Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.21.392621v1?rss=1 Authors: Chibani, C. M., Mahnert, A., Borrel, G., Almeida, A., Werner, A., Brugere, J.-F., Gribaldo, S., Finn, R. D., Schmitz, R. A., Moissl-Eichinger, C. Abstract: The human gut microbiome plays an important role in health and disease, but the archaeal diversity therein remains largely unexplored. Here we report the pioneering analysis of 1,167 non-redundant archaeal genomes recovered from human...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.21.392613v1?rss=1 Authors: Moussa, M. M. R., Mandoiu, I. I. Abstract: The variation in gene expression profiles of cells captured in different phases of the cell cycle can interfere with cell type identification and functional analysis of single cell RNA-Seq (scRNA-Seq) data. In this paper, we introduce SC1CC (SC1 - Cell Cycle analysis tool), a computational approach for clustering and ordering single cell transcriptional...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.21.392761v1?rss=1 Authors: Barthelson, K., Pederson, S. M., Newman, M., Jiang, H., Lardelli, M. Abstract: Background: Mutations in PRESENILIN 2 (PSEN2) cause early disease onset familial Alzheimer's disease (EOfAD) but their mode of action remains elusive. One consistent observation for all PRESENILIN gene mutations causing EOfAD is that a transcript is produced with a reading frame terminated by the normal stop codon :...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.21.392878v1?rss=1 Authors: Wojtowicz, D., Hoinka, J., Amgalan, B., Kim, Y.-A., Przytycka, T. M. Abstract: Many mutagenic processes leave characteristic imprints on cancer genomes known as mutational signatures. These signatures have been of recent interest regarding their applicability in studying processes shaping the mutational landscape of cancer. In particular, pinpointing the presence of altered DNA repair pathways...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.22.393108v1?rss=1 Authors: Loewenthal, G., Rapoport, D., Avram, O., Moshe, A., Itzkovitch, A., Israeli, O., Azouri, D., Cartwright, R. A., Mayrose, I., Pupko, T. Abstract: Insertions and deletions (indels) are common molecular evolutionary events. However, probabilistic models for indel evolution are under-developed due to their computational complexity. Here we introduce several improvements to indel modeling: (1) while...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.22.392217v1?rss=1 Authors: Armingol, E., Joshi, C. J., Baghdassarian, H., Shamie, I., Ghaddar, A., Chan, J., Her, H.-L., O'Rourke, E. J., Lewis, N. E. Abstract: Cell-cell interactions are crucial for multicellular organisms as they shape cellular function and ultimately organismal phenotype. However, the spatial code embedded in the molecular interactions that drive and sustain spatial organization, and in the...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.22.393074v1?rss=1 Authors: Roy, N., Kabir, A. H., Zahan, N., Mouna, S. T., Chakravarty, S., Rahman, A. H., Bayzid, M. S. Abstract: Rice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. We performed Genome Wide Association...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.22.393165v1?rss=1 Authors: Yan, H., Song, Q., Lee, J., Schiefelbein, J., Li, S. Abstract: An essential step of single-cell RNA sequencing analysis is to classify specific cell types with marker genes in order to dissect the biological functions of each individual cell. In this study, we integrated five published scRNA-seq datasets from the Arabidopsis root containing over 25,000 cells and 17 cell clusters. We have...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.19.390773v1?rss=1 Authors: Ge, X., Chen, Y. E., Song, D., McDermott, M., Woyshner, K., Manousopoulou, A., Wang, L. D., Li, W., Li, J. J. Abstract: High-throughput biological data analysis commonly involves the identification of "interesting" features (e.g., genes, genomic regions, and proteins), whose values differ between two conditions, from numerous features measured simultaneously. To ensure the reliability of such...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.20.391912v1?rss=1 Authors: Choudhary, K. S., Fahy, E., Coakley, K., Sud, M., Maurya, M. R., Subramaniam, S. Abstract: With the advent of high throughput mass spectrometric methods, metabolomics has emerged as an essential area of research in biomedicine with the potential to provide deep biological insights into normal and diseased functions in physiology. However, to achieve the potential offered by metabolomics...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.19.390542v1?rss=1 Authors: Burstein, D., Fullard, J., Roussos, P. Abstract: Prior to identifying clusters in single cell gene expression experiments, selecting the top principal components is a critical step for filtering out noise in the data set. Identifying these top principal components typically focuses on the total variance explained, and principal components that explain small clusters from rare populations will...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.367490v1?rss=1 Authors: Rizwan, S., Pike, D., Poudel, S., Nanda, V. Abstract: Cofactor binding sites in proteins often are composed of favorable interactions of specific cofactors with the sidechains and/or backbone protein fold motifs. In many cases these motifs contain left-handed conformations which enable tight turns of the backbone that present backbone amide protons in direct interactions with cofactors termed...