All Stories

  1. Cytokine-induced Chromatin Accessibility in Whole Blood Neutrophils Links to Sepsis Transcriptional States

    Article • February 2026, openRxiv

    Benjamin Berman

  2. Chromatin Changes Associated with Neutrophil Extracellular Trap (NET) Formation in Whole Blood Reflect Complex Immune Signaling

    Article • January 2025, Cold Spring Harbor Laboratory Press

    Benjamin Berman

  3. CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes

    Article • Genome Biology, June 2024, Springer Science + Business Media

    Benjamin Berman

  4. Understanding Complex Chromatin Dynamics of Primary Human Neutrophils During PMA Induced NETosis

    Article • June 2024, Cold Spring Harbor Laboratory Press

    Benjamin Berman

  5. Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer

    Article • May 2024, Cold Spring Harbor Laboratory Press

    Benjamin Berman

  6. Multi-cell type deconvolution using a probabilistic model for single-molecule DNA methylation haplotypes

    Article • August 2023, Cold Spring Harbor Laboratory Press

    Benjamin Berman

  7. Muscle injury causes long-term changes in stem-cell DNA methylation

    Article • Proceedings of the National Academy of Sciences, December 2022, Proceedings of the National Academy of Sciences

    Tal Falick Michaeli, Benjamin Berman

  8. A local sequence signature defines a subset of heterochromatin-associated CpGs with minimal loss of methylation in healthy tissues but extensive loss in cancer

    Article • August 2022, Cold Spring Harbor Laboratory Press

    Benjamin Berman

  9. Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

    Article • October 2021, Cold Spring Harbor Laboratory Press

    Benjamin Berman

  10. Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome

    Article • eLife, August 2021, eLife

    Benjamin Berman

  11. Publisher Correction: A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes

    Article • Nature Communications, June 2021, Springer Science + Business Media

    Benjamin Berman

  12. A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes

    Article • Nature Communications, April 2021, Springer Science + Business Media

    Benjamin Berman

  13. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

    Article • Science Advances, December 2018, American Association for the Advancement of Science

    Benjamin Berman

  14. Author Correction: Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A

    Article • Scientific Reports, April 2018, Springer Science + Business Media

    Benjamin Berman

  15. TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data

    Article • F1000Research, April 2018, Faculty of 1000, Ltd.

    Tiago Chedraoui Silva, Pr Gianluca Bontempi, Benjamin Berman, Dr Tathi Malta

  16. DNA methylation loss in late-replicating domains is linked to mitotic cell division

    Article • Nature Genetics, April 2018, Springer Science + Business Media

    Benjamin Berman

  17. Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A

    Article • Scientific Reports, March 2018, Springer Science + Business Media

    Benjamin Berman

  18. Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas

    Article • Gut, August 2017, BMJ

    Benjamin Berman

  19. Exosomal MicroRNA Transfer Into Macrophages Mediates Cellular Postconditioning

    Article • Circulation, July 2017, Wolters Kluwer Health

    Benjamin Berman

  20. ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Tiago Chedraoui Silva, Benjamin Berman

  21. TCGAbiolinksGUI: A graphical user interface to analyze GDC cancer molecular and clinical data

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Benjamin Berman

  22. Chromatin states simplified

    Article • April 2017, Cold Spring Harbor Laboratory Press

    Dennis Hazelett, Benjamin Berman

  23. Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma

    Article • Cancer Research, February 2017, American Association for Cancer Research (AACR)

    Benjamin Berman

  24. Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma

    Article • Nature Genetics, October 2016, Springer Science + Business Media

    Benjamin Berman

  25. The PsychENCODE project

    Article • Nature Neuroscience, November 2015, Springer Science + Business Media

    Benjamin Berman

  26. FOXC1 Activates Smoothened-Independent Hedgehog Signaling in Basal-like Breast Cancer

    Article • Cell Reports, November 2015, Elsevier

    Benjamin Berman

  27. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes

    Article • Critical Reviews in Biochemistry and Molecular Biology, October 2015, Taylor & Francis

    Benjamin Berman

  28. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

    Article • Genome Biology, May 2015, Springer Science + Business Media

    Benjamin Berman

  29. Gender-specific postnatal demethylation and establishment of epigenetic memory

    Article • Genes & Development, May 2015, Cold Spring Harbor Laboratory Press

    Benjamin Berman

  30. The role of DNA methylation in directing the functional organization of the cancer epigenome

    Article • Genome Research, March 2015, Cold Spring Harbor Laboratory Press

    Benjamin Berman

  31. Functional annotation of colon cancer risk SNPs

    Article • Nature Communications, September 2014, Springer Science + Business Media

    Benjamin Berman

  32. Multiscale representation of genomic signals

    Article • Nature Chemical Biology, April 2014, Springer Science + Business Media

    Benjamin Berman

  33. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue

    Article • Nature Communications, February 2014, Springer Science + Business Media

    Benjamin Berman

  34. Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes

    Article • Genome Biology, January 2014, Springer Science + Business Media

    Benjamin Berman

  35. Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1

    Article • Human Molecular Genetics, November 2013, Oxford University Press (OUP)

