diff --git a/2019/01/07/example-post-1.html b/2019/01/07/example-post-1.html index 747e4df..fe5a4fb 100644 --- a/2019/01/07/example-post-1.html +++ b/2019/01/07/example-post-1.html @@ -62,10 +62,10 @@ - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + Dashnow Lab + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
+

+Blog

+ +

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. +Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.

+
+ + + + + +
+ + +
+ + +
+ +
+ + + biology + + + + medicine + + + + big data + + +
+ +
+ +

2023

+ +
+ + + Example post 3 + +
+ + + + + +
+ + member portrait + + + + + + John Doe + + + + + + + + PhD Student + + + + + +
+ + + + + + + + + + + February 23, 2023 + + + + + + + January 02, 2024 + + +
+ + + + + +
+ + + biology + + + + medicine + + +
+ + + + + + + +

+ Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. + +

+
+ +

2021

+ +
+ + + Example post 2 + +
+ + + + + +
+ + member portrait + + + + + + Jane Smith + + + + + + + + Principal Investigator + + + + + +
+ + + + + + + + + + + September 30, 2021 + + + + + + + January 02, 2024 + + +
+ + + + + + + + + + + +

+ Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. + +

+
+ +

2019

+ +
+ + + Example post 1 + +
+ + + + + +
+ + member portrait + + + + + + Sarah Johnson + + + + + + + + Lead Programmer + + + + + +
+ + + + + + + + + + + January 07, 2019 + + + + + + + January 02, 2024 + + +
+ + + + + +
+ + + biology + + + + medicine + + + + big data + + +
+ + + + + + + +

+ Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. + +

+
+
+ + +
+ + + + + + + diff --git a/contact/index.html b/contact/index.html index 4a51071..8d24465 100644 --- a/contact/index.html +++ b/contact/index.html @@ -410,6 +410,12 @@ + + Blog + + + + Contact @@ -536,37 +542,6 @@

dark: true; size: 1; --> - -
- - -
- -
- - -
- -
- - -
- -
- -
diff --git a/feed.xml b/feed.xml index 4133499..4e21d1a 100644 --- a/feed.xml +++ b/feed.xml @@ -1 +1 @@ -Jekyll2024-01-01T23:27:42+00:00/feed.xmlDashnow LabThis is the website for the Dashnow Lab. We do computational genomics in the Department of Biomedical Informatics at the University of Colorado Anschutz Medical Campus.Example post 32023-02-23T00:00:00+00:002024-01-01T23:26:17+00:00/2023/02/23/example-post-3Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

]]>john-doeExample post 22021-09-30T00:00:00+00:002024-01-01T23:26:17+00:00/2021/09/30/example-post-2Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

]]>jane-smithExample post 12019-01-07T00:00:00+00:002024-01-01T23:26:17+00:00/2019/01/07/example-post-1Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

]]>sarah-johnson \ No newline at end of file +Jekyll2024-01-02T18:15:04+00:00/feed.xmlDashnow LabThis is the website for the Dashnow Lab. We do computational genomics in the Department of Biomedical Informatics at the University of Colorado Anschutz Medical Campus.Example post 32023-02-23T00:00:00+00:002024-01-02T18:13:33+00:00/2023/02/23/example-post-3Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

]]>john-doeExample post 22021-09-30T00:00:00+00:002024-01-02T18:13:33+00:00/2021/09/30/example-post-2Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

]]>jane-smithExample post 12019-01-07T00:00:00+00:002024-01-02T18:13:33+00:00/2019/01/07/example-post-1Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

