Back

Comment on "Solving the time-dependent protein distributions for autoregulated bursty gene expression using spectral decomposition"

Ferreira Ramos, A.

2025-02-08 systems biology
10.1101/2025.02.05.635946 bioRxiv
Show abstract

The authors of the commented article claim that the exact time-dependent solutions of the stochastic model for a self-repressing gene previously obtained by us are both "incomplete and incorrect" because their calculations issued complex numbers as decaying rates of the system to steady state. We show that the imaginary decaying rates result from a methodological artifact. We use a linear algebraic approach to show that the decaying rates are those reported in [ Exact time-dependent solutions for a self-regulating gene. Phys. Rev. E 83: 062902 (2011)]. Thus, our solution is both complete and correct. Additionally, the authors claim that they have discovered a new class of operator having complex eigenvalues and non-orthogonal eigenfunctions. We show that the operator can actually be written in the usual self-adjoint form, and, hence, it has real eigenvalues and orthogonal eigenfunctions.

Matching journals

The top 8 journals account for 50% of the predicted probability mass.

1
Journal of Mathematical Biology
37 papers in training set
Top 0.1%
19.7%
2
Bulletin of Mathematical Biology
84 papers in training set
Top 0.2%
8.5%
3
Physical Review E
95 papers in training set
Top 0.1%
6.5%
4
PLOS Computational Biology
1633 papers in training set
Top 9%
3.9%
5
Nature Communications
4913 papers in training set
Top 39%
3.6%
6
Physical Review Letters
43 papers in training set
Top 0.1%
3.6%
7
Scientific Reports
3102 papers in training set
Top 35%
3.6%
8
Mathematical Biosciences
42 papers in training set
Top 0.3%
2.8%
50% of probability mass above
9
Journal of The Royal Society Interface
189 papers in training set
Top 2%
2.6%
10
Proceedings of the National Academy of Sciences
2130 papers in training set
Top 25%
2.6%
11
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
15 papers in training set
Top 0.2%
2.6%
12
Frontiers in Molecular Biosciences
100 papers in training set
Top 1.0%
2.1%
13
Entropy
20 papers in training set
Top 0.1%
1.9%
14
Biophysical Journal
545 papers in training set
Top 3%
1.7%
15
Cell Systems
167 papers in training set
Top 8%
1.5%
16
Journal of Clinical Medicine
91 papers in training set
Top 4%
1.2%
17
The Journal of Chemical Physics
49 papers in training set
Top 0.3%
1.2%
18
Royal Society Open Science
193 papers in training set
Top 3%
1.2%
19
Physical Review Research
46 papers in training set
Top 0.5%
1.2%
20
Physical Biology
43 papers in training set
Top 1%
1.2%
21
Bioinformatics
1061 papers in training set
Top 8%
1.1%
22
The European Physical Journal Plus
13 papers in training set
Top 0.6%
1.0%
23
Chaos: An Interdisciplinary Journal of Nonlinear Science
16 papers in training set
Top 0.2%
1.0%
24
Communications Biology
886 papers in training set
Top 18%
0.9%
25
iScience
1063 papers in training set
Top 26%
0.9%
26
BMC Bioinformatics
383 papers in training set
Top 6%
0.8%
27
Journal of Theoretical Biology
144 papers in training set
Top 2%
0.8%
28
Journal of the Royal Society Interface
18 papers in training set
Top 0.1%
0.8%
29
PRX Life
34 papers in training set
Top 0.9%
0.8%
30
Mathematical Biosciences and Engineering
23 papers in training set
Top 0.7%
0.7%