Peter J Park
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Engineering Computer Science
Peter J Park's Degrees
- PhD Computer Science Stanford University
- Masters Electrical Engineering University of California, Berkeley
- Bachelors Computer Engineering University of California, Berkeley
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(Suggest an Edit or Addition)Peter J Park'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
- Comprehensive molecular portraits of human breast tumors (2012) (7791)
- Integrated Genomic Analyses of Ovarian Carcinoma (2011) (6411)
- Comprehensive molecular characterization of human colon and rectal cancer (2012) (6141)
- Comprehensive genomic characterization defines human glioblastoma genes and core pathways (2008) (5775)
- Comprehensive molecular characterization of gastric adenocarcinoma (2014) (4496)
- Comprehensive molecular profiling of lung adenocarcinoma (2014) (4095)
- Integrated genomic characterization of endometrial carcinoma (2013) (3708)
- Comprehensive genomic characterization of squamous cell lung cancers (2012) (2998)
- Comprehensive genomic characterization of head and neck squamous cell carcinomas (2015) (2860)
- Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. (2015) (2211)
- Genomic Classification of Cutaneous Melanoma (2015) (2143)
- The Molecular Taxonomy of Primary Prostate Cancer (2015) (2116)
- An integrated encyclopedia of DNA elements in the human genome (2012) (2080)
- Integrated Genomic Characterization of Papillary Thyroid Carcinoma (2014) (2007)
- ChIP–seq: advantages and challenges of a maturing technology (2009) (1851)
- Comprehensive molecular characterization of urothelial bladder carcinoma (2014) (1748)
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia (2012) (1701)
- Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma (2016) (1474)
- Comprehensive Characterization of Cancer Driver Genes and Mutations (2018) (1360)
- Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE (2010) (1211)
- Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. (2017) (1092)
- Design and analysis of ChIP-seq experiments for DNA-binding proteins (2008) (880)
- Comprehensive analysis of the chromatin landscape in Drosophila (2010) (868)
- Human Decidual Natural Killer Cells Are a Unique NK Cell Subset with Immunomodulatory Potential (2003) (820)
- Integrated genomic and molecular characterization of cervical cancer (2017) (762)
- Discovering statistically significant pathways in expression profiling studies. (2005) (678)
- The somatic genomic landscape of chromophobe renal cell carcinoma. (2014) (646)
- Landscape of Somatic Retrotransposition in Human Cancers (2012) (638)
- Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome (2013) (614)
- HiGlass: web-based visual exploration and analysis of genome interaction maps (2017) (518)
- Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain (2012) (480)
- Somatic mutation in single human neurons tracks developmental and transcriptional history (2015) (456)
- The 4D nucleome project (2017) (445)
- Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data (2005) (438)
- Aging and neurodegeneration are associated with increased mutations in single human neurons (2017) (425)
- A molecular portrait of microsatellite instability across multiple cancers (2016) (398)
- An assessment of histone-modification antibody quality (2010) (387)
- Postmeiotic Sex Chromatin in the Male Germline of Mice (2006) (380)
- Patterns of somatic structural variation in human cancer genomes (2020) (377)
- A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. (2017) (361)
- Comprehensive Characterization of Cancer Driver Genes and Mutations (2018) (340)
- A Region of the Human HOXD Cluster that Confers Polycomb-Group Responsiveness (2010) (335)
- Comparative analysis of metazoan chromatin organization (2014) (325)
- Hallmarks of pluripotency (2015) (322)
- Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (2018) (319)
- CpG Islands Recruit a Histone H3 Lysine 36 Demethylase (2010) (307)
- Characterization of HPV and host genome interactions in primary head and neck cancers (2014) (296)
- The Landscape of Microsatellite Instability in Colorectal and Endometrial Cancer Genomes (2013) (289)
- Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. (2016) (284)
- Clonal History and Genetic Predictors of Transformation Into Small-Cell Carcinomas From Lung Adenocarcinomas. (2017) (277)
- Comparative Analysis of the Transcriptome across Distant Species (2014) (268)
- Intron retention is a widespread mechanism of tumor-suppressor inactivation (2015) (263)
- Mechanisms and therapeutic implications of hypermutation in gliomas (2020) (256)
- A Sequence Motif within Chromatin Entry Sites Directs MSL Establishment on the Drosophila X Chromosome (2008) (254)
- Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. (2011) (245)
- Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes (2013) (245)
- Power comparisons for disease clustering tests (2003) (236)
- Integrative genome analysis reveals an oncomir/oncogene cluster regulating glioblastoma survivorship (2010) (235)
- ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice (2016) (230)
- The histone chaperone CAF-1 safeguards somatic cell identity (2015) (228)
- SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation (2016) (226)
- A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs (2015) (224)
- The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers (2017) (224)
- Spatiotemporal Evolution of the Primary Glioblastoma Genome. (2015) (223)
- Genomic basis for RNA alterations in cancer (2020) (221)
- Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (2020) (220)
- Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion (2011) (219)
- Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway (2010) (217)
- MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. (2007) (215)
- The Lkb1 metabolic sensor maintains haematopoietic stem cell survival (2010) (212)
- High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. (2006) (210)
- Cell Lineage Analysis in Human Brain Using Endogenous Retroelements (2015) (210)
- The Lkb1 metabolic sensor maintains haematopoietic stem cell survival (2011) (202)
- Apc inhibition of Wnt signaling regulates supernumerary tooth formation during embryogenesis and throughout adulthood (2009) (198)
- A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. (2011) (196)
- Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. (2013) (193)
- X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila (2010) (192)
- Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network (2017) (190)
- Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models (2007) (186)
- Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition (2020) (180)
- Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition (2020) (180)
- A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies (2006) (178)
- ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis (2011) (173)
- Expression, circulation, and excretion profile of microRNA-21, -155, and -18a following acute kidney injury. (2012) (170)
- MNase titration reveals differences between nucleosome occupancy and chromatin accessibility (2016) (170)
- Nature and function of insulator protein binding sites in the Drosophila genome (2012) (167)
- KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs. (2013) (161)
- Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells (2012) (158)
- Pathway analysis of primary central nervous system lymphoma. (2008) (158)
- Detecting the mutational signature of homologous recombination deficiency in clinical samples (2019) (156)
- Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters (2013) (155)
- Differential H3K4 methylation identifies developmentally poised hematopoietic genes. (2008) (154)
- Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster. (2005) (150)
- The mouse X chromosome is enriched for multi-copy testis genes exhibiting post-meiotic expression (2008) (146)
- A multivariate approach for integrating genome-wide expression data and biological knowledge (2006) (144)
- Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer (2020) (139)
- Thyroid hormone-related regulation of gene expression in human fatty liver. (2009) (137)
- Comparative analysis of metazoan chromatin (2014) (137)
- A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data (2000) (136)
- Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data (2018) (135)
- Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes (2013) (134)
- Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all–iPS cell mice from terminally differentiated B cells (2012) (134)
- Resolving rates of mutation in the brain using single-neuron genomics (2016) (132)
- Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. (2011) (130)
- Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) (128)
- Linking gene expression data with patient survival times using partial least squares (2002) (127)
- Drosophila MSL complex globally acetylates H4 Lys16 on the male X chromosome for dosage compensation (2009) (127)
- Large-Scale Quality Analysis of Published ChIP-seq Data (2013) (124)
- Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer (2015) (124)
- Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes (2014) (123)
- Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma (2019) (123)
- Prevalence and detection of low-allele-fraction variants in clinical cancer samples (2017) (122)
- Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis. (2011) (121)
- A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma. (2006) (113)
- Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. (2009) (111)
- Systematic Identification of Synergistic Drug Pairs Targeting HIV (2012) (109)
- Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. (2004) (108)
- A Wnt-Bmp Feedback Circuit Controls Intertissue Signaling Dynamics in Tooth Organogenesis (2012) (107)
- Estimating enrichment of repetitive elements from high-throughput sequence data (2010) (105)
- Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. (2012) (104)
- The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. (2013) (103)
- Genomic Profiling Reveals Alternative Genetic Pathways of Meningioma Malignant Progression Dependent on the Underlying NF2 Status (2010) (103)
- Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants (2016) (101)
- Mechanisms and Consequences of Cancer Genome Instability: Lessons from Genome Sequencing Studies. (2016) (97)
- BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors (2019) (95)
- StratomeX: Visual Analysis of Large‐Scale Heterogeneous Genomics Data for Cancer Subtype Characterization (2012) (94)
- Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast (2013) (92)
- iSyTE: integrated Systems Tool for Eye gene discovery. (2012) (92)
- Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming (2014) (88)
- The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila X chromosome (2008) (88)
- Genome-Wide Analysis of Wilms' Tumor 1-Controlled Gene Expression in Podocytes Reveals Key Regulatory Mechanisms. (2015) (86)
- Evidence for dosage compensation between the X chromosome and autosomes in mammals (2011) (86)
- Unphosphorylated SR-Like Protein Npl3 Stimulates RNA Polymerase II Elongation (2008) (80)
- Primate genome architecture influences structural variation mechanisms and functional consequences (2013) (79)
- A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity (2013) (79)
- Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation. (2017) (79)
- Detecting Somatic Mutations in Normal Cells. (2018) (79)
- Genomic footprints of activated telomere maintenance mechanisms in cancer (2017) (75)
- Combining gene expression data from different generations of oligonucleotide arrays (2004) (74)
- The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts (2016) (74)
- Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes (2008) (74)
- Phase II study of neoadjuvant bevacizumab and radiotherapy for resectable soft tissue sarcomas. (2011) (72)
- Impact of sequencing depth in ChIP-seq experiments (2014) (72)
- Angiogenic profile of soft tissue sarcomas based on analysis of circulating factors and microarray gene expression. (2006) (71)
- Specific genes expressed in association with progesterone receptors in meningioma. (2008) (70)
- Impact of chromatin structure on sequence variability in the human genome (2011) (69)
- Vector algebra in the analysis of genome-wide expression data (2002) (68)
- The 4 D nucleome project (2017) (68)
- Detecting structural variations in the human genome using next generation sequencing. (2010) (67)
- Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers (2009) (66)
- NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types (2017) (66)
- VEGF amplifies transcription through ETS1 acetylation to enable angiogenesis (2017) (65)
- Linked-read analysis identifies mutations in single-cell DNA-sequencing data (2019) (64)
- Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types (2016) (64)
- Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila (2015) (63)
- A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases. (2018) (60)
- p53 prevents neurodegeneration by regulating synaptic genes (2014) (59)
- The origins and genetic interactions of KRAS mutations are allele- and tissue-specific (2021) (59)
- Amniocytes can serve a dual function as a source of iPS cells and feeder layers (2010) (58)
- Numb Regulates Glioma Stem Cell Fate and Growth by Altering Epidermal Growth Factor Receptor and Skp1‐Cullin‐F‐Box Ubiquitin Ligase Activity (2012) (57)
- Identification of somatic mutations in single cell DNA-seq using a spatial model of allelic imbalance (2019) (56)
- DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. (2017) (56)
- Normalization and experimental design for ChIP-chip data (2007) (55)
- nuScore: a web-interface for nucleosome positioning predictions (2008) (54)
- Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain (2012) (54)
- Transcriptional control of a whole chromosome: emerging models for dosage compensation (2014) (54)
- rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data (2010) (53)
