University of North Carolina at Chapel Hill

Response eQTLs, chromatin accessibility, and 3D chromatin structure in chondrocytes provide mechanistic insight into osteoarthritis risk
Kramer N.E., Coryell P., D'Costa S., Thulson E., Byun S., Kim H., Parkus S.M., Bond M.L., Shine J., Chubinskaya S., Love M.I., Mohlke K.L., Diekman B.O., Loeser R.F., Phanstiel D.H. Cell Genomics, 2025.
preprint web
Gaussian processes for time series with lead-lag effects with applications to biology data
Mu W, Chen J, Davis ES, Reed K, Phanstiel D, Love MI, Li D. Biometrics , 2024.
web
Response splicing QTLs in primary human chondrocytes identifies putative osteoarthritis risk genes
Byun S, Coryell P, Kramer N, D'Costa S, Thulson E, Shine J, Parkus S, Chubinskaya S, Loeser RF, Diekman BO, Phanstiel DH. Biometrics , 2024.
web
Targeting the 3D genome by anthracyclines for chemotherapeutic effects
Tan M, Sun S, Liu Y, Perreault AA, Phanstiel DH, Dou L, Pang B. bioRxiv , 2024.
preprint
Deciphering the functional impact of Alzheimer's Disease-associated variants in resting and proinflammatory immune cells
Bond ML, Quiroga-Barber IY, D'Costa S, Wu Y, Bell JL, McAfee JC, Kramer NE, Lee S, Patrucco M, Phanstiel DH, Won H. medRxiv, 2024.
preprint
CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression
Lewis MW, King CM, Wisniewska K, Regner MJ, Coffey A, Kelly MR, Mendez-Giraldez R, Davis ES, Phanstiel DH, Franco HL. Cancer Research , 2024.
web
Mariner: explore the Hi-Cs.
Davis ES, Parker SM, Kramer NE, Flores JP, Kiran M, Phanstiel DH. Bioinformatics , 2024.
web
TDP-43 pathology links innate and adaptive immunity in amyotrophic lateral sclerosis
Evangelista BA, Ragusa JV, Pellegrino K, Wu Y, Quiroga-Barber IY, Cahalan SR, Arooji OK, Madren JA, Schroeter S, Cozzarin J, Xie L, Chen X, White KK, Ezzell JA, Iannone MA, Cohen S, Traub RE, Li X, Bedlack R, Phanstiel DH, Meeker R, Stanley N, Cohen TJ. bioRxiv, 2024.
preprint
Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants
McAfee JC, Lee S, Lee J, Bell JL, Krupa O, Davis J, Insigne K, Bond ML, Zhao N, Boyle AP, Phanstiel DH, Love MI, Stein JL, Ruzicka WB, Davila-Velderrain J, Kosuri S, Won H. Cell Genomics, 2023.
web
Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features
Bond M.L., Davis E.S., Quiroga I.Y., Kiran M, Love M.I., Won H, Phanstiel D.H. Genome Research , 2023.
preprint web
Proximity-dependent recruitment of Polycomb repressive complexes by the lncRNA Airn
Braceros AK, Schertzer MD, Omer A, Trotman JB, Davis ES, Dowen JM, Phanstiel DH, Aiden EL, Calabrese JM. Cell Reports, 2023.
web
Chromatin alternates between A and B compartments at kilobase scale for subgenic organization
Harris HL, Gu H, Olshansky M, Wang A, Farabella I, Eliaz Y, Kalluchi A, Krishna A, Jacobs M, Cauer G, Pham M, Rao SSP, Dudchenko O, Omer A, Mohajeri K, Kim S, Nichols MH, Davis ES, Gkountaroulis D, Udupa D, Aiden AP, Corces VG, Phanstiel DH, Noble WS, Nir G, Di Pierro M, Seo JS, Talkowski ME, Aiden EL, Rowley MJ. Nature Communications, 2023.
web
matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling
Davis ES, Mu W, Lee S, Dozmorov MG, Love MI, Phanstiel DH. Bioinformatics , 2023.
web
excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies
Ogata JD, Mu W, Davis ES, Xue B, Harrell JC, Sheffield NC, Phanstiel DH, Love MI, Dozmorov MG. Bioinformatics , 2023.
web
bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing
Mu W, Davis ES, Lee S, Dozmorov MG, Phanstiel DH, Love MI. Bioinformatics , 2023.
web
Guiding the design of well-powered Hi-C experiments to detect differential loops
Parker S.M., Davis E.S., Phanstiel D.H. Bioinformatics Advances , 2023.
preprint web
CTCF: an R/bioconductor data package of human and mouse CTCF binding sites
Dozmorov MG, Mu W, Davis ES, Lee S, Triche TJ Jr, Phanstiel DH, Love MI. Bioinformatics Advances , 2022.
web
Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription
Reed K. S. M.*, Davis E. S.*, Bond M. L., Cabrera A., Thulson E., Quiroga I. Y., Cassel S., Woolery K. T., Hilton I., Won H., Love M. I., Phanstiel D. H. Cell Reports , 2022.
preprint web
3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes
Thulson E, Davis ES, D'Costa S, Coryell PR, Kramer NE, Mohlke KL, Loeser RF, Diekman BO, Phanstiel DH. Genetics , 2022.
web
A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer
Kelly MR, Wisniewska K, Regner MJ, Lewis MW, Perreault AA, Davis ES, Phanstiel DH, Parker JS, Franco HL. Nature Communications, 2022.
web
Synthetic amyloid beta does not induce a robust transcriptional response in innate immune cell culture systems
Quiroga I. Y., Cruikshank A. E., Bond M. L., Reed K. S. M., Evangelista B. A., Tseng J. H., Ragusa J. V., Meeker R. B., Won H., Cohen S., Cohen T. J., Phanstiel D. H. Journal of Neuroinflammation , 2022.
web
Oncogenic fusion proteins and their role in three-dimensional chromatin structure, phase separation, and cancer
Quiroga I.Y., Ahn J.H., Wang G.G., Phanstiel D.H. Current Opinion in Genetics & Development, 2022.
web
Cell type-specific chromatin topology and gene regulation
Phanstiel DH, Wang GG. Trends in Genetics , 2022.
web
Plotgardener: cultivating precise multi-panel figures in R
Nicole E Kramer, Eric S Davis, Craig D Wenger, Erika M Deoudes, Sarah M Parker, Michael I Love, Douglas H Phanstiel Bioinformatics , 2023.
web
Phase separation drives aberrant chromatin looping and cancer development
Ahn H.A., Davis E.S., Daugird S.Z., Zhao S., Quiroga I.Y., Uryu H., Li J., Storey A.J., Tsai Y., Keeley, D.P., Mackintosh S.G., Edmondson R.D., Byrum S.D., Cai L., Tackett A.J., Zheng D., Legant W.R., Phanstiel D.H., Wang G.G. Nature , 2021.
web
Transcriptional response of human articular chondrocytes treated with fibronectin fragments: an in vitro model of the osteoarthritis phenotype
Metz K.S., Ulici V., Kim C, Chubinskaya S, Loeser R.F., Phanstiel D.H. Osteoarthritis and Cartilage , 2020.
preprint web
Bedtoolsr: An R package for genomic data analysis and manipulation
Patwardhan M.N., Wenger C., Davis E.S., Phanstiel D.H. Journal of Open Source Software, 2019.
pdf web

