Michael Q Zhang
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Computer Science
Michael Q Zhang's Degrees
- PhD Computer Science Stanford University
- Masters Computer Science Stanford University
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(Suggest an Edit or Addition)Michael Q Zhang's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Integrative analysis of 111 reference human epigenomes (2015) (4979)
- Combinatorial patterns of histone acetylations and methylations in the human genome (2008) (2263)
- ESEfinder: a web resource to identify exonic splicing enhancers (2003) (1574)
- Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome (2007) (1051)
- The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. (2002) (916)
- CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function (2015) (775)
- Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications (2010) (673)
- Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells (2013) (670)
- A long nuclear‐retained non‐coding RNA regulates synaptogenesis by modulating gene expression (2010) (656)
- Network-based global inference of human disease genes (2008) (650)
- Regulating Gene Expression through RNA Nuclear Retention (2005) (648)
- A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells (2003) (561)
- NONCODE 2016: an informative and valuable data source of long non-coding RNAs (2015) (505)
- An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. (2006) (499)
- Critical roles for Dicer in the female germline. (2007) (499)
- A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes (2001) (491)
- Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing (2006) (479)
- SCPD: a promoter database of the yeast Saccharomyces cerevisiae (1999) (472)
- Direct coupling of the cell cycle and cell death machinery by E2F (2002) (458)
- An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia (2009) (439)
- Use of Chromatin Immunoprecipitation To Clone Novel E2F Target Promoters (2001) (401)
- Large-scale structure of genomic methylation patterns. (2005) (370)
- Using quality scores and longer reads improves accuracy of Solexa read mapping (2008) (366)
- NONCODEV5: a comprehensive annotation database for long non-coding RNAs (2017) (333)
- HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. (2014) (329)
- Allelic reprogramming of 3D chromatin architecture during early mammalian development (2017) (324)
- BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data (2013) (322)
- TRED: a transcriptional regulatory element database, new entries and other development (2007) (319)
- Large-scale human promoter mapping using CpG islands (2000) (291)
- Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. (2008) (290)
- Computational prediction of eukaryotic protein-coding genes (2002) (268)
- Recurrently deregulated lncRNAs in hepatocellular carcinoma (2017) (256)
- Novel Foxo1-dependent transcriptional programs control Treg cell function (2012) (255)
- Exonic Splicing Enhancer Motif Recognized by Human SC35 under Splicing Conditions (2000) (244)
- Genome-wide map of regulatory interactions in the human genome (2014) (242)
- Computational identification of promoters and first exons in the human genome (2001) (237)
- High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. (2009) (231)
- Development of the human cancer microRNA network (2010) (230)
- Determination of enriched histone modifications in non-genic portions of the human genome (2009) (230)
- TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies (2004) (210)
- In Situ Capture of Chromatin Interactions by Biotinylated dCas9 (2017) (207)
- Integrative analysis of haplotype-resolved epigenomes across human tissues (2015) (205)
- Evaluation and comparison of clustering algorithms in analyzing es cell gene expression data (2002) (200)
- Comparative transcriptome profiling of the human and mouse dorsal root ganglia: An RNA-seq-based resource for pain and sensory neuroscience research (2017) (197)
- A weight array method for splicing signal analysis (1993) (196)
- Updates to the RMAP short-read mapping software (2009) (185)
- Novel Foxo 1 – dependent transcriptional programs control T reg cell function (2013) (176)
- Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription (2019) (166)
- Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain (2012) (165)
- Identifying tissue-selective transcription factor binding sites in vertebrate promoters. (2005) (163)
- Computational prediction of methylation status in human genomic sequences. (2006) (162)
- Identifying cooperativity among transcription factors controlling the cell cycle in yeast. (2003) (159)
- The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. (2013) (155)
- Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes (2005) (153)
- Identifying combinatorial regulation of transcription factors and binding motifs (2004) (144)
- Purification and characterization of human RNPS1: a general activator of pre‐mRNA splicing (1999) (144)
- Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery. (2015) (139)
- Interacting models of cooperative gene regulation. (2004) (137)
- Current Topics in Computational Molecular Biology (2002) (135)
- DNA motifs in human and mouse proximal promoters predict tissue-specific expression. (2006) (130)
- SCALE method for single-cell ATAC-seq analysis via latent feature extraction (2019) (127)
- Co‐inhibitory Molecule B7 Superfamily Member 1 Expressed by Tumor‐Infiltrating Myeloid Cells Induces Dysfunction of Anti‐tumor CD8+ T Cells (2018) (127)
- Similarity of position frequency matrices for transcription factor binding sites (2005) (125)
- Interferon regulatory factors are transcriptional regulators of adipogenesis. (2008) (123)
- Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. (2007) (120)
- OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds (2013) (115)
- Reconstructing cell cycle pseudo time-series via single-cell transcriptome data (2017) (115)
- Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4 (2014) (113)
- The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development (2013) (113)
- Mining ChIP-chip data for transcription factor and cofactor binding sites (2005) (105)
- Activity-dependent FUS dysregulation disrupts synaptic homeostasis (2014) (104)
- RNA landscape of evolution for optimal exon and intron discrimination (2008) (104)
- Predicting methylation status of CpG islands in the human brain (2006) (104)
- High-resolution human core-promoter prediction with CoreBoost_HM. (2009) (104)
- Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit (2015) (103)
- Profiling alternatively spliced mRNA isoforms for prostate cancer classification (2006) (101)
- Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer (2011) (98)
- CD36-dependent Regulation of Muscle FoxO1 and PDK4 in the PPARδ/β-mediated Adaptation to Metabolic Stress* (2008) (97)
- CGmapTools improves the precision of heterozygous SNV calls and supports allele‐specific methylation detection and visualization in bisulfite‐sequencing data (2018) (97)
- Statistical significance of cis-regulatory modules (2007) (97)
- Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification (2015) (95)
- Regulation of the PDK4 Isozyme by the Rb-E2F1 Complex* (2008) (94)
- SpliceTrap: a method to quantify alternative splicing under single cellular conditions (2011) (93)
- Poly A- Transcripts Expressed in HeLa Cells (2008) (90)
- DNA methylation data analysis and its application to cancer research. (2013) (89)
- Chd5 orchestrates chromatin remodelling during sperm development (2014) (88)
- Super-resolution dipole orientation mapping via polarization demodulation (2016) (85)
- PAF1 regulation of promoter-proximal pause release via enhancer activation (2017) (83)
- Functional genomics as applied to mapping transcription regulatory networks. (2002) (81)
- ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis (2016) (80)
- Neural Potential of a Stem Cell Population in the Hair Follicle (2007) (79)
- Adaptively inferring human transcriptional subnetworks (2006) (78)
- Epigenome-wide association of liver methylation patterns and complex metabolic traits in mice. (2015) (78)
- Genome-wide promoter extraction and analysis in human, mouse, and rat (2005) (73)
- A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome (2006) (71)
- Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. (2009) (69)
- Design and bioinformatics analysis of genome-wide CLIP experiments (2015) (69)
- Tissue-specific regulatory elements in mammalian promoters (2007) (66)
- Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development (2011) (66)
- Promoter Analysis of Co-regulated Genes in the Yeast Genome (1999) (65)
- CDKN2A/p16 Inactivation Mechanisms and Their Relationship to Smoke Exposure and Molecular Features in Non–Small-Cell Lung Cancer (2013) (65)
- Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data (2012) (64)
- ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor (2011) (63)
- From worm to human: bioinformatics approaches to identify FOXO target genes (2005) (60)
- Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain (2012) (59)
- Histone methylation marks play important roles in predicting the methylation status of CpG islands. (2008) (55)
- BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions (2017) (53)
