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- repo_url: https://github.com/quinlan-lab/mutator-epistasis-manuscript
html_url: https://quinlan-lab.github.io/mutator-epistasis-manuscript/
preprint_citation: doi:10.1101/2023.04.25.537217
journal_citation: doi:10.7554/eLife.89096
- repo_url: https://github.com/greenelab/ccc-manuscript
html_url: https://greenelab.github.io/ccc-manuscript/
preprint_citation: 10.1101/2022.06.15.496326
- repo_url: https://github.com/laurentperrinet/2023-01-31_formes-et-perception
html_url: https://laurentperrinet.github.io/2023-01-31_formes-et-perception/
- repo_url: https://github.com/jaybee84/ml-in-rd
html_url: https://jaybee84.github.io/ml-in-rd/
journal_citation: doi:10.1038/s41592-023-01886-z
- repo_url: https://github.com/greenelab/deep-review
html_url: https://greenelab.github.io/deep-review/
preprint_citation: doi:10.1101/142760
journal_citation: doi:10.1098/rsif.2017.0387
- repo_url: https://github.com/greenelab/meta-review
html_url: https://greenelab.github.io/meta-review/
thumbnail_url: https://raw.githubusercontent.com/greenelab/meta-review/master/thumbnail.png
journal_citation: doi:10.1371/journal.pcbi.1007128
- repo_url: https://github.com/dhimmel/bitcoin-whitepaper/
html_url: https://dhimmel.github.io/bitcoin-whitepaper/
comments: https://steemit.com/manubot/@dhimmel/how-i-used-the-manubot-to-reproduce-the-bitcoin-whitepaper
- repo_url: https://github.com/greenelab/scihub-manuscript
html_url: https://greenelab.github.io/scihub-manuscript/
# https://github.com/crosscite/content-negotiation/issues/104
preprint_citation: doi:10.7287/peerj.preprints.3100
journal_citation: doi:10.7554/eLife.32822
- repo_url: https://github.com/greenelab/scihub-manuscript-es
html_url: https://greenelab.github.io/scihub-manuscript-es/
thumbnail_url: https://raw.githubusercontent.com/greenelab/scihub-manuscript/master/thumbnail.png
- repo_url: https://github.com/simonvh/gimmemotifs-manuscript
html_url: https://simonvh.github.io/gimmemotifs-manuscript/
preprint_citation: doi:10.1101/474403
- repo_url: https://github.com/zietzm/Vagelos2017
html_url: https://zietzm.github.io/Vagelos2017/
preprint_citation: doi:10.6084/m9.figshare.5346577
- repo_url: https://github.com/Benjamin-Lee/deep-rules
html_url: https://benjamin-lee.github.io/deep-rules/
preprint_citation: arxiv:2105.14372
journal_citation: doi:10.1371/journal.pcbi.1009803
- repo_url: https://github.com/zietzm/integration-review
html_url: https://zietzm.github.io/integration-review/
- repo_url: https://github.com/dhimmel/rephetio-manuscript/
html_url: https://dhimmel.github.io/rephetio-manuscript/
preprint_citation: doi:10.1101/087619
journal_citation: doi:10.7554/eLife.26726
# - repo_url: https://github.com/openclimatedata/global-emissions
# html_url: https://openclimatedata.github.io/global-emissions/
# thumbnail_url: https://user-images.githubusercontent.com/8326331/64821751-888dc280-d581-11e9-8d8b-37233f7b087a.png
- repo_url: https://github.com/yt-project/yt-4.0-paper
html_url: https://yt-project.github.io/yt-4.0-paper/
thumbnail_url: https://user-images.githubusercontent.com/8326331/64820041-96414900-d57d-11e9-9b57-325f89b548df.png
- repo_url: https://github.com/trangdata/tpot-fss-ms
html_url: https://trangdata.github.io/tpot-fss-ms/
thumbnail_url: https://raw.githubusercontent.com/trangdata/tpot-fss-ms/master/thumbnail.png
preprint_citation: doi:10.1101/502484
journal_citation: doi:10.1093/bioinformatics/btz470
- repo_url: https://github.com/greenelab/manufund-2018
html_url: https://greenelab.github.io/manufund-2018/
- repo_url: https://github.com/slochower/smirnoff-host-guest-manuscript
html_url: https://slochower.github.io/smirnoff-host-guest-manuscript/
thumbnail_url: https://raw.githubusercontent.com/slochower/smirnoff-host-guest-manuscript/master/thumbnail.png