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
Matoba N., Quiroga I.Y., Phanstiel D.H., Won H The Journal of Visualized Experiments ,2020.
web

CoralP: Flexible visualization of the human phosphatome
Min A., Deoudes E.M., Bond M.L., Davis E.S., Phanstiel D.H. Journal of Open Source Software,
pdf preprint web

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
Tycko J, Wainberg M, Marinov GK, Ursu O, Hess GT, Ego BK, Aradhana, Li A, Truong A, Trevino AE, Spees K, Yao D, Kaplow IM, Greenside PG, Morgens DW, Phanstiel DH, Snyder MP, Bintu L, Greenleaf WJ, Kundaje A, Bassik MC. Nat. Commun. 2019.
pdf preprint web

Coral: Clear and Customizable Visualization of Human Kinome Data

Metz, K.S., Deoudes, E.M., Berginsky, M.E., Jimenez-Ruiz, I., Aksoy, B.A., Hammerbacher, J., Gomez, S.M., Phanstiel, D.H. Cell Systems, 2018.

Protein kinases represent one of the largest gene families in eukaryotes and play roles in a wide range of cell signaling processes and human diseases. Current tools for visualizing kinase data in the context of the human kinome superfamily are limited to encoding data through the addition of nodes to a low-resolution image of the kinome tree. We present Coral, a user-friendly interactive web application for visualizing both quantitative and qualitative data. Unlike previous tools, Coral can encode data in three features (node color, node size, and branch color), allows three modes of kinome visualization (the traditional kinome tree as well as radial and dynamic force networks), and generates high-resolution scalable vector graphics files suitable for publication without the need for refinement using graphics editing software. Due to its user-friendly, interactive, and highly customizable design, Coral is broadly applicable to high-throughput studies of the human kinome. The source code and web application are available at github.com/dphansti/CORAL and phanstiel-lab.med.unc.edu/Coral, respectively.

pdf preprint web

Stanford University

Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation.
Van Bortle K, Phanstiel DH, Snyder MP. Genome Biology, 2017.
web

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

Phanstiel, D.H.*, Van Bortle, K.*, Spacek D.V., Hess G.T., Saad Shamim M., Machol I., Love M.I., Lieberman Aiden E., Bassik M.C., Snyder, M.P. Molecular Cell, 2017.

The three-dimensional arrangement of the human genome comprises a complex network of structural and regulatory chromatin loops important for coordinating changes in transcription during human development. To better understand the mechanisms underlying context-specific 3D chromatin structure and transcription during cellular differentiation, we generated comprehensive in situ Hi-C maps of DNA loops in human monocytes and differentiated macrophages. We demonstrate that dynamic looping events are regulatory rather than structural in nature and uncover widespread coordination of dynamic enhancer activity at preformed and acquired DNA loops. Enhancer-bound loop formation and enhancer-activation of preformed loops together form multi-loop activation hubs at key macrophage genes. Activation hubs connect 3.4 enhancers per promoter and exhibit a strong enrichment for Activator Protein 1 (AP-1) binding events, suggesting multi-loop activation hubs involving cell-type specific transcription factors may represent an important class of regulatory chromatin structures for the spatiotemporal control of transcription.

pdf preprint web

Mango: a bias-correcting ChIA-PET analysis pipeline

Phanstiel, D.H., Boyle,A.P., Heidari, N., Snyder, M.P. Bioinformatics, 2015

Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data processing. We present Mango, a complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity.

Comparison to the existing software packages, ChIA-PET Tool and ChiaSig, revealed that Mango interactions exhibit much better agreement with high-resolution Hi-C data. Importantly, Mango executes all steps required for processing ChIA-PET datasets, whereas ChiaSig only completes 20% of the required steps. Application of Mango to multiple available ChIA-PET datasets permitted the independent rediscovery of known trends in chromatin loops including enrichment of CTCF, RAD21, SMC3 and ZNF143 at the anchor regions of interactions and strong bias for convergent CTCF motifs.

Mango is open source and distributed through github at https://github.com/dphansti/mango.

pdf pubmed web

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

Phanstiel, D.H., Boyle A.P., Araya C.L., Snyder M.P. Bioinformatics, 2014.

Interpretation and communication of genomic data require flexible and quantitative tools to analyze and visualize diverse data types, and yet, a comprehensive tool to display all common genomic data types in publication quality figures does not exist to date. To address this shortcoming, we present Sushi.R, an R/Bioconductor package that allows flexible integration of genomic visualizations into highly customizable, publication-ready, multi-panel figures from common genomic data formats including Browser Extensible Data (BED), bedGraph, and Browser Extensible Data Paired-End (BEDPE). Sushi.R is open source and made publicly available through GitHub (https://github.com/dphansti/Sushi) and Bioconductor (http://bioconductor.org/packages/release/bioc/html/Sushi.html).

pdf pubmed web

Genome-wide map of regulatory interactions in the human genome

Heidari N.*, Phanstiel, D.H.*, He C., Grubert F., Jahanbani F., Kasowski M., Zhang M.Q., Snyder M.P. Genome Research, 2014.

Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer-promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus.

pdf pubmed web

Proteomic and phosphoproteomic comparison of human ES and iPS cells

Phanstiel, D.H.*, Brumbaugh J.*, Wenger C.D., Tian S., Probasco M.D., Bailey D.J., Swaney D.L., Tervo M.A., Bolin J.M., Ruotti V., Stewart R., Thomson J.A., Coon J.J. Nature Methods (2011)

Combining high-mass-accuracy mass spectrometry, isobaric tagging and software for multiplexed, large-scale protein quantification, we report deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate. This 24-sample comparison resulted in a very large set of identified proteins and phosphorylation sites in pluripotent cells. The statistical analysis afforded by our approach revealed subtle but reproducible differences in protein expression and protein phosphorylation between embryonic stem cells and induced pluripotent cells. Merging these results with RNA-seq analysis data, we found functionally related differences across each tier of regulation. We also introduce the Stem Cell-Omics Repository (SCOR), a resource to collate and display quantitative information across multiple planes of measurement, including mRNA, protein and post-translational modifications.

pdf pubmed web

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells

Phanstiel, D.H., Brumbaugh, J., Berggren, W.T., Conard, K., Feng, X., Levenstein, M.E., McAlister, G.C., Thomson, J.A., Coon, J.J. Proceedings of the National Academy of Sciences (2008)

Epigenetic regulation through chromatin is thought to play a critical role in the establishment and maintenance of pluripotency. Traditionally, antibody-based technologies were used to probe for specific posttranslational modifications (PTMs) present on histone tails, but these methods do not generally reveal the presence of multiple modifications on a single-histone tail (combinatorial codes). Here, we describe technology for the discovery and quantification of histone combinatorial codes that is based on chromatography and mass spectrometry. We applied this methodology to decipher 74 discrete combinatorial codes on the tail of histone H4 from human embryonic stem (ES) cells. Finally, we quantified the abundances of these codes as human ES cells undergo differentiation to reveal striking changes in methylation and acetylation patterns. For example, H4R3 methylation was observed only in the presence of H4K20 dimethylation; such context-specific patterning exemplifies the power of this technique.

pdf pubmed web

Peptide quantification using 8-plex isobaric tags and electron transfer dissociation tandem mass spectrometry

Phanstiel, D.H., Unwin, R., McAlister, G.C., Coon, J.J. Analytical Chemistry (2009)

Isobaric tags for absolute and relative quantitation (iTRAQ) allow for simultaneous relative quantification of peptides from up to eight different samples. Typically peptides labeled with 8-plex iTRAQ tags are pooled and fragmented using beam-type collision activated dissociation (CAD) which, in addition to cleaving the peptide backbone bonds, cleaves the tag to produce reporter ions. The relative intensities of the reporters are directly proportional to the relative abundances of each peptide in the solution phase. Recently, studies using the 4-plex iTRAQ tagging reagent demonstrated that electron transfer dissociation (ETD) of 4-plex iTRAQ labeled peptides cleaves at the N-C alpha bond in the tag and allows for up to three channels of quantification. In this paper we investigate the ETD fragmentation patterns of peptides labeled with 8-plex iTRAQ tags. We demonstrate that upon ETD, peptides labeled with 8-plex iTRAQ tags fragment to produce unique reporter ions that allow for five channels of quantification. ETD-MS/MS of these labeled peptides also produces a peak at 322 m/z which, upon resonant excitation (CAD), gives rise to all eight iTRAQ reporter ions and allows for eight channels of quantification. Comparison of this method to beam-type CAD quantification shows a good correlation (y = 0.91x + 0.01, R(2) = 0.9383).

pdf pubmed web

Peptide and protein quantification using iTRAQ with electron transfer dissociation

Phanstiel, D.H., Zhang, Y., Marto, J.A., Coon, J.J. Journal of The American Society for Mass Spectrometry (2008)

