@article{14689,
  author       = {Ing-Simmons, Elizabeth and Machnik, Nick N and Vaquerizas, Juan M.},
  issn         = {1546-1718},
  journal      = {Nature Genetics},
  number       = {12},
  pages        = {2053--2055},
  publisher    = {Springer Nature},
  title        = {{Reply to: Revisiting the use of structural similarity index in Hi-C}},
  doi          = {10.1038/s41588-023-01595-5},
  volume       = {55},
  year         = {2023},
}

@techreport{8151,
  abstract     = {The main idea behind the Core Project is to teach first year students at IST scientific communication skills and let them practice by presenting their research within an interdisciplinary environment. Over the course of the first semester, students participated in seminars, where they shared their results with the colleagues from other fields and took part in discussions on relevant subjects. The main focus during this sessions was on delivering the information in a simplified and comprehensible way, going into the very basics of a subject if necessary. At the end, the students were asked to present their research in the written form to exercise their writing skills. The reports were gathered in this document. All of them were reviewed by the  teaching assistants and write-ups illustrating unique stylistic features and, in general, an outstanding level of writing skills, were honorably mentioned in the section "Selected Reports".},
  author       = {Maslov, Mikhail and Kondrashov, Fyodor and Artner, Christina and Hennessey-Wesen, Mike and Kavcic, Bor and Machnik, Nick N and Satapathy, Roshan K and Tomanek, Isabella},
  pages        = {425},
  publisher    = {IST Austria},
  title        = {{Core Project Proceedings}},
  year         = {2020},
}

@article{8707,
  abstract     = {Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.},
  author       = { Galan, Silvia and Machnik, Nick N and Kruse, Kai and Díaz, Noelia and Marti-Renom, Marc A and Vaquerizas, Juan M},
  issn         = {15461718},
  journal      = {Nature Genetics},
  pages        = {1247--1255},
  publisher    = {Springer Nature},
  title        = {{CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction}},
  doi          = {10.1038/s41588-020-00712-y},
  volume       = {52},
  year         = {2020},
}