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.386813v1?rss=1 Authors: Dragan, I., Sparso, T., Kuznetsov, D., Slieker, R., Ibberson, M. Abstract: Summary: dsSwissKnife is an R package that enables several powerful analyses to be performed on federated datasets. The package works alongside DataSHIELD and extends its functionality. We have developed and implemented dsSwissKnife in a large IMI project on type 2 diabetes, RHAPSODY, where data from 10 observational...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.20.391045v1?rss=1 Authors: Planell, N., Lagani, V., Sebastian-Leon, P., van der Kloet, F., Ewing, E., Karathanasis, N., Urdangarin, A., Arozarena, I., Jagodic, M., Tsamardinos, I., Tarazona, S., Conesa, A., tegner, j., Gomez-Cabrero, D. Abstract: Technologies for profiling samples using different omics platforms have been at the forefront since the human genome project. Large-scale multi-omics data hold the promise of...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.20.390930v1?rss=1 Authors: Das Roy, R., Hallikas, O., Christensen, M. M., Renvoise, E., Jernvall, J. Abstract: Exploration of genetically modified organisms, developmental processes, diseases or responses to various treatments require accurate measurement of changes in gene expression. This can be done for thousands of genes using high throughput technologies such as microarray and RNAseq. However, identification of...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.20.391011v1?rss=1 Authors: Laws, R. L., Paul, P., Mosites, E., Scobie, H., Clarke, K. E. N., Slayton, R. B. Abstract: Background : Congregate settings are at risk for coronavirus disease 2019 (COVID-19) outbreaks. Diagnostic testing can be used as a tool in these settings to identify outbreaks and to control transmission. Methods : We used transmission modeling to estimate the minimum number of persons to test and the...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.20.391029v1?rss=1 Authors: Covell, D. G. Abstract: A joint analysis of NCI60 small molecule screening data, their genetically defective genes and mechanisms of action (MOA) of FDA approved cancer drugs screened in the NCI60 is proposed for identifying links between chemosensitivity, genomic defects and MOA. Self-organizing-maps (SOMs) are used to organize the chemosensitivity data. Students t-tests are used to identify...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.20.391300v1?rss=1 Authors: Neely, B. A., Stemmer, P., Searle, B. C., Herring, L. E., Martin, L., Midha, M. K., Phinney, B. S., Shan, B., Palmblad, M., Wang, Y., Jagtap, P. D., Kirkpatrick, J. M. Abstract: Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample, as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in core...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.19.389981v1?rss=1 Authors: Ness-Cohn, E., Braun, R. Abstract: The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues. The recent revolution in high-throughput transcriptomics, coupled with the significant implications of the circadian clock for human health, has sparked an interest in circadian profiling studies to discover genes under circadian control. Here we present TimeCycle:...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.20.391318v1?rss=1 Authors: Karatzas, E., Baltoumas, F. A., Panayiotou, N. A., Schneider, R., Pavlopoulos, G. A. Abstract: Efficient integration and visualization of heterogeneous biomedical information in a single view is a key challenge. In this study, we present Arena3Dweb, the first, fully interactive and dependency-free, web application which allows the visualization of multilayered graphs in 3D space. With...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.387795v1?rss=1 Authors: Sun, T., Song, D., Li, W. V., Li, J. J. Abstract: In the burgeoning field of single-cell transcriptomics, a pressing challenge is to benchmark various experimental protocols and numerous computational methods in an unbiased manner. Although dozens of simulators have been developed for single-cell RNA-seq (scRNA-seq) data, they lack the capacity to simultaneously achieve all the three goals:...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.20.387738v1?rss=1 Authors: Arslan, A. Abstract: Motivation: The transport of proteins plays a crucial role in the cellular phenotype. Changes in the protein targeting sequence can result in missing protein delivery to the right destination and at the right time, and can disrupt various cellular pathways. Given the importance of single residue change(s) in the protein targeting sequence we developed a missing computational...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.18.389213v1?rss=1 Authors: Srinivas, R., Verma, N., Larson, E. C., Kraka, E. Abstract: In their previous work , Srinivas et al have shown that implicit fingerprints capture ligands and proteins in a shared latent space, typically for the purposes of virtual screening with collaborative filtering models applied on known bioactivity data. In this work, we extend these implicit fingerprints/descriptors using deep learning...

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.19.390401v1?rss=1 Authors: Geread, R. S., Sivanandarajah, A., Brouwer, E., Wood, G., Androutsos, D., Faragalla, H., Khademi, A. Abstract: In this work, a novel proliferation index (PI) calculator for Ki67 images called piNET is proposed. It is successfully tested on four datasets, from three scanners comprised of patches, tissue microarrays (TMAs) and wholeslide images (WSI), representing a diverse multicentre dataset for...