and evolution

scientific article

Ancient DNA analysis of mid-holocene individuals from the Northwest Coast of North America reveals different evolutionary paths for mitogenomes

scientific article published on 3 July 2013

BLESS 2: accurate, memory-efficient and fast error correction method.

scientific article published on 24 March 2016

BLESS: bloom filter-based error correction solution for high-throughput sequencing reads.

scientific article

Biomedical informatics and computational biology for high-throughput data analysis

scientific article published on 12 February 2014

CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity

scientific article published on 15 June 2020

CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci.

scientific article

Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee,

article

Comparative and demographic analysis of orang-utan genomes

scientific article

Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF

scientific article published on 01 June 2019

Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data

scientific article published on 20 June 2018

Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer

scientific article published on 25 June 2015

DawnRank: discovering personalized driver genes in cancer.

scientific article published on 31 July 2014

Discriminative bag-of-cells for imaging-genomics.

scientific article published in January 2018

Draft genome sequence of the Tibetan antelope

scientific article published on January 2013

Erratum: Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

scientific article published in Nature Communications

Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

scientific article published on 13 February 2019

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Exploiting sequence-based features for predicting enhancer-promoter interactions

scientific article published on July 2017

Fasting-induced FGF21 signaling activates hepatic autophagy and lipid degradation via JMJD3 histone demethylase

scientific article published on 10 February 2020

Fasting-induced JMJD3 histone demethylase epigenetically activates mitochondrial fatty acid β-oxidation

scientific article published on 18 June 2018

Finding the missing honey bee genes: lessons learned from a genome upgrade

scientific article

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.

scientific article

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax.

scientific article published on 3 June 2014

Greedy selection of species for ancestral state reconstruction on phylogenies: elimination is better than insertion

scientific article

Identifying gene regulatory network rewiring using latent differential graphical models.

scientific article

Identifying micro-inversions using high-throughput sequencing reads

scientific article published on 11 January 2016

Intestinal FGF15/19 physiologically repress hepatic lipogenesis in the late fed-state by activating SHP and DNMT3A

scientific article published on 24 November 2020

Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2.

scientific article

LncRNA-mediated regulation of SOX9 expression in basal subtype breast cancer cells

scientific article published on 05 November 2019

Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex.

scientific article published on 18 April 2018

MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome

scientific article published on 06 January 2020

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler.

scientific article published on 28 August 2018

MicroRNA-210 Promotes Bile Acid-Induced Cholestatic Liver Injury by Targeting Mixed-Lineage Leukemia-4 Methyltransferase in Mice

scientific article published on 24 September 2019

Mulan: multiple-sequence local alignment and visualization for studying function and evolution

scientific article

Multiscale and integrative single-cell Hi-C analysis with Higashi

scientific article published on 11 October 2021

Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee.

scientific article

Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome

scientific article published in 2022

PSAR-align: improving multiple sequence alignment using probabilistic sampling.

scientific article

PSAR: measuring multiple sequence alignment reliability by probabilistic sampling.

scientific article

PSIP1/p75 promotes tumorigenicity in breast cancer cells by promoting the transcription of cell cycle genes

scientific article published on 17 June 2017

Personalized ovarian cancer disease surveillance and detection of candidate therapeutic drug target in circulating tumor DNA.

scientific article published on January 2014

Predicting CTCF-mediated chromatin loops using CTCF-MP.

scientific article published in July 2018

Privacy Challenges of Genomic Big Data.

scientific article published in January 2017

RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee

scientific article

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.

scientific article

Reconstructing the history of large-scale genomic changes: biological questions and computational challenges.

scientific article published on 12 May 2011

Reconstruction and evolutionary history of eutherian chromosomes

scientific article

Reference-assisted chromosome assembly ⬇️

scientific article published on January 10, 2013

Replication Timing Becomes Intertwined with 3D Genome Organization

scientific article published on 01 February 2019

Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions

scientific article published on 07 November 2019

Rotation equivariant and invariant neural networks for microscopy image analysis

scientific article published on 01 July 2019

SPIN reveals genome-wide landscape of nuclear compartmentalization

scientific article published on 14 January 2021

Search for chromosome rearrangements: New approaches toward discovery of novel translocations in head and neck squamous cell carcinoma ⬇️

scientific article published on July 17, 2012

Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription

scientific article published on 29 April 2022

Single-molecule analysis reveals widespread structural variation in multiple myeloma.

scientific article published on 8 June 2015

TIGER: tiled iterative genome assembler

scientific article

TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

scientific article published on 18 December 2020

The yak genome and adaptation to life at high altitude

scientific article

Toward Recovering Allele-specific Cancer Genome Graphs

scientific article published on 16 April 2018

Transcriptional regulation of autophagy by an FXR-CREB axis

scientific article

UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing.

scientific article

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