diff --git a/_data/citations.yaml b/_data/citations.yaml index 572f79aa..2895b19d 100644 --- a/_data/citations.yaml +++ b/_data/citations.yaml @@ -1,699 +1,710 @@ # DO NOT EDIT, GENERATED AUTOMATICALLY - id: doi:10.1111/jvim.70133 - title: 'The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization' + title: "The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization" authors: - - Kathleen R. Mullen - - Imke Tammen - - Nicolas A. Matentzoglu - - Marius Mather - - James P. Balhoff - - Elizabeth Esdaile - - Gregoire Leroy - - Carissa A. Park - - Halie M. Rando - - Nadia T. Saklou - - Tracy L. Webb - - Nicole A. Vasilevsky - - Christopher J. Mungall - - Melissa A. Haendel - - Frank W. Nicholas - - Sabrina Toro + - Kathleen R. Mullen + - Imke Tammen + - Nicolas A. Matentzoglu + - Marius Mather + - James P. Balhoff + - Elizabeth Esdaile + - Gregoire Leroy + - Carissa A. Park + - Halie M. Rando + - Nadia T. Saklou + - Tracy L. Webb + - Nicole A. Vasilevsky + - Christopher J. Mungall + - Melissa A. Haendel + - Frank W. Nicholas + - Sabrina Toro publisher: Journal of Veterinary Internal Medicine - date: '2025-07-01' + date: "2025-07-01" link: https://doi.org/hbwvfw - plugin: sources.py - file: sources.yaml -- type: journal paper + type: journal paper + image: images/m_jvim70133-fig-0003.jpeg tags: - - ontology - - animals - - domestication + - ontology + - animals + - domestication plugin: sources.py file: sources.yaml - id: doi:10.2460/ajvr.24.10.0315 - title: Standardizing canine breed data in veterinary records is challenging, but + title: + Standardizing canine breed data in veterinary records is challenging, but computer vision offers an alternative perspective on breed assignment authors: - - Glenvelis Perez - - Yixuan He - - Zihan Lyu - - Yilin Chen - - Nicholas R. Howe - - Halie M. Rando + - Glenvelis Perez + - Yixuan He + - Zihan Lyu + - Yilin Chen + - Nicholas R. Howe + - Halie M. Rando publisher: American Journal of Veterinary Research - date: '2025-03-01' + date: "2025-03-01" link: https://doi.org/g85s7s type: journal paper + image: images/full-ajvr.24.10.0315.figure1.jpg tags: - - genetics - - dogs - - machine learning + - genetics + - dogs + - machine learning plugin: sources.py file: sources.yaml - id: doi:10.1093/jhered/esae022 - title: 'Missing history of a modern domesticate: Historical demographics and genetic - diversity in farm-bred red fox populations' + title: + "Missing history of a modern domesticate: Historical demographics and genetic + diversity in farm-bred red fox populations" authors: - - Halie M Rando - - Emmarie P Alexander - - Sophie Preckler-Quisquater - - Cate B Quinn - - Jeremy T Stutchman - - Jennifer L Johnson - - Estelle R Bastounes - - Beata Horecka - - Kristina L Black - - Michael P Robson - - Darya V Shepeleva - - Yury E Herbeck - - Anastasiya V Kharlamova - - Lyudmila N Trut - - Jonathan N Pauli - - Benjamin N Sacks - - Anna V Kukekova + - Halie M Rando + - Emmarie P Alexander + - Sophie Preckler-Quisquater + - Cate B Quinn + - Jeremy T Stutchman + - Jennifer L Johnson + - Estelle R Bastounes + - Beata Horecka + - Kristina L Black + - Michael P Robson + - Darya V Shepeleva + - Yury E Herbeck + - Anastasiya V Kharlamova + - Lyudmila N Trut + - Jonathan N Pauli + - Benjamin N Sacks + - Anna V Kukekova publisher: Journal of Heredity - date: '2024-04-16' + date: "2024-04-16" link: https://doi.org/gtq55b type: journal paper image: images/jhered_2024_red_fox_map.jpeg tags: - - domestication - - foxes - - wildlife + - domestication + - foxes + - wildlife plugin: sources.py file: sources.yaml - id: doi:10.2460/javma.23.07.0372 - title: Many direct-to-consumer canine genetic tests can identify the breed of purebred + title: + Many direct-to-consumer canine genetic tests can identify the breed of purebred dogs authors: - - Halie M. Rando - - Kiley Graim - - Greg Hampikian - - Casey S. Greene + - Halie M. Rando + - Kiley Graim + - Greg Hampikian + - Casey S. Greene publisher: Journal of the American Veterinary Medical Association - date: '2024-05-01' + date: "2024-05-01" link: https://doi.org/gtn72p type: journal paper image: https://user-images.githubusercontent.com/8975841/250271905-4eed44ba-528a-4a61-a4ec-fa90d51e61f9.jpg tags: - - reproducibility - - genetics - - dogs + - reproducibility + - genetics + - dogs plugin: sources.py file: sources.yaml - id: url:https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_1882.pdf title: Classifying animal breeds with the vertebrate breed ontology (VBO) authors: - - Sabrina Toro - - Nicolas Matentzoglu - - Kathleen R. Mullen - - Nicole Vasilevsky - - Halie M. Rando - - Melissa Haendel - - Christopher J. Mungall - - Zhi-Liang Hu - - Gregoire Leroy - - Imke Tammen - - Frank W. Nicholas + - Sabrina Toro + - Nicolas Matentzoglu + - Kathleen R. Mullen + - Nicole Vasilevsky + - Halie M. Rando + - Melissa Haendel + - Christopher J. Mungall + - Zhi-Liang Hu + - Gregoire Leroy + - Imke Tammen + - Frank W. Nicholas publisher: Proceedings of the International Conference on Biomedical Ontology - date: '2022-09-25' + date: "2022-09-25" link: https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_1882.pdf type: conference paper image: https://user-images.githubusercontent.com/8975841/260512613-910f7bcd-2648-48db-8874-d37bca58c8f1.png tags: - - ontology - - animals - - domestication + - ontology + - animals + - domestication plugin: sources.py file: sources.yaml - id: doi:10.1016/j.ebiom.2021.103722 - title: 'Characterizing Long COVID: Deep Phenotype of a Complex Condition' + title: "Characterizing Long COVID: Deep Phenotype of a Complex Condition" authors: - - Rachel R Deer - - Madeline A Rock - - Nicole Vasilevsky - - Leigh Carmody - - Halie Rando - - Alfred J Anzalone - - Marc D Basson - - Tellen D Bennett - - Timothy Bergquist - - Eilis A Boudreau - - Carolyn T Bramante - - James Brian Byrd - - Tiffany J Callahan - - Lauren E Chan - - Haitao Chu - - Christopher G Chute - - Ben D Coleman - - Hannah E Davis - - Joel Gagnier - - Casey S Greene - - William B Hillegass - - Ramakanth Kavuluru - - Wesley D Kimble - - Farrukh M Koraishy - - "Sebastian K\xF6hler" - - Chen Liang - - Feifan Liu - - Hongfang Liu - - Vithal Madhira - - Charisse R Madlock-Brown - - Nicolas Matentzoglu - - Diego R Mazzotti - - Julie A McMurry - - Douglas S McNair - - Richard A Moffitt - - Teshamae S Monteith - - Ann M Parker - - Mallory A Perry - - Emily Pfaff - - Justin T Reese - - Joel Saltz - - Robert A Schuff - - Anthony E Solomonides - - Julian Solway - - Heidi Spratt - - Gary S Stein - - Anupam A Sule - - Umit Topaloglu - - George D. Vavougios - - Liwei Wang - - Melissa A Haendel - - Peter N Robinson + - Rachel R Deer + - Madeline A Rock + - Nicole Vasilevsky + - Leigh Carmody + - Halie Rando + - Alfred J Anzalone + - Marc D Basson + - Tellen D Bennett + - Timothy Bergquist + - Eilis A Boudreau + - Carolyn T Bramante + - James Brian Byrd + - Tiffany J Callahan + - Lauren E Chan + - Haitao Chu + - Christopher G Chute + - Ben D Coleman + - Hannah E Davis + - Joel Gagnier + - Casey S Greene + - William B Hillegass + - Ramakanth Kavuluru + - Wesley D Kimble + - Farrukh M Koraishy + - "Sebastian K\xF6hler" + - Chen Liang + - Feifan Liu + - Hongfang Liu + - Vithal Madhira + - Charisse R Madlock-Brown + - Nicolas Matentzoglu + - Diego R Mazzotti + - Julie A McMurry + - Douglas S McNair + - Richard A Moffitt + - Teshamae S Monteith + - Ann M Parker + - Mallory A Perry + - Emily Pfaff + - Justin T Reese + - Joel Saltz + - Robert A Schuff + - Anthony E Solomonides + - Julian Solway + - Heidi Spratt + - Gary S Stein + - Anupam A Sule + - Umit Topaloglu + - George D. Vavougios + - Liwei Wang + - Melissa A Haendel + - Peter N Robinson publisher: eBioMedicine - date: '2021-12-01' + date: "2021-12-01" link: https://doi.org/gnmkm7 type: journal paper image: https://www.medrxiv.org/content/medrxiv/early/2021/06/29/2021.06.23.21259416/F1.large.jpg?width=800&height=600&carousel=1 tags: - - ontology - - disease - - humans + - ontology + - disease + - humans plugin: sources.py file: sources.yaml - id: url:http://ceur-ws.org/Vol-2976/paper-2.pdf title: An Open-Publishing Response to the COVID-19 Infodemic authors: - - Halie M. Rando - - Simina M. Boca - - Lucy D'Agostino McGowan - - Daniel S. Himmelstein - - Michael P. Robson - - Vincent Rubinetti - - Ryan Velazquez - - Casey S. Greene - - Anthony Gitter + - Halie M. Rando + - Simina M. Boca + - Lucy D'Agostino McGowan + - Daniel S. Himmelstein + - Michael P. Robson + - Vincent Rubinetti + - Ryan Velazquez + - Casey S. Greene + - Anthony Gitter publisher: Digital Infrastructures for Scholarly Content Objects 2021 - date: '2021-09-30' + date: "2021-09-30" link: http://ceur-ws.org/Vol-2976/paper-2.pdf type: conference paper image: https://user-images.githubusercontent.com/8975841/137757668-cf24b018-5539-4969-965f-305fee56b2d3.png tags: - - manubot - - reproducibility - - documents + - manubot + - reproducibility + - documents plugin: sources.py file: sources.yaml - id: doi:10.1128/mSystems.00122-21 - title: Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention + title: + Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment authors: - - Ronan Lordan - - Halie M. Rando - - Casey S. Greene + - Ronan Lordan + - Halie M. Rando + - Casey S. Greene publisher: mSystems - date: '2021-06-29' + date: "2021-06-29" link: https://doi.org/gj9qvs image: https://greenelab.github.io/covid19-review/images/N000-overview.png tags: - - manubot - - COVID-19 + - manubot + - COVID-19 plugin: sources.py file: sources.yaml - id: doi:10.1128/msystems.00095-21 - title: Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis + title: + Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure authors: - - Halie M. Rando - - Adam L. MacLean - - Alexandra J. Lee - - Ronan Lordan - - Sandipan Ray - - Vikas Bansal - - Ashwin N. Skelly - - Elizabeth Sell - - John J. Dziak - - Lamonica Shinholster - - "Lucy D\u2019Agostino McGowan" - - Marouen Ben Guebila - - Nils Wellhausen - - Sergey Knyazev - - Simina M. Boca - - Stephen Capone - - Yanjun Qi - - YoSon Park - - David Mai - - Yuchen Sun - - Joel D. Boerckel - - Christian Brueffer - - James Brian Byrd - - Jeremy P. Kamil - - Jinhui Wang - - Ryan Velazquez - - Gregory L. Szeto - - John P. Barton - - Rishi Raj Goel - - Serghei Mangul - - Tiago Lubiana - - Anthony Gitter - - Casey S. Greene + - Halie M. Rando + - Adam L. MacLean + - Alexandra J. Lee + - Ronan Lordan + - Sandipan Ray + - Vikas Bansal + - Ashwin N. Skelly + - Elizabeth Sell + - John J. Dziak + - Lamonica Shinholster + - "Lucy D\u2019Agostino McGowan" + - Marouen Ben Guebila + - Nils Wellhausen + - Sergey Knyazev + - Simina M. Boca + - Stephen Capone + - Yanjun Qi + - YoSon Park + - David Mai + - Yuchen Sun + - Joel D. Boerckel + - Christian Brueffer + - James Brian Byrd + - Jeremy P. Kamil + - Jinhui Wang + - Ryan Velazquez + - Gregory L. Szeto + - John P. Barton + - Rishi Raj Goel + - Serghei Mangul + - Tiago Lubiana + - Anthony Gitter + - Casey S. Greene publisher: mSystems - date: '2021-10-26' + date: "2021-10-26" link: https://doi.org/gm8k9b image: https://greenelab.github.io/covid19-review/images/N000-overview.png tags: - - manubot - - COVID-19 + - manubot + - COVID-19 plugin: sources.py file: sources.yaml - id: doi:10.1128/mSystems.00233-21 title: Identification and Development of Therapeutics for COVID-19 authors: - - Halie M. Rando - - Nils Wellhausen - - Soumita Ghosh - - Alexandra J. Lee - - Anna Ada Dattoli - - Fengling Hu - - James Brian Byrd - - Diane N. Rafizadeh - - Ronan Lordan - - Yanjun Qi - - Yuchen Sun - - Christian Brueffer - - Jeffrey M. Field - - Marouen Ben Guebila - - Nafisa M. Jadavji - - Ashwin N. Skelly - - Bharath Ramsundar - - Jinhui Wang - - Rishi Raj Goel - - YoSon Park - - Simina M. Boca - - Anthony Gitter - - Casey S. Greene + - Halie M. Rando + - Nils Wellhausen + - Soumita Ghosh + - Alexandra J. Lee + - Anna Ada Dattoli + - Fengling