    Benjamin Berman

  36. The Cancer Genome Atlas Pan-Cancer analysis project

    Article • Nature Genetics, September 2013, Springer Science + Business Media

    Benjamin Berman

  37. Comprehensive molecular characterization of clear cell renal cell carcinoma

    Article • Nature, June 2013, Springer Science + Business Media

    Benjamin Berman

  38. Integrated Transcriptomic and Epigenomic Analysis of Primary Human Lung Epithelial Cell Differentiation

    Article • PLoS Genetics, June 2013, PLOS

    Benjamin Berman

  39. Comprehensive molecular portraits of human breast tumours

    Article • Nature, September 2012, Springer Science + Business Media

    Benjamin Berman

  40. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

    Article • Genome Research, September 2012, Cold Spring Harbor Laboratory Press

    Benjamin Berman

  41. Comprehensive molecular characterization of human colon and rectal cancer

    Article • Nature, July 2012, Springer Science + Business Media

    Benjamin Berman

  42. FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs

    Article • Nucleic Acids Research, June 2012, Oxford University Press (OUP)

    Benjamin Berman

  43. An Evaluation of the Cost and Performance of Scientific Workflows on Amazon EC2

    Article • Journal of Grid Computing, March 2012, Springer Science + Business Media

    Benjamin Berman

  44. Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

    Article • Genome Biology, January 2012, Springer Science + Business Media

    Benjamin Berman

  45. Exploring the cancer methylome

    Article • BMC Proceedings, January 2012, Springer Science + Business Media

    Benjamin Berman

  46. Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion

    Article • Nucleic Acids Research, December 2011, Oxford University Press (OUP)

    Benjamin Berman

  47. Opposing Effects of Runx2 and Estradiol on Breast Cancer Cell Proliferation: In Vitro Identification of Reciprocally Regulated Gene Signature Related to Clinical Letrozole Responsiveness

    Article • Clinical Cancer Research, December 2011, American Association for Cancer Research (AACR)

    Benjamin Berman

  48. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

    Article • Nature Genetics, November 2011, Springer Science + Business Media

    Benjamin Berman

  49. Dynamic Nucleosome-Depleted Regions at Androgen Receptor Enhancers in the Absence of Ligand in Prostate Cancer Cells

    Article • Molecular and Cellular Biology, October 2011, ASM Journals

    Benjamin Berman

  50. Data Sharing Options for Scientific Workflows on Amazon EC2

    Article • November 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Benjamin Berman

  51. Vitamin C Promotes Widespread Yet Specific DNA Demethylation of the Epigenome in Human Embryonic Stem Cells

    Article • Stem Cells, October 2010, Wiley

    Benjamin Berman

  52. H2A.Z Maintenance during Mitosis Reveals Nucleosome Shifting on Mitotically Silenced Genes

    Article • Molecular Cell, September 2010, Elsevier

    Benjamin Berman

  53. Androgen receptor responsive enhancers are flanked by consistently-positioned H3-acetylated nucleosomes

    Article • Cell Cycle, June 2010, Taylor & Francis

    Benjamin Berman

  54. Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

    Article • Cancer Cell, May 2010, Elsevier

    Benjamin Berman

  55. Scientific workflow applications on Amazon EC2

    Article • December 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Benjamin Berman

  56. Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus

    Article • PLoS Genetics, August 2009, PLOS

    Benjamin Berman

  57. Location, location, (ChIP-)location! Mapping chromatin landscapes one immunoprecipitation at a time

    Article • Journal of Cellular Biochemistry, May 2009, Wiley

    Benjamin Berman

  58. Locking in on the human methylome

    Article • Nature Biotechnology, April 2009, Springer Science + Business Media

    Benjamin Berman

  59. Genomic Androgen Receptor-Occupied Regions with Different Functions, Defined by Histone Acetylation, Coregulators and Transcriptional Capacity

    Article • PLOS One, November 2008, PLOS

    Benjamin Berman

  60. Global analysis of patterns of gene expression during Drosophila embryogenesis

    Article • Genome Biology, January 2007, Springer Science + Business Media

    Benjamin Berman

  61. Article • Genome Biology, January 2004, Springer Science + Business Media

    Benjamin Berman

  62. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

    Article • Proceedings of the National Academy of Sciences, January 2002, Proceedings of the National Academy of Sciences

    Benjamin Berman

  63. Article • Genome Biology, January 2002, Springer Science + Business Media

    Benjamin Berman

  64. Article • Genome Biology, January 2002, Springer Science + Business Media

    Benjamin Berman

  65. A BAC-Based Physical Map of the Major Autosomes of Drosophila melanogaster

    Article • Science, March 2000, American Association for the Advancement of Science

    Benjamin Berman

  66. The Genome Sequence of Drosophila melanogaster

    Article • Science, March 2000, American Association for the Advancement of Science

    Benjamin Berman

  67. Optical character recognition for typeset mathematics

    Article • January 1994, ACM (Association for Computing Machinery)

    Benjamin Berman