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fixed errors identified by JOSS editorial process
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243 changes: 91 additions & 152 deletions paper/paper.bib
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@@ -1,115 +1,21 @@
@inproceedings{kour2014real,
title={Real-time segmentation of on-line handwritten arabic script},
author={Kour, George and Saabne, Raid},
booktitle={Frontiers in Handwriting Recognition (ICFHR), 2014 14th International Conference on},
pages={417--422},
year={2014},
organization={IEEE}
}

@inproceedings{kour2014fast,
title={Fast classification of handwritten on-line Arabic characters},
author={Kour, George and Saabne, Raid},
booktitle={Soft Computing and Pattern Recognition (SoCPaR), 2014 6th International Conference of},
pages={312--318},
year={2014},
organization={IEEE}
}

@article{hadash2018estimate,
title={Estimate and Replace: A Novel Approach to Integrating Deep Neural Networks with Existing Applications},
author={Hadash, Guy and Kermany, Einat and Carmeli, Boaz and Lavi, Ofer and Kour, George and Jacovi, Alon},
journal={arXiv preprint arXiv:1804.09028},
year={2018}
}


@article{HyDe,
abstract = {{The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e., their difference is 0), producing a set of functions called phylogenetic invariants. In this article, we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available as an open source Python package under the GNU GPL v3 on both GitHub (https://github.com/pblischak/HyDe) and the Python Package Index (PyPI: https://pypi.python.org/pypi/phyde).}},
author = {Blischak, Paul D and Chifman, Julia and Wolfe, Andrea D and Kubatko, Laura S},
doi = {10.1093/sysbio/syy023},
eprint = {https://academic.oup.com/sysbio/article-pdf/67/5/821/25517390/syy023.pdf},
issn = {1063-5157},
journal = {Systematic Biology},
month = {03},
number = {5},
pages = {821-829},
title = {{HyDe: A Python Package for Genome-Scale Hybridization Detection}},
url = {https://doi.org/10.1093/sysbio/syy023},
volume = {67},
year = {2018},
bdsk-url-1 = {https://doi.org/10.1093/sysbio/syy023}}


@misc{lev1athan,
doi = {10.48550/ARXIV.0910.4067},

url = {https://arxiv.org/abs/0910.4067},

author = {Huber, Katharina T. and van Iersel, Leo and Kelk, Steven and Suchecki, Radoslaw},

keywords = {Populations and Evolution (q-bio.PE), FOS: Biological sciences, FOS: Biological sciences},

title = {A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks},

publisher = {arXiv},

year = {2009},

copyright = {arXiv.org perpetual, non-exclusive license}
}
####################################
@article{kurtz2015sparse,
title={Sparse and compositionally robust inference of microbial ecological networks},
author={Kurtz, Zachary D and M{\"u}ller, Christian L and Miraldi, Emily R and Littman, Dan R and Blaser, Martin J and Bonneau, Richard A},
journal={PLoS computational biology},
volume={11},
number={5},
pages={e1004226},
year={2015},
publisher={Public Library of Science San Francisco, CA USA}
}


@inproceedings{chen2020gppial,
title={GPPIAL: A New Global PPI Network Aligner Based on Orthologs},
author={Chen, Yaoran and Zhu, Yuanyuan and Zhong, Ming and Peng, Rong and Liu, Juan},
booktitle={2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
pages={100--107},
year={2020},
organization={IEEE}
organization={IEEE},
doi={10.1109/bibm49941.2020.9313552}
}

@article{ma2020review,
title={A review of protein--protein interaction network alignment: From pathway comparison to global alignment},
author={Ma, Cheng-Yu and Liao, Chung-Shou},
journal={Computational and Structural Biotechnology Journal},
volume={18},
pages={2647--2656},
year={2020},
publisher={Elsevier}
}

@article{peschel2021netcomi,
title={NetCoMi: network construction and comparison for microbiome data in R},
author={Peschel, Stefanie and M{\"u}ller, Christian L and von Mutius, Erika and Boulesteix, Anne-Laure and Depner, Martin},
journal={Briefings in bioinformatics},
volume={22},
number={4},
pages={bbaa290},
year={2021},
publisher={Oxford University Press}
}

@article{yang2019meta,
title={Meta-network: optimized species-species network analysis for microbial communities},
author={Yang, Pengshuo and Yu, Shaojun and Cheng, Lin and Ning, Kang},
journal={BMC genomics},
volume={20},
number={2},
pages={143--151},
year={2019},
publisher={BioMed Central}
@article{hovcevar2016computation,
title={Computation of graphlet orbits for nodes and edges in sparse graphs},
author={Ho{\v{c}}evar, Toma{\v{z}} and Dem{\v{s}}ar, Janez},
journal={Journal of Statistical Software},
volume={71},
pages={1--24},
year={2016},
doi={10.18637/jss.v071.i10 }
}

@article{kuchaiev2010topological,
Expand All @@ -120,7 +26,20 @@ @article{kuchaiev2010topological
number={50},
pages={1341--1354},
year={2010},
publisher={The Royal Society}
publisher={The Royal Society},
doi={10.1098/rsif.2010.0063}
}

@article{kuchaiev2011graphcrunch,
title={GraphCrunch 2: software tool for network modeling, alignment and clustering},
author={Kuchaiev, Oleksii and Stevanovi{\'c}, Aleksandar and Hayes, Wayne and Pr{\v{z}}ulj, Nata{\v{s}}a},
journal={BMC bioinformatics},
volume={12},
number={1},
pages={1--13},
year={2011},
publisher={Springer},
doi={10.1186/1471-2105-12-24}
}

