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.

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(sorted by most recently updated)
Multi-Dataset Integration and Residual Connections Improve Proteome Prediction from Transcriptomics Using Deep Learning
Cranney, Meyer
Jul 2024
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
Jul 2024
An efficient not-only-linear correlation coefficient based on clustering
Pividori, Ritchie, Milone, Greene
Jun 2024
A publishing infrastructure for AI-assisted academic authoring
Pividori, Greene
Jun 2024
Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry
Jiang, Rex, Schuster, Neely, Rosano, Volkmar, Momenzadeh, Peters-Clarke, Egbert, Kreimer, Doud, et al
May 2024
Analysis of science journalism reveals gender and regional disparities in coverage
Davidson, Greene
Mar 2024
A Platform for the Biomedical Application of Large Language Models
Lobentanzer, Feng, Consortium, Maier, Wang, Baumbach, Krehl, Ma, Saez-Rodriguez
Feb 2024
Edit me to practice contributing to a collaborative Manubot manuscript
Doe, Roe
Feb 2024
The probability of edge existence due to node degree: a baseline for network-based predictions
Zietz, Himmelstein, Kloster, Williams, Nagle, Greene
Feb 2024
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
Feb 2024
Optimizer's dilemma: optimization strongly influences model selection in transcriptomic prediction
Crawford, Chikina, Greene
Nov 2023
Formes & perception
Nov 2023
Epistasis between mutator alleles contributes to germline mutation rate variability in laboratory mice
Sasani, Quinlan, Harris
Oct 2023
Microtomographic investigation of a large corpus of cichlids
Haberthür, Law, Ford, Häsler, Seehausen, Hlushchuk
Oct 2023
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
Sep 2023
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Himmelstein, Zietz, Rubinetti, Kloster, Heil, Alquaddoomi, Hu, Nicholson, Hao, Sullivan, Nagle, et al
Jul 2023
OpenPBTA: An Open Pediatric Brain Tumor Atlas
Shapiro, Gaonkar, Spielman, Savonen, Bethell, Jin, Rathi, Zhu, Egolf, Farrow, Miller, Yang, Koganti, et al
Apr 2023
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution
Braga, Hébert, Hudgins, Scott, Edwards, Reyes, Grainger, Foroughirad, Hillemann, Binley, Brookson, et al
Apr 2023
Machine learning in rare disease
Banerjee, Taroni, Allaway, Prasad, Guinney, Greene
Mar 2023
A set of Common Software Quality Assurance Baseline Criteria for Research Projects
Orviz, David, Campos, Gomes, Moltó, Tykhonov, Duma, Lopez, Donvito
Feb 2023
Morphofunctional changes at the active zone during synaptic vesicle exocytosis
Radecke, Seeger, Kádková, Laugks, Khosrozadeh, Goldie, Lučić, Sørensen, Zuber
Feb 2023
Sourmash Branchwater Enables Lightweight Petabyte-Scale Sequence Search
Irber, Pierce-Ward, Brown
Nov 2022
Protein k-mers enable assembly-free microbial metapangenomics
Reiter, Pierce-Ward, Irber, Botvinnik, Brown
Nov 2022
Integrative Analytical and Computational Strategies for Qualitative and Semi-quantitative Plant Metabolome Characterization
Oct 2022
Expanding a Database-derived Biomedical Knowledge Graph via Multi-relation Extraction from Biomedical Abstracts
Nicholson, Himmelstein, Greene
Sep 2022
Accurate prediction of transition metal ion location via deep learning
Dürr, Levy, Rothlisberger
Aug 2022
Widespread redundancy in -omics profiles of cancer mutation states
Crawford, Christensen, Chikina, Greene
Jun 2022
Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for Label-Free Detection of Molecules across Entire Cell Sections
Elferich, Schiroli, Scadden, Grigorieff
Jun 2022
The LOTUS Initiative for Open Knowledge Management in Natural Products Research
Rutz, Sorokina, Galgonek, Mietchen, Willighagen, Gaudry, Graham, Stephan, Page, Vondrášek, Steinbeck, et al
Mar 2022
Automated segmentation and description of the internal morphology of human permanent teeth by means of micro-CT
Haberthür, Hlushchuk, Wolf
Jan 2022
Pulmonary acini exhibit complex changes during postnatal rat lung development
Haberthür, Yao, Barré, Cremona, Tschanz, Schittny
Jan 2022
Packaging research artefacts with RO-Crate
Soiland-Reyes, Sefton, Crosas, Castro, Coppens, Fernández, Garijo, Grüning, Rosa, Leo, Carragáin, et al
Jan 2022
Opportunities and obstacles for deep learning in biology and medicine [update in progress]
Christensen, Gitter, Himmelstein, Titus, Levy, Greene, Elton
Dec 2021
Ten Quick Tips for Deep Learning in Biology
Lee, Gitter, Greene, Raschka, Maguire, Titus, Kessler, Lee, Chevrette, Stewart, Britto-Borges, Cofer, et al
Nov 2021
Examining linguistic shifts between preprints and publications
Nicholson, Rubinetti, Hu, Thielk, Hunter, Greene
Nov 2021
Towards a pragmatic definition of cell type
Lubiana, Nakaya
Oct 2021
Analysis of scientific society-awarded honors reveals disparities
Le, Himmelstein, Hippen, Gazzara, Greene
Sep 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
New Technology and Tools to Enhance Collaborative Video Analysis in Live ‘Data Sessions’
Mar 2021
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
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
Genotyping structural variants in pangenome graphs using the vg toolkit
Hickey, Heller, Monlong, Sibbesen, Sirén, Eizenga, Dawson, Garrison, Novak, Paten
Feb 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
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
Sci-Hub provides access to nearly all scholarly literature
Himmelstein, Romero, Levernier, Munro, McLaughlin, Tzovaras, Greene
Feb 2018
Manubot 2018 development proposal
Himmelstein, Greene
Dec 2017
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Himmelstein, Lizee, Hessler, Brueggeman, Chen, Hadley, Green, Khankhanian, Baranzini
Sep 2017
Bitcoin: A Peer-to-Peer Electronic Cash System
Oct 2008
Vagelos Report Summer 2017