- Genome-wide prediction and analysis of function-specific transcription factor binding sites (2004) (53)
- Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells (2013) (52)
- Identification of Synaptic Targets of Drosophila Pumilio (2008) (51)
- Computing exact P-values for DNA motifs (2007) (49)
- Algorithmic Approaches to Clustering Gene Expression Data (2002) (44)
- FIND: difFerential chromatin INteractions Detection using a spatial Poisson process (2018) (44)
- Neighbor number, valley seeking and clustering (2007) (44)
- Identification of Novel Androgen-Regulated Pathways and mRNA Isoforms through Genome-Wide Exon-Specific Profiling of the LNCaP Transcriptome (2011) (41)
- Differential connectivity of splicing activators and repressors to the human spliceosome (2015) (41)
- A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information (2011) (41)
- Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells (2008) (40)
- Quantitative combination of natural anti-oxidants prevents metabolic syndrome by reducing oxidative stress (2015) (40)
- Dual-specificity splice sites function alternatively as 5′ and 3′ splice sites (2007) (39)
- SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles (2019) (39)
- Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation. (2016) (39)
- Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression (2011) (39)
- SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment (2020) (38)
- DWE: Discriminating Word Enumerator (2005) (38)
- Emergent Lévy behavior in single-cell stochastic gene expression. (2017) (38)
- Boosting with stumps for predicting transcription start sites (2007) (37)
- Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes (2011) (37)
- Network embedding-based representation learning for single cell RNA-seq data (2017) (37)
- Computational comparison of two mouse draft genomes and the human golden path (2002) (36)
- Computational analyses of eukaryotic promoters (2007) (35)
- New Fusion Transcripts Identified in Normal Karyotype Acute Myeloid Leukemia (2012) (34)
- Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro (2014) (34)
- Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing (2015) (33)
- Gene set-based module discovery in the breast cancer transcriptome (2009) (32)
- Global transcriptional activity dynamics reveal functional enhancer RNAs (2018) (31)
- Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes (2019) (31)
- The landscape of RNA polymerase II associated chromatin interactions in prostate cancer. (2020) (31)
- Major Chromosomal Breakpoint Intervals in Breast Cancer Co-Localize with Differentially Methylated Regions (2012) (31)
- A common set of distinct features that characterize noncoding RNAs across multiple species (2014) (30)
- MTGIpick allows robust identification of genomic islands from a single genome (2016) (30)
- Purification and characterization of human RNPS 1 : a general activator of pre-mRNA splicing (1999) (29)
- Population dynamics of cancer cells with cell state conversions (2013) (29)
- De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles (2016) (29)
- Inferring Gene Regulatory Networks (2008) (28)
- Stochastic fluctuations can reveal the feedback signs of gene regulatory networks at the single-molecule level (2017) (28)
- The transcriptome of human CD34+ hematopoietic stem-progenitor cells (2009) (28)
- OSCAR: One-class SVM for accurate recognition of cis-elements (2007) (28)
- Computational Methods for Protein Folding: Scaling a Hierarchy of Complexities (2002) (28)
- Relaxation rates of gene expression kinetics reveal the feedback signs of autoregulatory gene networks (2018) (28)
- Correlated evolution of transcription factors and their binding sites (2011) (27)
- Extracting functional information from microarrays: A challenge for functional genomics (2002) (27)
- Developing novel methods to image and visualize 3D genomes (2018) (26)
- MICC: an R package for identifying chromatin interactions from ChIA-PET data (2015) (26)
- HiCDB: a sensitive and robust method for detecting contact domain boundaries (2018) (26)
- Discriminant Analysis and Its Application in DNA Sequence Motif Recognition (2000) (25)
- A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. (2006) (25)
- Single-cell stochastic gene expression kinetics with coupled positive-plus-negative feedback. (2019) (25)
- Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species (2008) (24)
- Finding Genes by Computer: Probabilistic and Discriminative Approaches (2002) (24)
- ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks (2015) (24)
- Putative Zinc Finger Protein Binding Sites Are Over-Represented in the Boundaries of Methylation-Resistant CpG Islands in the Human Genome (2007) (24)
