reviews

public peer reviews.

Peer review is a good idea. Gatekeeping is not. As a reviewer, I see my job as sharpening the work by defining the boundaries of what can be supported, not dictating what I want the work to be. I aim to be attentive, courteous, and constructive. As a mentor, I try to involve trainees in the review process as well.

See the peer review section of the Fraser lab compact for a lot more on this topic that I agree with, along with the Peer Review in the Life Sciences course we co-taught in 2023. Also see the polemically-titled “Is Peer Review a Good Idea?” by Remco Heesen and Liam Kofi Bright for an interesting argument.

The genetic architecture of protein stability.
Faure AJ, Martí-Aranda A, Hidalgo-Carcedo C, Beltran A, Schmiedel JM, Lehner B.

Reviewed by: Macdonald CB, Coyote-Maestas W (Referee #1).


Representative Image
    Post-Review
    Access the paper
  • PMID: 39322666

The simplicity of protein sequence-function relationships.
Park Y, Metzger BPH, Thornton JW.

Reviewed by: Lam A, Macdonald CB, Sanchez R, Coyote-Maestas W.


Representative Image
    Post-Review
    Access the paper
  • PMID: 39261454

FusOn-pLM: A Fusion Oncoprotein-Specific Language Model via Focused Probabilistic Masking.
Vincoff S, Goel S, Kholina K, Pulugurta R, Vure P, Chatterjee P.

Reviewed by: Bajaj P, Macdonald CB.


Representative Image
    Peer Review
  • Biorxiv Preprint v597245: 597245
  • PREreview.org: 12658078

Heterogeneous folding landscapes and predetermined breaking points within a protein family.
Pechmann S.

Reviewed by: Macdonald CB, San Felipe CJ.


Representative Image

The conserved protein CBA1 is required for vitamin B12 uptake in different algal lineages.
Sayer AP, Llavero-Pasquina M, Geisler K, Holzer A, Bunbury F, Mendoza-Ochoa GI, Lawrence AD, Warren MJ, Mehrshahi P, Smith AG.

Reviewed by: Student 1, Student 2, Macdonald CB, Fraser J.


Representative Image

Phosphorylation of pyruvate dehydrogenase marks the inhibition of in vivo neuronal activity.
Yang D, Wang Y, Qi T, Zhang X, Shen L, Ma J, Pang Z, Lal NK, McClatchy DB, Wang K, Xie Y, Polli F, Maximov A, Augustine V, Cline HT, Yates JR III, Ye L.

Reviewed by: Liu Z, Shin C, Macdonald CB, Fraser J.


Representative Image
    Post-Review
    Access the paper
  • PMID: 38266644

The Herbicide Acetochlor Causes Lipid Peroxidation by Inhibition of Glutathione Peroxidase 4.
Mesmar F, Muhsen M, Tourigny JP, Tennessen JM, Bondesson M.

Reviewed by: Byun D, Zheng J, Macdonald CB, Fraser J.


Representative Image

Decoding the Cure-all Effects of Ginseng.
Loo S, Kam A, Dutta B, Zhang X, Feng N, Sze SK, Liu CF, Wang X, Tam JP.

Reviewed by: Chavez I, Rodea D, Ravikumar A, Macdonald CB, Fraser J.


Representative Image

Deep Boosted Molecular Dynamics (DBMD): Accelerating molecular simulations with Gaussian boost potentials generated using probabilistic Bayesian deep neural network.
Do, H and Miao, Y.

Reviewed by: Alkislar I, Freitas N, Macdonald CB, Fraser J.


Representative Image

Mutation in glutamate transporter homologue GltTk provides insights into pathologic mechanism of episodic ataxia 6.
Colucci E, Anshari ZR, Patino-Ruiz MF, Nemchinova M, Whittaker J, Slotboom DJ, Guskov A.

Reviewed by: Macdonald CB.


Representative Image
    Post-Review
    Access the paper
  • PMID: 37002226

Nitrogenase resurrection and the evolution of a singular enzymatic mechanism.
Garcia AK, Harris DF, Rivier AJ, Carruthers BM, Pinochet-Barros A, Seefeldt L, Kaçar B.

Reviewed by: Macdonald CB, Lee S.


Representative Image
    Peer Review
  • Biorxiv Preprint v3: 492308
  • Reviewer: #3
    Post-Review
    Access the paper
  • PMID: 36799917

Activating alternative transport modes in a multidrug resistance efflux pump to confer chemical susceptibility.
Spreacker PJ, Thomas N, Beeninga WF, Brousseau M, Porter CJ, Hibbs KM, Henzler-Wildman KA.

Reviewed by: Macdonald CB.


Representative Image
    Post-Review
    Access the paper
  • PMID: 36496486

Higher-order epistasis creates idiosyncrasy, confounding predictions in protein evolution.
Buda K, Miton CM, Tokuriki N.

Reviewed by: Macdonald CB, Lee S, Fraser JS.


Representative Image
    Post-Review
    Access the paper
  • PMID: 38129396

Interpreting the molecular mechanisms of disease variants in human membrane proteins.
Tiemann JKS, Zschach H, Lindorff-Larsen K, Stein A.

Reviewed by: Macdonald CB, Trinidad D, Grimes PR, Howard M, Melo A, Coyote-Maestas W.


Representative Image
    Peer Review
  • Biorxiv Preprint v1: 499731
    Post-Review
    Access the paper
  • PMID: 36600598

Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms.
Flynn JM, Samant N, Schneider-Nachum G, Barkan DT, Yilmaz NK, Schiffer CA, Moquin SA, Dovala D, Bolon DNA.

Reviewed by: Macdonald CB, Fraser JS.


Representative Image
    Peer Review
  • Biorxiv Preprint v2: 477860
  • Reviewer: #1