{"results":[{"id":"arxiv_2501.04596","title":"Fast Directed $q$-Analysis for Brain Graphs","authors":[{"name":"Felix Windisch"},{"name":"Florian Unger"}],"abstract":"Recent innovations in reconstructing large scale, full-precision, neuron-synapse-scale connectomes demand subsequent improvements to graph analysis methods to keep up with the growing complexity and size of the data. One such tool is the recently introduced directed $q$-analysis. We present numerous improvements, theoretical and applied, to this technique: on the theoretical side, we introduce modified definitions for key elements of directed $q$-analysis, which remedy a well-hidden and previously undetected bias. This also leads to new, beneficial perspectives to the associated computational challenges. Most importantly, we present a high-speed, publicly available, low-level implementation that provides speed-ups of several orders of magnitude on C. Elegans. Furthermore, the speed gains grow with the size of the considered graph. This is made possible due to the mathematical and algorithmic improvements as well as a carefully crafted implementation. These speed-ups enable, for the first time, the analysis of full-sized connectomes such as those obtained by recent reconstructive methods. Additionally, the speed-ups allow comparative analysis to corresponding null models, appropriately designed randomly structured artificial graphs that do not correspond to actual brains. This, in turn, allows for assessing the efficacy and usefulness of directed $q$-analysis for studying the brain. We report on the results in this paper.","source":"arXiv","year":2025,"language":"en","subjects":["q-bio.QM","math.AT"],"url":"https://arxiv.org/abs/2501.04596","pdf_url":"https://arxiv.org/pdf/2501.04596","is_open_access":true,"published_at":"2025-01-08T16:24:23Z","score":69},{"id":"crossref_10.1038/s41598-025-32638-y","title":"Green CO2-capture cluster model using bioengineering of carbonic anhydrase enzyme: QM and QM/QM′ approach","authors":[{"name":"Mina Ghiasi"},{"name":"Hanane Sadat Eghtedari"}],"abstract":"","source":"CrossRef","year":2025,"language":"en","subjects":null,"doi":"10.1038/s41598-025-32638-y","url":"https://doi.org/10.1038/s41598-025-32638-y","pdf_url":"https://www.nature.com/articles/s41598-025-32638-y.pdf","is_open_access":true,"published_at":"","score":69},{"id":"arxiv_2411.04684","title":"Strong anomalous diffusion for free-ranging birds","authors":[{"name":"Ohad Vilk"},{"name":"Motti Charter"},{"name":"Sivan Toledo"},{"name":"Eli Barkai"},{"name":"Ran Nathan"}],"abstract":"Diffusion and anomalous diffusion are widely observed and used to study movement across organisms, resulting in extensive use of the mean and mean-squared displacement (MSD). However, these measures - corresponding to specific displacement moments - do not capture the full complexity of movement behavior. Using high-resolution data from over 70 million localizations of young and adult free-ranging Barn Owls (\\textit{Tyto alba}), we reveal strong anomalous diffusion as nonlinear growth of displacement moments. The moment spectrum function $λ_t(q)$ -- defined by $\\left\u003c|\\bm{x}(t)|^q\\right\u003e \\sim t^{λ_t(q)}$ -- displays piecewise linearity in $q$, with a critical moment marking the crossover between scaling regimes. This highlights the need of a broad spectrum of displacement moments to characterize movement, which we link to age-specific ecological drivers. Furthermore, a characteristic timescale of five minutes marks an unexpected transition from a convex to a concave $λ_t(q)$. Using two stochastic models - a bounded Lévy walk and a multi-mode behavioral model - we account for the observed phenomena, showing good agreement with data, relating age-specific behavioral states to environmentally confined movement, and demonstrating how Lévy walk-like patterns can arise from underlying behavioral structure. Finally, we discuss the ecological significance of our results, arguing that strong anomalous diffusion may be widespread in animal movement.","source":"arXiv","year":2024,"language":"en","subjects":["q-bio.PE","cond-mat.stat-mech","physics.bio-ph","physics.data-an","q-bio.QM"],"url":"https://arxiv.org/abs/2411.04684","pdf_url":"https://arxiv.org/pdf/2411.04684","is_open_access":true,"published_at":"2024-11-07T13:14:42Z","score":68},{"id":"crossref_10.1051/bioconf/202414504043","title":"Analysis of interconnections between Lean and QM standards within LCIA framework","authors":[{"name":"Tatyana Burtseva"},{"name":"Nataliya Mironova"},{"name":"Anzhelika Borisova"},{"name":"Asiiat Mottaeva"}],"abstract":"The ubiquitous approaches of lean management and environmental management (lean and green management) stem from the same sentiment, their driving force is of great importance in government and Russian practice, they have different tools and a general view of waste processes. However, the final result, as a rule, meets the needs of these concepts. The article is devoted to searching and beginning to correlate these approaches and find the presence (or absence) of a direct relationship through the mechanisms of built-in indicators reflecting both connections. This indicates the identity of the approaches to total social responsibility. The authors show the possibility of forming integrated indicators that reflect the results of lower approaches at each stage of the product life cycle from its planning and production to after-sales service. The results of the study, firstly, set the vector for further development of a single integrated model that unites both governments, and secondly, using an example, they simplify the interaction of traditional line-functional managers of production enterprises and heads of environmental departments, limit barriers to mutual understanding and show the goals of unity, although excellent in terms of implementation of the approach.","source":"CrossRef","year":2024,"language":"en","subjects":null,"doi":"10.1051/bioconf/202414504043","url":"https://doi.org/10.1051/bioconf/202414504043","is_open_access":true,"published_at":"","score":68},{"id":"crossref_10.1088/2516-1075/acb02c","title":"QM-cluster model study of CO\u003csub\u003e2\u003c/sub\u003e hydration mechanisms in metal-substituted human carbonic anhydrase II","authors":[{"name":"Thomas J Summers"},{"name":"Nathan J DeYonker"}],"abstract":"Abstract Human carbonic anhydrase (CA) metalloenzymes utilize a Zn2+-containing active site to catalyze the interconversion of carbon dioxide to bicarbonate. The Zn2+ ion may be replaced with other divalent transition metals, though the catalytic efficiency of the enzyme will be reduced. In this work, quantum mechanical cluster models of the active site are used to map the reaction profile for the hydration mechanism of carbon dioxide. The Lipscomb proton transfer and Lindskog rotation mechanisms were examined for the native Zn2+-enzyme along with variants where the metal was substituted with Cd2+, Ni2+, Fe2+, and Fe3+. The findings highlight the impact the metal coordination geometry has on the reaction profile. The results also suggest Fe2+, which is the functional metal for a prototypical CA of an anaerobic bacterium, might also be functional for human CA if cultured within an anaerobic environment.","source":"CrossRef","year":2023,"language":"en","subjects":null,"doi":"10.1088/2516-1075/acb02c","url":"https://doi.org/10.1088/2516-1075/acb02c","pdf_url":"https://iopscience.iop.org/article/10.1088/2516-1075/acb02c/pdf","is_open_access":true,"citations":5,"published_at":"","score":67.15},{"id":"arxiv_2308.13171","title":"Q-Drug: a Framework to bring Drug Design into Quantum Space using Deep Learning","authors":[{"name":"Zhaoping Xiong"},{"name":"Xiaopeng Cui"},{"name":"Xinyuan Lin"},{"name":"Feixiao Ren"},{"name":"Bowen Liu"},{"name":"Yunting Li"},{"name":"Manhong Yung"},{"name":"Nan Qiao"}],"abstract":"Optimizing the properties of molecules (materials or drugs) for stronger toughness, lower toxicity, or better bioavailability has been a long-standing challenge. In this context, we propose a molecular optimization framework called Q-Drug (Quantum-inspired optimization algorithm for Drugs) that leverages quantum-inspired algorithms to optimize molecules on discrete binary domain variables. The framework begins by encoding the molecules into binary embeddings using a discrete VAE. The binary embeddings are then used to construct an Ising energy-like objective function, over which the state-of-the-art quantum-inspired optimization algorithm is adopted to find the optima. The binary embeddings corresponding to the optima are decoded to obtain the optimized molecules. We have tested the framework for optimizing drug molecule properties and have found that it outperforms other molecular optimization methods, finding molecules with better properties in 1/20th to 1/10th of the time previously required. The framework can also be deployed directly on various quantum computing equipment, such as laser pulses CIMs, FPGA Ising Machines, and quantum computers based on quantum annealing, among others. Our work demonstrates a new paradigm that leverages the advantages of quantum computing and AI to solve practically useful problems.","source":"arXiv","year":2023,"language":"en","subjects":["quant-ph","q-bio.MN","q-bio.QM"],"url":"https://arxiv.org/abs/2308.13171","pdf_url":"https://arxiv.org/pdf/2308.13171","is_open_access":true,"published_at":"2023-08-25T04:26:02Z","score":67},{"id":"crossref_10.26434/chemrxiv-2023-bm8lv-v2","title":"Protein network centralities as descriptor for QM region construction in QM/MM simulations of enzymes","authors":[{"name":"Felix Brandt"},{"name":"Christoph Jacob"}],"abstract":"","source":"CrossRef","year":2023,"language":"en","subjects":null,"doi":"10.26434/chemrxiv-2023-bm8lv-v2","url":"https://doi.org/10.26434/chemrxiv-2023-bm8lv-v2","is_open_access":true,"published_at":"","score":67},{"id":"arxiv_2202.07307","title":"Simplicial $q$-connectivity of directed graphs with applications to network analysis","authors":[{"name":"Henri Riihimäki"}],"abstract":"Directed graphs are ubiquitous models for networks, and topological spaces they generate, such as the directed flag complex, have become useful objects in applied topology. The simplices are formed from directed cliques. We extend Atkin's theory of $q$-connectivity to the case of directed simplices. This results in a preorder where simplices are related by sequences of simplices that share a $q$-face with respect to directions specified by chosen face maps. We leverage the Alexandroff equivalence between preorders and topological spaces to introduce a new class of topological spaces for directed graphs, enabling to assign new homotopy types different from those of directed flag complexes as seen by simplicial homology. We further introduce simplicial path analysis enabled by the connectivity preorders. As an application we characterise structural differences between various brain networks by computing their longest simplicial paths.","source":"arXiv","year":2022,"language":"en","subjects":["math.AT","math.CO","q-bio.QM"],"url":"https://arxiv.org/abs/2202.07307","pdf_url":"https://arxiv.org/pdf/2202.07307","is_open_access":true,"published_at":"2022-02-15T10:54:59Z","score":66},{"id":"crossref_10.26434/chemrxiv-2021-tn7cq-v2","title":"Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification","authors":[{"name":"Felix Brandt"},{"name":"Christoph Jacob"}],"abstract":"","source":"CrossRef","year":2022,"language":"en","subjects":null,"doi":"10.26434/chemrxiv-2021-tn7cq-v2","url":"https://doi.org/10.26434/chemrxiv-2021-tn7cq-v2","is_open_access":true,"published_at":"","score":66},{"id":"arxiv_2111.15082","title":"Application of Equal Local Levels to Improve Q-Q Plot Testing Bands with R Package qqconf","authors":[{"name":"Eric Weine"},{"name":"Mary Sara McPeek"},{"name":"Mark Abney"}],"abstract":"Quantile-Quantile (Q-Q) plots are often difficult to interpret because it is unclear how large the deviation from the theoretical distribution must be to indicate a lack of fit. Most Q-Q plots could benefit from the addition of meaningful global testing bands, but the use of such bands unfortunately remains rare because of the drawbacks of current approaches and packages. These drawbacks include incorrect global Type I error rate, lack of power to detect deviations in the tails of the distribution, relatively slow computation for large data sets, and limited applicability. To solve these problems, we apply the equal local levels global testing method, which we have implemented in the R Package qqconf, a versatile tool to create Q-Q plots and probability-probability (P-P) plots in a wide variety of settings, with simultaneous testing bands rapidly created using recently-developed algorithms. qqconf can easily be used to add global testing bands to Q-Q plots made by other packages. In addition to being quick to compute, these bands have a variety of desirable properties, including accurate global levels, equal sensitivity to deviations in all parts of the null distribution (including the tails), and applicability to a range of null distributions. We illustrate the use of qqconf in several applications: assessing normality of residuals from regression, assessing accuracy of p values, and use of Q-Q plots in genome-wide association studies.","source":"arXiv","year":2021,"language":"en","subjects":["stat.CO","q-bio.QM","stat.AP"],"url":"https://arxiv.org/abs/2111.15082","pdf_url":"https://arxiv.org/pdf/2111.15082","is_open_access":true,"published_at":"2021-11-30T02:55:48Z","score":65},{"id":"crossref_10.26434/chemrxiv-2021-tn7cq","title":"Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification","authors":[{"name":"Felix Brandt"},{"name":"Christoph Jacob"}],"abstract":"","source":"CrossRef","year":2021,"language":"en","subjects":null,"doi":"10.26434/chemrxiv-2021-tn7cq","url":"https://doi.org/10.26434/chemrxiv-2021-tn7cq","is_open_access":true,"published_at":"","score":65},{"id":"crossref_10.26434/chemrxiv.11857668.v1","title":"Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase","authors":[{"name":"Rimsha Mehmood"},{"name":"Heather Kulik"}],"abstract":"","source":"CrossRef","year":2020,"language":"en","subjects":null,"doi":"10.26434/chemrxiv.11857668.v1","url":"https://doi.org/10.26434/chemrxiv.11857668.v1","is_open_access":true,"published_at":"","score":64},{"id":"arxiv_1904.00353","title":"Long-range temporal correlation in Auditory Brainstem Responses to Spoken Syllable /da/","authors":[{"name":"Marjan Mozaffarilegha"},{"name":"S. M. S. Movahed"}],"abstract":"The speech auditory brainstem response (sABR) is an objective clinical tool to diagnose particular impairments along the auditory brainstem pathways. We explore the scaling behavior of the brainstem in response to synthetic /da/ stimuli using a proposed pipeline including Multifractal Detrended Moving Average Analysis (MFDMA) modified by Singular Value Decomposition. The scaling exponent confirms that all normal sABR are classified into the non-stationary process. The average Hurst exponent is $H=0.77\\pm0.12$ at 68\\% confidence interval indicating long-range correlation which shows the first universality behavior of sABR. Our findings exhibit that fluctuations in the sABR series are dictated by a mechanism associated with long-term memory of the dynamic of the auditory system in the brainstem level. The $q-$dependency of $h(q)$ demonstrates that underlying data sets have multifractal nature revealing the second universality behavior of the normal sABR samples. Comparing Hurst exponent of original sABR with the results of the corresponding shuffled and surrogate series, we conclude that its multifractality is almost due to the long-range temporal correlations which are devoted to the third universality. Finally, the presence of long-range correlation which is related to the slow timescales in the subcortical level and integration of information in the brainstem network is confirmed.","source":"arXiv","year":2019,"language":"en","subjects":["q-bio.QM","physics.bio-ph","q-bio.NC"],"doi":"10.1038/s41598-018-38215-w","url":"https://arxiv.org/abs/1904.00353","pdf_url":"https://arxiv.org/pdf/1904.00353","is_open_access":true,"published_at":"2019-03-31T07:36:56Z","score":63},{"id":"arxiv_1805.01735","title":"Optimizing Native Ion Mobility Q-TOF in Helium and Nitrogen for Very Fragile Noncovalent Interactions","authors":[{"name":"Valérie Gabelica"},{"name":"Sandrine Livet"},{"name":"Frédéric Rosu"}],"abstract":"The meaningful comparison of ion mobility (IM) results and of collision cross section (CCS) values on different platforms is a prerequisite for using CCS for identification or structural assignment. The amount of internal energy imparted to the ions prior to the ion mobility cell is a source of experimental variation. Here we investigated the effects of virtually all tuning parameters of the Agilent 6560 IM-Q-TOF on the arrival time distributions of Ubiquitin7+, and found conditions in which the native state prevails. We will discuss the effects of solvent evaporation conditions in the source, in the entire pre-IM DC voltage gradient, and with the funnel RF amplitudes, and will also report on ubiquitin7+ conformations in different solvents, including native supercharging conditions. Collision-induced unfolding (CIU) can be conveniently provoked in two distinct regions: behind the source capillary (by changing the fragmentor voltage) and in the trapping funnel (by changing the trap entrance grid delta voltage). The softness of the instrumental conditions were then optimized with the benchmark DNA G-quadruplex [(dG4T4G4)2.(NH4+)3-8H]5-, for which ion activation results in ammonia loss. To reduce the ion internal energy and obtain the intact 3-NH4+ complex, we reduced the post-IM voltage gradient, but this resulted in a lower IM resolving power due to increased diffusion behind the drift tube. The article thus describes the various trade-offs between ion activation, ion transmission, and ion mobility performance for native MS of very fragile structures.","source":"arXiv","year":2018,"language":"en","subjects":["q-bio.QM","q-bio.BM"],"doi":"10.1007/s13361-018-2029-4","url":"https://arxiv.org/abs/1805.01735","pdf_url":"https://arxiv.org/pdf/1805.01735","is_open_access":true,"published_at":"2018-05-04T12:15:42Z","score":62},{"id":"arxiv_1809.02872","title":"Optimal vaccine allocation during the mumps outbreak in two SIR centers","authors":[{"name":"A. Chernov"},{"name":"M. Kelbert"},{"name":"A. Shemendyuk"}],"abstract":"The aim of this work is to investigate the optimal vaccine sharing between two SIR centers in the presence of migration fluxes of susceptibles and infected individuals during the mumps outbreak. Optimality of the vaccine allocation means the minimization of the total number of lost working days during the whole period of epidemic outbreak $[0,t_f]$, which can be described by the functional $Q=\\int_0^{t_f}I(t){\\rm d}t$ where $I(t)$ stands for the number of infectives at time $t$. We explain the behavior of the optimal allocation, which depends on the model parameters and the amount of available vaccine.","source":"arXiv","year":2018,"language":"en","subjects":["q-bio.QM","q-bio.PE"],"url":"https://arxiv.org/abs/1809.02872","pdf_url":"https://arxiv.org/pdf/1809.02872","is_open_access":true,"published_at":"2018-09-08T20:46:13Z","score":62},{"id":"arxiv_1804.02454","title":"Affinity-based extension of non-extensive entropy and statistical mechanics","authors":[{"name":"Keisuke Okamura"}],"abstract":"Tsallis' non-extensive entropy is extended to incorporate the dependence on affinities between the microstates of a system. At the core of our construction of the extended entropy ($\\mathcal{H}$) is the concept of the effective number of dissimilar states, termed the effective diversity ($\\mathitΔ$). It is a unique integrated measure derived from the probability distribution among states and the affinities between states. The effective diversity is related to the extended entropy through the Boltzmann's-equation-like relation, $\\mathcal{H}=\\ln_{q}\\mathitΔ$, in terms of the Tsallis' $q$-logarithm. A new principle called the Nesting Principle is established, stating that the effective diversity remains invariant under an arbitrary grouping of the constituent states. It is shown that this invariance property holds only for $q=2$; however, the invariance is recovered for general $q$ in the zero-affinity limit (i.e. the Tsallis and Boltzmann-Gibbs case). Using the affinity-based extended Tsallis entropy, the microcanonical and the canonical ensembles are constructed in the presence of general between-state affinities. It is shown that the classic postulate of equal a priori probabilities no longer holds but is modified by affinity-dependent terms. As an illustration, a two-level system is investigated by the extended canonical method, which manifests that the thermal behaviours of the thermodynamic quantities at equilibrium are affected by the between-state affinity. Furthermore, some applications and implications of the affinity-based extended diversity/entropy for information theory and biodiversity theory are addressed in appendices.","source":"arXiv","year":2018,"language":"en","subjects":["q-bio.QM","q-bio.PE"],"doi":"10.1016/j.physa.2020.124849","url":"https://arxiv.org/abs/1804.02454","pdf_url":"https://arxiv.org/pdf/1804.02454","is_open_access":true,"published_at":"2018-03-29T16:23:23Z","score":62},{"id":"doaj_10.46298/dmtcs.1329","title":"Permutation Pattern matching in (213, 231)-avoiding permutations","authors":[{"name":"Both Neou"},{"name":"Romeo Rizzi"},{"name":"Stéphane Vialette"}],"abstract":"Given permutations σ of size k and π of size n with k \u003c n, the permutation pattern matching problem is to decide whether σ occurs in π as an order-isomorphic subsequence. We give a linear-time algorithm in case both π and σ avoid the two size-3 permutations 213 and 231. For the special case where only σ avoids 213 and 231, we present a O(max(kn 2 , n 2 log log n)-time algorithm. We extend our research to bivincular patterns that avoid 213 and 231 and present a O(kn 4)-time algorithm. Finally we look at the related problem of the longest subsequence which avoids 213 and 231.","source":"DOAJ","year":2017,"language":"","subjects":["Mathematics"],"doi":"10.46298/dmtcs.1329","url":"https://dmtcs.episciences.org/1329/pdf","pdf_url":"https://dmtcs.episciences.org/1329/pdf","is_open_access":true,"published_at":"","score":61},{"id":"arxiv_1602.08183","title":"Non-Identifiable Pedigrees and a Bayesian Solution","authors":[{"name":"B. Kirkpatrick"}],"abstract":"Some methods aim to correct or test for relationships or to reconstruct the pedigree, or family tree. We show that these methods cannot resolve ties for correct relationships due to identifiability of the pedigree likelihood which is the probability of inheriting the data under the pedigree model. This means that no likelihood-based method can produce a correct pedigree inference with high probability. This lack of reliability is critical both for health and forensics applications.   In this paper we present the first discussion of multiple typed individuals in non-isomorphic pedigrees, $\\mathcal{P}$ and $\\mathcal{Q}$, where the likelihoods are non-identifiable, $Pr[G~|~\\mathcal{P},θ] = Pr[G~|~\\mathcal{Q},θ]$, for all input data $G$ and all recombination rate parameters $θ$. While there were previously known non-identifiable pairs, we give an example having data for multiple individuals.   Additionally, deeper understanding of the general discrete structures driving these non-identifiability examples has been provided, as well as results to guide algorithms that wish to examine only identifiable pedigrees. This paper introduces a general criteria for establishing whether a pair of pedigrees is non-identifiable and two easy-to-compute criteria guaranteeing identifiability. Finally, we suggest a method for dealing with non-identifiable likelihoods: use Bayes rule to obtain the posterior from the likelihood and prior. We propose a prior guaranteeing that the posterior distinguishes all pairs of pedigrees.   Shortened version published as: B. Kirkpatrick. Non-identifiable pedigrees and a Bayesian solution. Int. Symp. on Bioinformatics Res. and Appl. (ISBRA), 7292:139-152 2012.","source":"arXiv","year":2016,"language":"en","subjects":["q-bio.QM","q-bio.PE"],"url":"https://arxiv.org/abs/1602.08183","pdf_url":"https://arxiv.org/pdf/1602.08183","is_open_access":true,"published_at":"2016-02-26T02:56:34Z","score":60},{"id":"arxiv_1510.00675","title":"Stochastic modeling of gene expression, protein modification, and polymerization","authors":[{"name":"Andrew Mugler"},{"name":"Sean Fancher"}],"abstract":"Many fundamental cellular processes involve small numbers of molecules. When numbers are small, fluctuations dominate, and stochastic models, which account for these fluctuations, are required. In this chapter, we describe minimal stochastic models of three fundamental cellular processes: gene expression, protein modification, and polymerization. We introduce key analytic tools for solving each model, including the generating function, eigenfunction expansion, and operator methods, and we discuss how these tools are extended to more complicated models. These analytic tools provide an elegant, efficient, and often insightful alternative to stochastic simulation.","source":"arXiv","year":2015,"language":"en","subjects":["q-bio.MN","physics.bio-ph","q-bio.QM"],"url":"https://arxiv.org/abs/1510.00675","pdf_url":"https://arxiv.org/pdf/1510.00675","is_open_access":true,"published_at":"2015-10-02T18:31:32Z","score":59},{"id":"arxiv_1202.0048","title":"P-values, q-values and posterior probabilities for equivalence in genomics studies","authors":[{"name":"J. Tuke"},{"name":"G. F. V. Glonek"},{"name":"P. J. Solomon"}],"abstract":"Equivalence testing is of emerging importance in genomics studies but has hitherto been little studied in this content. In this paper, we define the notion of equivalence of gene expression and determine a `strength of evidence' measure for gene equivalence. It is common practice in genome-wide studies to rank genes according to observed gene-specific P-values or adjusted P-values, which are assumed to measure the strength of evidence against the null hypothesis of no differential gene expression. We show here, both empirically and formally, that the equivalence P-value does not satisfy the basic consistency requirements for a valid strength of evidence measure for equivalence. This means that the widely-used q-value (Storey, 2002) defined for each gene to be the minimum positive false discovery rate that would result in the inclusion of the corresponding P-value in the discovery set, cannot be translated to the equivalence testing framework. However, when represented as a posterior probability, we find that the q-value does satisfy some basic consistency requirements needed to be a credible measure of evidence for equivalence. We propose a simple estimate for the q-value from posterior probabilities of equivalence, and analyse data from a mouse stem cell microarray experiment which demonstrate the theory and methods presented here.","source":"arXiv","year":2012,"language":"en","subjects":["stat.AP","math.ST","q-bio.QM","stat.ME"],"url":"https://arxiv.org/abs/1202.0048","pdf_url":"https://arxiv.org/pdf/1202.0048","is_open_access":true,"published_at":"2012-01-31T23:10:04Z","score":56}],"total":276759,"page":1,"page_size":20,"sources":["arXiv","DOAJ","CrossRef"],"query":"q-bio.QM"}