Electron transfer dissociation (ETD) has become increasingly used in proteomic analyses due to its complementarity to collision-activated dissociation (CAD) and its ability to sequence peptides with post-translation modifications (PTMs). It was previously unknown, however, whether ETD would be compatible with a commonly employed quantification technique, isobaric tags for relative and absolute quantification (iTRAQ), since the fragmentation mechanisms and pathways of ETD differ significantly from CAD. We demonstrate here that ETD of iTRAQ labeled peptides produces c- and z-type fragment ions as well as reporter ions that are unique from those produced by CAD. Exact molecular formulas of product ions were determined by ETD fragmentation of iTRAQ-labeled synthetic peptides followed by high mass accuracy orbitrap mass analysis. These experiments revealed that ETD cleavage of the N-C(alpha) bond of the iTRAQ tag results in fragment ions that could be used for quantification. Synthetic peptide work demonstrates that these fragment ions provide up to three channels of quantification and that the quality is similar to that provided by beam-type CAD. Protein standards were used to evaluate peptide and protein quantification of iTRAQ labeling in conjunction with ETD, beam-type CAD, and pulsed Q dissociation (PQD) on a hybrid ion trap-orbitrap mass spectrometer. For reporter ion intensities above a certain threshold all three strategies provided reliable peptide quantification (average error <10%). Approximately 36%, 8%, and 16% of scans identified fall below this threshold for ETD, HCD, and PQD, respectively. At the protein level, average errors were 2.3%, 1.7%, and 3.6% for ETD, HCD, and PQD, respectively.

pdf pubmed web

Publications

University of North Carolina at Chapel Hill

Response eQTLs, chromatin accessibility, and 3D chromatin structure in chondrocytes provide mechanistic insight into osteoarthritis risk

Gaussian processes for time series with lead-lag effects with applications to biology data

Response splicing QTLs in primary human chondrocytes identifies putative osteoarthritis risk genes

Targeting the 3D genome by anthracyclines for chemotherapeutic effects

Deciphering the functional impact of Alzheimer's Disease-associated variants in resting and proinflammatory immune cells

CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression

Mariner: explore the Hi-Cs.

TDP-43 pathology links innate and adaptive immunity in amyotrophic lateral sclerosis

Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants

Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features

Proximity-dependent recruitment of Polycomb repressive complexes by the lncRNA Airn

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling

excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing

Guiding the design of well-powered Hi-C experiments to detect differential loops

CTCF: an R/bioconductor data package of human and mouse CTCF binding sites

Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription

3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes

A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer

Synthetic amyloid beta does not induce a robust transcriptional response in innate immune cell culture systems

Oncogenic fusion proteins and their role in three-dimensional chromatin structure, phase separation, and cancer

Cell type-specific chromatin topology and gene regulation

Plotgardener: cultivating precise multi-panel figures in R

Phase separation drives aberrant chromatin looping and cancer development

Transcriptional response of human articular chondrocytes treated with fibronectin fragments: an in vitro model of the osteoarthritis phenotype

Bedtoolsr: An R package for genomic data analysis and manipulation

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

CoralP: Flexible visualization of the human phosphatome

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements

Coral: Clear and Customizable Visualization of Human Kinome Data

Stanford University

Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation.

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

Mango: a bias-correcting ChIA-PET analysis pipeline

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

Genome-wide map of regulatory interactions in the human genome

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias

University of Wisconsin–Madison

Proteomic and phosphoproteomic comparison of human ES and iPS cells

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells

Peptide quantification using 8-plex isobaric tags and electron transfer dissociation tandem mass spectrometry

Peptide and protein quantification using iTRAQ with electron transfer dissociation

Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer

The Hutch

A mouse to human search for plasma proteome changes associated with pancreatic tumor development

Identification of 14-3-3 theta as an antigen that induces a humoral response in lung cancer

Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes

Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS

US Patents

Mass Spectrometry Data Acquisition Mode for Obtaining More Reliable Protein Quantitation

Probability-based Mass Spectrometry Data Acquisition.

External Links