- MyoD is a 3D genome structure organizer for muscle cell identity (2022) (23)
- Evolutionary impact of limited splicing fidelity in mammalian genes. (2007) (22)
- EpiRegNet: Constructing epigenetic regulatory network from high throughput gene expression data for humans (2011) (22)
- Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT) (2016) (22)
- Scanning the human genome at kilobase resolution. (2008) (21)
- 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process (2015) (20)
- Web3DMol: interactive protein structure visualization based on WebGL (2017) (20)
- Computational Identification of Active Enhancers in Model Organisms (2013) (19)
- FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer (2013) (19)
- Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure (2008) (19)
- Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073 (2015) (19)
- Sox2 and Klf4 as the Functional Core in Pluripotency Induction without Exogenous Oct4. (2019) (19)
- Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9 (2020) (19)
- 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome (2020) (18)
- EVALUATION AND COMPARISON OF CLUSTERING ALGORITHMS IN ANGLYZING ES CELL GENE EXPRESSION DATA (2003) (18)
- Computational prediction of novel components of lung transcriptional networks (2007) (18)
- Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation (2018) (18)
- The mouse genome: experimental examination of gene predictions and transcriptional start sites. (2004) (17)
- A novel epigenetic AML1‐ETO/THAP10/miR‐383 mini‐circuitry contributes to t(8;21) leukaemogenesis (2017) (17)
- Computational Structural Biology (2002) (16)
- Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes (2001) (16)
- Transcription factor binding element detection using functional clustering of mutant expression data. (2004) (16)
- FAT10 Is Critical in Influenza A Virus Replication by Inhibiting Type I IFN (2016) (15)
- The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence (2021) (15)
- Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions (2014) (14)
- A highly conserved regulatory element controls hematopoietic expression of GATA-2 in zebrafish (2007) (14)
- HiC-3DViewer: a new tool to visualize Hi-C data in 3D space (2017) (14)
- MIROR: a method for cell-type specific microRNA occupancy rate prediction. (2014) (14)
- Computational Methods for Promoter Recognition (2002) (14)
- Regulation of the PDK 4 Isozyme by the RbE 2 F 1 Complex * (2008) (14)
- Evidence and characteristics of putative human α recombination hotspots (2004) (14)
- Analysis and visualization of DNA spectrograms: open possibilities for the genome research (2006) (14)
- A novel method to identify topological domains using Hi-C data (2015) (14)
- Regulation by competition: a hidden layer of gene regulatory network (2018) (14)
- HCSGD: An integrated database of human cellular senescence genes. (2017) (13)
- Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers (2016) (13)
- CDKN 2 A / p 16 Inactivation Mechanisms and Their Relationship to Smoke Exposure and Molecular Features in Non – Small-Cell Lung Cancer (2013) (13)
- Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence (2018) (12)
- Computer software to find genes in plant genomic DNA. (2003) (12)
- Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. (2014) (12)
- GFScan: a gene family search tool at genomic DNA level. (2002) (11)
- Computing exact p-values for DNA motifs ( Part I ) (2006) (11)
- Polarization-based super-resolution imaging of surface-enhanced Raman scattering nanoparticles with orientational information. (2018) (11)
- Prediction of transcription start sites based on feature selection using AMOSA. (2007) (11)
- Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development (2020) (11)
- Phylogenetics and the Quartet Method (2002) (11)
- Integrative Genomic Analysis of Gemcitabine Resistance in Pancreatic Cancer by Patient-derived Xenograft Models (2021) (11)
- Pan‐genome isolation of low abundance transcripts using SAGE tag (2006) (11)
- LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency (2020) (10)
- Prioritizing Disease Genes and Understanding Disease Pathways (2012) (10)
- High-Order Interactions in Rheumatoid Arthritis Detected by Bayesian Method using Genome-Wide Association Studies Data (2012) (10)
- Predictive models of gene regulation: application of regression methods to microarray data. (2007) (10)
- Molecular basis for histone H3 “K4me3-K9me3/2” methylation pattern readout by Spindlin1 (2020) (9)
- Evidence and characteristics of putative human alpha recombination hotspots. (2004) (9)
- factors Fox-1 and Fox-2 Defining the regulatory network of the tissue-specific splicing Material Supplemental (2008) (9)
- CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming. (2022) (9)
- Regulatory elements of Caenorhabditis elegans ribosomal protein genes (2012) (9)
- Identifying the 3'-terminal exon in human DNA (2001) (9)
- CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9 (2018) (9)
- 3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia (2021) (9)
- DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes (2017) (9)
- Deciphering hierarchical organization of topologically associated domains through change-point testing (2021) (8)
- ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks (2014) (8)
- Algorithmic Methods for Multiple Sequence Alignment (2002) (8)
- A Bayesian Method for Disentangling Dependent Structure of Epistatic Interaction (2012) (8)
- Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index (2021) (8)
- Bio-Sequence Comparison and Applications (2002) (8)
- Assembly and Validation of Versatile Transcription Activator-Like Effector Libraries (2014) (8)
- Datamining: Discovering Information from Bio-Data (2002) (7)
- The Seventh Asia Pacific Bioinformatics Conference (APBC2009) (2009) (7)
- Integrative molecular analysis of metastatic hepatocellular carcinoma (2019) (7)
- Bayesian Modeling and Computation in Bioinformatics Research (2002) (7)
- Developing bioimaging and quantitative methods to study 3D genome (2016) (7)
- Reconfigurable hybrid interface for molecular marker diagnostics and in-situ reporting. (2015) (7)
- SFSSClass: an integrated approach for miRNA based tumor classification (2010) (6)
- Gene expression profiling in developing human hippocampus (2002) (6)
- Challenges in Understanding Genome-Wide DNA Methylation (2010) (6)
- Single-cell alternative polyadenylation analysis delineates GABAergic neuron types (2021) (6)
- CoreBoost _ HM High-resolution human core-promoter prediction with Material Supplemental (2009) (6)
- Analytic theory of stochastic oscillations in single-cell gene expression (2019) (6)
- developmental control, stem cell maintenance, and tumorigenesis The Argonaute family: tentacles that reach into RNAi, (2007) (6)
- Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits (2020) (6)
- RNA Secondary Structure Prediction (2002) (6)
- Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming (2011) (6)
- Murine in vivo CD8+ T Cell Killing Assay. (2014) (6)
- A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass (2019) (6)
- KEGG for Computational Genomics (2002) (6)
- Small C-terminal Domain Phosphatase 3 Dephosphorylates the Linker Sites of Receptor-regulated Smads (R-Smads) to Ensure Transforming Growth Factor β (TGFβ)-mediated Germ Layer Induction in Xenopus Embryos* (2015) (5)
- Advances in computational ChIA-PET data analysis (2016) (5)
- Erratum: Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements (2017) (5)
- Inferring Haplotypes of Copy Number Variations From High-Throughput Data With Uncertainty (2011) (5)
- Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index (2020) (5)
- Basics of Bioinformatics (2013) (5)
- Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits. (2021) (5)
- Large-scale structure of genomic methylation patterns Material Supplemental (2006) (4)
- capture and single molecule bisulfite sequencing High definition profiling of mammalian DNA methylation by array Material Supplemental (2009) (4)
- Krainer proteins by individual SR Identification of functional exonic splicing enhancer motifs recognized (1998) (4)
- Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. (2013) (4)
- ProteoMirExpress: Inferring MicroRNA and Protein-centered Regulatory Networks from High-throughput Proteomic and mRNA Expression Data* (2013) (4)
- Bivalent-Like Chromatin Markers Are Predictive for Transcription Start Site Distribution in Human (2012) (4)
- Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. (2012) (4)
- A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types. (2012) (4)
- 09-05 FastDMA : An Infinium Humanmethylation 450 Beadchip Analyzer (2014) (4)
- Genome wide mapping of Foxo1 binding-sites in murine T lymphocytes (2014) (4)
- Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements (2016) (4)
- Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models (2004) (3)
- Single-cell RNA sequencing of t(8;21) acute myeloid leukemia for risk prediction (2020) (3)
- Integrating Hi-C and FISH data for modeling 3D organizations of chromosomes (2018) (3)
- Deep sequencing analysis of CRISPR-escaping plasmid transconjugants in Enterococcus faecalis (2018) (3)
- Computational Methods for Docking and Applications to Drug Design: Functional Epitopes and Combinatorial Libraries (2002) (3)