]]>sarah-johnson \ No newline at end of file diff --git a/images/Data-Interlocking.png b/images/Data-Interlocking.png new file mode 100644 index 0000000..236ea4d Binary files /dev/null and b/images/Data-Interlocking.png differ diff --git a/images/ejhg2017123f1.jpg b/images/ejhg2017123f1.jpg new file mode 100644 index 0000000..e654a5b Binary files /dev/null and b/images/ejhg2017123f1.jpg differ diff --git a/images/elegantscipy-cover.jpg b/images/elegantscipy-cover.jpg new file mode 100644 index 0000000..a4935d1 Binary files /dev/null and b/images/elegantscipy-cover.jpg differ diff --git a/index.html b/index.html index de6f2bc..eb5f849 100644 --- a/index.html +++ b/index.html @@ -410,6 +410,12 @@ + + Blog + + + + Contact @@ -470,7 +476,7 @@

Highlights

- Our Research + Our Research
@@ -492,7 +498,7 @@

Highlights

- Our Projects and Software + Our Projects and Software
@@ -514,7 +520,7 @@

Highlights

- Our Team + Our Team
diff --git a/members/harriet-dashnow.html b/members/harriet-dashnow.html index a045e17..b6ad800 100644 --- a/members/harriet-dashnow.html +++ b/members/harriet-dashnow.html @@ -358,6 +358,12 @@ + + Blog + + + + Contact diff --git a/members/jane-smith.html b/members/jane-smith.html new file mode 100644 index 0000000..6c0883d --- /dev/null +++ b/members/jane-smith.html @@ -0,0 +1,598 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Jane Smith | Dashnow Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + Dashnow Lab + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
+
+ +
+ + member portrait + + + + + + Jane Smith + + + + + + + + Principal Investigator + + + + + +
+ +
+ + + + + + + +
+ + + + Home Page + + +
+ +
+ + + + + + + +
+ + + + ORCID + + +
+ +
+ +
+ + +
+ + +

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. +Faucibus purus in massa tempor nec feugiat nisl pretium fusce. +Elit at imperdiet dui accumsan. +Duis tristique sollicitudin nibh sit amet commodo nulla facilisi. +Vitae elementum curabitur vitae nunc sed velit dignissim sodales. +Lacinia at quis risus sed vulputate odio ut. +Magna eget est lorem ipsum.

+ + + + + + +

+ + Search for Jane Smith's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/members/john-doe.html b/members/john-doe.html new file mode 100644 index 0000000..5b8eec2 --- /dev/null +++ b/members/john-doe.html @@ -0,0 +1,575 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +John Doe | Dashnow Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + Dashnow Lab + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
+
+ +
+ + member portrait + + + + + + John Doe + + + + + + + + PhD Student + + + + + +
+ +
+ + + + + + + +
+ + + + GitHub + + +
+ +
+ +
+ + +
+ + +

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

+ + + + + + +

+ + Search for John Doe's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/members/laurel-hiatt.html b/members/laurel-hiatt.html index 6ee065f..32fba97 100644 --- a/members/laurel-hiatt.html +++ b/members/laurel-hiatt.html @@ -358,6 +358,12 @@ + + Blog + + + + Contact diff --git a/members/sarah-johnson.html b/members/sarah-johnson.html new file mode 100644 index 0000000..0a88f0a --- /dev/null +++ b/members/sarah-johnson.html @@ -0,0 +1,592 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Sarah Johnson | Dashnow Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + Dashnow Lab + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
+
+ +
+ + member portrait + + + + + + Sarah Johnson + + + + + + + + Lead Programmer + + + + + +
+ +
+ + + + + + + +
+ + + + Email + + +
+ +
+ + + + + + + +
+ + + + Twitter + + +
+ +
+ +
+ + +
+ + +

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

+ + + + + + +

+ + Search for Sarah Johnson's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/projects/index.html b/projects/index.html index e5c7392..57fe3ee 100644 --- a/projects/index.html +++ b/projects/index.html @@ -410,6 +410,12 @@ + + Blog + + + + Contact diff --git a/research/index.html b/research/index.html index 7bd10b5..0178c41 100644 --- a/research/index.html +++ b/research/index.html @@ -410,6 +410,12 @@ + + Blog + + + + Contact @@ -461,95 +467,35 @@