@article{kuhn1955hungarian,
Expand All @@ -131,16 +50,42 @@ @article{kuhn1955hungarian
number={1-2},
pages={83--97},
year={1955},
publisher={Wiley Online Library}
publisher={Wiley Online Library},
doi={10.1002/nav.20053}
}

@article{Pilgrim1995,
author = {Pilgrim, Robert},
year = {1995},
month = {08},
journal = {Lecture notes},
title = {Tutorial on Implementation of Munkres' Assignment Algorithm},
doi = {10.13140/RG.2.1.3572.3287}
@article{ma2020review,
title={A review of protein--protein interaction network alignment: From pathway comparison to global alignment},
author={Ma, Cheng-Yu and Liao, Chung-Shou},
journal={Computational and Structural Biotechnology Journal},
volume={18},
pages={2647--2656},
year={2020},
publisher={Elsevier},
doi={10.1016/j.csbj.2020.09.011}
}

@article{malod2015graal,
title={L-GRAAL: Lagrangian graphlet-based network aligner},
author={Malod-Dognin, No{\"e}l and Pr{\v{z}}ulj, Nata{\v{s}}a},
journal={Bioinformatics},
volume={31},
number={13},
pages={2182--2189},
year={2015},
publisher={Oxford University Press}.
doi={10.1093/bioinformatics/btv130}
}

@article{milenkovic2008uncovering,
title={Uncovering biological network function via graphlet degree signatures},
author={Milenkovi{\'c}, Tijana and Pr{\v{z}}ulj, Nata{\v{s}}a},
journal={Cancer informatics},
volume={6},
pages={CIN--S680},
year={2008},
publisher={SAGE Publications Sage UK: London, England},
doi={10.4137/cin.s680}
}

@article{neyshabur2013netal,
Expand All @@ -151,18 +96,29 @@ @article{neyshabur2013netal
number={13},
pages={1654--1662},
year={2013},
publisher={Oxford University Press}
publisher={Oxford University Press},
doi={10.1093/bioinformatics/btt202}
}

@article{malod2015graal,
title={L-GRAAL: Lagrangian graphlet-based network aligner},
author={Malod-Dognin, No{\"e}l and Pr{\v{z}}ulj, Nata{\v{s}}a},
journal={Bioinformatics},
volume={31},
number={13},
pages={2182--2189},
year={2015},
publisher={Oxford University Press}
@article{peschel2021netcomi,
title={NetCoMi: network construction and comparison for microbiome data in R},
author={Peschel, Stefanie and M{\"u}ller, Christian L and von Mutius, Erika and Boulesteix, Anne-Laure and Depner, Martin},
journal={Briefings in bioinformatics},
volume={22},
number={4},
pages={bbaa290},
year={2021},
publisher={Oxford University Press},
doi={10.1101/2020.07.15.195248}
}

@article{Pilgrim1995,
author = {Pilgrim, Robert},
year = {1995},
month = {08},
journal = {Lecture notes},
title = {Tutorial on Implementation of Munkres' Assignment Algorithm},
doi = {10.13140/RG.2.1.3572.3287}
}

@article{prvzulj2007biological,
Expand All @@ -173,35 +129,18 @@ @article{prvzulj2007biological
number={2},
pages={e177--e183},
year={2007},
publisher={Oxford University Press}
publisher={Oxford University Press},
doi={10.1093/bioinformatics/btq091}
}

@article{kuchaiev2011graphcrunch,
title={GraphCrunch 2: software tool for network modeling, alignment and clustering},
author={Kuchaiev, Oleksii and Stevanovi{\'c}, Aleksandar and Hayes, Wayne and Pr{\v{z}}ulj, Nata{\v{s}}a},
journal={BMC bioinformatics},
volume={12},
number={1},
pages={1--13},
year={2011},
publisher={Springer}
}

@article{hovcevar2016computation,
title={Computation of graphlet orbits for nodes and edges in sparse graphs},
author={Ho{\v{c}}evar, Toma{\v{z}} and Dem{\v{s}}ar, Janez},
journal={Journal of Statistical Software},
volume={71},
pages={1--24},
year={2016}
}

@article{milenkovic2008uncovering,
title={Uncovering biological network function via graphlet degree signatures},
author={Milenkovi{\'c}, Tijana and Pr{\v{z}}ulj, Nata{\v{s}}a},
journal={Cancer informatics},
volume={6},
pages={CIN--S680},
year={2008},
publisher={SAGE Publications Sage UK: London, England}
@article{yang2019meta,
title={Meta-network: optimized species-species network analysis for microbial communities},
author={Yang, Pengshuo and Yu, Shaojun and Cheng, Lin and Ning, Kang},
journal={BMC genomics},
volume={20},
number={2},
pages={143--151},
year={2019},
publisher={BioMed Central},
doi={10.1186/s12864-019-5471-1}
}
6 changes: 3 additions & 3 deletions paper/paper.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,11 @@ authors:
email: [email protected]
affiliation: "2,3"
affiliations:
- name: Department of Computer Science, University of Wisconsin-Madison
- name: Department of Computer Science, University of Wisconsin-Madison, Madison, WI, United States of America
index: 1
- name: Wisconsin Institute for Discovery, University of Wisconsin-Madison
- name: Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States of America
index: 2
- name: Department of Plant Pathology, University of Wisconsin-Madison
- name: Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States of America
index: 3
date: 12 December 2022
bibliography: paper.bib
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