Hu + - James Brian Byrd + - Diane N. Rafizadeh + - Ronan Lordan + - Yanjun Qi + - Yuchen Sun + - Christian Brueffer + - Jeffrey M. Field + - Marouen Ben Guebila + - Nafisa M. Jadavji + - Ashwin N. Skelly + - Bharath Ramsundar + - Jinhui Wang + - Rishi Raj Goel + - YoSon Park + - Simina M. Boca + - Anthony Gitter + - Casey S. Greene publisher: mSystems - date: '2021-12-21' + date: "2021-12-21" link: https://doi.org/gnbhqq image: https://greenelab.github.io/covid19-review/images/N000-overview.png tags: - - manubot - - COVID-19 + - manubot + - COVID-19 plugin: sources.py file: sources.yaml - id: doi:10.48550/ARXIV.2204.12598 title: Molecular and Serologic Diagnostic Technologies for SARS-CoV-2 authors: - - Halie M. Rando - - Christian Brueffer - - Ronan Lordan - - Anna Ada Dattoli - - David Manheim - - Jesse G. Meyer - - Ariel I. Mundo - - Dimitri Perrin - - David Mai - - Nils Wellhausen - - COVID-19 Review Consortium - - Anthony Gitter - - Casey S. Greene + - Halie M. Rando + - Christian Brueffer + - Ronan Lordan + - Anna Ada Dattoli + - David Manheim + - Jesse G. Meyer + - Ariel I. Mundo + - Dimitri Perrin + - David Mai + - Nils Wellhausen + - COVID-19 Review Consortium + - Anthony Gitter + - Casey S. Greene publisher: arXiv - date: '2022-01-01' + date: "2022-01-01" link: https://doi.org/gp4ftc image: https://greenelab.github.io/covid19-review/images/N000-overview.png tags: - - manubot - - COVID-19 + - manubot + - COVID-19 plugin: sources.py file: sources.yaml - id: doi:10.1128/msystems.00927-22 title: Application of Traditional Vaccine Development Strategies to SARS-CoV-2 authors: - - Halie M. Rando - - Ronan Lordan - - Alexandra J. Lee - - Amruta Naik - - Nils Wellhausen - - Elizabeth Sell - - Likhitha Kolla - - Anthony Gitter - - Casey S. Greene - - Vikas Bansal - - John P. Barton - - Simina M. Boca - - Joel D. Boerckel - - Christian Brueffer - - James Brian Byrd - - Stephen Capone - - Shikta Das - - Anna Ada Dattoli - - John J. Dziak - - Jeffrey M. Field - - Soumita Ghosh - - Anthony Gitter - - Rishi Raj Goel - - Casey S. Greene - - Marouen Ben Guebila - - Daniel S. Himmelstein - - Fengling Hu - - Nafisa M. Jadavji - - Jeremy P. Kamil - - Sergey Knyazev - - Likhitha Kolla - - Alexandra J. Lee - - Ronan Lordan - - Tiago Lubiana - - Temitayo Lukan - - Adam L. MacLean - - David Mai - - Serghei Mangul - - David Manheim - - "Lucy D\u2019Agostino McGowan" - - Jesse G. Meyer - - Ariel I. Mundo - - Amruta Naik - - YoSon Park - - Dimitri Perrin - - Yanjun Qi - - Diane N. Rafizadeh - - Bharath Ramsundar - - Halie M. Rando - - Sandipan Ray - - Michael P. Robson - - Vincent Rubinetti - - Elizabeth Sell - - Lamonica Shinholster - - Ashwin N. Skelly - - Yuchen Sun - - Yusha Sun - - Gregory L. Szeto - - Ryan Velazquez - - Jinhui Wang - - Nils Wellhausen + - Halie M. Rando + - Ronan Lordan + - Alexandra J. Lee + - Amruta Naik + - Nils Wellhausen + - Elizabeth Sell + - Likhitha Kolla + - Anthony Gitter + - Casey S. Greene + - Vikas Bansal + - John P. Barton + - Simina M. Boca + - Joel D. Boerckel + - Christian Brueffer + - James Brian Byrd + - Stephen Capone + - Shikta Das + - Anna Ada Dattoli + - John J. Dziak + - Jeffrey M. Field + - Soumita Ghosh + - Anthony Gitter + - Rishi Raj Goel + - Casey S. Greene + - Marouen Ben Guebila + - Daniel S. Himmelstein + - Fengling Hu + - Nafisa M. Jadavji + - Jeremy P. Kamil + - Sergey Knyazev + - Likhitha Kolla + - Alexandra J. Lee + - Ronan Lordan + - Tiago Lubiana + - Temitayo Lukan + - Adam L. MacLean + - David Mai + - Serghei Mangul + - David Manheim + - "Lucy D\u2019Agostino McGowan" + - Jesse G. Meyer + - Ariel I. Mundo + - Amruta Naik + - YoSon Park + - Dimitri Perrin + - Yanjun Qi + - Diane N. Rafizadeh + - Bharath Ramsundar + - Halie M. Rando + - Sandipan Ray + - Michael P. Robson + - Vincent Rubinetti + - Elizabeth Sell + - Lamonica Shinholster + - Ashwin N. Skelly + - Yuchen Sun + - Yusha Sun + - Gregory L. Szeto + - Ryan Velazquez + - Jinhui Wang + - Nils Wellhausen publisher: mSystems - date: '2023-04-27' + date: "2023-04-27" link: https://doi.org/grv3d9 image: https://greenelab.github.io/covid19-review/images/N000-overview.png tags: - - manubot - - COVID-19 + - manubot + - COVID-19 plugin: sources.py file: sources.yaml - id: doi:10.1128/msystems.00928-22 title: The Coming of Age of Nucleic Acid Vaccines during COVID-19 authors: - - Halie M. Rando - - Ronan Lordan - - Likhitha Kolla - - Elizabeth Sell - - Alexandra J. Lee - - Nils Wellhausen - - Amruta Naik - - Jeremy P. Kamil - - Anthony Gitter - - Casey S. Greene - - John P. Barton - - Simina M. Boca - - Joel D. Boerckel - - Christian Brueffer - - James Brian Byrd - - Stephen Capone - - Shikta Capone - - Anna Ada Dattoli - - John J. Dziak - - Jeffrey M. Field - - Soumita Ghosh - - Anthony Gitter - - Rishi Raj Goel - - Casey S. Greene - - Marouen Ben Guebila - - Daniel S. Himmelstein - - Fengling Hu - - Nafisa M. Jadavji - - Jeremy P. Kamil - - Sergey Knyazev - - Likhitha Kolla - - Alexandra J. Lee - - Ronan Lordan - - Tiago Lubiana - - Temitayo Lukan - - Adam L. MacLean - - David Mai - - Serghei Mangul - - David Manheim - - "Lucy D\u2019Agostino McGowan" - - Jesse G. Meyer - - Ariel I. Mundo - - Amruta Naik - - YoSon Park - - Dimitri Perrin - - Yanjun Qi - - Diane N. Rafizadeh - - Bharath Ramsundar - - Halie M. Rando - - Sandipan Ray - - Michael P. Robson - - Vincent Rubinetti - - Elizabeth Sell - - Lamonica Shinholster - - Ashwin N. Skelly - - Yuchen Sun - - Yusha Sun - - Gregory L. Szeto - - Ryan Velazquez - - Jinhui Wang - - Nils Wellhausen + - Halie M. Rando + - Ronan Lordan + - Likhitha Kolla + - Elizabeth Sell + - Alexandra J. Lee + - Nils Wellhausen + - Amruta Naik + - Jeremy P. Kamil + - Anthony Gitter + - Casey S. Greene + - John P. Barton + - Simina M. Boca + - Joel D. Boerckel + - Christian Brueffer + - James Brian Byrd + - Stephen Capone + - Shikta Capone + - Anna Ada Dattoli + - John J. Dziak + - Jeffrey M. Field + - Soumita Ghosh + - Anthony Gitter + - Rishi Raj