Highlighted

- - Resolving the unsolved: Comprehensive assessment of tandem repeats at scale + + citation image
- + - - Resolving the unsolved: Comprehensive assessment of tandem repeats at scale + + [no title info] -
- Egor Dolzhenko, Adam English, Harriet Dashnow, Guilherme De Sena Brandine, Tom Mokveld, ..., Stephan Zuchner, Tomi Pastinen, Aaron R. Quinlan, Fritz J. Sedlazeck, Michael A Eberle +
+ [no author info]
- Cold Spring Harbor Laboratory + [no publisher info]   ·   - 14 May 2023 + [no date info]   ·   - doi:10.1101/2023.05.12.540470 + [no id info]
-
- TRGT genotypes tandem repeats from PacBio HiFi long read data and visualizes them with TRVZ. - -
- -
- - - - - -
- - - - Manuscript Supporting Code - - -
- - - - - - - -
- - - - Website - - -
- - - -
- - - - - - -
- - - long reads - - - - STRs - - - - VNTRs - - -
- @@ -583,107 +529,8 @@

2023

- - Resolving the unsolved: Comprehensive assessment of tandem repeats at scale - - - -
- - - - - Resolving the unsolved: Comprehensive assessment of tandem repeats at scale - - -
- Egor Dolzhenko, Adam English, Harriet Dashnow, Guilherme De Sena Brandine, Tom Mokveld, ..., Stephan Zuchner, Tomi Pastinen, Aaron R. Quinlan, Fritz J. Sedlazeck, Michael A Eberle -
- -
- Cold Spring Harbor Laboratory -   ·   - 14 May 2023 -   ·   - doi:10.1101/2023.05.12.540470 -
- - - -
- TRGT genotypes tandem repeats from PacBio HiFi long read data and visualizes them with TRVZ. - -
- - - -
- - - - - -
- - - - Manuscript Supporting Code - - -
- - - - - - - -
- - - - Website - - -
- - - -
- - - - - - -
- - - long reads - - - - STRs - - - - VNTRs - - -
- - - - -
-
- -

2022

- -
- - - STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci + + MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes @@ -691,20 +538,20 @@

2022

- - STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci + + MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes -
- Harriet Dashnow, Brent S. Pedersen, Laurel Hiatt, Joe Brown, Sarah J. Beecroft, ..., Miriam J. Rodrigues, Mark Davis, Heather C. Mefford, Nigel G. Laing, Aaron R. Quinlan +
+ Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu
- Genome Biology + Nucleic Acids Research   ·   - 14 Dec 2022 + 18 Apr 2023   ·   - doi:10.1186/s13059-022-02826-4 + doi:10.1093/nar/gkad289
@@ -713,33 +560,14 @@

2022

- - - -
- - - short reads - - - - STRs - - -
- - -
-

2021

-
- - Effective variant filtering and expected candidate variant yield in studies of rare human disease + + Hetnet connectivity search provides rapid insights into how two biomedical entities are related @@ -747,20 +575,20 @@

2021

- - Effective variant filtering and expected candidate variant yield in studies of rare human disease + + Hetnet connectivity search provides rapid insights into how two biomedical entities are related -
- Brent S. Pedersen, Joe M. Brown, Harriet Dashnow, Amelia D. Wallace, Matt Velinder, ..., Tatiana Tvrdik, Rong Mao, D. Hunter Best, Pinar Bayrak-Toydemir, Aaron R. Quinlan +
+ Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, ..., David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene
- npj Genomic Medicine + Cold Spring Harbor Laboratory   ·   - 15 Jul 2021 + 07 Jan 2023   ·   - doi:10.1038/s41525-021-00227-3 + doi:10.1101/2023.01.05.522941
@@ -773,12 +601,12 @@

2021

-

2019

+

2022

- - Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software + + Hetnet connectivity search provides rapid insights into how biomedical entities are related @@ -786,20 +614,20 @@