- A bioinformatics approach identifies signal transducer and activator of transcription-3 and checkpoint kinase 1 as upstream regulators of kidney injury molecule-1 after kidney injury. (2014) (53)
- Identification of Chromatin-Associated Regulators of MSL Complex Targeting in Drosophila Dosage Compensation (2012) (53)
- Intravenous Leiomyomatosis: An Unusual Intermediate between Benign and Malignant Uterine Smooth Muscle Tumors (2016) (52)
- Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila. (2013) (52)
- Expression profiling of uterine leiomyomata cytogenetic subgroups reveals distinct signatures in matched myometrium: transcriptional profilingof the t(12;14) and evidence in support of predisposing genetic heterogeneity. (2012) (51)
- Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context (2012) (50)
- Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation. (2015) (48)
- Epigenetics meets next-generation sequencing (2008) (47)
- CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms (2008) (45)
- MicroRNA mir-16 is anti-proliferative in enterocytes and exhibits diurnal rhythmicity in intestinal crypts. (2010) (42)
- MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues (2003) (42)
- Evaluation of somatic copy number estimation tools for whole-exome sequencing data (2016) (42)
- Failure to replicate the STAP cell phenomenon (2015) (42)
- Sex differences in oncogenic mutational processes (2019) (41)
- Efficacy of sunitinib and radiotherapy in genetically engineered mouse model of soft-tissue sarcoma. (2009) (41)
- hiHMM: Bayesian non-parametric joint inference of chromatin state maps (2015) (41)
- Nucleosome positioning in human HOX gene clusters. (2008) (41)
- Overcoming evasive resistance from vascular endothelial growth factor a inhibition in sarcomas by genetic or pharmacologic targeting of hypoxia-inducible factor 1α (2012) (40)
- Improving identification of differentially expressed genes in microarray studies using information from public databases (2004) (40)
- Advances in analysis of transcriptional regulatory networks (2011) (38)
- MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. (2019) (38)
- Comparing expression profiles of genes with similar promoter regions (2002) (37)
- Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. (2009) (37)
- Accurate detection of mosaic variants in sequencing data without matched controls (2019) (37)
- HiNT: a computational method for detecting copy number variations and translocations from Hi-C data (2019) (37)
- Landmarks of human embryonic development inscribed in somatic mutations (2021) (37)
- "Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts. (2013) (35)
- Identification of rare germline copy number variations over-represented in five human cancer types (2015) (35)
- Analyzing Somatic Genome Rearrangements in Human Cancers by Using Whole-Exome Sequencing. (2016) (34)
- High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations (2020) (34)
- BIC-seq: a fast algorithm for detection of copy number alterations based on high-throughput sequencing data (2010) (32)
- Variable Requirements for DNA-Binding Proteins at Polycomb-Dependent Repressive Regions in Human HOX Clusters (2013) (31)
- Identifying the molecular signature of the interstitial deletion 7q subgroup of uterine leiomyomata using a paired analysis (2009) (31)
- A Survey of Copy‐Number Variation Detection Tools Based on High‐Throughput Sequencing Data (2012) (29)
- Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer. (2017) (29)
- Large mosaic copy number variations confer autism risk (2020) (29)
- An enhanced genetic model of colorectal cancer progression history (2019) (28)
- Loss of Sh3gl2/endophilin A1 is a common event in urothelial carcinoma that promotes malignant behavior. (2013) (28)
- Alternative splicing of CHEK2 and codeletion with NF2 promote chromosomal instability in meningioma. (2012) (27)
- Guided visual exploration of genomic stratifications in cancer (2014) (26)
- Small-Molecule and CRISPR Screening Converge to Reveal Receptor Tyrosine Kinase Dependencies in Pediatric Rhabdoid Tumors. (2019) (25)
- A permutation test for determining significance of clusters with applications to spatial and gene expression data (2009) (24)
- Comment on “Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters” (2013) (23)
- Microarrays and clinical dentistry. (2003) (22)
- Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (2020) (22)
- The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data (2021) (22)
- Aging elevates metabolic gene expression in brain cholinergic neurons (2008) (22)
- Bivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in Drosophila (2017) (22)
- Comprehensive identification of transposable element insertions using multiple sequencing technologies (2021) (21)
