RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0, i.e. whose minimum free energy secondary identical to 0. Here we consider ensemble all have low with respect given 0.We introduce program RNAdualPF, which computes dual partition function Z ∗, defined as sum Boltzmann factors exp(-E(a,s 0)/RT) nucleotide compatible Using efficiently sample approximately where additionally user can specify IUPAC sequence constraints at...

We describe the first dynamic programming algorithm that computes expected degree for network, or graph G = (V, E) of all secondary structures a given RNA sequence a1, …, an. Here, nodes V correspond to a, while an edge exists between s, t if structure can be obtained from s by adding, removing shifting base pair. Since kinetics programs implement Gillespie algorithm, which simulates random walk on network structures, may provide better understanding folding when allowing defect diffusion,...

Alignment of structural RNAs is an important problem with a wide range applications. Since function often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for homology identification. This paper describes C++ software, RNAmountAlign, sequence/structure that runs in O(n3) time O(n2) space two sequences length n; moreover, our software returns p-value (transformable to expect value E) based on Karlin-Altschul...

Abstract Alignment of structural RNAs is an important problem with a wide range applications. Since function often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for homology identification. A number successful are heuristic versions Sankoff’s optimal algorithm. Most them require O ( n 4 ) run time. This paper describes C++ software, RNAmountAlign , sequence/structure that runs in 3 time 2 space; moreover, our...

Abstract Background Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires slippery sequence an immediate downstream stem-loop secondary structure, together called stimulating signal (FSS). It follows that molecular evolution of this genomic region HIV-1 is highly constrained, since retroviral genome must contain (sequence constraint), code appropriate peptides in reading frames 0 1 (coding...

RNA molecules can be designed by applying an optimization method (adaptive walk, Monte-Carlo, genetic algorithm, constraint programming, etc) to compute sequences that are likely fold into a given target structure. Since suboptimal structures quite distinct from desired structure, it is more important minimize the structural diversity around than ensure minimum free energy structure equal A number of measures have been introduced in literature, ranging positional entropy ensemble defect....

Abstract The aim of this work is to elucidate the role CXCR4-CXCL12 axis in ER+ breast cancer with spatial proteomics profiling. signaling pathway has emerged as an interest tumorigenesis 1,2,3. Current clinical trials increase immune cell inflammation solid tumors by blocking pathway. Our analysis bulk-RNAseq revealed high gene expression levels CXCL12 transcripts, making it a potential tumor indication investigate. We spatially characterized 20 FFPE samples developing 13-plex antibody...

RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as hok/sok system in E. coli. Although linear algebra provides an exact computational solution with respect Turner energy model tiny (~ 20 nt) sequences, larger sequences can only approximated by binning structures into macrostates a coarse-grained model, or repeatedly simulating either Monte Carlo algorithm Gillespie algorithm. Here we investigate relation between and We...

The Kinfold and KFOLD programs for RNA folding kinetics implement the Gillespie algorithm to generate stochastic trajectories from an initial structure s a target t, in which each intermediate secondary is obtained its predecessor by addition, removal or shift of single base pair. Define MS2 distance between structures t be minimum path length refold where move applied step. We describe algorithms compute shortest trajectory any two given structures. These include optimal integer programming...

Alignment of structural RNAs is an important problem with a wide range applications. Since function often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for homology identi^Lcation. A number successful are heuristic versions Sanko^K's optimal algorithm. Most them require O(n4) run time. This paper describes C++ software, RNAmountAlign, sequence/structure that runs in O(n3) time O(n2) space; moreover, our software...

Abstract Performance of Single Cell RNA sequencing (scRNA-seq) experiments depends on multiple factors including the number cells loaded, cell recovery rates, and coverage. We optimized such in 10x Genomics gene expression profiling compared targeted panels to whole transcriptome using Human donor PBMC samples. expect that our findings will apply scRNA-seq studies other sample types as well. Optimizing is essential order ensure changes low-abundance populations (e.g. Treg) can be accurately...

<h3>Background</h3> Natural killer (NK) cell can serve as an effective anti-cancer treatment,^1,2 and enhancing NK function has been shown to enhance patient outcomes.^1,2 Therefore, insight into states subtypes may lead new treatment options. Initial characterization of cells relied on flow cytometry with surface markers dividing less mature CD56^bright NKs more CD56^dim NKs.⁴ More recently, single-cell RNAseq profiling enabled deeper...

<h3>Background</h3> Spatial transcriptomics technology may improve our ability to understand the organization of tumor microenvironment (TME) and uncover recurrent interaction patterns across diverse cell types. While naturally complementing traditional scRNA-Seq, recent popular spatial platforms (such as 10x visium) fail achieve single-cell resolution require deconvolution methods calculate underlying type distributions. There are dozens whereas systematic benchmarks comparing lacking....