2019

- - Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software + + Hetnet connectivity search provides rapid insights into how biomedical entities are related -
- Peter Georgeson, Anna Syme, Clare Sloggett, Jessica Chung, Harriet Dashnow, Michael Milton, Andrew Lonsdale, David Powell, Torsten Seemann, Bernard Pope +
+ Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, ..., David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene
GigaScience   ·   - 01 Sep 2019 + 28 Dec 2022   ·   - doi:10.1093/gigascience/giz109 + doi:10.1093/gigascience/giad047
@@ -812,242 +640,120 @@

2019

+

2020

+
- - Elegant SciPy + + Open collaborative writing with Manubot
- + - - Elegant SciPy + + Open collaborative writing with Manubot
- [no author info] + Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
- O'Reilly Media, Inc. + PLOS Computational Biology   ·   - 01 Aug 2019 + 04 Dec 2020   ·   - : + doi:10.1371/journal.pcbi.1007128
+
+ Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. +
- -
-
- -
- - - Pooled-parent exome sequencing to prioritise <i>de novo</i> variants in genetic disease - - - -
- - +
+ + - - Pooled-parent exome sequencing to prioritise de novo variants in genetic disease - -
- Harriet Dashnow, Katrina M. Bell, Zornitza Stark, Tiong Y. Tan, Susan M. White, Alicia Oshlack -
- -
- Cold Spring Harbor Laboratory -   ·   - 07 Apr 2019 -   ·   - doi:10.1101/601740 -
- - - +
+ + - + Manubot - -
-
- -

2018

- -
- - - STRetch: detecting and discovering pathogenic short tandem repeat expansions - - -
- - +
- - STRetch: detecting and discovering pathogenic short tandem repeat expansions - -
- Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, ..., Phillipa Lamont, Joshua S. Clayton, Nigel G. Laing, Daniel G. MacArthur, Alicia Oshlack -
+ + -
- Genome Biology -   ·   - 21 Aug 2018 -   ·   - doi:10.1186/s13059-018-1505-2 -
- - +
+ + - + Manuscript Source - -
-
- -

2017

- -
- - - A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data - - -
- - +
- - A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data - -
- Zornitza Stark, Harriet Dashnow, Sebastian Lunke, Tiong Y Tan, Alison Yeung, ..., Ivan Macciocca, Clara Gaff, Alicia Oshlack, Susan M White, Paul A James -
+ + -
- European Journal of Human Genetics -   ·   - 23 Aug 2017 -   ·   - doi:10.1038/ejhg.2017.123 -
- - +
+ + - + Website - -
-
- -

2016

- -
- - - Ten Simple Rules for a Bioinformatics Journal Club - - -
- - - - - Ten Simple Rules for a Bioinformatics Journal Club - - -
- Andrew Lonsdale, Jocelyn Sietsma Penington, Timothy Rice, Michael Walker, Harriet Dashnow -
- -
- PLOS Computational Biology -   ·   - 28 Jan 2016 -   ·   - doi:10.1371/journal.pcbi.1004526 -
+
- - + +
- -
-
+ -

2015

-
- - - Cpipe: a shared variant detection pipeline designed for diagnostic settings - - - -
+
+ + open science + - - - Cpipe: a shared variant detection pipeline designed for diagnostic settings - - -
- Simon P. Sadedin, Harriet Dashnow, Paul A. James, Melanie Bahlo, Denis C. Bauer, ..., Susan M. White, Graham Taylor, Clara Gaff, Alicia Oshlack, Natalie P. Thorne -
- -
- Genome Medicine -   ·   - 10 Jul 2015 -   ·   - doi:10.1186/s13073-015-0191-x -
- + + collaboration + - +
-
-

2014

-
- - Data Interlocking: Coupling Analytics to the Data + + Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations @@ -1055,20 +761,20 @@