- Comprehensive identification of somatic nucleotide variants in human brain tissue (2020) (21)
- Global impact of somatic structural variation on the DNA methylome of human cancers (2019) (21)
- MicroRNA-29a activates a multi-component growth and invasion program in glioblastoma (2019) (20)
- Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance (2009) (20)
- Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours (2017) (19)
- Supplemental Data MSL Complex Is Attracted to Genes Marked by H 3 K 36 Trimethylation Using a Sequence-Independent Mechanism (2007) (19)
- Nozzle: a report generation toolkit for data analysis pipelines (2013) (19)
- Dysregulation of cancer genes by recurrent intergenic fusions (2020) (19)
- EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering (2015) (18)
- Upregulation of Proapoptotic MicroRNA mir-125a After Massive Small Bowel Resection in Rats (2012) (18)
- Experimental Design and Data Analysis for Array Comparative Genomic Hybridization (2008) (18)
- A genome-wide view of microsatellite instability: old stories of cancer mutations revisited with new sequencing technologies. (2014) (18)
- Functional Relationships Between Gene Pairs in Oral Squamous Cell Carcinoma (2003) (18)
- Systematic Assessment of Tumor Purity and Its Clinical Implications (2020) (17)
- AR egion of the Human HOXD Cluster that Confers Polycomb-Group (2010) (17)
- CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays (2005) (17)
- Gene expression levels in different stages of progression in oral squamous cell carcinoma (2002) (17)
- A user guide for the online exploration and visualization of PCAWG data (2020) (16)
- Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications (2021) (15)
- Clinical Application of Targeted Deep Sequencing in Solid-Cancer Patients and Utility for Biomarker-Selected Clinical Trials. (2017) (15)
- EED, a member of the polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells (2018) (15)
- Parallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain (2020) (14)
- Deletions in CWH43 cause idiopathic normal pressure hydrocephalus (2021) (14)
- Essential histone chaperones collaborate to regulate transcription and chromatin integrity (2020) (13)
- A Genome-Wide Screen Reveals Functional Gene Clusters in the Cancer Genome and Identifies EphA 2 as a Mitogen in Glioblastoma (2006) (13)
- Genomics of MPNST (GeM) Consortium: Rationale and Study Design for Multi-Omic Characterization of NF1-Associated and Sporadic MPNSTs (2020) (13)
- Gene Expression Analysis Reveals the Cell Cycle and Kinetochore Genes Participating in Ischemia Reperfusion Injury and Early Development in Kidney (2011) (12)
- Ultraspecific somatic SNV and indel detection in single neurons using primary template-directed amplification (2021) (12)
- Computational analysis of cancer genome sequencing data (2021) (12)
- upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks (2017) (11)
- Analysis of primary structure of chromatin with next-generation sequencing. (2010) (11)
- A small subunit processome protein promotes cancer by altering translation (2014) (11)
- The Landscape of Mutational Mosaicism in Autistic and Normal Human Cerebral Cortex (2020) (11)
- The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae (2020) (11)
- Tibanna: software for scalable execution of portable pipelines on the cloud (2018) (11)
- PaSD-qc: quality control for single cell whole-genome sequencing data using power spectral density estimation (2017) (10)
- Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability (2022) (10)
- DUSP 9 Modulates DNA Hy pomethylation in Female Mouse Pluripotent Stem Cells (10)
- Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation. (2020) (10)
- Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells (2021) (10)
- A dynamic H 3 K 27 ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP 300 activity Citation (2013) (9)
- Parallel RNA and DNA analysis after Deep-sequencing (PRDD-seq) reveals cell type specific lineage patterns in human brain (2020) (9)
- Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury (2020) (8)
- Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements (2022) (8)
- Abstract 1167: Development of BT1718, a novel Bicycle Drug Conjugate for the treatment of lung cancer (2017) (8)
- Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder (2021) (8)
- Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. (2022) (8)
- A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA (2019) (8)
- Rearranging the chromatin for pluripotency (2013) (7)
- The modENCODE Consortium modENCODE Drosophila Identification of Functional Elements and Regulatory Circuits (2011) (7)
- Author Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data (2022) (7)
- Next-generation sequencing-based detection of germline L1-mediated transductions (2016) (7)