- Widespread transcriptional responses to the thermal stresses are prewired in human 3D genome (2019) (3)
- MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data with transition pathway and critical point detection (2020) (3)
- Properties and Prediction of Protein Secondary Structure (2002) (3)
- Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition (2020) (2)
- Integrative analysis of 111 reference human epigenomes Open (2015) (2)
- Dissecting splicing regulatory network by integrative analysis of CLIP-seq data (2012) (2)
- Group-Sparsity-Based Super-Resolution Dipole Orientation Mapping (2019) (2)
- Biomedical Literature Mining (2009) (2)
- Predictive models in gene regulation (2007) (2)
- ScaffComb: A Phenotype‐Based Framework for Drug Combination Virtual Screening in Large‐Scale Chemical Datasets (2021) (2)
- Stochastic fluctuations can reveal the auto-regulatory characteristics of gene networks at the single-molecule level (2017) (2)
- Macroscopic limits, analytical distributions, and noise structure for stochastic gene expression with coupled feedback loops (2019) (2)
- Mathematics of Genome Analysis.Cambridge Studies in Mathematical Biology, Volume 17.ByJerome K Percus.Cambridge and New York: Cambridge University Press. $59.95 (hardcover); $19.95 (paper). x + 139 p; ill.; index. ISBN: 0–521–58517–1 (hc); 0–521–58526–0 (pb). 2002. (2003) (2)
- Protein Structure Prediction by Protein Threading and Partial Experimental Data (2002) (2)
- Evolutionary outcomes of plasmid-CRISPR conflicts in an opportunistic pathogen (2017) (2)
- SuperCT: A supervised-learning-framework to enhance the characterization of single-cell transcriptomic profiles (2018) (2)
- Functional in Silico Analysis of Gene Regulatory Polymorphism (2007) (2)
- Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT 073 (2015) (2)
- Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1. (2020) (2)
- Murine In vitro Memory T Cell Differentiation. (2014) (2)
- Genome mapping by random anchoring: A discrete theoretical analysis (1993) (1)
- Computational Molecular Biology of Genome Expression and Regulation (2005) (1)
- Prostate cancer transcriptomic regulation by the interplay of germline risk alleles, somatic mutations and 3D-genomic architecture. (2022) (1)
- Gene predictions and annotations (2004) (1)
- Histone Deacetylases Pos itively Regulate Transcription through the Elongation Machinery Graphical Abstract Highlights (2015) (1)
- Comparative Sequence and Genome Analysis (2002) (1)
- Quantitative understanding of molecular competition as a hidden layer of gene regulatory network (2018) (1)
- MyoD is a structure organizer of 3D genome architecture in muscle cells (2020) (1)
- Constructing Hepitypes: Phasing Local Genotype and DNA Methylation (2013) (1)
- A data-driven method to learn a jump diffusion process from aggregate biological gene expression data (2021) (1)
- Imaging chromatin interactions at sub-kilobase resolution Via Tn5-FISH (2019) (1)
- A personal journey on cracking the genomic codes (2021) (1)
- The Challenges Facing Genomic Informatics (2002) (1)
- Computational Promoter Prediction in a Vertebrate Genome (2011) (1)
- Identification of Splicing Factor Target Genes by High-Throughput Sequencing (2012) (1)
- 3D Genome Analysis Identifies Enhancer Hijacking Mechanism for High-Risk Factors in Human T-Lineage Acute Lymphoblastic Leukemia (2020) (1)
- Compressing DNA Sequences (2002) (1)
- Protein Structure Prediction by Comparison: Homology-Based Modeling (2002) (1)
- Population dynamics of cancer cells with cell-state conversions between cancer stem cells and non-stem cancer cells (2013) (1)
- QB: A new inter- and multi-disciplinary forum for modeling, engineering and understanding life (2013) (1)
- RSQ: a statistical method for quantification of isoform-specific structurome using transcriptome-wide structural profiling data (2016) (1)
- A data-driven method to learn a jump diffusion process from aggregate biological gene expression data. (2021) (1)
- CREAD: Comprehensive Regulatory Element Analysis and Detection (2005) (0)
- Transcription Regulatory Networks in Yeast Cell Cycle (2005) (0)
- Integration of single cell data by disentangled representation learning (2021) (0)
- 675 Unveiling of DNA Repair Gene Alterations in Non-Lynch Hereditary Colorectal Cancer Through Exome Sequencing (2014) (0)
- () Digestions of the splicing products with RNase R, RNase II and PNPase (2011) (0)
- Inferring Combinatorial Regulation of Binding Sites and Transcription Factors on Gene Expression (2002) (0)
- P1.01-072 Epithelial-To-Mesenchymal Transition (EMT) in Lung Cancer: Classic Reproduction (2017) (0)