2014

- - Data Interlocking: Coupling Analytics to the Data + + Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
- Yousef Kowsar, Harriet Dashnow, Andrew Lonie + Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
- 2014 IEEE/ACM 7th International Conference on Utility and Cloud Computing + Genome Biology   ·   - 01 Dec 2014 + 11 May 2020   ·   - doi:10.1109/ucc.2014.113 + doi:10.1186/s13059-020-02021-3
@@ -1083,8 +789,8 @@

2014

- - SRST2: Rapid genomic surveillance for public health and hospital microbiology labs + + Constructing knowledge graphs and their biomedical applications @@ -1092,20 +798,20 @@

2014

- - SRST2: Rapid genomic surveillance for public health and hospital microbiology labs + + Constructing knowledge graphs and their biomedical applications
- Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel, Kathryn E Holt + David N. Nicholson, Casey S. Greene
- Genome Medicine + Computational and Structural Biotechnology Journal   ·   - 20 Nov 2014 + 01 Jan 2020   ·   - doi:10.1186/s13073-014-0090-6 + doi:10.1016/j.csbj.2020.05.017
@@ -1118,10 +824,12 @@

2014

+

2019

+
- - Ten Simple Rules for Writing a PLOS Ten Simple Rules Article + + Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality @@ -1129,20 +837,20 @@

2014

- - Ten Simple Rules for Writing a PLOS Ten Simple Rules Article + + Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
- Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne + Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
- PLoS Computational Biology + Cold Spring Harbor Laboratory   ·   - 23 Oct 2014 + 11 Mar 2019   ·   - doi:10.1371/journal.pcbi.1003858 + doi:10.1101/573782
@@ -1155,12 +863,12 @@

2014

-

2012

+

2018

- - Development of Transgenic Mice Containing an Introduced Stop Codon on the Human Methylmalonyl-CoA Mutase Locus + + Sci-Hub provides access to nearly all scholarly literature @@ -1168,20 +876,20 @@

2012

- - Development of Transgenic Mice Containing an Introduced Stop Codon on the Human Methylmalonyl-CoA Mutase Locus + + Sci-Hub provides access to nearly all scholarly literature
- Nicole E. Buck, Harriet Dashnow, James J. Pitt, Leonie R. Wood, Heidi L. Peters + Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
- PLoS ONE + eLife   ·   - 14 Sep 2012 + 01 Mar 2018   ·   - doi:10.1371/journal.pone.0044974 + doi:10.7554/eLife.32822
diff --git a/sitemap.xml b/sitemap.xml index a1d9026..f32134d 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -2,46 +2,62 @@ /members/harriet-dashnow.html -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 + + +/members/jane-smith.html +2024-01-02T18:13:33+00:00 + + +/members/john-doe.html +2024-01-02T18:13:33+00:00 /members/laurel-hiatt.html -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 + + +/members/sarah-johnson.html +2024-01-02T18:13:33+00:00 /2019/01/07/example-post-1.html -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 /2021/09/30/example-post-2.html -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 /2023/02/23/example-post-3.html -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 /research/ -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 + + +/blog/ +2024-01-02T18:13:33+00:00 /contact/ -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 /projects/ -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 /team/ -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 / -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 /testbed.html -2024-01-01T23:26:17+00:00 +2024-01-02T18:13:33+00:00 diff --git a/team/index.html b/team/index.html index 012b292..9358525 100644 --- a/team/index.html +++ b/team/index.html @@ -410,6 +410,12 @@ + + Blog + + + + Contact @@ -522,6 +528,54 @@

+
+ + member portrait + + + + + + Jane Smith + + + + + + + + Principal Investigator + + + + + +
+ +
+ + member portrait + + + + + + John Doe + + + + + + + + PhD Student + + + + + +
+
member portrait @@ -546,6 +600,30 @@

+
+ + member portrait + + + + + + Sarah Johnson + + + + + + + + Lead Programmer + + + + + +
+

Values

+

2019

+
@@ -1389,27 +1223,27 @@

2014

- - Ten Simple Rules for Writing a PLOS Ten Simple Rules Article + + Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
- Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne + Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
- PLoS Computational Biology + Cold Spring Harbor Laboratory   ·   - 23 Oct 2014 + 11 Mar 2019   ·   - doi:10.1371/journal.pcbi.1003858 + doi:10.1101/573782
-

2012

+

2018

@@ -1418,20 +1252,20 @@

2012

- - Development of Transgenic Mice Containing an Introduced Stop Codon on the Human Methylmalonyl-CoA Mutase Locus + + Sci-Hub provides access to nearly all scholarly literature
- Nicole E. Buck, Harriet Dashnow, James J. Pitt, Leonie R. Wood, Heidi L. Peters + Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
- PLoS ONE + eLife   ·   - 14 Sep 2012 + 01 Mar 2018   ·   - doi:10.1371/journal.pone.0044974 + doi:10.7554/eLife.32822
@@ -1638,6 +1472,54 @@

List team members

+
+ + member portrait + + + + + + Jane Smith + + + + + + + + Principal Investigator + + + + + +
+ +
+ + member portrait + + + + + + John Doe + + + + + + + + PhD Student + + + + + +
+
member portrait @@ -1662,6 +1544,30 @@

List team members
+
+ + member portrait + + + + + + Sarah Johnson + + + + + + + + Lead Programmer + + + + + +
+

List blog posts

@@ -1677,11 +1583,33 @@

2023

- - - john-doe + + +
+ + member portrait + + + + + + John Doe + + + + + + + + PhD Student + + + +
+ + @@ -1697,7 +1625,7 @@

2023

- January 01, 2024 + January 02, 2024
@@ -1741,11 +1669,33 @@

2021

- - - jane-smith + + +
+ + member portrait + + + + + + Jane Smith + + + + + + + + Principal Investigator + + + +
+ + @@ -1761,7 +1711,7 @@

2021

- January 01, 2024 + January 02, 2024
@@ -1793,11 +1743,33 @@

2019

- - - sarah-johnson + + +
+ + member portrait + + + + + + Sarah Johnson + + + + + + + + Lead Programmer + + + +
+ + @@ -1813,7 +1785,7 @@

2019

- January 01, 2024 + January 02, 2024
@@ -1871,20 +1843,20 @@

Citation

- - [no title info] + + Constructing knowledge graphs and their biomedical applications
- [no author info] + David N. Nicholson, Casey S. Greene
- [no publisher info] + Computational and Structural Biotechnology Journal   ·   - [no date info] + 01 Jan 2020   ·   - [no id info] + doi:10.1016/j.csbj.2020.05.017
@@ -1893,37 +1865,108 @@

Citation

- - citation image + + Open collaborative writing with Manubot
- + - - [no title info] + + Open collaborative writing with Manubot
- [no author info] + Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
- [no publisher info] + PLOS Computational Biology   ·   - [no date info] + 04 Dec 2020   ·   - [no id info] + doi:10.1371/journal.pcbi.1007128
+
+ Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. + +
+ + + +
+ + + + + +
+ + + + Manubot + + +
+ + + + + + + +
+ + + + Manuscript Source + + +
+ + + + + + + +
+ + + + Website + + +
+ + +
+ + + +
+ + + open science + + + + collaboration + + +
+ + +
@@ -2052,18 +2095,50 @@

Card

Portrait

- - member portrait + + member portrait + + + + Jane Smith + + + + + + + + Principal Investigator + + + +
- - member portrait + + member portrait + + + + John Doe + + + + + + + + PhD Student + + + +
@@ -2116,11 +2191,33 @@

Post Excerpt

- - - sarah-johnson + + +
+ + member portrait + + + + + + Sarah Johnson + + + + + + + + Lead Programmer + + + +
+ + @@ -2136,7 +2233,7 @@

Post Excerpt

- January 01, 2024 + January 02, 2024
@@ -2472,109 +2569,22 @@

2023

- - - - Resolving the unsolved: Comprehensive assessment of tandem repeats at scale - - -
- Egor Dolzhenko, Adam English, Harriet Dashnow, Guilherme De Sena Brandine, Tom Mokveld, ..., Stephan Zuchner, Tomi Pastinen, Aaron R. Quinlan, Fritz J. Sedlazeck, Michael A Eberle -
- -
- Cold Spring Harbor Laboratory -   ·   - 14 May 2023 -   ·   - doi:10.1101/2023.05.12.540470 -
- -
-
- -

2022

- -
- -
- - - - - STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci - - -
- Harriet Dashnow, Brent S. Pedersen, Laurel Hiatt, Joe Brown, Sarah J. Beecroft, ..., Miriam J. Rodrigues, Mark Davis, Heather C. Mefford, Nigel G. Laing, Aaron R. Quinlan -
- -
- Genome Biology -   ·   - 14 Dec 2022 -   ·   - doi:10.1186/s13059-022-02826-4 -
- - -
-
- -

2021

- -
- - -
- - - - - Effective variant filtering and expected candidate variant yield in studies of rare human disease - - -
- Brent S. Pedersen, Joe M. Brown, Harriet Dashnow, Amelia D. Wallace, Matt Velinder, ..., Tatiana Tvrdik, Rong Mao, D. Hunter Best, Pinar Bayrak-Toydemir, Aaron R. Quinlan -
- -
- npj Genomic Medicine -   ·   - 15 Jul 2021 -   ·   - doi:10.1038/s41525-021-00227-3 -
- - -
-
- -

2019

- -
- - -
- - - - - Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software + + MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
- Peter Georgeson, Anna Syme, Clare Sloggett, Jessica Chung, Harriet Dashnow, Michael Milton, Andrew Lonsdale, David Powell, Torsten Seemann, Bernard Pope + Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu
- GigaScience + Nucleic Acids Research   ·   - 01 Sep 2019 + 18 Apr 2023   ·   - doi:10.1093/gigascience/giz109 + doi:10.1093/nar/gkad289
@@ -2588,83 +2598,27 @@

2019

- - Elegant SciPy + + Hetnet connectivity search provides rapid insights into how two biomedical entities are related -
- [no author info] -
- -
- O'Reilly Media, Inc. -   ·   - 01 Aug 2019 -   ·   - : -
- - -
-
- -
- - -
- - - - - Pooled-parent exome sequencing to prioritise de novo variants in genetic disease - - -
- Harriet Dashnow, Katrina M. Bell, Zornitza Stark, Tiong Y. Tan, Susan M. White, Alicia Oshlack +
+ Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, ..., David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene
Cold Spring Harbor Laboratory   ·   - 07 Apr 2019 + 07 Jan 2023   ·   - doi:10.1101/601740 + doi:10.1101/2023.01.05.522941
-

2018

- -
- - -
- - - - - STRetch: detecting and discovering pathogenic short tandem repeat expansions - - -
- Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, ..., Phillipa Lamont, Joshua S. Clayton, Nigel G. Laing, Daniel G. MacArthur, Alicia Oshlack -
- -
- Genome Biology -   ·   - 21 Aug 2018 -   ·   - doi:10.1186/s13059-018-1505-2 -
- - -
-
- -

2017

+

2022

@@ -2673,86 +2627,55 @@

2017

- - A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data + + Hetnet connectivity search provides rapid insights into how biomedical entities are related -
- Zornitza Stark, Harriet Dashnow, Sebastian Lunke, Tiong Y Tan, Alison Yeung, ..., Ivan Macciocca, Clara Gaff, Alicia Oshlack, Susan M White, Paul A James +
+ Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, ..., David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene
- European Journal of Human Genetics + GigaScience   ·   - 23 Aug 2017 + 28 Dec 2022   ·   - doi:10.1038/ejhg.2017.123 + doi:10.1093/gigascience/giad047
-