Goel + - Casey S. Greene + - Marouen Ben Guebila + - Daniel S. Himmelstein + - Fengling Hu + - Nafisa M. Jadavji + - Jeremy P. Kamil + - Sergey Knyazev + - Likhitha Kolla + - Alexandra J. Lee + - Ronan Lordan + - Tiago Lubiana + - Temitayo Lukan + - Adam L. MacLean + - David Mai + - Serghei Mangul + - David Manheim + - "Lucy D\u2019Agostino McGowan" + - Jesse G. Meyer + - Ariel I. Mundo + - Amruta Naik + - YoSon Park + - Dimitri Perrin + - Yanjun Qi + - Diane N. Rafizadeh + - Bharath Ramsundar + - Halie M. Rando + - Sandipan Ray + - Michael P. Robson + - Vincent Rubinetti + - Elizabeth Sell + - Lamonica Shinholster + - Ashwin N. Skelly + - Yuchen Sun + - Yusha Sun + - Gregory L. Szeto + - Ryan Velazquez + - Jinhui Wang + - Nils Wellhausen publisher: mSystems - date: '2023-04-27' + date: "2023-04-27" link: https://doi.org/grv5vq image: https://greenelab.github.io/covid19-review/images/N000-overview.png tags: - - manubot - - COVID-19 + - manubot + - COVID-19 plugin: sources.py file: sources.yaml - id: doi:10.1101/2021.03.20.21253896 - title: 'Challenges in defining Long COVID: Striking differences across literature, - Electronic Health Records, and patient-reported information' + title: + "Challenges in defining Long COVID: Striking differences across literature, + Electronic Health Records, and patient-reported information" authors: - - Halie M. Rando - - Tellen D. Bennett - - James Brian Byrd - - Carolyn Bramante - - Tiffany J. Callahan - - Christopher G. Chute - - Hannah E. Davis - - Rachel Deer - - Joel Gagnier - - Farrukh M Koraishy - - Feifan Liu - - Julie A. McMurry - - Richard A. Moffitt - - Emily R. Pfaff - - Justin T. Reese - - Rose Relevo - - Peter N. Robinson - - Joel H. Saltz - - Anthony Solomonides - - Anupam Sule - - Umit Topaloglu - - Melissa A. Haendel + - Halie M. Rando + - Tellen D. Bennett + - James Brian Byrd + - Carolyn Bramante + - Tiffany J. Callahan + - Christopher G. Chute + - Hannah E. Davis + - Rachel Deer + - Joel Gagnier + - Farrukh M Koraishy + - Feifan Liu + - Julie A. McMurry + - Richard A. Moffitt + - Emily R. Pfaff + - Justin T. Reese + - Rose Relevo + - Peter N. Robinson + - Joel H. Saltz + - Anthony Solomonides + - Anupam Sule + - Umit Topaloglu + - Melissa A. Haendel publisher: openRxiv - date: '2021-03-26' + date: "2021-03-26" link: https://doi.org/gjk3ng image: https://user-images.githubusercontent.com/8975841/112666874-013a3400-8e33-11eb-9be9-5c74f3e397ea.png type: preprint tags: - - ontology - - disease - - humans + - ontology + - disease + - humans plugin: sources.py file: sources.yaml - id: doi:10.3390/genes10060409 title: The Red Fox Y-Chromosome in Comparative Context authors: - - Halie M. Rando - - William H. Wadlington - - Jennifer L. Johnson - - Jeremy T. Stutchman - - Lyudmila N. Trut - - "Marta Farr\xE9" - - Anna V. Kukekova + - Halie M. Rando + - William H. Wadlington + - Jennifer L. Johnson + - Jeremy T. Stutchman + - Lyudmila N. Trut + - "Marta Farr\xE9" + - Anna V. Kukekova publisher: Genes - date: '2019-05-28' + date: "2019-05-28" link: https://doi.org/gk67ng image: images/thumbnails/Red_fox_ychromosome_genes10060409.png tags: - - foxes - - genomes - - machine learning + - foxes + - genomes + - machine learning plugin: sources.py file: sources.yaml - id: doi:10.3390/genes12010097 - title: Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative + title: + Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography authors: - - Benjamin N. Sacks - - Zachary T. Lounsberry - - Halie M. Rando - - Kristopher Kluepfel - - Steven R. Fain - - Sarah K. Brown - - Anna V. Kukekova + - Benjamin N. Sacks + - Zachary T. Lounsberry + - Halie M. Rando + - Kristopher Kluepfel + - Steven R. Fain + - Sarah K. Brown + - Anna V. Kukekova publisher: Genes - date: '2021-01-14' + date: "2021-01-14" link: https://doi.org/gtj95c image: images/thumbnails/sequencing_red_fox.png tags: - - foxes - - genomes - - wildlife + - foxes + - genomes + - wildlife plugin: sources.py file: sources.yaml - id: doi:10.1111/age.12755 - title: "Four structural variants associated with human\u2010directed sociability\ + title: + "Four structural variants associated with human\u2010directed sociability\ \ in dogs are not found in tame red foxes (Vulpes vulpes)" authors: - - Estelle R. Bastounes - - Halie M. Rando - - Jennifer L. Johnson - - Lyudmila N. Trut - - Benjamin N. Sacks - - Carlos A. Driscoll - - Bridgett vonHoldt - - Anna V. Kukekova + - Estelle R. Bastounes + - Halie M. Rando + - Jennifer L. Johnson + - Lyudmila N. Trut + - Benjamin N. Sacks + - Carlos A. Driscoll + - Bridgett vonHoldt + - Anna V. Kukekova publisher: Animal Genetics - date: '2018-12-10' + date: "2018-12-10" link: https://doi.org/gtj95d image: images/thumbnails/Four_structural_variants.png tags: - - foxes - - genomes - - dogs - - behavior - - domestication + - foxes + - genomes + - dogs + - behavior + - domestication plugin: sources.py file: sources.yaml - id: doi:10.1038/s41559-018-0611-6 - title: Red fox genome assembly identifies genomic regions associated with tame and + title: + Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours authors: - - Anna V. Kukekova - - Jennifer L. Johnson - - Xueyan Xiang - - Shaohong Feng - - Shiping Liu - - Halie M. Rando - - Anastasiya V. Kharlamova - - Yury Herbeck - - Natalya A. Serdyukova - - Zijun Xiong - - Violetta Beklemischeva - - Klaus-Peter Koepfli - - Rimma G. Gulevich - - Anastasiya V. Vladimirova - - Jessica P. Hekman - - Polina L. Perelman - - Aleksander S. Graphodatsky - - "Stephen J. O\u2019Brien" - - Xu Wang - - Andrew G. Clark - - Gregory M. Acland - - Lyudmila N. Trut - - Guojie Zhang + - Anna V. Kukekova + - Jennifer L. Johnson + - Xueyan Xiang + - Shaohong Feng + - Shiping Liu + - Halie M. Rando + - Anastasiya V. Kharlamova + - Yury Herbeck + - Natalya A. Serdyukova + - Zijun Xiong + - Violetta Beklemischeva + - Klaus-Peter Koepfli + - Rimma G. Gulevich + - Anastasiya V. Vladimirova + - Jessica P. Hekman + - Polina