- Abstract 773: Analysis of oncogene affected networks in tumorigenesis of lung cancer (2016) (0)
- Abstract 1855: SCT methylation is a potential cancer biomarker for lung cancer (2014) (0)
- DE MERVLs are Enriched Around Two-Cell-Specific Genes During Zygotic Genome Activation in Mouse (2018) (0)
- Data Mining and Pattern Discovery (2002) (0)
- BIOINFORMATICS and Research Opportunities (2006) (0)
- Scanning the human genome at kilobase resolution Material Supplemental (2008) (0)
- Histone code or not? Combinatorial pattern analyses of histone modifications (2008) (0)
- Computational Modeling of Mammalian Promoters - (Invited Keynote Talk) (2012) (0)
- A method for finding novel associations between genome-wide copy number and dna methylation patterns (2011) (0)
- Silico Identification of Human Gene Core Promoters in (2014) (0)
- FP02.09 Effects of Chinese Reimbursement Policy on Molecular Diagnosis and Therapy of NSCLC from the Northern Part of Henan Province (2021) (0)
- A change-point approach to identify hierarchical organization of topologically associated domains in chromatin interaction (2019) (0)
- Biologists Large-Scale Gene Expression Data Analysis : A New Challenge to Related Content (1999) (0)
- visualizing multiple genomic loci using UCNPs and low-power super-resolution STED microscopy (2017) (0)
- Scanning the human genome at kilobase resolution data (2008) (0)
- Major chromosomal breakpoint intervals in breast cancer tumors co-localize with differentially methylated regions. (2012) (0)
- Model-based analysis of chromatin interactions from dCas9-Based CAPTURE-3C-seq (2020) (0)
- Clone Novel E2F Target Promoters Use of Chromatin Immunoprecipitation To (2014) (0)
- Global inference of human phenotype-genotype associations by integrating interactome , phenome and diseasome (2010) (0)
- A novelmethod to identify topological domains using Hi-C data (2015) (0)
- Resource In Situ Capture of Chromatin Interactions by Biotinylated dCas 9 Graphical (2017) (0)
- Integrative Method for Identifying Combinatorial Regulation of Transcription Factors (2003) (0)
- Chromosomal breakpoints in breast cancer co-localize with differentially methylated regions (2016) (0)
- Extracting functional informa A challenge for functional ge (2016) (0)
- Neural potential of stem cells in the hair follicle (2005) (0)
- COMPUTATIONAL DISSECTION OF MAMMALIAN REGULATION NETWORKS (2007) (0)
- The Statistical Distribution of the Length of DNA Segments That are Identical-by-Descent Using a Single Crossover Model (0)
- Abstract 30: Identification of genomic and epigenetic features of tumor suppressors and oncogenes in ovarian cancer (2011) (0)
- OSCAR: One-class SVM for Cis-elements Accu- rate Recognition (2007) (0)
- Erratum: Extracting functional information from microarrays: A challenge for functional genomics (Proceedings of the National Academy of Sciences of the United States of America (October 1, 2002) 99:20 (12509-12511)) (2002) (0)
- Accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features (2022) (0)
- P2.01-117 Concurrent Gene Alterations in Treatment-Naïve EGFR-Mutant Advanced Non-Small Cell Lung Cancer (2018) (0)
- Advanced Topics in Bioinformatics and Computational Biology (2013) (0)
- Protocadherin Gene Clusters Comparative DNA Sequence Analysis of Mouse and Human (2001) (0)
- Yeast Sequencing Report A 38 kb segment containing the cdc 2 gene from the left arm of ® ssion yeast chromosome II : sequence analysis and characterization of the genomic DNA and cDNAs encoded on the segment (1999) (0)
- : A Gene Family Search Tool at Genomic DNA LevelGFScan (2002) (0)
- PREDICTION OF EUKARYOTIC PROTEIN-CODING GENES (2002) (0)
- A Stochastic Segmentation Model for the Indentification of Histone Modification and DNase I Hypersensitive Sites in Chromatin (2015) (0)
- Super-resolution fluorescence dipole orientation microscopy (2016) (0)
- Large-scale structure of genomic methylation patterns data (2005) (0)
- Co-inhibitory Molecule B 7 Superfamily Member 1 Expressed by Tumor-Infiltrating Myeloid Cells Induces Dysfunction of Anti-tumor CD 8 + T Cells Graphical (2018) (0)
- Modern Epigenomics DNA Methylomics (2012) (0)
- MARSMotif: Deciphering Transcriptional Subnetworks from Microarray Expression Data using Regression Splines (2006) (0)
- Title ChIP-Array 2 : integrating multiple omics data to construct generegulatory networks (2015) (0)
- Deciphering hierarchical organization of topologically associated domains through change-point testing (2021) (0)
- Topics in Computational Genomics (2013) (0)
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What Schools Are Affiliated With Michael Q Zhang?
Michael Q Zhang is affiliated with the following schools:
