Analytical tools and current challenges in the modern era of neuroepigenomics

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works

Cutadapt removes adapter sequences from high-throughput sequencing reads

Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889 · see citing works

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055 · see citing works

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1883 · Cited by 20,776 · see citing works

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works

Differential expression analysis for sequence count data

Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581 · see citing works

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556 · see citing works

Integrative genomics viewer

Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390 · see citing works

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696 · see citing works

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382 · see citing works

TopHat: discovering splice junctions with RNA-Seq

Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,477 · see citing works

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898 · see citing works

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

Eng, J. K., McCormack, A. L., & Yates, J. R. (1994) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(94)80016-2 · Cited by 6,484 · see citing works

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

Law, C. W., Chen, Y., Shi, W., & Smyth, G. K. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r29 · Cited by 6,155 · see citing works

limma: Linear Models for Microarray Data

Smyth, G. K. (2005) · Statistics for Biology and Health · doi:10.1007/0-387-29362-0_23 · Cited by 5,796 · see citing works

A General Framework for Weighted Gene Co-Expression Network Analysis

Zhang, B., & Horvath, S. (2005) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1128 · Cited by 5,684 · see citing works

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular &amp; Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574 · see citing works

Cerebral organoids model human brain development and microcephaly

Lancaster, M. A., Renner, M., Martin, C.-A., Wenzel, D., Bicknell, L. S., Hurles, M. E., Homfray, T., Penninger, J. M., Jackson, A. P., & Knoblich, J. A. (2013) · Nature · doi:10.1038/nature12517 · Cited by 5,372 · see citing works

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

Krueger, F., & Andrews, S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr167 · Cited by 5,161 · see citing works

miRBase: annotating high confidence microRNAs using deep sequencing data

Kozomara, A., & Griffiths-Jones, S. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1181 · Cited by 4,629 · see citing works

Mutational landscape and significance across 12 major cancer types

Kandoth, C., McLellan, M. D., Vandin, F., Ye, K., Niu, B., Lu, C., Xie, M., Zhang, Q., McMichael, J. F., Wyczalkowski, M. A., et al. (2013) · Nature · doi:10.1038/nature12634 · Cited by 4,419 · see citing works

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716 · see citing works

Differential analysis of gene regulation at transcript resolution with RNA-seq

Trapnell, C., Hendrickson, D. G., Sauvageau, M., Goff, L., Rinn, J. L., & Pachter, L. (2013) · Nature Biotechnology · doi:10.1038/nbt.2450 · Cited by 3,492 · see citing works

Bioinformatics and Computational Biology Solutions Using R and Bioconductor

Gentleman, R. C., Carey, V. J., Huber, W. K., Irizarry, R. A., & Dudoit, S. (2005) · Statistics in the health sciences · doi:10.1007/0-387-29362-0 · Cited by 3,470 · see citing works

Evolution at Two Levels in Humans and Chimpanzees: Their macromolecules are so alike that regulatory mutations may account for their biological differences

King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815 · see citing works

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008) · Genome Research · doi:10.1101/gr.079558.108 · Cited by 2,771 · see citing works

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

Kriaucionis, S., & Heintz, N. (2009) · Science · doi:10.1126/science.1169786 · Cited by 2,700 · see citing works

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533 · see citing works

ChromHMM: automating chromatin-state discovery and characterization

Ernst, J., & Kellis, M. (2012) · Nature Methods · doi:10.1038/nmeth.1906 · Cited by 2,489 · see citing works

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., & Snyder, M. (2008) · Science · doi:10.1126/science.1158441 · Cited by 2,479 · see citing works

Initial sequence of the chimpanzee genome and comparison with the human genome

The Chimpanzee Sequencing and Analysis Consortium (2005) · Nature · doi:10.1038/nature04072 · Cited by 2,459 · see citing works

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research · doi:10.1101/gr.136184.111 · Cited by 2,033 · see citing works

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

Tan, M., Luo, H., Lee, S., Jin, F., Yang, J. S., Montellier, E., Buchou, T., Cheng, Z., Rousseaux, S., Rajagopal, N., et al. (2011) · Cell · doi:10.1016/j.cell.2011.08.008 · Cited by 1,902 · see citing works

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2Preprint

Love, M. I., Huber, W. K., & Anders, S. (2014) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/002832 · Cited by 1,849 · see citing works

Global epigenomic reconfiguration during mammalian brain development

Lister, R., Mukamel, E. A., Nery, J. R., Urich, M., Puddifoot, C. A., Johnson, N. D., Lucero, J., Huang, Y., Dwork, A. J., Schultz, M. D., et al. (2013) · Science · doi:10.1126/science.1237905 · Cited by 1,830 · see citing works

Wisdom of crowds for robust gene network inference

The DREAM5 Consortium, Marbach, D., Costello, J. C., Küffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., Allison, K. R., Kellis, M., Collins, J. J., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2016 · Cited by 1,667 · see citing works

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

Zhang, B., Gaiteri, C., Bodea, L.-G., Wang, Z., McElwee, J., Podtelezhnikov, A. A., Zhang, C., Xie, T., Tran, L., Dobrin, R., et al. (2013) · Cell · doi:10.1016/j.cell.2013.03.030 · Cited by 1,657 · see citing works

ChIP-seq accurately predicts tissue-specific activity of enhancers

Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639 · see citing works

A probability-based approach for high-throughput protein phosphorylation analysis and site localization

Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., & Gygi, S. P. (2006) · Nature Biotechnology · doi:10.1038/nbt1240 · Cited by 1,577 · see citing works

Genome-wide association analysis identifies 13 new risk loci for schizophrenia

Multicenter Genetic Studies of Schizophrenia Consortium, Ripke, S., Psychosis Endophenotypes International Consortium, Wellcome Trust Case Control Consortium 2, O'Dushlaine, C., Chambert, K., Moran, J. L., Kähler, A. K., Akterin, S., Bergen, S. E., et al. (2013) · Nature Genetics · doi:10.1038/ng.2742 · Cited by 1,496 · see citing works

Open Mass Spectrometry Search Algorithm

Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M. Q., Maynard, D., Yang, X., Shi, W., & Bryant, S. H. (2004) · Journal of Proteome Research · doi:10.1021/pr0499491 · Cited by 1,420 · see citing works

Analysis and design of RNA sequencing experiments for identifying isoform regulation

Katz, Y., Wang, E. T., Airoldi, E. M., & Burge, C. B. (2010) · Nature Methods · doi:10.1038/nmeth.1528 · Cited by 1,353 · see citing works

BSMAP: whole genome bisulfite sequence MAPping program

Xi, Y., & Li, W. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-232 · Cited by 1,216 · see citing works

A high-resolution map of the three-dimensional chromatin interactome in human cells

Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208 · see citing works

Discovering microRNAs from deep sequencing data using miRDeep

Friedländer, M. R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., & Rajewsky, N. (2008) · Nature Biotechnology · doi:10.1038/nbt1394 · Cited by 1,189 · see citing works

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

Zhu, L., Gazin, C., Lawson, N., Pagès, H., Lin, S. M., Lapointe, D. S., & Green, M. R. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-237 · Cited by 1,144 · see citing works

PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

Zhang, J., Xin, L., Shan, B., Chen, W., Xie, M., Yuen, D., Zhang, W., Zhang, Z., Lajoie, G., & Ma, B. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.010587 · Cited by 1,073 · see citing works

An integrative genomics approach to infer causal associations between gene expression and disease

Schadt, E. E., Lamb, J., Yang, X., Zhu, J., Edwards, S., GuhaThakurta, D., Sieberts, S. K., Monks, S., Reitman, M., Zhang, C., et al. (2005) · Nature Genetics · doi:10.1038/ng1589 · Cited by 1,043 · see citing works

Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism

Parikshak, N. N., Luo, R., Zhang, A., Won, H., Lowe, J. K., Chandran, V., Horvath, S., & Geschwind, D. H. (2013) · Cell · doi:10.1016/j.cell.2013.10.031 · Cited by 1,039 · see citing works

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

Wilhelm, B. T., Marguerat, S., Watt, S. B., Schubert, F., Wood, V., Goodhead, I., Penkett, C. J., Rogers, J., & Bähler, J. (2008) · Nature · doi:10.1038/nature07002 · Cited by 974 · see citing works

Altered Histone Acetylation Is Associated with Age-Dependent Memory Impairment in Mice

Peleg, S., Sananbenesi, F., Zovoilis, A., Burkhardt, S., Bahari-Javan, S., Agis-Balboa, R. C., Cota, P., Wittnam, J. L., Gogol-Doering, A., Opitz, L., et al. (2010) · Science · doi:10.1126/science.1186088 · Cited by 951 · see citing works

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

Zhao, S., Fung‐Leung, W., Bittner, A., Ngo, K., & Liu, X. (2014) · PLoS ONE · doi:10.1371/journal.pone.0078644 · Cited by 945 · see citing works

ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression

Shi, X., Hong, T., Walter, K. L., Ewalt, M. D., Michishita, E., Hung, T., Carney, D., Peña, P. V., Lan, F., Kaadige, M. R., et al. (2006) · Nature · doi:10.1038/nature04835 · Cited by 944 · see citing works

MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system

Mellén, M., Ayata, P., Dewell, S., Kriaucionis, S., & Heintz, N. (2012) · Cell · doi:10.1016/j.cell.2012.11.022 · Cited by 943 · see citing works

Common Genetic Variation and Human Traits

Goldstein, D. B. (2009) · New England Journal of Medicine · doi:10.1056/nejmp0806284 · Cited by 918 · see citing works

RNA-SeQC: RNA-seq metrics for quality control and process optimization

DeLuca, D. S., Levin, J. Z., Sivachenko, A., Fennell, T., Nazaire, M.-D., Williams, C., Reich, M., Winckler, W., & Getz, G. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts196 · Cited by 899 · see citing works

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

Chan, P. P., & Lowe, T. M. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn787 · Cited by 867 · see citing works

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

Shen, L., Shao, N., Liu, X., & Nestler, E. J. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-284 · Cited by 852 · see citing works

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

Szulwach, K. E., Li, X., Li, Y., Song, C., Wu, H., Dai, Q., Irier, H. A., Upadhyay, A. K., Gearing, M., Levey, A. I., et al. (2011) · Nature Neuroscience · doi:10.1038/nn.2959 · Cited by 818 · see citing works

Rfam 11.0: 10 years of RNA families

Burge, S., Daub, J., Eberhardt, R. Y., Tate, J. G., Barquist, L., Nawrocki, E. P., Eddy, S. R., Gardner, P. P., & Bateman, A. G. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1005 · Cited by 807 · see citing works

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

Rapaport, F., Khanin, R., Liang, Y., Pirun, M., Krek, A., Zumbo, P., Mason, C. E., Socci, N. D., & Betel, D. (2013) · Genome Biology · doi:10.1186/gb-2013-14-9-r95 · Cited by 733 · see citing works

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

Guo, J. U., Su, Y., Shin, J. H., Shin, J., Li, H., Xie, B., Zhong, C., Hu, S., Le, T., Fan, G., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3607 · Cited by 714 · see citing works

Neuronal activity modifies the DNA methylation landscape in the adult brain

Guo, J. U., Ma, D. K., Mo, H., Ball, M. P., Jang, M.-H., Bonaguidi, M. A., Balazer, J. A., Eaves, H. L., Xie, B., Ford, E., et al. (2011) · Nature Neuroscience · doi:10.1038/nn.2900 · Cited by 669 · see citing works

Essential Role of the Histone Methyltransferase G9a in Cocaine-Induced Plasticity

Maze, I., Covington, H. E., Dietz, D. M., LaPlant, Q., Renthal, W., Russo, S. J., Mechanic, M., Mouzon, E., Neve, R. L., Haggarty, S. J., et al. (2010) · Science · doi:10.1126/science.1179438 · Cited by 665 · see citing works

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

Down, T. A., Rakyan, V. K., Turner, D., Flicek, P., Li, H., Kulesha, E., Gräf, S., Johnson, N., Herrero, J., Tomazou, E. M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1414 · Cited by 651 · see citing works

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

Yaffe, E., & Tanay, A. (2011) · Nature Genetics · doi:10.1038/ng.947 · Cited by 645 · see citing works

Analysis of oncogenic signaling networks in glioblastoma identifies <i>ASPM</i> as a molecular target

Horvath, S., Zhang, B., Carlson, M., Lu, K. V., Zhu, S., Felciano, R. M., Laurance, M. F., Zhao, W., Qi, S., Chen, Z., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608396103 · Cited by 641 · see citing works

Lysine succinylation and lysine malonylation in histones

Xie, Z., Dai, J., Dai, L., Tan, M., Cheng, Z., Wu, Y., Boeke, J. D., & Zhao, Y. (2012) · Molecular &amp; Cellular Proteomics · doi:10.1074/mcp.m111.015875 · Cited by 613 · see citing works

lncRNAdb: a reference database for long noncoding RNAs

Amaral, P., Clark, M. B., Gascoigne, D. K., Dinger, M. E., & Mattick, J. S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1138 · Cited by 584 · see citing works

Analysing and interpreting DNA methylation data

Bock, C. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3273 · Cited by 580 · see citing works

Genome-wide chromatin state transitions associated with developmental and environmental cues

Zhu, J., Adli, M., Zou, J., Verstappen, G., Coyne, M. J., Zhang, X.-L., Durham, T. J., Miri, M., Deshpande, V., Jager, P. D., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.033 · Cited by 553 · see citing works

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

Zhu, J., Zhang, B., Smith, E. N., Drees, B., Brem, R. B., Kruglyak, L., Bumgarner, R. E., & Schadt, E. E. (2008) · Nature Genetics · doi:10.1038/ng.167 · Cited by 549 · see citing works

Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

Evrony, G. D., Cai, X., Lee, E., Hills, L. B., Elhosary, P. C., Lehmann, H. S., Parker, J. J., Atabay, K. D., Gilmore, E. C., Poduri, A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.035 · Cited by 548 · see citing works

Purification of Proteins Associated with Specific Genomic Loci

Déjardin, J., & Kingston, R. E. (2009) · Cell · doi:10.1016/j.cell.2008.11.045 · Cited by 545 · see citing works

Human-specific loss of regulatory DNA and the evolution of human-specific traits

McLean, C. Y., Reno, P. L., Pollen, A. A., Bassan, A. I., Capellini, T. D., Guenther, C., Indjeian, V. B., Lim, X., Menke, D. B., Schaar, B. T., et al. (2011) · Nature · doi:10.1038/nature09774 · Cited by 535 · see citing works

Systematic evaluation of spliced alignment programs for RNA-seq data

The RGASP Consortium, Engström, P. G., Steijger, T., Sipos, B., Grant, G. R., Kahles, A., Rätsch, G., Goldman, N., Hubbard, T. J., Harrow, J., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2722 · Cited by 513 · see citing works

snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs

Lestrade, L. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj002 · Cited by 504 · see citing works

RNA-seq differential expression studies: more sequence or more replication?

Liu, Y., Zhou, J., & White, K. P. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt688 · Cited by 497 · see citing works

Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways

Miller, J. A., Horvath, S., & Geschwind, D. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914257107 · Cited by 480 · see citing works

Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark

Dai, L., Peng, C., Montellier, E., Lu, Z., Chen, Y., Ishii, H., Debernardi, A., Buchou, T., Rousseaux, S., Jin, F., et al. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1497 · Cited by 460 · see citing works

Asymmetrically Modified Nucleosomes

Voigt, P., LeRoy, G., Drury, W. J., Zee, B. M., Son, J., Beck, D. B., Young, N. L., Garcia, B. A., & Reinberg, D. (2012) · Cell · doi:10.1016/j.cell.2012.09.002 · Cited by 457 · see citing works

RNA-sequencing from single nuclei

Grindberg, R. V., Yee-Greenbaum, J. L., McConnell, M. J., Novotny, M., O’Shaughnessy, A. L., Lambert, G. M., Araúzo-Bravo, M. J., Lee, J., Fishman, M., Robbins, G. E., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319700110 · Cited by 422 · see citing works

Comparison of software packages for detecting differential expression in RNA-seq studies

Seyednasrollah, F., Laiho, A., & Elo, L. L. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbt086 · Cited by 421 · see citing works

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencingPreprint

Chen, K.-F., Xi, Y., Pan, X.-W., Li, Z.-Y., Kaestner, K., Tyler, J. K., Dent, S., He, X.-W., & Li, W. (2013) · Genome Research · doi:10.1101/gr.142067.112 · Cited by 415 · see citing works

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

Shen, L., Shao, N., Liu, X., Maze, I. S., Feng, J., & Nestler, E. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065598 · Cited by 403 · see citing works

NONCODEv4: exploring the world of long non-coding RNA genes

Xie, C., Yuan, J., Li, H., Li, M., Zhao, G., Bu, D., Zhu, W., Wu, W., Chen, R., & Zhao, Y. C. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1222 · Cited by 401 · see citing works

A Systems Level Analysis of Transcriptional Changes in Alzheimer's Disease and Normal Aging

Miller, J. A., Oldham, M. C., & Geschwind, D. H. (2008) · The Journal of Neuroscience · doi:10.1523/jneurosci.4098-07.2008 · Cited by 385 · see citing works

piRNABank: a web resource on classified and clustered Piwi-interacting RNAs

Lakshmi, S. S., & Agrawal, S. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm696 · Cited by 381 · see citing works

A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue

Deal, R. B., & Henikoff, S. (2010) · Developmental Cell · doi:10.1016/j.devcel.2010.05.013 · Cited by 379 · see citing works

MeCP2 binds to 5hmc enriched within active genes and accessible chromatin in the nervous system

Mellén, M., Ayata, P., Dewell, S. B., Kriaučionis, S., & Heintz, N. (2013) · Epigenetics & Chromatin · doi:10.1186/1756-8935-6-s1-p52 · Cited by 345 · see citing works

High Throughput Characterization of Combinatorial Histone Codes

Young, N. L., DiMaggio, P. A., Plazas-Mayorca, M. D., Baliban, R. C., Floudas, C. A., & Garcia, B. A. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900238-mcp200 · Cited by 312 · see citing works

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

Nookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlén, M., & Nielsen, J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks804 · Cited by 309 · see citing works

MOABS: model based analysis of bisulfite sequencing data

Sun, D., Xi, Y., Rodriguez, B. A. T., Park, H. J., Tong, P., Meong, M., Goodell, M. A., & Li, W. (2014) · Genome biology · doi:10.1186/gb-2014-15-2-r38 · Cited by 299 · see citing works

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

Saint-André, V., Batsché, E., Rachez, C., & Muchardt, C. (2011) · Nature Structural &amp; Molecular Biology · doi:10.1038/nsmb.1995 · Cited by 278 · see citing works

Genes and pathways underlying regional and cell type changes in Alzheimer’s disease

Miller, J. A., Woltjer, R. L., Goodenbour, J. M., Horvath, S., & Geschwind, D. H. (2013) · Genome Medicine · doi:10.1186/gm452 · Cited by 275 · see citing works

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

Hackenberg, M., Rodríguez‐Ezpeleta, N., & Aransay, A. M. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr247 · Cited by 272 · see citing works

The Genotype-Tissue Expression (GTEx) project

Lonsdale, J., Thomas, J., Salvatore, M., Phillips, R., Lo, E., Shad, S., Hasz, R., Walters, G., Garcia, F., Young, N., et al. (2013) · Nature Genetics · doi:10.1038/ng.2653 · Cited by 263 · see citing works

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

Carroll, T. S., Liang, Z., Salama, R. A., Stark, R., & de Santiago, I. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00075 · Cited by 254 · see citing works

Modeling gene expression using chromatin features in various cellular contexts

Dong, X., Greven, M. C., Kundaje, A. B., Djebali, S., Brown, J., Cheng, C., Gingeras, T., Gerstein, M., Guigó, R., Birney, E., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-9-r53 · Cited by 254 · see citing works

Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex

Cheung, I., Shulha, H. P., Jiang, Y., Matevossian, A., Wang, J., Weng, Z., & Akbarian, S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001702107 · Cited by 235 · see citing works

ΔFosB Mediates Epigenetic Desensitization of the c-fosGene After Chronic Amphetamine Exposure

Renthal, W. R., Carle, T. L., Maze, I. S., Covington, H. E., Truong, H.-T., Alibhai, I. N., Kumar, A., Montgomery, R. L., Olson, E. N., & Nestler, E. J. (2008) · Journal of Neuroscience · doi:10.1523/jneurosci.1043-08.2008 · Cited by 234 · see citing works

Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation

Tanizawa, H., Iwasaki, O., Tanaka, A., Capizzi, J. R., Wickramasinghe, P., Lee, M., Fu, Z., & Noma, K.-I. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq955 · Cited by 223 · see citing works

Substance-specific and shared transcription and epigenetic changes in the human hippocampus chronically exposed to cocaine and alcohol

Zhou, Z., Yuan, Q., Mash, D. C., & Goldman, D. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1018514108 · Cited by 220 · see citing works

pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry

Wang, L., Li, D., Fu, Y., Wang, H., Zhang, J., Yuan, Z., Sun, R., Zeng, R., He, S., & Gao, W. (2007) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.3173 · Cited by 218 · see citing works

Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

Feng, J., Wilkinson, M., Liu, X., Purushothaman, I., Ferguson, D., Vialou, V., Maze, I., Shao, N., Kennedy, P., Koo, J., et al. (2014) · Genome Biology · doi:10.1186/gb-2014-15-4-r65 · Cited by 198 · see citing works

Isolation of neuronal chromatin from brain tissue

Jiang, Y., Matevossian, A., Huang, H.-S., Straubhaar, J., & Akbarian, S. (2008) · BMC Neuroscience · doi:10.1186/1471-2202-9-42 · Cited by 193 · see citing works

Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens

Maze, I. S., Feng, J., Wilkinson, M. B., Sun, H., Shen, L., & Nestler, E. J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1015483108 · Cited by 191 · see citing works

Acute stress and hippocampal histone H3 lysine 9 trimethylation, a retrotransposon silencing response

Hunter, R. G., Murakami, G., Dewell, S. B., Seligsohn, M., Baker, M. E. R., Datson, N. A., McEwen, B. S., & Pfaff, D. W. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1215810109 · Cited by 173 · see citing works

Genome-wide Transcriptome Profiling Reveals the Functional Impact of Rare De Novo and Recurrent CNVs in Autism Spectrum Disorders

Luo, R., Sanders, S. J., Tian, Y., Voineagu, I., Huang, N., Chu, S. H., Klei, L., Cai, C., Ou, J., Lowe, J. K., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.05.011 · Cited by 167 · see citing works

Systematic evaluation of factors influencing ChIP-seq fidelity

Chen, Y., Negre, N. N., Li, Q., Mieczkowska, J. O., Slattery, M. G., Liu, T., Zhang, Y., Kim, T.-K., He, H. H., Zieba, J. T., et al. (2012) · Nature Methods · doi:10.1038/nmeth.1985 · Cited by 164 · see citing works

Identification of Combinatorial Patterns of Post-Translational Modifications on Individual Histones in the Mouse Brain

Tweedie‐Cullen, R. Y., Brunner, A. M., Grossmann, J., Mohanna, S., Sichau, D., Nanni, P., Panse, C., & Mansuy, I. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036980 · Cited by 162 · see citing works

Morphine Epigenomically Regulates Behavior through Alterations in Histone H3 Lysine 9 Dimethylation in the Nucleus Accumbens

Sun, H., Maze, I. S., Dietz, D., Scobie, K. N., Kennedy, P., Damez-Werno, D. M., Neve, R. L., Zachariou, V., Shen, L., & Nestler, E. J. (2012) · Journal of Neuroscience · doi:10.1523/jneurosci.1357-12.2012 · Cited by 146 · see citing works

Proteomic and genomic characterization of chromatin complexes at a boundary

Tackett, A. J., Dilworth, D. J., Davey, M. J., O’Donnell, M. E., Aitchison, J. D., Rout, M. P., & Chait, B. T. (2005) · The Journal of Cell Biology · doi:10.1083/jcb.200502104 · Cited by 142 · see citing works

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

Cheng, C., Yan, K., Yip, K. Y.-L., Rozowsky, J. S., Alexander, R. P., Shou, C., & Gerstein, M. (2011) · Genome biology · doi:10.1186/gb-2011-12-2-r15 · Cited by 137 · see citing works

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs

Mitsuyama, T., Yamada, K. H., Hattori, E., Okida, H., Ono, Y., Terai, G., Yoshizawa, A., Komori, T., & Asai, K. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn805 · Cited by 136 · see citing works

Enhanced top-down characterization of histone post-translational modifications

Tian, Z., Tolić, N., Zhao, R., Moore, R. J., Hengel, S. M., Robinson, E. W., Stenoien, D. L., Wu, S., Smith, R. D., & Paša‐Tolić, L. (2012) · Genome biology · doi:10.1186/gb-2012-13-10-r86 · Cited by 127 · see citing works

Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons

Shulha, H. P., Crisci, J. L., Reshetov, D. A., Tushir, J. S., Cheung, I. K., Bharadwaj, R. A., Chou, H.-J., Houston, I. B., Peter, C. J., Mitchell, A., et al. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001427 · Cited by 123 · see citing works

Archiving next generation sequencing data

Shumway, M. F., Cochrane, G., & Sugawara, H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1078 · Cited by 120 · see citing works

Modeling psychiatric disorders at the cellular and network levels

Brennand, K. J., Simone, A., Tran, N., & Gage, F. H. (2012) · Molecular Psychiatry · doi:10.1038/mp.2012.20 · Cited by 119 · see citing works

Chromatin proteins captured by ChIP–mass spectrometry are linked to dosage compensation in Drosophila

Wang, C. I., Alekseyenko, A. A., LeRoy, G., Elia, A. E. H., Gorchakov, A. A., Britton, L.-M. P., Elledge, S. J., Kharchenko, P. V., Garcia, B. A., & Kuroda, M. I. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2477 · Cited by 116 · see citing works

PTMap—A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites

Chen, Y., Chen, W., Cobb, M. H., & Zhao, Y. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811739106 · Cited by 102 · see citing works

A Mixed Integer Linear Optimization Framework for the Identification and Quantification of Targeted Post-translational Modifications of Highly Modified Proteins Using Multiplexed Electron Transfer Dissociation Tandem Mass Spectrometry

DiMaggio, P. A., Young, N. L., Baliban, R. C., Garcia, B. A., & Floudas, C. A. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900144-mcp200 · Cited by 90 · see citing works

Detecting differential binding of transcription factors with ChIP-seq

Liang, K., & Keleş, S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr605 · Cited by 90 · see citing works

Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans

Khrameeva, E. E., Bożek, K., He, L., Zheng, Y., Jiang, X., Wei, Y., Tang, K., Gelfand, M. S., Prüfer, K., Kelso, J. F., et al. (2014) · Nature Communications · doi:10.1038/ncomms4584 · Cited by 89 · see citing works

Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins

LeRoy, G., Chepelev, I., DiMaggio, P. A., Blanco, M. A., Zee, B. M., Zhao, K., & Garcia, B. A. (2012) · Genome Biology · doi:10.1186/gb-2012-13-8-r68 · Cited by 84 · see citing works

Interpreting Top-Down Mass Spectra Using Spectral Alignment

Frank, A. M., Pesavento, J. J., Mizzen, C. A., Kelleher, N. L., & Pevzner, P. A. (2008) · Analytical Chemistry · doi:10.1021/ac702324u · Cited by 77 · see citing works

Comparison of two-dimensional electrophoresis patterns of heat shock protein Hsp27 species in normal and cardiomyopathic hearts

Scheler, C., Li, X., Salnikow, J., Dunn, M. J., & Jungblut, P. R. (1999) · Electrophoresis · doi:10.1002/(sici)1522-2683(19991201)20:18 · Cited by 72 · see citing works

Identification and interrogation of combinatorial histone modifications

Karch, K. R., DeNizio, J. E., Black, B. E., & Garcia, B. A. (2013) · Frontiers in Genetics · doi:10.3389/fgene.2013.00264 · Cited by 70 · see citing works

Essential role of poly(ADP-ribosyl)ation in cocaine action

Scobie, K. N., Damez-Werno, D. M., Sun, H., Shao, N., Gancarz, A. M., Panganiban, C. H., Dias, C., Koo, J., Caiafa, P., Kaufman, L., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319703111 · Cited by 63 · see citing works

Intact MicroRNA Analysis Using High Resolution Mass Spectrometry

Kullolli, M., Knouf, E. C., Arampatzidou, M., et al. (2013) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-013-0759-x · Cited by 62 · see citing works

Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions

Gehlen, L. R., Gruenert, G., Jones, B., Rodley, C. D. M., Langowski, J., & O'Sullivan, J. M. (2012) · Nucleus · doi:10.4161/nucl.20971 · Cited by 61 · see citing works

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq

Xu, A. G., He, L., Li, Z., Xu, Y., Li, M., Fu, X., Zheng, Y., Yuan, Y., Menzel, C., Li, N., et al. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000843 · Cited by 58 · see citing works

Purification of a specific native genomic locus for proteomic analysis

Byrum, S. D., Taverna, S. D., & Tackett, A. J. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt822 · Cited by 57 · see citing works

Genome-wide analysis of H4K5 acetylation associated with fear memory in mice

Park, C., Rehrauer, H., & Mansuy, I. M. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-539 · Cited by 56 · see citing works

Insertional chromatin immunoprecipitation: A method for isolating specific genomic regions

Hoshino, A., & Fujii, H. (2009) · Journal of Bioscience and Bioengineering · doi:10.1016/j.jbiosc.2009.05.005 · Cited by 53 · see citing works

Decoding neural transcriptomes and epigenomes via high-throughput sequencing

Shin, J., Ming, G., & Song, H. (2014) · Nature Neuroscience · doi:10.1038/nn.3814 · Cited by 52 · see citing works

Characterization of neurohistone variants and post-translational modifications by electron capture dissociation mass spectrometry

Garcia, B. A., Siuti, N., Thomas, C. E., Mizzen, C. A., & Kelleher, N. L. (2006) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2006.07.022 · Cited by 44 · see citing works

Initial characterization of histone H3 serine 10 O-acetylation

Britton, L.-M. P., Newhart, A., Bhanu, N. V., Sridharan, R., Gonzales-Cope, M., Plath, K., Janicki, S. M., & Garcia, B. A. (2013) · Epigenetics · doi:10.4161/epi.26025 · Cited by 30 · see citing works

Modern approaches for investigating epigenetic signaling pathways

Evertts, A. G., Zee, B. M., & Garcia, B. A. (2010) · Journal of Applied Physiology · doi:10.1152/japplphysiol.00007.2010 · Cited by 30 · see citing works

Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains

Li, Z., Bammann, H., Li, M., Liang, H., Zheng, Y., Chen, Y. P., Zhao, M., & Khaitovich, P. (2013) · RNA · doi:10.1261/rna.039206.113 · Cited by 29 · see citing works

From big data to mechanism

Swarup, V., & Geschwind, D. H. (2013) · Nature · doi:10.1038/nature12457 · Cited by 24 · see citing works

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

Silbereis, J. C., Pochareddy, S., Zhu, Y., Li, M., & Sestan, N. (2016) · Neuron · doi:10.1016/j.neuron.2015.12.008 · Cited by 818 · see citing works

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

Mo, A., Mukamel, E. A., Davis, F. P., Luo, C., Henry, G. L., Picard, S., Urich, M. A., Nery, J. R., Sejnowski, T. J., Lister, R., et al. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.018 · Cited by 739 · see citing works

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

Parikshak, N. N., Gandal, M. J., & Geschwind, D. H. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3934 · Cited by 430 · see citing works

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics

Farlik, M., Sheffield, N. C., Nuzzo, A., Datlinger, P., Schönegger, A., Klughammer, J., & Bock, C. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.001 · Cited by 422 · see citing works

Epigenetic basis of mental illness

Nestler, E. J., Peña, C. J., Kundakovic, M., Mitchell, A., & Akbarian, S. (2016) · The Neuroscientist · doi:10.1177/1073858415608147 · Cited by 342 · see citing works

Peripheral biomarkers of major depression and antidepressant treatment response: Current knowledge and future outlooks

Gadad, B. S., Jha, M. K., Czysz, A., Furman, J. L., Mayes, T. L., Emslie, M. P., & Trivedi, M. H. (2018) · Journal of Affective Disorders · doi:10.1016/j.jad.2017.07.001 · Cited by 205 · see citing works

Axonal Degeneration during Aging and Its Functional Role in Neurodegenerative Disorders

Salvadores, N., Sanhueza, M., Manque, P., & Court, F. A. (2017) · Frontiers in Neuroscience · doi:10.3389/fnins.2017.00451 · Cited by 182 · see citing works

Biomarkers in Substance Use Disorders

Volkow, N. D., Koob, G., & Baler, R. (2015) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.5b00067 · Cited by 141 · see citing works

Role of the Brain's Reward Circuitry in Depression

Nestler, E. J. (2015) · International review of neurobiology · doi:10.1016/bs.irn.2015.07.003 · Cited by 108 · see citing works

Neuroepigenetic Editing

Hamilton, P. J., Lim, C. J., Nestler, E. J., & Heller, E. A. (2018) · Methods in Molecular Biology · doi:10.1007/978-1-4939-7774-1_5 · Cited by 28 · see citing works

Emerging techniques in single-cell epigenomics and their applications to cancer research.

Lo, P., & Zhou, Q. Y. (2018) · PubMed · doi:10.4172/jcg.1000103 · Cited by 41 · see citing works

Chromatin Epigenomics in Muscle Development and Disease

Perovanović, J. (2019) · Springer eBooks · doi:10.1007/978-1-4939-9802-9_3

Characterizing cis-regulatory elements using single-cell epigenomics

Preissl, S., Gaulton, K. J., & Ren, B. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-022-00509-1 · Cited by 251 · see citing works

Self-functional gold nanoprobes for intra-nuclear epigenomic monitoring of cancer stem-like cells

Verma, A. H., Ganesh, S., Venkatakrishnan, K., & Tan, B. (2021) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2021.113644 · Cited by 8 · see citing works

Institutional Profile: The Einstein Center for Epigenomics: Studying the Role of Epigenomic Dysregulation in Human Disease

McLellan, A. S., Dubin, R. A., Jing, Q., Maqbool, S. B., Olea, R., Westby, G., Broin, P. Ó., Fazzari, M. J., Zheng, D., Suzuki, M., et al. (2009) · Epigenomics · doi:10.2217/epi.09.9 · Cited by 1 · see citing works