preprint_citation: doi:10.26434/chemrxiv.9159872
journal_citation: doi:10.1021/acs.jctc.9b00748
- repo_url: https://github.com/laurentperrinet/2019-05_illusions-visuelles
html_url: https://laurentperrinet.github.io/2019-05_illusions-visuelles/
thumbnail_url: https://raw.githubusercontent.com/laurentperrinet/2019-05_illusions-visuelles/master/thumbnail.png
journal_citation: url:https://theconversation.com/illusions-et-hallucinations-visuelles-une-porte-sur-la-perception-117389
- repo_url: https://github.com/jmonlong/manu-vgsv
html_url: https://jmonlong.github.io/manu-vgsv/
thumbnail_url: https://raw.githubusercontent.com/jmonlong/manu-vgsv/master/thumbnail.png
preprint_citation: doi:10.1101/654566
- repo_url: https://github.com/zach-hensel/low-noise-manuscript
html_url: https://zach-hensel.github.io/low-noise-manuscript/
preprint_citation: doi:10.1101/515940
thumbnail_url: https://user-images.githubusercontent.com/8326331/64823430-64cc7b80-d585-11e9-9986-e76256b2bac1.png
journal_citation: doi:10.1128/mSphere.00340-19
- repo_url: https://github.com/vsmalladi/tfsee-manuscript
html_url: https://vsmalladi.github.io/tfsee-manuscript/
journal_citation: doi:10.1177/1177932220938063
- repo_url: https://github.com/indigo-dc/sqa-baseline
html_url: https://indigo-dc.github.io/sqa-baseline/
preprint_citation: doi:10.20350/digitalCSIC/12543
- repo_url: https://github.com/greenelab/czi-hca-report
html_url: https://greenelab.github.io/czi-hca-report/
- repo_url: https://github.com/dhimmel/psb-manuscript
html_url: https://git.dhimmel.com/psb-manuscript/
- repo_url: https://github.com/manubot/try-manubot
html_url: https://manubot.github.io/try-manubot/
thumbnail_url: https://raw.githubusercontent.com/manubot/try-manubot/master/thumbnail.png
- repo_url: https://github.com/greenelab/text_mined_hetnet_manuscript
html_url: https://greenelab.github.io/text_mined_hetnet_manuscript/
preprint_citation: doi:10.1101/730085
journal_citation: doi:10.1186/s13040-022-00311-z
- repo_url: https://github.com/lelaboratoire/rethink-prs-ms
html_url: https://lelaboratoire.github.io/rethink-prs-ms/
thumbnail_url: https://raw.githubusercontent.com/lelaboratoire/rethink-prs-ms/master/thumbnail.png
- repo_url: https://github.com/sbonaretti/FAIR_metrics
html_url: https://rawcdn.githack.com/sbonaretti/FAIR_metrics/c12a837e1b0505ffa7a3cd311e3fa69b5b940d2e/paper/manubot/webpage/v/local/index.html
thumbnail_url: https://raw.githubusercontent.com/sbonaretti/FAIR_metrics/master/thumbnail.png
preprint_citation: doi:10.1101/739334
journal_citation: doi:10.3390/nano10102068
- repo_url: https://github.com/greenelab/xswap-manuscript
html_url: https://greenelab.github.io/xswap-manuscript/
preprint_citation: doi:10.1101/2023.01.05.522939
journal_citation: doi:10.1093/gigascience/giae001
- repo_url: https://github.com/greenelab/connectivity-search-manuscript
html_url: https://greenelab.github.io/connectivity-search-manuscript/
preprint_citation: doi:10.1101/2023.01.05.522941
journal_citation: doi:10.1093/gigascience/giad047
- repo_url: https://github.com/greenelab/biopriors-review
html_url: https://greenelab.github.io/biopriors-review
thumbnail_url: https://raw.githubusercontent.com/greenelab/biopriors-review/master/content/images/ontology_simple.png
preprint_citation: arxiv:1910.06738
journal_citation: doi:10.1016/j.copbio.2019.12.021
- repo_url: https://github.com/czbiohub/kmer-homology-paper
html_url: https://czbiohub.github.io/kmer-homology-paper/
- repo_url: https://github.com/greenelab/iscb-diversity-manuscript
html_url: https://greenelab.github.io/iscb-diversity-manuscript/
preprint_citation: doi:10.1101/2020.04.14.927251
journal_citation: doi:10.1016/j.cels.2021.07.007
- repo_url: https://github.com/greenelab/covid19-review
html_url: https://greenelab.github.io/covid19-review/
