1. Designing biochemical circuits with tree search

    This article has 2 authors:
    1. Pranav S. Bhamidipati
    2. Matthew Thomson
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This manuscript presents a valuable computational tool for identifying 3-5 gene regulatory network topologies capable of generating oscillatory dynamics. The application of Monte Carlo Tree Search to circuit design is novel and effectively expands the scale at which non-linear behaviours can be explored in silico. The efficiency of the proposed algorithm is convincing, and the work will be of interest to the systems and synthetic biology communities. While the evolutionary implications remain unclear, the methodological contribution represents a significant advance in the field.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  2. A mathematical model for ketosis-prone diabetes suggests the existence of multiple pancreatic β-cell inactivation mechanisms

    This article has 3 authors:
    1. Sean A Ridout
    2. Priyathama Vellanki
    3. Ilya Nemenman
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This theoretical study makes a useful contribution to our understanding of a subtype of type 2 diabetes - ketosis-prone diabetes mellitus (KPD) - with a potential impact on our broader understanding of diabetes and glucose regulation. The article presents an ordinary differential equation-based model for KPD that incorporates a number of distinct timescales - fast, slow, as well as intermediate, incorporating a key hypothesis of reversible beta cell deactivation. The presented evidence is solid and shows that observed clinical disease trajectories may be explained by a simple mathematical model in a particular parameter regime.

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  3. Dynamic sensitivity analysis of a mathematical model describing the effect of the macroalgae Asparagopsis taxiformis on rumen fermentation and methane production under in vitro continuous conditions

    This article has 4 authors:
    1. Paul Blondiaux
    2. Tristan Senga Kiessé
    3. Maguy Eugène
    4. Rafael Muñoz-Tamayo

    Reviewed by Peer Community in Animal Science

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  4. A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell Model

    This article has 12 authors:
    1. James D Pearce
    2. Sara E Simmonds
    3. Gita Mahmoudabadi
    4. Lakshmi Krishnan
    5. Giovanni Palla
    6. Ana-Maria Istrate
    7. Alexander Tarashansky
    8. Benjamin Nelson
    9. Omar Valenzuela
    10. Donghui Li
    11. Stephen R. Quake
    12. Theofanis Karaletsos

    Reviewed by Arcadia Science

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  5. Amino acid repeat signatures underlying human-pathogen interactions

    This article has 7 authors:
    1. Anjali Kumari Singh
    2. Nagashree Rachote
    3. Anushka Agrawal
    4. Vaidehi Sharma
    5. Keertana Sai Kappagantula
    6. Rajashekar Varma Kadumuri
    7. Sreenivas Chavali

    Reviewed by Arcadia Science

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  6. Exploiting fluctuations in gene expression to detect causal interactions between genes

    This article has 6 authors:
    1. Euan Joly-Smith
    2. Mir Mikdad Talpur
    3. Paige Allard
    4. Fotini Papazotos
    5. Laurent Potvin-Trottier
    6. Andreas Hilfinger
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      By taking advantage of noise in gene expression, this important study introduces a new approach for detecting directed causal interactions between two genes without perturbing either. The main theoretical result is supported by a proof. Preliminary simulations and experiments on small circuits are solid, but further investigations are needed to demonstrate the broad applicability and scalability of the method.

    Reviewed by eLife

    This article has 6 evaluationsAppears in 1 listLatest version Latest activity
  7. Perturbation-response analysis of in silico metabolic dynamics revealed hard-coded responsiveness in the cofactors and network sparsity

    This article has 2 authors:
    1. Yusuke Himeoka
    2. Chikara Furusawa
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study uses dynamic metabolic models to compare perturbation responses in a bacterial system, analyzing whether they return to their steady state or amplify beyond the initial perturbation. The evidence supporting the emergent properties of perturbed metabolic systems to network topology and sensitivity to specific metabolites is solid.

    Reviewed by eLife

    This article has 11 evaluationsAppears in 1 listLatest version Latest activity
  8. Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns

    This article has 6 authors:
    1. Ken-ichiro F Kamei
    2. Koseki J Kobayashi-Kirschvink
    3. Takashi Nozoe
    4. Hidenori Nakaoka
    5. Miki Umetani
    6. Yuichi Wakamoto
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This paper reports the fundamental finding of how Raman spectral patterns correlate with proteome profiles. The authors then go further to show that this can be used to infer global stochiometric regulation of the proteomes. These findings are likely general and the authors provide compelling evidence by analyzing bacterial and human cells but there are some suggestions provided below to make the work clearer and more accessible for it to reach a broader audience.

    Reviewed by eLife, Arcadia Science

    This article has 5 evaluationsAppears in 2 listsLatest version Latest activity
  9. Passive shaping of intra- and intercellular m6A dynamics via mRNA metabolism

    This article has 14 authors:
    1. David Dierks
    2. Ran Shachar
    3. Ronit Nir
    4. Miguel Angel Garcia-Campos
    5. Anna Uzonyi
    6. David Wiener
    7. Ursula Toth
    8. Walter Rossmanith
    9. Lior Lasman
    10. Boris Slobodin
    11. Jacob H Hanna
    12. Yaron Antebi
    13. Ruth Scherz-Shouval
    14. Schraga Schwartz
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents a fundamental finding on how levels of m6A levels are controlled, invoking a consolidated model where degradation of modified RNAs in the cytoplasm plays a primary role in shaping m6A patterns and dynamics, rather than needing active regulation by m6A erasers and other related processes. The evidence is compelling through its use of transcriptome-wide data and mechanistic modeling. Relevant for any reader with an interest in RNA metabolism, this new framework consolidates previous observations and highlights the importance of careful experimentation for evaluation m6A levels.

    Reviewed by eLife

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
  10. An Hfq-dependent post-transcriptional mechanism fine tunes RecB expression in Escherichia coli

    This article has 6 authors:
    1. Irina Kalita
    2. Ira Alexandra Iosub
    3. Lorna McLaren
    4. Louise Goossens
    5. Sander Granneman
    6. Meriem El Karoui
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      Combining experimental and computation approaches, this manuscript provides convincing evidence for a post-transcriptional mechanism that provides robust control over the protein expression level of RecB in E. coli. In addition to uncovering how DNA damage drives higher levels of RecB protein, this work also reveals important tenets for how broader mechanisms that suppress noise and underlie responsive tuning of protein levels can be achieved.

    Reviewed by eLife

    This article has 10 evaluationsAppears in 1 listLatest version Latest activity
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