L. Perelman + - Aleksander S. Graphodatsky + - "Stephen J. O\u2019Brien" + - Xu Wang + - Andrew G. Clark + - Gregory M. Acland + - Lyudmila N. Trut + - Guojie Zhang publisher: Nature Ecology & Evolution - date: '2018-08-06' + date: "2018-08-06" link: https://doi.org/csvn image: images/thumbnails/red_fox_genome_assembly.png tags: - - foxes - - genomes - - behavior - - domestication + - foxes + - genomes + - behavior + - domestication plugin: sources.py file: sources.yaml - id: doi:10.3390/genes9060308 - title: Construction of Red Fox Chromosomal Fragments from the Short-Read Genome + title: + Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly authors: - - Halie M. Rando - - "Marta Farr\xE9" - - Michael P. Robson - - Naomi B. Won - - Jennifer L. Johnson - - Ronak Buch - - Estelle R. Bastounes - - Xueyan Xiang - - Shaohong Feng - - Shiping Liu - - Zijun Xiong - - Jaebum Kim - - Guojie Zhang - - Lyudmila N. Trut - - Denis M. Larkin - - Anna V. Kukekova + - Halie M. Rando + - "Marta Farr\xE9" + - Michael P. Robson + - Naomi B. Won + - Jennifer L. Johnson + - Ronak Buch + - Estelle R. Bastounes + - Xueyan Xiang + - Shaohong Feng + - Shiping Liu + - Zijun Xiong + - Jaebum Kim + - Guojie Zhang + - Lyudmila N. Trut + - Denis M. Larkin + - Anna V. Kukekova publisher: Genes - date: '2018-06-20' + date: "2018-06-20" link: https://doi.org/gf4p6z image: images/thumbnails/red_fox_chromosomal_fragments.png tags: - - foxes - - genomes - - high-performance computing + - foxes + - genomes + - high-performance computing plugin: sources.py file: sources.yaml - id: doi:10.1002/ece3.3583 - title: "Development of a genotype\u2010by\u2010sequencing immunogenetic assay as\ + title: + "Development of a genotype\u2010by\u2010sequencing immunogenetic assay as\ \ exemplified by screening for variation in red fox with and without endemic rabies\ \ exposure" authors: - - Michael E. Donaldson - - Yessica Rico - - Karsten Hueffer - - Halie M. Rando - - Anna V. Kukekova - - Christopher J. Kyle + - Michael E. Donaldson + - Yessica Rico + - Karsten Hueffer + - Halie M. Rando + - Anna V. Kukekova + - Christopher J. Kyle publisher: Ecology and Evolution - date: '2017-12-02' + date: "2017-12-02" link: https://doi.org/gctwp9 image: images/thumbnails/immunogenetic_assay.png tags: - - foxes - - genomes - - wildlife + - foxes + - genomes + - wildlife plugin: sources.py file: sources.yaml - id: doi:10.1093/jhered/esx066 title: Y-Chromosome Markers for the Red Fox authors: - - Halie M Rando - - Jeremy T Stutchman - - Estelle R Bastounes - - Jennifer L Johnson - - Carlos A Driscoll - - Christina S Barr - - Lyudmila N Trut - - Benjamin N Sacks - - Anna V Kukekova + - Halie M Rando + - Jeremy T Stutchman + - Estelle R Bastounes + - Jennifer L Johnson + - Carlos A Driscoll + - Christina S Barr + - Lyudmila N Trut + - Benjamin N Sacks + - Anna V Kukekova publisher: Journal of Heredity - date: '2017-08-14' + date: "2017-08-14" link: https://doi.org/gbt6tq image: images/thumbnails/y_chromosome_markers.png tags: - - foxes - - genomes - - wildlife + - foxes + - genomes + - wildlife plugin: sources.py file: sources.yaml diff --git a/_data/sources.yaml b/_data/sources.yaml index ac80ce65..74abfe5a 100644 --- a/_data/sources.yaml +++ b/_data/sources.yaml @@ -1,5 +1,5 @@ - id: doi:10.1111/jvim.70133 -- type: journal paper + type: journal paper tags: - ontology - animals diff --git a/_includes/citation.html b/_includes/citation.html index ea62b17e..7383edf6 100644 --- a/_includes/citation.html +++ b/_includes/citation.html @@ -1,22 +1,35 @@ -{% assign citation = site.data.citations +{% assign matched_citation = site.data.citations | where_exp: "citation", "citation.id == include.lookup or citation.title contains include.lookup" | first - | default: include %}
+ {% assign citation_link = include.link | default: matched_citation.link %} + {% assign citation_title = include.title | default: matched_citation.title %} + {% assign citation_image = include.image | default: matched_citation.image %} + {% assign citation_authors = include.authors | default: matched_citation.authors %} + {% assign citation_publisher = include.publisher | default: matched_citation.publisher %} + {% assign citation_date = include.date | default: matched_citation.date %} + {% assign citation_id = include.id | default: matched_citation.id %} + {% assign citation_description = include.description | default: matched_citation.description %} + {% assign citation_buttons = include.buttons | default: matched_citation.buttons %} + {% assign citation_tags = include.tags | default: matched_citation.tags %} + {% assign citation_repo = include.repo | default: matched_citation.repo %} + {% assign citation_type_key = include.type | default: matched_citation.type %} + {% assign citation_type = site.data.types[citation_type_key] %} + {% if include.style == "rich" %} {{ citation.title | default: @@ -24,27 +37,26 @@ {% endif %}
- {% assign type = site.data.types[citation.type] %} - {% include icon.html icon=type.icon %} + {% include icon.html icon=citation_type.icon %} - {{ citation.title | default: "[no title info]" }} + {{ citation_title | default: "[no title info]" }}
10 %} - data-tooltip="{{ citation.authors | join: ", " }} " + {% if citation_authors.size > 10 %} + data-tooltip="{{ citation_authors | join: ", " }} " {% endif %} tabindex="0" > {{ - citation.authors + citation_authors | join: "," | split: "," | array_carve: 5 @@ -54,18 +66,18 @@
- {{ citation.publisher | default: "[no publisher info]" }} + {{ citation_publisher | default: "[no publisher info]" }}   ·   - {{ citation.date | default: "[no date info]" | date: "%d %b %Y" }} + {{ citation_date | default: "[no date info]" | date: "%d %b %Y" }}   ·   - {{ citation.id | default: "[no id info]" }} + {{ citation_id | default: "[no id info]" }}
{% if include.style == "rich" %} - {% if citation.description %} + {% if citation_description %}
{{ - citation.description + citation_description | markdownify | remove: "