- Publisher Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (2020) (6)
- Publisher Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (2020) (6)
- Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors. (2021) (6)
- Author Correction: BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors (2019) (5)
- Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications (2021) (5)
- Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data (2020) (5)
- Gene Expression Data and Survival Analysis (2005) (5)
- Genomic Determinants of De Novo Resistance to Immune Checkpoint Blockade in Mismatch Repair–Deficient Endometrial Cancer (2020) (5)
- Prevalence and detection of low-allele-fraction variants in clinical cancer samples (2017) (5)
- Author Correction: Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer (2020) (5)
- The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework. (2013) (5)
- Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs (2021) (4)
- HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data (2020) (4)
- Whole-genome analysis of de novo and polymorphic retrotransposon insertions in Autism Spectrum Disorder (2021) (4)
- Corrigendum: The 4D nucleome project (2017) (4)
- Mutational Signature 3 Detected from Clinical Panel Sequencing is Associated with Responses to Olaparib in Breast and Ovarian Cancers (2022) (3)
- Quantized correlation coefficient for measuring reproducibility of ChIP-chip data (2010) (3)
- MSL complex associates with clusters of actively transcribed genes along the Drosophila male X chromosome. (2006) (3)
- Identification of rare germline copy number variations over-represented in five human cancer types (2015) (3)
- Linked-read analysis identifies mutations in single-cell DNA-sequencing data (2017) (3)
- Analysis of somatic retrotransposition in human cancers (2012) (2)
- Single-cell gene fusion detection by scFusion (2020) (2)
- A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG) (2019) (2)
- Correspondence of Drosophila polycomb group proteins with broad H3K27me3 silent domains (2015) (2)
- Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer (2020) (2)
- Author Correction: The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing (2021) (2)
- modENCODE and ENCODE resources for analysis of metazoan chromatin organization (2013) (2)
- Abstract B135: The mechanism of action of BT1718, a novel small-molecule drug conjugate for the treatment of solid tumors expressing MT1-MMP (2018) (2)
- Genome-Wide Disease Screening in Early Human Embryos with Primary Template-Directed Amplification (2021) (2)
- GiniQC: a measure for quantifying noise in single-cell Hi-C data (2020) (2)
- Response to Brosch et al. (2012) (2)
- StratomeX : Enabling Visualization-Driven Cancer Subtype Analysis (2012) (1)
- Dosage compensation in drosophila: Sequence-specific initiation and sequence-independent spreading of MSL complex to the active genes on the male X chromosome (2010) (1)
- Resources and challenges for integrative analysis of nuclear architecture data. (2021) (1)
- Genome‐Wide Mapping of Protein–DNA Interactions by ChIP‐Seq (2012) (1)
- Corrigendum: Failure to replicate the STAP cell phenomenon (2015) (1)
- modENCODE consortia ChIP-seq guidelines and practices of the ENCODE and Material Supplemental (2012) (1)
- endothelial enhancers and requires EP 300 activity A dynamic H 3 K 27 ac signature identifies VEGFA-stimulated Material Supplemental (2013) (1)
- BamSnap: a lightweight viewer for sequencing reads in BAM files (2021) (1)
- Mechanisms and therapeutic implications of hypermutation in gliomas (2020) (1)
- Seqeyes : A multi-scale interactive visualization tool for structural variations (2011) (1)
- Alternative Splicing of CHEK 2 and Codeletion with NF 2 Promote Chromosomal Instability in Meningioma 1 (2012) (1)
- Enrichment of somatic mutations in schizophrenia brain targets prenatally active transcription factor bindings sites (2022) (1)
- Author Correction: Pan-cancer analysis of whole genomes (2023) (1)
- HiNT: a computational method for detecting copy number variations and translocations from Hi-C data (2020) (1)
- An enhanced genetic model of colorectal cancer progression history (2019) (1)
- KDM2B controls tumorigenesis in pancreatic cancer via Polycomb-dependent and -independent transcriptional programs (2012) (1)
- Comprehensive identification of somatic nucleotide variants in human brain tissue (2021) (1)
- Advantages and challenges of using Galaxy CloudMan within an integrated data analysis and visualization platform (2016) (0)
- MicroRNA-29a activates a multi-component growth and invasion program in glioblastoma (2019) (0)
- Abstract 3719: Bicyclic peptides for PET imaging of MT1-MMP expressing tumors (2017) (0)
