Author

J. Freeman

University of Colorado Boulder

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Ecology· 3 Microbiology· 3 Bioinformatics· 1 Cancer Biology· 1 Cell Biology· 1 Plant Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Approach:experimental assay· 4 Organism:C. elegans· 3 Organism:human· 2 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cancer & tumor microenvironment· 1

Frequent Co-Authors

D. Cullenward· 3 shared G. Badgley· 3 shared J. J. Hamman· 3 shared A. T. Trugman· 2 shared M. H. Wilcox· 2 shared O. S. Chegwidden· 2 shared W. R. L. Anderegg· 2 shared A. De Haven Brandon· 1 shared

Activity by Year

2019-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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3 shared papersEcology

D. Cullenward

Mutual co-authors in cluster

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10 papers

Recent·Most cited

Macrophages undergo functionally significant reprogramming of nucleotide metabolism upon classical activation

S. V. John, G. L. Seim, B. J. Erazo-Flores, J. Steill, J. Freeman, J. A. Votava, N. L. Arp, X. Qing, R. Stewart, L. J. Knoll, J. Fan

This study identifies significant reprogramming of nucleotide metabolism in classically activated macrophages, revealing key regulatory mechanisms and functional consequences.

bioRxiv · Dec 27, 2023 · PreprintCell Biology

Transcription dosage compensation does not occur in Down syndrome

Samuel Hunter, Robin D. Dowell, Josephina Hendrix, J. Freeman, Mary Ann Allen

The paper shows that transcriptional dosage compensation is absent in Down syndrome using real and simulated data, and highlights issues with standard analysis methods.

BMC Biology · Nov 9, 2023Peer-reviewedBioinformatics

A high soluble-fibre allele in wheat encodes a defective cell wall peroxidase responsible for dimerization of ferulate moieties on arabinoxylan

R. A. C. Mitchell, M. Oszvald, T. K. Pellny, J. Freeman, K. Halsey, C. A. Sparks, A. K. Huttly, S. Specel, M. Leverington-Waite, S. Griffiths, P. R. Shewry, A. Lovegrove

This study identifies a wheat peroxidase variant that reduces ferulate dimerization in arabinoxylan, increasing soluble dietary fibre content.

bioRxiv · Mar 8, 2023Plant Biology

Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile

A. O. Olaitan, C. Dureja, M. Youngblom, M. A. Topf, W.-J. Shen, A. J. Gonzales-Luna, A. Deshpande, K. E. Hevener, J. Freeman, M. H. Wilcox, K. L. Palmer, K. W. Garey, C. S. Pepperell, J. G. Hurdle

This study identifies a mutation in C. difficile that causes metronidazole resistance and links it to fluoroquinolone resistance, contributing to the spread of drug-resistant strains.

bioRxiv · Sep 23, 2022Microbiology

Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile

K. E. Dingle, J. Freeman, X. Didelot, D. W. Eyre, J. Swann, W. Spittal, E. V. Clark, K. A. Jolley, A. S. Walker, M. H. Wilcox, D. W. Crook

The paper identifies amino acid substitutions in penicillin binding proteins (PBPs) PBP1 and PBP3 as a mechanism of cephalosporin resistance in C. difficile, which co-occurs with fluoroquinolone resistance in epidemic lineages.

bioRxiv · May 23, 2022 · PreprintMicrobiology

California's forest carbon offsets buffer pool is severely undercapitalized

G. Badgley, F. Chay, O. S. Chegwidden, J. J. Hamman, J. Freeman, D. Cullenward

This paper analyzes California's forest carbon offset buffer pool, finding it severely undercapitalized due to wildfire and disease risks, threatening the program's 100-year permanence guarantee.

bioRxiv · Apr 27, 2022Ecology

Climate risks to carbon sequestration in US forests

W. R. L. Anderegg, O. S. Chegwidden, G. Badgley, A. T. Trugman, D. Cullenward, J. T. Abatzoglou, J. A. Hicke, J. Freeman, J. J. Hamman

The paper quantifies climate-driven risks to forest carbon sequestration in the US, projecting increased wildfire, drought, and insect disturbances under different emission scenarios.

bioRxiv · May 11, 2021 · PreprintEcology

Systematic over-crediting in California's forest carbon offsets program

G. Badgley, J. Freeman, J. J. Hamman, B. Haya, A. T. Trugman, W. R. L. Anderegg, D. Cullenward

This paper evaluates California's forest carbon offsets program and finds systematic over-crediting due to flawed regional average comparisons, resulting in 29.4% excess credits worth $410 million.

bioRxiv · Apr 28, 2021Ecology

Heme is crucial for medium-dependent metronidazole resistance in clinical isolates of C. difficile

I. M. Boekhoud, I. Sidorov, S. Nooij, C. Harmanus, I. M. J. G. Bos-Sanders, V. Viprey, B. Spittal, E. Clark, K. Davies, J. Freeman, E. J. Kuijper, W. K. Smits, COMBACTE-CDI Consortium, European Study Group for Clostridioides difficile

The paper shows heme dependence in metronidazole resistance in C. difficile clinical isolates, linked to a SNP in hsmA and associated with a resistant lineage.

bioRxiv · Nov 18, 2020Microbiology

Signalling involving MET and FAK supports cell division independent of the activity of the cell cycle-regulating CDK4/6 kinases

C. Zhang, S. R. Stockwell, M. Elbanna, R. Ketteler, J. Freeman, B. Al-Lazikani, S. Eccles, A. De Haven Brandon, F. Raynaud, A. Hayes, P. A. Clarke, P. Workman, S. Mittnacht

This study shows that MET/FAK signaling can activate CDK2 independently of CDK4/6, leading to cell division, and suggests targeting MET/FAK could enhance CDK4/6 inhibitor therapies.

bioRxiv · Apr 8, 2019Cancer Biology