" | remove: "

" @@ -73,9 +85,9 @@
{% endif %} - {% if citation.buttons.size > 0 %} + {% if citation_buttons.size > 0 %}
- {% for button in citation.buttons %} + {% for button in citation_buttons %} {% include button.html type=button.type @@ -88,8 +100,8 @@
{% endif %} - {% if citation.tags.size > 0 or citation.repo %} - {% include tags.html tags=citation.tags repo=citation.repo %} + {% if citation_tags.size > 0 or citation_repo %} + {% include tags.html tags=citation_tags repo=citation_repo %} {% endif %} {% endif %}
diff --git a/_includes/course-excerpt.html b/_includes/course-excerpt.html new file mode 100644 index 00000000..59525d96 --- /dev/null +++ b/_includes/course-excerpt.html @@ -0,0 +1,65 @@ +
+ {% assign course_website = include.course_website | default: empty %} + {% assign url = include.url | default: include.link | default: course_website %} + {% assign title = include.title | default: "[no course title]" %} + {% assign subtitle = include.subtitle %} + {% capture display_title %} + {% if subtitle %}{{ subtitle }}: {% endif %}{{ title }} + {% endcapture %} + {% if url %} + {{ display_title | strip }} + {% else %} + {{ display_title | strip }} + {% endif %} + + {% if course_website %} +

+ Course website: + {{ course_website }} +

+ {% endif %} + + {% if include.distribution %} +

Distribution: {{ include.distribution }}

+ {% endif %} + + {% if include.next_offered %} +

Next offering: {{ include.next_offered }}

+ {% endif %} + + {% assign terms_offered = include.terms_offered | default: empty %} + {% if terms_offered.size > 0 %} + {% assign teaching_link = "/teaching" | relative_url %} +

Previously offered:

+
+ {% for term in terms_offered %} + + {{ term }} + + {% endfor %} +
+ {% endif %} + + {% assign body = include.content | default: "" %} + {% if body != "" %} + {% assign excerpt = body + | regex_scan: "(.*)", true + | default: include.excerpt + | default: include.description + | default: "" + | strip_html + %} + {% assign search = body + | strip_html + | strip_newlines + | regex_strip + %} +

+ {{ excerpt }} +

+ {% endif %} +
diff --git a/_includes/post-excerpt.html b/_includes/post-excerpt.html index f62849af..195bfed1 100644 --- a/_includes/post-excerpt.html +++ b/_includes/post-excerpt.html @@ -1,77 +1,56 @@ -{% assign post = site.posts +{% assign matched_post = site.posts | where_exp: "post", "post.slug == include.lookup" | first - | default: include %}
- {% assign course_website = post.course_website | default: empty %} - {% assign url = post.url | default: post.link | default: course_website %} - {% assign title = post.title %} - {% assign subtitle = post.subtitle %} - {% capture display_title %} - {% if subtitle %}{{ subtitle }}: {% endif %}{{ title }} - {% endcapture %} + {% assign url = matched_post.url | default: include.url | default: include.link %} + {% assign title = matched_post.title | default: include.title | default: include.lookup %} {% if url %} - {{ display_title | strip }} + {{ title }} {% else %} - {{ display_title | strip }} + {{ title }} {% endif %} - {% if course_website %} -

- Course website: - {{ course_website }} -

- {% endif %} - - {% if post.distribution %} -

Distribution: {{ post.distribution }}

- {% endif %} - - {% if post.next_offered %} -

Next offering: {{ post.next_offered }}

- {% endif %} - - {% assign terms_offered = post.terms_offered | default: empty %} - {% if terms_offered.size > 0 %} - {% assign teaching_link = "/teaching" | relative_url %} -

Previously offered:

-
- {% for term in terms_offered %} - - {{ term }} - - {% endfor %} -
- {% endif %} + {% assign info_author = matched_post.author | default: include.author %} + {% assign info_people = matched_post.people | default: include.people %} + {% assign info_published = matched_post.date | default: include.date %} + {% assign info_updated = matched_post.last_modified_at | default: include.last_modified_at %} + {% assign info_tags = matched_post.tags | default: include.tags %} {% include post-info.html - author=post.author - published=post.date - updated=post.last_modified_at - tags=post.tags + author=info_author + people=info_people + published=info_published + updated=info_updated + tags=info_tags + hide_author_image=true + hide_updated=true %} - {% assign excerpt = post.content - | default: "" - | regex_scan: "(.*)", true - | default: post.excerpt - | default: post.description - | default: "" - | strip_html - %} - {% assign search = post.content - | strip_html - | strip_newlines - | regex_strip - %} -

- {{ excerpt }} -

+ {% assign body = matched_post.content | default: include.content | default: "" %} + {% if include.show_full_content %} +
+ {{ body | markdownify }} +
+ {% else %} + {% assign excerpt = body + | regex_scan: "(.*)", true + | default: matched_post.excerpt + | default: matched_post.description + | default: include.excerpt + | default: include.description + | default: "" + | strip_html + %} + {% assign search = body + | strip_html + | strip_newlines + | regex_strip + %} +

+ {{ excerpt }} +

+ {% endif %}
diff --git a/_includes/post-info.html b/_includes/post-info.html index c0585d70..10dfb093 100644 --- a/_includes/post-info.html +++ b/_includes/post-info.html @@ -5,7 +5,13 @@ | first %} {% if member %} - {% include portrait.html lookup=include.author style="tiny" %} + {% unless include.hide_author_image %} + {% include portrait.html lookup=include.author style="tiny" %} + {% endunless %} + + {% include icon.html icon="fa-solid fa-feather-pointed" %} + {{ member.name }} + {% else %} {% include icon.html icon="fa-solid fa-feather-pointed" %} @@ -24,14 +30,36 @@ {% endif %} + {% unless include.hide_updated %} {% if updated and updated != "" and updated != published %} {% include icon.html icon="fa-solid fa-clock-rotate-left" %} {{ updated }} {% endif %} + {% endunless %}
+{% assign tagged_people = include.people | default: empty %} +{% assign tagged_people = tagged_people | join: "," | split: "," | array_filter %} + +{% if tagged_people.size > 0 %} +

+ Mentioned: + {% for person in tagged_people %} + {% assign member = site.members + | where_exp: "member", "member.slug == person" + | first + %} + {% if member %} + {{ member.name }}{% unless forloop.last %}, {% endunless %} + {% else %} + {{ person }}{% unless forloop.last %}, {% endunless %} + {% endif %} + {% endfor %} +

+{% endif %} + {% if include.tags %} - {% include tags.html tags=include.tags link="blog" %} + {% include tags.html tags=include.tags link="news" %} {% endif %} diff --git a/_layouts/member.html b/_layouts/member.html index 034b5d08..9eefb506 100644 --- a/_layouts/member.html +++ b/_layouts/member.html @@ -20,6 +20,20 @@ {{ content }} +{% assign related_posts = site.posts + | where_exp: "post", "post.author == page.slug or post.people contains page.slug" +%} + +{% if related_posts.size > 0 %} +{% include section.html %} + +## News + +{% for post in related_posts %} +{% include post-excerpt.html lookup=post.slug %} +{% endfor %} +{% endif %} + {% assign aliases = page.aliases | default: page.name | default: page.title @@ -39,13 +53,17 @@

{% capture search -%} - blog/?search={{ page.name }} + news/?search={{ page.name }} {%- endcapture %} - +{% endif %} diff --git a/_layouts/post.html b/_layouts/post.html index 9b1641a9..f4bbe277 100644 --- a/_layouts/post.html +++ b/_layouts/post.html @@ -7,10 +7,13 @@

{{ page.title }}

{% include post-info.html author=page.author + people=page.people member=page.member published=page.date updated=page.last_modified_at tags=page.tags + hide_author_image=true + hide_updated=true %} {% include section.html %} diff --git a/_posts/.gitkeep b/_posts/.gitkeep new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/_posts/.gitkeep @@ -0,0 +1 @@ + diff --git a/_posts/2024-04-28-hildana-mckinley-honors-fellowship.md b/_posts/2024-04-28-hildana-mckinley-honors-fellowship.md new file mode 100644 index 00000000..ab9a5da3 --- /dev/null +++ b/_posts/2024-04-28-hildana-mckinley-honors-fellowship.md @@ -0,0 +1,17 @@ +--- +title: Hildana Shiferaw Selected for the McKinley Honors Fellowship Program +author: halie_rando +people: + - hildana_shiferaw +tags: + - announcement + - honors +--- + + +Hildana Shiferaw has been selected for the McKinley Honors Fellowship Program. + + +We are excited to share that Hildana Shiferaw has been selected for the McKinley Honors Fellowship Program. + +The fellowship will support Hildana's honors thesis work in the VBIL. More information about Smith's AEMES programs is available [here](https://www.smith.edu/academics/departments-programs-courses/aemes). diff --git a/_posts/2025-04-28-hildana-thesis-presentation.md b/_posts/2025-04-28-hildana-thesis-presentation.md new file mode 100644 index 00000000..a7b47f84 --- /dev/null +++ b/_posts/2025-04-28-hildana-thesis-presentation.md @@ -0,0 +1,16 @@ +--- +title: Hildana Shiferaw Presents Honors Thesis +author: halie_rando +people: + - hildana_shiferaw +tags: + - announcement + - honors + - thesis +--- + + +Hildana Shiferaw gave an excellent presentation of her honors thesis on a urine-based screening approach for ovarian cancer. + + +On Monday, April 28, 2025, Hildana Shiferaw gave an excellent presentation of her honors thesis, "System Design of a Urine-Based Screening Approach for Ovarian Cancer Informed by Computational Identification of miRNAs as Biomarkers." diff --git a/_posts/2025-04-29-alina-mckinley-honors-fellowship.md b/_posts/2025-04-29-alina-mckinley-honors-fellowship.md new file mode 100644 index 00000000..3657c2d9 --- /dev/null +++ b/_posts/2025-04-29-alina-mckinley-honors-fellowship.md @@ -0,0 +1,17 @@ +--- +title: Alina Yildirim Selected for the McKinley Honors Fellowship Program +author: halie_rando +people: + - alina_yildirim +tags: + - announcement + - honors +--- + + +Alina Yildirim has been selected for the McKinley Honors Fellowship Program. + + +We are excited to share that Alina Yildirim has been selected for the McKinley Honors Fellowship Program. + +The fellowship will support Alina's honors thesis work in the VBIL. More information about Smith's AEMES programs is available [here](https://www.smith.edu/academics/departments-programs-courses/aemes). diff --git a/images/full-ajvr.24.10.0315.figure1.jpg b/images/full-ajvr.24.10.0315.figure1.jpg new file mode 100644 index 00000000..80ca8ec5 Binary files /dev/null and b/images/full-ajvr.24.10.0315.figure1.jpg differ diff --git a/images/m_jvim70133-fig-0003.jpeg b/images/m_jvim70133-fig-0003.jpeg new file mode 100644 index 00000000..9931d9fb Binary files /dev/null and b/images/m_jvim70133-fig-0003.jpeg differ diff --git a/index.md b/index.md index 175f172c..b78dbdad 100644 --- a/index.md +++ b/index.md @@ -7,6 +7,27 @@ Here in the VBIL within the Computer Science Department at Smith, we are interes {% include section.html %} +## Latest News + +{% if site.posts.size > 0 %} +{% for post in site.posts limit: 3 %} +{% include post-excerpt.html lookup=post.slug %} +{% endfor %} +{% else %} +Future lab announcements, milestones, publications, and event updates will appear here. +{% endif %} + +{% + include button.html + link="news" + text="View all news" + icon="fa-solid fa-arrow-right" + flip=true + style="bare" +%} + +{% include section.html %} + ## Highlights {% capture text %} diff --git a/news/index.md b/news/index.md new file mode 100644 index 00000000..b48495aa --- /dev/null +++ b/news/index.md @@ -0,0 +1,41 @@ +--- +title: News +nav: + order: 4 + tooltip: Lab updates and announcements +redirect_from: + - /blog + - /blog/ +--- + +# {% include icon.html icon="fa-regular fa-newspaper" %}News + +Use this page for lab updates, student milestones, publications, talks, and other announcements from the VBIL. + +{% if site.posts.size > 0 %} + +{% include search-box.html %} + +{% include search-info.html %} + +{% assign current_year = "" %} + +{% for post in site.posts %} +{% assign post_year = post.date | date: "%Y" %} +{% if post_year != current_year %} +{% assign current_year = post_year %} +## {{ current_year }} +{% endif %} +{% include post-excerpt.html + lookup=post.slug + show_full_content=true +%} +{% endfor %} + +{% else %} + +No news posts have been published yet. + +To publish one, add a Markdown file to `_posts/` using the filename format `YYYY-MM-DD-title.md`. + +{% endif %} diff --git a/teaching/index.md b/teaching/index.md index d84d5a6e..51d87c38 100644 --- a/teaching/index.md +++ b/teaching/index.md @@ -17,4 +17,4 @@ Here is some information about the classes that Prof. Rando has taught at Smith. {% include search-info.html %} -{% include list.html data="courses" component="post-excerpt" %} +{% include list.html data="courses" component="course-excerpt" %}