Results 11 to 20 of about 5,448,839 (367)

Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions [PDF]

arXiv, 2017
Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true ...
A Fuente de la, A Morgun, A Morgun, A Mortazavi, A Perez-Diez, A Yambartsev, AR Erickson, AR Joyce, B Buchfink, B Langmead, BJ Haas, C Trapnell, CL Poirel, CL Schoch, DH Huson, DJ Lane, DJ McCarthy, E Saccenti, E Stackebrandt, ER Mardis, F Imhann, F Meyer, Gautier, J Kuczynski, J Skinner, JG Caporaso, JL Brookman, JN Paulson, KL Mine, LD Thomas, M Martin, M Schirmer, MA Moreno-Risueno, ML Metzker, N Gehlenborg, N Krumm, N Segata, N Shulzhenko, O Morozova, P Li, PD Schloss, PW Laird, R Greer, R Schmieder, Ritchie, RL Greer, RR Rodrigues, S Anders, S Goodwin, S Lindgreen, S Weiss, S Zhao, SC Schuster, TJ Sharpton, W Zhang, X Dong, YJ Hua   +56 more
arxiv   +3 more sources

RxRx1: A Dataset for Evaluating Experimental Batch Correction Methods [PDF]

2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW), 2023
High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens
Maciej Sypetkowski, Morteza Rezanejad, Saber Saberian, Oren Z. Kraus, John Urbanik, J. Taylor, Ben Mabey, Mason L. Victors, J. Yosinski, A. R. Sereshkeh, I. Haque, Berton A. Earnshaw   +11 more
semanticscholar   +1 more source

A monograph of the British Uredineæ and Ustilagineæ, with an account of their biology including the methods of observing the germination of their spores and of their experimental culture

, 1889
Charles B. Plowright
openalex   +6 more sources

Standardization of Synthetic Biology Tools and Assembly Methods for Saccharomyces cerevisiae and Emerging Yeast Species

ACS Synthetic Biology, 2022
As redesigning organisms using engineering principles is one of the purposes of synthetic biology (SynBio), the standardization of experimental methods and DNA parts is becoming increasingly a necessity.
K. Malcı, Emma J. Watts, T. Roberts, Jamie Auxillos, Behnaz Nowrouzi, Heloísa Oss Boll, Cibele Zolnier Sousa do Nascimento, Andreas I. Andreou, Peter Vegh, S. Donovan, R. Fragkoudis, S. Panke, Edward W. J. Wallace, A. Elfick, L. Rios‐Solis   +14 more
semanticscholar   +1 more source

Organoids as host models for infection biology – a review of methods

Experimental and Molecular Medicine, 2021
Infectious diseases are a major threat worldwide. With the alarming rise of antimicrobial resistance and emergence of new potential pathogens, a better understanding of the infection process is urgently needed.
Carmen Aguilar, Marta Alves da Silva, M. Saraiva, Mastura Neyazi, I. Olsson, S. Bartfeld   +5 more
semanticscholar   +1 more source

Assessment of Prediction Uncertainty Quantification Methods in Systems Biology

IEEE/ACM Transactions on Computational Biology & Bioinformatics, 2022
Biological processes are often modelled using ordinary differential equations. The unknown parameters of these models are estimated by optimizing the fit of model simulation and experimental data. The resulting parameter estimates inevitably possess some
A. F. Villaverde, E. Raimúndez, J. Hasenauer, J. Banga   +3 more
semanticscholar   +1 more source

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

bioRxiv, 2023
An analysis of AlphaFold protein structure predictions shows that while in many cases the predictions are highly accurate, there are also many instances where the predicted structures or parts of predicted structures do not agree with experimentally ...
T. Terwilliger, D. Liebschner, T. Croll, Christopher J. Williams, A. McCoy, B. Poon, P. Afonine, R. Oeffner, J. Richardson, Randy J. Read, P. Adams   +10 more
semanticscholar   +1 more source

A Framework for Directional and Higher-Order Reconstruction in Photoacoustic Tomography [PDF]

, 2017
Photoacoustic tomography is a hybrid imaging technique that combines high optical tissue contrast with high ultrasound resolution. Direct reconstruction methods such as filtered backprojection, time reversal and least squares suffer from curved line ...
Boink, Yoeri E., Brune, Christoph, Lagerwerf, Marinus J., Manohar, Srirang, Steenbergen, Wiendelt, van Gils, Stephan A.   +5 more
core   +10 more sources

Combining Experimental Data and Computational Methods for the Non-Computer Specialist

Molecules, 2020
Experimental methods are indispensable for the study of the function of biological macromolecules, not just as static structures, but as dynamic systems that change conformation, bind partners, perform reactions, and respond to different stimulus ...
Reinier Cárdenas, Javier Martínez-Seoane, Carlos Amero   +2 more
doaj   +1 more source

A structural biology community assessment of AlphaFold2 applications

bioRxiv, 2021
Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods have led to protein structure predictions that have reached the accuracy of ...
Mehmet Akdel, Douglas E. V. Pires, Eduard Porta Pardo, Jürgen Jänes, Arthur O. Zalevsky, Bálint Mészáros, P. Bryant, Lydia L. Good, R. Laskowski, G. Pozzati, Aditi Shenoy, Wensi Zhu, P. Kundrotas, Victoria Ruiz Serra, Carlos H. M. Rodrigues, Alistair S. Dunham, D. Burke, N. Borkakoti, S. Velankar, A. Frost, K. Lindorff-Larsen, A. Valencia, S. Ovchinnikov, J. Durairaj, D. Ascher, J. Thornton, Norman E. Davey, Amelie Stein, A. Elofsson, T. Croll, P. Beltrão   +30 more
semanticscholar   +1 more source