- BIOINFORMATICS Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance (2009) (0)
- Reproducible Research in the Cloud with the Refinery Platform (2016) (0)
- Abstract P002: Timing onset of homologous recombination deficiency before cancer diagnosis in BRCA1/2 mutation carriers (2023) (0)
- Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. (2023) (0)
- Supplementary Materials for Landscape of Somatic Retrotransposition in Human Cancers (2012) (0)
- Abstract LB-378: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (2018) (0)
- chipchipnorm: normalization for chip-chip data (2009) (0)
- Title Comparative analysis of metazoan chromatin organization Permalink (2014) (0)
- StratomeX : Guided Visual Exploration for Tumor Subtype Identification in The Cancer Genome Atlas (2012) (0)
- Gene expression Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance (2009) (0)
- Fission Yeast and Histone Modifications Genome-Wide in Transcription , Nucleosome Positioning , Spt 6 Regulates Intragenic and Antisense (2013) (0)
- Clinical Cancer esearch an Cancer Biology omic Profiling Reveals Alternative Genetic Pathways of ingioma Malignant Progression Dependent R he Underlying NF 2 Status (2010) (0)
- Global impact of somatic structural variation on the DNA methylome of human cancers (2019) (0)
- Identification of regions in the HOX cluster that can confer repression in a Polycomb-dependent manner (2013) (0)
- Rank-Based Nonlinear Normalization of Oligonucleotide Arrays (2003) (0)
- Contrasting patterns of somatic mutations in neurons and glia reveal differential predisposition to disease in the aging human brain (2023) (0)
- Accurate and sensitive mutational signature analysis with MuSiCal (2022) (0)
- Abstract SY10-01: How aneuploidy drives cancer (2016) (0)
- Abstract 6084: Recurrent genomic patterns of MPNST evolution correlate with clinical outcome (2022) (0)
- Faculty Opinions recommendation of Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. (2012) (0)
- An analysis of the chemical-mechanical polishing process (1998) (0)
- Author Correction: Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications (2021) (0)
- Guided Visual Analysis for the Identification of Cancer Subtypes (2012) (0)
- Genomic basis for RNA alterations in cancer (2020) (0)
- Abstract SY36-03: How aneuploidy drives tumorigenesis (2014) (0)
- VEGF amplifies transcription through ETS1 acetylation to enable angiogenesis (2017) (0)
- Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (2020) (0)
- Author Correction: Inferring structural variant cancer cell fraction (2022) (0)
- Refinery: a data management, analysis, and visualization platform utilizing the Galaxy workbench (2018) (0)
- perspectiVes The 4D nucleome project (2017) (0)
- Next-generation sequencing-based detection of germline L1-mediated transductions (2016) (0)
- Integrated genomic characterization of oesophageal carcinoma (2017) (0)
- Correction: Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context (2014) (0)
- HiGlass: web-based visual exploration and analysis of genome interaction maps (2018) (0)
- Abstract 4066: Loss of Sh3gl2/endophilin A1 is an early event in urothelial carcinoma that regulates malignant behavior. (2013) (0)
- Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder (2021) (0)
- Data integration and visualization at the 4D nucleome data portal (2019) (0)
- A user guide for the online exploration and visualization of PCAWG data (2020) (0)
- Local Hosts and Organizing Committee (2015) (0)
- Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (2020) (0)
- Dysregulation of cancer genes by recurrent intergenic fusions (2020) (0)
- EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering (2015) (0)
- Supplemental Information Spt 5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation (2017) (0)
- Corrigendum: Hallmarks of pluripotency (2015) (0)
- The two complementary methods of understanding a transcription profile (2011) (0)
- CHROMATIN MARKERS IN REPETITIVE REGIONS OF DNA (2009) (0)
- A potential serum panel for breast cancer diagnosis: ongoing clinical validation for its clinical implication. (2009) (0)
- Somatic mutation accumulation seen through a single-molecule lens (2021) (0)
- Otx2 and Oc1 directly regulate the transcriptional program of cone photoreceptor development (2020) (0)
- Abstract 2404: Cumulative dosage effect of TSGs and OGs drives aneuploidy patterns in cancer (2014) (0)
- Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types (2016) (0)
- Abstract 3257: Activation of CD137 using multivalent and tumor targeted Bicyclic peptides (2019) (0)
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What Schools Are Affiliated With Peter J Park?
Peter J Park is affiliated with the following schools:
