yggdrasil: a Python package for integrating computational models across languages and scales

JOURNAL ARTICLE published 1 January 2019 in in silico Plants

Research funded by Foundation for Food and Agriculture Research (515760) | Gordon and Betty Moore Foundation (GBMF4561)

Authors: Meagan Lang

Soybean-BioCro: a semi-mechanistic model of soybean growth

JOURNAL ARTICLE published 1 January 2022 in in silico Plants

Research funded by Foundation for Food and Agriculture Research (602757) | Bill and Melinda Gates Foundation (OPP1172157) | UK Foreign, Commonwealth and Development Office (OPP1172157)

Authors: Megan L Matthews | Amy Marshall-Colón | Justin M McGrath | Edward B Lochocki | Stephen P Long

Editors: Graeme Hammer

Yield dissection models to improve yield: a case study in tomato

JOURNAL ARTICLE published 1 January 2021 in in silico Plants

Authors: Yutaka Tsutsumi-Morita | Ep Heuvelink | Sedighehsadat Khaleghi | Daniela Bustos-Korts | Leo F M Marcelis | Kim M C A Vermeer | Hannelore van Dijk | Frank F Millenaar | George A K Van Voorn | Fred A Van Eeuwijk

Editors: Carlos Messina | Stephen P Long

Informative community structure revealed using Arabidopsis time series transcriptome data via partitioned local depth

JOURNAL ARTICLE published 1 January 2024 in in silico Plants

Research funded by National Science Foundation (MCB 1716279)

Authors: Maleana G Khoury | Kenneth S Berenhaut | Katherine E Moore | Edward E Allen | Alexandria F Harkey | Joëlle K Mühlemann | Courtney N Craven | Jiayi Xu | Suchi S Jain | David J John | James L Norris | Gloria K Muday

Editors: Amy Marshall-Colon

Phloem anatomy restricts root system architecture development: theoretical clues from in silico experiments

JOURNAL ARTICLE published 1 July 2023 in in silico Plants

Authors: Xiao-Ran Zhou | Andrea Schnepf | Jan Vanderborght | Daniel Leitner | Harry Vereecken | Guillaume Lobet

Editors: Xin-Guang Zhu

Polar auxin transport dynamics of primary and secondary vein patterning in dicot leaves

JOURNAL ARTICLE published 1 July 2021 in in silico Plants

Authors: David M Holloway | Carol L Wenzel

Editors: Amy Marshall-Colon

Integrating genomic prediction and genotype specific parameter estimation in ecophysiological models: overview and perspectives

JOURNAL ARTICLE published 1 January 2023 in in silico Plants

Authors: Pratishtha Poudel | Bryan Naidenov | Charles Chen | Phillip D Alderman | Stephen M Welch

Editors: Graeme Hammer

Within- and cross-species predictions of plant specialized metabolism genes using transfer learning

JOURNAL ARTICLE published 1 January 2020 in in silico Plants

Research funded by National Science Foundation (IOS-1546617,IOS-1811055,DEB-1655386) | National Institutes of Health (T32-GM110523) | U.S. Department of Energy Great Lakes Bioenergy Research Center (DE-SC0018409) | National Institute of Food and Agriculture (MICL02552)

Authors: Bethany M Moore | Peipei Wang | Pengxiang Fan | Aaron Lee | Bryan Leong | Yann-Ru Lou | Craig A Schenck | Koichi Sugimoto | Robert Last | Melissa D Lehti-Shiu | Cornelius S Barry | Shin-Han Shiu

Editors: Amy Marshall-Colon

Bottom-up multiscale modelling of guard cell walls reveals molecular mechanisms of stomatal biomechanics

JOURNAL ARTICLE published 1 July 2023 in in silico Plants

Authors: Hojae Yi | Charles T Anderson

Editors: Xin-Guang Zhu

The mechanical origin of the radial shape in distichous phyllotaxy grass plants

JOURNAL ARTICLE published 1 July 2021 in in silico Plants

Authors: Yoshiki Tokuyama | Yohei Koide | Kazumitsu Onishi | Kiwamu Hikichi | Miku Omachi | Itsuro Takamure | Yuji Kishima

Editors: Przemyslaw Prusinkiewicz

Phenomics data processing: extracting dose–response curve parameters from high-resolution temperature courses and repeated field-based wheat height measurements

JOURNAL ARTICLE published 1 January 2022 in in silico Plants

Research funded by Innosuisse (KTI P-Nr 27059.2 PFLS-LS) | Deutsche Forschungsgemeinschaft (PI 377/24-1)

Authors: Lukas Roth | Hans-Peter Piepho | Andreas Hund

Editors: Xin-Guang Zhu

Limiting transpiration rate in high evaporative demand conditions to improve Australian wheat productivity

JOURNAL ARTICLE published 1 January 2021 in in silico Plants

Research funded by Grains Research and Development Corporation (CSP00179)

Authors: Brian Collins | Scott Chapman | Graeme Hammer | Karine Chenu

Editors: Vincent Vadez | Stephen P Long

Investigations into the emergent properties of gene-to-phenotype networks across cycles of selection: a case study of shoot branching in plants

JOURNAL ARTICLE published 1 January 2022 in in silico Plants

Research funded by Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture (CE200100015) | Australian Grains Research and Development Corporation (UOQ1903-008RTX) | Australian Research Council Georgina Sweet Laureate Fellowship (FL180100139) | Australian Research Council Discovery Early Career Researcher Award (DE210101407)

Authors: Owen M Powell | Francois Barbier | Kai P Voss-Fels | Christine Beveridge | Mark Cooper

Editors: Amy Marshall-Colon

Identifying transcription factor–DNA interactions using machine learning

JOURNAL ARTICLE published 1 July 2022 in in silico Plants

Research funded by National Science Foundation (IOS-1856627,IOS-2026554,IOS-1916804)

Authors: Sohyun Bang | Mary Galli | Peter A Crisp | Andrea Gallavotti | Robert J Schmitz

Editors: Amy Marshall-Colon

Biological reality and parsimony in crop models—why we need both in crop improvement!

JOURNAL ARTICLE published 1 January 2019 in in silico Plants

Authors: Graeme Hammer | Charlie Messina | Alex Wu | Mark Cooper

The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation

JOURNAL ARTICLE published 1 July 2022 in in silico Plants

Research funded by European Commission (245143) | BBSRC FLIP (BB/M017605) | BBSRC Institute Strategic Programme (BB/J004561/1) | Swiss National Science Foundation (31003A_162555) | Marie Skłodowska-Curie (GA-2010-267243)

Authors: Yin Hoon Chew | Daniel D Seaton | Virginie Mengin | Anna Flis | Sam T Mugford | Gavin M George | Michael Moulin | Alastair Hume | Samuel C Zeeman | Teresa B Fitzpatrick | Alison M Smith | Mark Stitt | Andrew J Millar

Editors: Amy Marshall-Colon

Corrigendum to: Researcher Profile: Przemysław Prusinkiewicz

JOURNAL ARTICLE published 1 January 2021 in in silico Plants

Authors: Rachel G Shekar

SIMPLACE—a versatile modelling and simulation framework for sustainable crops and agroecosystems

JOURNAL ARTICLE published 1 January 2023 in in silico Plants

Research funded by SUSCAP (FKZ 031B0809) | DAKIS (FKZ 031B0729E) | PhenoRob (EXC 2070-390732324) | DETECT (450058266) | African Union (AURG II-1-074-2016)

Authors: Andreas Enders | Murilo Vianna | Thomas Gaiser | Gunther Krauss | Heidi Webber | Amit Kumar Srivastava | Sabine Julia Seidel | Andreas Tewes | Ehsan Eyshi Rezaei | Frank Ewert

Editors: Amy Marshall-Colon

A theoretical analysis of how plant growth is limited by carbon allocation strategies and respiration

JOURNAL ARTICLE published 1 January 2019 in in silico Plants

Research funded by Leverhulme Centre for Advanced Biological Modelling (X/009780-11-22)

Authors: Bethany L Holland | Nicholas A M Monk | Richard H Clayton | Colin P Osborne

Simulating organ biomass variability and carbohydrate distribution in perennial fruit crops: a comparison between the common assimilate pool and phloem carbohydrate transport models

JOURNAL ARTICLE published 1 July 2021 in in silico Plants

Research funded by European Regional Development Fund-Project ‘SINGING PLANT’ (CZ.02.1.01/0.0/0.0/16_026/0008446)

Authors: Junqi Zhu | Fang Gou | Gerhard Rossouw | Fareeda Begum | Michael Henke | Ella Johnson | Bruno Holzapfel | Stewart Field | Alla Seleznyova

Editors: Kathy Steppe | Stephen P Long | Kathy Steppe