From 266d73edfedf01bce1f1de1dcef11da952d91fb0 Mon Sep 17 00:00:00 2001 From: David Kouril Date: Thu, 29 Jan 2026 11:18:59 -0500 Subject: [PATCH 1/4] citation section --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 97f01c3..18063c0 100644 --- a/README.md +++ b/README.md @@ -27,3 +27,5 @@ pnpm run docs Led by [David Kouřil](https://davidkouril.com) @ [HIDIVE lab](http://hidivelab.org) (Harvard Medical School). The name **uchimata** roughly abbreviates "**u**nderstanding **ch**romatin **i**n **m**odels **a**pproximating **t**hree-dimensional **a**rchitecture". The tool was previously known as *chromospace*. + +### Citation From bb65ea27a034ce19e3eaadaeb055009ec494a0c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Kou=C5=99il?= Date: Thu, 29 Jan 2026 11:25:30 -0500 Subject: [PATCH 2/4] Add citation section to README Added citation information for the uchimata tool. --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 18063c0..c1d78cb 100644 --- a/README.md +++ b/README.md @@ -29,3 +29,6 @@ Led by [David Kouřil](https://davidkouril.com) @ [HIDIVE lab](http://hidivelab. The name **uchimata** roughly abbreviates "**u**nderstanding **ch**romatin **i**n **m**odels **a**pproximating **t**hree-dimensional **a**rchitecture". The tool was previously known as *chromospace*. ### Citation +If you use uchimata, please consider citing our Bioinformatics paper: + +> David Kouřil, Trevor Manz, Tereza Clarence, Nils Gehlenborg. "Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks", Bioinformatics *btag035* (2026), [doi.org/10.1093/bioinformatics/btag035](https://doi.org/10.1093/bioinformatics/btag035) From 4e73a5aabde054b4b593001429b2835ad9bca1ef Mon Sep 17 00:00:00 2001 From: David Kouril Date: Thu, 29 Jan 2026 14:12:45 -0500 Subject: [PATCH 3/4] add citation.cff file --- CITATION.cff | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..caf85de --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,43 @@ +cff-version: 1.2.0 +title: uchimata +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software +authors: + - given-names: David + family-names: Kouřil + email: david.kouril@gmail.com + affiliation: Harvard Medical School + orcid: 'https://orcid.org/0000-0003-4043-3487' + - given-names: Trevor + family-names: Manz + affiliation: Harvard Medical School + orcid: 'https://orcid.org/0000-0001-7694-5164' +repository-code: 'https://github.com/hms-dbmi/dvdkouril' +url: 'http://hms-dbmi.github.io/uchimata/' +license: MIT +preferred-citation: + type: article + title: "Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks" + authors: + - given-names: "David" + family-names: "Kouril" + orcid: "https://orcid.org/0000-0003-4043-3487" + affiliation: "Harvard Medical School" + - given-names: "Trevor" + family-names: "Manz" + orcid: "https://orcid.org/0000-0001-7694-5164" + affiliation: "Harvard Medical School" + - given-names: "Tereza" + family-names: "Clarence" + orcid: "https://orcid.org/0000-0002-0099-2797" + affiliation: "Icahn School of Medicine at Mount Sinai" + - given-names: "Nils" + family-names: "Gehlenborg" + affiliation: "Harvard Medical School" + orcid: "https://orcid.org/0000-0003-0327-8297" + doi: "10.1093/bioinformatics/btag035" + journal: "Bioinformatics" + month: 1 + year: 2026 From 0e519c3ea28c8d965e22c9e22cd9b47f61e19ab9 Mon Sep 17 00:00:00 2001 From: David Kouril Date: Tue, 17 Feb 2026 15:34:19 -0500 Subject: [PATCH 4/4] volume and issue numbers --- CITATION.cff | 7 +++++-- README.md | 2 +- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index caf85de..990e66c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -22,7 +22,7 @@ preferred-citation: title: "Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks" authors: - given-names: "David" - family-names: "Kouril" + family-names: "Kouřil" orcid: "https://orcid.org/0000-0003-4043-3487" affiliation: "Harvard Medical School" - given-names: "Trevor" @@ -39,5 +39,8 @@ preferred-citation: orcid: "https://orcid.org/0000-0003-0327-8297" doi: "10.1093/bioinformatics/btag035" journal: "Bioinformatics" - month: 1 + month: 2 year: 2026 + volume: 42 + issue: 2 + diff --git a/README.md b/README.md index c1d78cb..f73a43a 100644 --- a/README.md +++ b/README.md @@ -31,4 +31,4 @@ The name **uchimata** roughly abbreviates "**u**nderstanding **ch**romatin **i** ### Citation If you use uchimata, please consider citing our Bioinformatics paper: -> David Kouřil, Trevor Manz, Tereza Clarence, Nils Gehlenborg. "Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks", Bioinformatics *btag035* (2026), [doi.org/10.1093/bioinformatics/btag035](https://doi.org/10.1093/bioinformatics/btag035) +> David Kouřil, Trevor Manz, Tereza Clarence, Nils Gehlenborg. "Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks", Bioinformatics **42**(2):*btag035* (2026), [doi.org/10.1093/bioinformatics/btag035](https://doi.org/10.1093/bioinformatics/btag035)