- repo_url: https://github.com/fmaguire/mag_sim_paper
html_url: https://finlaymagui.re/mag_sim_paper/
- repo_url: https://github.com/AlexsLemonade/OpenPBTA-manuscript
html_url: https://alexslemonade.github.io/OpenPBTA-manuscript/
preprint_citation: doi:10.1101/2022.09.13.507832
journal_citation: doi:10.1016/j.xgen.2023.100340
- repo_url: https://github.com/jperkel/mymanuscript
html_url: https://jperkel.github.io/mymanuscript/
journal_citation: doi:10.1038/d41586-020-00916-6
- repo_url: https://github.com/zietzm/abo_covid
html_url: https://zietzm.com/abo_covid/
preprint_citation: doi:10.1101/2020.04.08.20058073
journal_citation: doi:10.1038/s41467-020-19623-x
- repo_url: https://github.com/CompGenomeLab/lemur-manuscript-archive
html_url: https://compgenomelab.github.io/lemur-manuscript-archive/webpage/
thumbnail_url: https://user-images.githubusercontent.com/1117703/79069949-19578880-7ca0-11ea-8a3f-d727696718ae.png
preprint_citation: doi:10.1101/2020.04.06.027201
- repo_url: https://github.com/trangdata/treeheatr-manuscript
html_url: https://trangdata.github.io/treeheatr-manuscript/
preprint_citation: doi:10.1101/2020.07.10.196352
journal_citation: doi:10.1093/bioinformatics/btaa662
- repo_url: https://github.com/Mangul-Lab-USC/enhancing_reproducibility
html_url: https://mangul-lab-usc.github.io/enhancing_reproducibility/
preprint_citation: arxiv:2001.05127
journal_citation: doi:10.1093/gigascience/giaa056
- repo_url: https://github.com/chemical-roles/manuscript
html_url: https://chemical-roles.github.io/manuscript/
preprint_citation: doi:10.26434/chemrxiv.12591221
- repo_url: https://github.com/dib-lab/2020-workflows-paper
html_url: https://dib-lab.github.io/2020-workflows-paper/
preprint_citation: doi:10.1101/2020.06.30.178673
- repo_url: https://github.com/data2health/contributorship
html_url: https://data2health.github.io/contributorship/
journal_citation: doi:10.1080/08989621.2020.1779591
- repo_url: https://github.com/apeltzer/eager2-paper
html_url: https://apeltzer.github.io/eager2-paper
preprint_citation: doi:10.1101/2020.06.11.145615
journal_citation: doi:10.7717/peerj.10947
- repo_url: https://github.com/QUIVIRR/Enhanced-Data-Sessions
html_url: https://quivirr.github.io/Enhanced-Data-Sessions/
preprint_citation: doi:10.31235/osf.io/eu7yw
journal_citation: doi:10.5278/ojs.quivirr.v1.2020.a0001
- repo_url: https://github.com/Sage-Bionetworks/governanceGreenPaper
html_url: https://sage-bionetworks.github.io/governanceGreenPaper/
- repo_url: https://github.com/lubianat/ann_sprint
html_url: https://lubianat.github.io/ann_sprint/
- repo_url: https://github.com/lubianat/technotype
html_url: https://lubianat.github.io/technotype/
preprint_citation: doi:10.22541/au.160979530.02627436/v1
- repo_url: https://github.com/habi/acinar-analysis-manuscript
html_url: https://habi.github.io/acinar-analysis-manuscript/
preprint_citation: doi:10.1101/786681
journal_citation: doi:10.1371/journal.pone.0257349
- repo_url: https://github.com/habi/zmk-tooth-cohort-method-manuscript
html_url: https://habi.github.io/zmk-tooth-cohort-method-manuscript/
preprint_citation: doi:10.1101/2020.10.27.356998
journal_citation: doi:10.1186/s12903-021-01551-x
- repo_url: https://github.com/habi/EAWAG-manuscript
html_url: https://habi.github.io/EAWAG-manuscript/
preprint_citation: doi:10.1101/2023.03.30.534917
journal_citation: doi:10.1371/journal.pone.0291003
- repo_url: https://github.com/greenelab/annorxiver_manuscript
html_url: https://greenelab.github.io/annorxiver_manuscript/
preprint_citation: doi:10.1101/2021.03.04.433874
- repo_url: https://github.com/lotusnprod/lotus-manuscript
html_url: https://lotusnprod.github.io/lotus-manuscript
preprint_citation: doi:10.1101/2021.02.28.433265
journal_citation: doi:10.7554/eLife.70780
- repo_url: https://github.com/laurentperrinet/Perrinet20PredictiveProcessing_manubot
html_url: https://laurentperrinet.github.io/Perrinet20PredictiveProcessing_manubot
preprint_citation: doi:10.5281/zenodo.4680675
journal_citation: doi:10.5040/9781350099784.ch-005
- repo_url: https://github.com/andtheWings/IRB_for_Indy_Housing_Interviews
html_url: https://andthewings.github.io/IRB_for_Indy_Housing_Interviews/
thumbnail_url: https://i.postimg.cc/BZkXjryx/redline-the-ave.png
- repo_url: https://github.com/greenelab/nature_news_manuscript
html_url: https://greenelab.github.io/nature_news_manuscript/
preprint_citation: doi:10.1101/2021.06.21.449261
- repo_url: https://github.com/fmsabatini/sPlotOpen_Manuscript
html_url: https://fmsabatini.github.io/sPlotOpen_Manuscript/
# https://github.com/crosscite/content-negotiation/issues/104
journal_citation: doi:10.1111/geb.13346
- repo_url: https://github.com/greenelab/phenoplier_manuscript
html_url: https://greenelab.github.io/phenoplier_manuscript/
preprint_citation: doi:10.1101/2021.07.05.450786
- repo_url: https://github.com/greenelab/mpmp-manuscript
html_url: https://greenelab.github.io/mpmp-manuscript/
preprint_citation: doi:10.1101/2021.10.27.466140
journal_citation: doi:10.1186/s13059-022-02705-y
- repo_url: https://github.com/aseedb/synaptic_tomo_ms
html_url: https://aseedb.github.io/synaptic_tomo_ms/
preprint_citation: doi:10.1101/2022.03.07.483217
- repo_url: https://github.com/stain/ro-crate-paper
html_url: https://www.researchobject.org/2021-packaging-research-artefacts-with-ro-crate/manuscript.html
preprint_citation: doi:10.5281/zenodo.5146227
journal_citation: doi:10.3233/DS-210053
thumbnail_url: https://www.researchobject.org/2021-packaging-research-artefacts-with-ro-crate/images/ro-crate-overview.svg
- repo_url: https://github.com/SORTEE-Github-Hackathon/manuscript
html_url: https://sortee-github-hackathon.github.io/manuscript/v/latest/
preprint_citation: doi:10.31222/osf.io/x3p2q
- repo_url: https://github.com/lcbc-epfl/metal-site-prediction
html_url: https://lcbc-epfl.github.io/metal-site-prediction/
preprint_citation: doi:10.1101/2022.08.22.504853
- repo_url: https://github.com/dib-lab/2022-paper-branchwater-software
html_url: https://dib-lab.github.io/2022-paper-branchwater-software/
preprint_citation: doi:10.1101/2022.11.02.514947
- repo_url: https://github.com/dib-lab/2021-paper-metapangenomes
html_url: https://dib-lab.github.io/2021-paper-metapangenomes/
preprint_citation: doi:10.1101/2022.06.27.497795
- repo_url: https://github.com/jojoelfe/deco_lace_template_matching_manuscript
html_url: https://jojoelfe.github.io/deco_lace_template_matching_manuscript/
preprint_citation: doi:10.1101/2022.06.13.495969
journal_citation: doi:10.7554/eLife.80980
- repo_url: https://github.com/greenelab/manubot-gpt-manuscript
html_url: https://greenelab.github.io/manubot-gpt-manuscript/
preprint_citation: doi:10.1101/2023.01.21.525030
journal_citation: doi:10.1093/jamia/ocae139
- repo_url: https://github.com/greenelab/optimizer-manuscript
html_url: https://greenelab.github.io/optimizer-manuscript/
preprint_citation: doi:10.1101/2023.06.26.546586
- repo_url: https://github.com/Adafede/thesis-manuscript
html_url: https://archive-ouverte.unige.ch/unige:165668
journal_citation: 10.13097/archive-ouverte/unige:165668
- repo_url: https://github.com/jessegmeyerlab/proteomics-tutorial
html_url: https://jessegmeyerlab.github.io/proteomics-tutorial/
preprint_citation: arxiv:2311.07791
journal_citation: 10.1021/acsmeasuresciau.3c00068
- repo_url: https://github.com/biocypher/biochatter-paper
html_url: https://biocypher.github.io/biochatter-paper/
preprint_citation: arxiv:2305.06488
- repo_url: https://github.com/xomicsdatascience/transcriptome-proteome-nas-manubot
html_url: https://xomicsdatascience.github.io/transcriptome-proteome-nas-manubot/
preprint_citation: doi:10.1101/2024.07.08.602560