2016

+

2020

- + - - Ten Simple Rules for a Bioinformatics Journal Club + + Open collaborative writing with Manubot
- Andrew Lonsdale, Jocelyn Sietsma Penington, Timothy Rice, Michael Walker, Harriet Dashnow + Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology   ·   - 28 Jan 2016 -   ·   - doi:10.1371/journal.pcbi.1004526 -
- - -
-
- -

2015

- -
- - -
- - - - - Cpipe: a shared variant detection pipeline designed for diagnostic settings - - -
- Simon P. Sadedin, Harriet Dashnow, Paul A. James, Melanie Bahlo, Denis C. Bauer, ..., Susan M. White, Graham Taylor, Clara Gaff, Alicia Oshlack, Natalie P. Thorne -
- -
- Genome Medicine -   ·   - 10 Jul 2015 + 04 Dec 2020   ·   - doi:10.1186/s13073-015-0191-x + doi:10.1371/journal.pcbi.1007128
-

2014

-
@@ -2760,20 +2683,20 @@

2014

- - Data Interlocking: Coupling Analytics to the Data + + Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
- Yousef Kowsar, Harriet Dashnow, Andrew Lonie + Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
- 2014 IEEE/ACM 7th International Conference on Utility and Cloud Computing + Genome Biology   ·   - 01 Dec 2014 + 11 May 2020   ·   - doi:10.1109/ucc.2014.113 + doi:10.1186/s13059-020-02021-3
@@ -2787,26 +2710,28 @@

2014

- - SRST2: Rapid genomic surveillance for public health and hospital microbiology labs + + Constructing knowledge graphs and their biomedical applications
- Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel, Kathryn E Holt + David N. Nicholson, Casey S. Greene
- Genome Medicine + Computational and Structural Biotechnology Journal   ·   - 20 Nov 2014 + 01 Jan 2020   ·   - doi:10.1186/s13073-014-0090-6 + doi:10.1016/j.csbj.2020.05.017
+

2019

+
@@ -2814,27 +2739,27 @@

2014

- - Ten Simple Rules for Writing a PLOS Ten Simple Rules Article + + Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
- Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne + Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
- PLoS Computational Biology + Cold Spring Harbor Laboratory   ·   - 23 Oct 2014 + 11 Mar 2019   ·   - doi:10.1371/journal.pcbi.1003858 + doi:10.1101/573782
-

2012

+

2018

@@ -2843,20 +2768,20 @@

2012

- - Development of Transgenic Mice Containing an Introduced Stop Codon on the Human Methylmalonyl-CoA Mutase Locus + + Sci-Hub provides access to nearly all scholarly literature
- Nicole E. Buck, Harriet Dashnow, James J. Pitt, Leonie R. Wood, Heidi L. Peters + Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
- PLoS ONE + eLife   ·   - 14 Sep 2012 + 01 Mar 2018   ·   - doi:10.1371/journal.pone.0044974 + doi:10.7554/eLife.32822
@@ -2881,11 +2806,33 @@

2023

- - - john-doe + + +
+ + member portrait + + + + + + John Doe + + + + + + + + PhD Student + + + +
+ + @@ -2901,7 +2848,7 @@

2023

- January 01, 2024 + January 02, 2024
@@ -2945,11 +2892,33 @@

2021

- - - jane-smith + + +
+ + member portrait + + + + + + Jane Smith + + + + + + + + Principal Investigator + + + +
+ + @@ -2965,7 +2934,7 @@

2021

- January 01, 2024 + January 02, 2024 @@ -2997,11 +2966,33 @@

2019

- - - sarah-johnson + + +
+ + member portrait + + + + + + Sarah Johnson + + + + + + + + Lead Programmer + + + +
+ + @@ -3017,7 +3008,7 @@

2019

- January 01, 2024 + January 02, 2024