Here is a list of manuscripts that have been created with Manubot. Click on a thumbnail to view the interactive web version of the paper. Or use the other buttons to view the journal, preprint, pdf, and other versions. Note that some of these manuscripts are still works-in-progress.

Don't see your manuscript here? Is a manuscript missing a preprint or journal link? Suggest an addition or change to the catalog here.

(sorted by most recently updated)
An Open Pediatric Brain Tumor Atlas
Shapiro, Savonen, Bethell, Gaonkar, Zhu, Brown, Duong, Rathi, Noureen, Zhang, Ennis, Spielman, et al
Oct 2021
SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics
Rando, Greene, Robson, Boca, Wellhausen, Lordan, Brueffer, Ray, McGowan, Gitter, Dattoli, Velazquez, et al
Oct 2021
Ten Quick Tips for Deep Learning in Biology
Lee, Gitter, Greene, Raschka, Maguire, Titus, Kessler, Lee, Chevrette, Stewart, Britto-Borges, Cofer, et al
Oct 2021
Introducing yt 4.0: Analysis and Visualization of Volumetric Data
Project, Turk, Goldbaum, ZuHone, Hummels, Ji, Lang, Munk, Smith, Kowalik, Val-Borro, Coughlin, et al
Oct 2021
Machine learning in rare disease
Banerjee, Taroni, Allaway, Prasad, Guinney, Greene
Oct 2021
The LOTUS Initiative for Open Natural Products Research: Knowledge Management through Wikidata
Rutz, Sorokina, Galgonek, Mietchen, Willighagen, Gaudry, Graham, Stephan, Page, Vondrášek, Steinbeck, et al
Oct 2021
Towards a pragmatic definition of cell type
Lubiana, Nakaya
Oct 2021
Linguistic Analysis of the bioRxiv Preprint Landscape
Nicholson, Rubinetti, Hu, Thielk, Hunter, Greene
Oct 2021
Pulmonary acini exhibit complex changes during postnatal rat lung development
Haberthür, Yao, Barré, Cremona, Tschanz, Schittny
Sep 2021
Analysis of scientific society-awarded honors reveals disparities
Le, Himmelstein, Hippen, Gazzara, Greene
Sep 2021
Edit me to practice contributing to a collaborative Manubot manuscript
Doe, Roe
Sep 2021
Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms
Pividori, Lu, Li, Su, Johnson, Wei, Feng, Namjou, Kiryluk, Kullo, Luo, Sullivan, Voight, Skarke, et al
Aug 2021
Analysis of science journalism reveals gender and regional disparities in coverage
Davidson, Greene
Jul 2021
sPlotOpen – An environmentally-balanced, open-access, global dataset of vegetation plots
Sabatini, Lenoir, Hattab, Arnst, Chytrý, Dengler, Ruffray, Hennekens, Jandt, Jansen, Jiménez-Alfaro, et al
Jul 2021
IRB Protocol: Understanding Black Indianapolis Community Members’ Vision for Housing in their Neighborhoods
Riggins, Wilkinson
Jun 2021
From the retina to action: Dynamics of predictive processing in the visual system
Apr 2021
Automated segmentation and description of the internal morphology of human permanent teeth by means of micro-CT
Haberthür, Hlushchuk, Wolf
Apr 2021
New Technology and Tools to Enhance Collaborative Video Analysis in Live ‘Data Sessions’
Mar 2021
A set of Common Software Quality Assurance Baseline Criteria for Research Projects
Orviz, Lopez, Duma, David, Gomes, Donvito
Jan 2021
$k$-mer homology is a transcriptome-first method enabling functional prediction of transcriptomic 'dark matter' across species
Botvinnik, Vemuri, Pierce, Logan, Nafees, Karanam, Brown, Karkanias
Dec 2020
ANN: A platform to annotate text with Wikidata IDs
Lubiana, Weber, Paranhos, Araújo, Dorrego-Rivas, Franzen, Viçosa, Ghosh, García-Plaza
Nov 2020
Streamlining Data-Intensive Biology With Workflow Systems
Reiter, Brooks, Irber, Joslin, Reid, Scott, Brown, Pierce
Nov 2020
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
Yates, Lamnidis, Borry, Valtueña, Fagernäs, Clayton, Garcia, Neukamm, Peltzer
Nov 2020
Opportunities and obstacles for deep learning in biology and medicine [update in progress]
Greene, Himmelstein, Elton, Christensen, Gitter, Titus, Levy
Nov 2020
Des illusions visuelles aux hallucinations: une porte sur la perception
Oct 2020
Mechanisms to Govern Responsible Sharing of Open Data: A Progress Report
Mangravite, Sen, Wilbanks, Team &dagger,
Oct 2020
Extension of Roles in the ChEBI Ontology
Hoyt, Mungall, Vasilevsky, Domingo-Fernández, Healy, Colluru
Sep 2020
Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic Islands
Maguire*, Jia*, Gray, Lau, Beiko, Brinkman
Sep 2020
Major challenges on authorship and concept of authorship - why is something more needed on contributorship?
Vasilevsky, Hosseini, Teplitzky, Ilik, Mohammadi, Schneider, Kern, Colomb, Edmunds, Gutzman, et al
Aug 2020
treeheatr: an R package for interpretable decision tree visualizations
Le, Moore
Jun 2020
Open collaborative writing with Manubot
Himmelstein, Rubinetti, Slochower, Hu, Malladi, Greene, Gitter
May 2020
Recommendations to enhance rigor and reproducibility in biomedical research
Brito, Li, Moore, Greene, Nogoy, Garmire, Mangul
May 2020
Testing the association between blood type and COVID-19 infection, intubation, and death
Zietz, Tatonetti
Apr 2020
Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV ...
Akkose, Kaya, Lindsey-Boltz, Karagoz, Brown, Larsen, Yoder, Sancar, Adebali
Apr 2020
Collaborative Writing with Manubot
Mar 2020
Sci-Hub provides access to nearly all scholarly literature
Himmelstein, Romero, Levernier, Munro, McLaughlin, Tzovaras, Greene
Mar 2020
The probability of edge existence due to node degree: a baseline for network-based predictions
Zietz, Himmelstein, Kloster, Williams, Nagle, Sullivan, Greene
Mar 2020
Genotyping structural variants in pangenome graphs using the vg toolkit
Hickey, Heller, Monlong, Sibbesen, Sirén, Eizenga, Dawson, Garrison, Novak, Paten
Feb 2020
Expanding a Database-derived Biomedical Knowledge Graph via Multi-relation Extraction from Biomedical Abstracts
Nicholson, Himmelstein, Greene
Jan 2020
Incorporating biological structure into machine learning models in biomedicine
Crawford, Greene
Dec 2019
Expanding polygenic risk scores to include automatic genotype encodings and gene-gene interactions
Le, Gong, Orzechowski, Manduchi, Moore
Dec 2019
Total Functional Score of Enhancer Elements Identifies Lineage-Specific Enhancers that Drive Differentiation of Pancreatic Cells
Malladi, Nagari, Franco, Kraus
Dec 2019
The people of the 24ᵗʰ annual Pacific Symposium on Biocomputing in Hawaii
Byrd, Fu, Greene, Himmelstein, Hu, Hunter, Jain, Kurkiewicz, Le, Li, Miller, Pinello, Ramola, Taroni, et al
Nov 2019
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Himmelstein, Lizee, Hessler, Brueggeman, Chen, Hadley, Green, Khankhanian, Baranzini
Nov 2019
Bitcoin: A Peer-to-Peer Electronic Cash System
Nov 2019
Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative
Slochower, Henriksen, Wang, Chodera, Mobley, Gilson
Oct 2019
Scaling tree-based automated machine learning to biomedical big data with a feature set selector
Le, Fu, Moore
Sep 2019
Sci-Hub proporciona acceso a casi toda la literatura académica
Himmelstein, Romero, Levernier, Munro, McLaughlin, Tzovaras, Greene
Sep 2019
Two real use cases of FAIR maturity indicators in the life sciences
Bonaretti, Willighagen
Aug 2019
GimmeMotifs: an analysis framework for transcription factor motif analysis
Bruse, Heeringen
Jul 2019
Plasmids for independently tunable, low-noise expression of two genes
Silva, Lopes, Grilo, Hensel
May 2019
Network Methods for Multiomic Data Integration
Dec 2018
Progress Report: Genome-wide hypothesis generation for single-cell expression via latent spaces of deep neural networks
Hu, Greene
Aug 2018
Manubot 2018 development proposal
Himmelstein, Greene
Dec 2017
Vagelos Report Summer 2017