Projects search

Optimal pathway reconstruction on 3D NMR maps

Authors:

Marta Szachniuk, Maria Cristina De Cola, Giovanni Felici, Dominique de Werra, Jacek Błażewicz

Academic press:

Discrete Applied Mathematics (year: 2015, volume: 182, pages: 134-149), Publisher: Elsevier

Status:

Published

DOI:

10.1016/j.dam.2014.04.010 – link to the publication

Selection of reference genes for qPCR- and ddPCR-based analyses of gene expression in senescing barley leaves

Authors:

Agnieszka Żmieńko, Anna Samelak-Czajka, Michał Góralski, Ewa Sobieszczuk- Nowicka, Piotr Kozłowski, Marek Figlerowicz

Academic press:

PLoS ONE (year: 2015, volume: 10, pages: Article ID e0118226), Publisher: Public Library of Science

Status:

Published

DOI:

10.1371/journal.pone.0118226 – link to the publication

Building the library of RNA 3D nucleotide conformations using the clustering approach

Authors:

Tomasz Żok, Maciej Antczak, Martin Riedel, David Nebel, Thomas Villmann, Piotr Łukasiak, Jacek Błażewicz, Marta Szachniuk

Academic press:

International Journal of Applied Mathematics and Computer Science (year: 2015, volume: 25, pages: 689-700), Publisher: Uniwersytet Zielonogórski

Status:

Published

DOI:

10.1515/amcs-2015-0050 – link to the publication

RNAssess - a web server for quality assessment of RNA 3D structures

Authors:

Piotr Łukasiak, Maciej Antczak, Tomasz Ratajczak, Marta Szachniuk, Mariusz Popenda, Ryszard W. Adamiak, Jacek Błażewicz

Academic press:

Nucleic Acids Research (year: 2015, volume: 43, pages: W502-W506), Publisher: Oxford University Press

Status:

Published

DOI:

10.1093/nar/gkv557 – link to the publication

Inferring mathematical equations using crowdsourcing

Authors:

Szymon Wąsik, Filip Frątczak, Jakub Krzyśków, Jarosław Wulnikowski

Academic press:

PLoS ONE (year: 2015, volume: 10, pages: Article ID e0145557), Publisher: Public Library of Science

Status:

Published

DOI:

10.1371/journal.pone.0145557 – link to the publication

Computer Representations of Bioinformatics Models

Authors:

Tomasz Prejzendanc, Szymon Wąsik, Jacek Błażewicz

Academic press:

Current Bioinformatics (year: 2016, volume: 11, pages: 551-560), Publisher: Bentham Science Publishers

Status:

Published

DOI:

10.2174/1574893610666150928193510 – link to the publication

Unified encoding for hyper-heuristics with application to bioinformatics

Authors:

Aleksandra Świercz, Edmund K. Burke, Mateusz Cicheński, Grzegorz Pawlak, Sanja Petrovic, Tomasz Żurkowski, Jacek Błażewicz

Academic press:

Central European Journal of Operations Research (year: 2014, volume: 22, pages: 567-589), Publisher: Springer

Status:

Published

DOI:

10.1007/s10100-013-0321-8 – link to the publication

Assigning NMR spectra of irregular RNAs by heuristic algorithms

Authors:

Marta Szachniuk

Academic press:

Bulletin of the Polish Academy of Sciences - Technical Sciences (year: 2015, volume: 63, pages: 329-338), Publisher: Polska Akademia Nauk, Wydział IV Nauk Technicznych

Status:

Published

DOI:

10.1515/bpasts-2015-0037 – link to the publication

New in silico approach to assessing RNA secondary structures with non-canonical base pairs

Authors:

Agnieszka Rybarczyk, Natalia Szóstak, Maciej Antczak, Tomasz Żok, Mariusz Popenda, Ryszard Adamiak, Jacek Błażewicz, Marta Szachniuk

Academic press:

BMC Bioinformatics (year: 2015, volume: 16, pages: Article ID 276), Publisher: BioMed Central

Status:

Published

DOI:

10.1186/s12859-015-0718-6 – link to the publication

Graph algorithms for DNA sequencing - origins, current models and the future

Authors:

Jacek Błażewicz, Marta Kasprzak, Michał Kierzynka, Wojciech Frohmberg, Aleksandra Świercz, Paweł Wojciechowski, Piotr Żurkowski

Academic press:

European Journal of Operational Research (year: 2018, volume: 264, pages: 799-812), Publisher: Elsevier

Status:

Published

DOI:

10.1016/j.ejor.2016.06.043 – link to the publication

Tabu search for the RNA Partial Degradation Problem

Authors:

Agnieszka Rybarczyk, Alain Hertz, Marta Kasprzak, Jacek Błażewicz

Academic press:

International Journal of Applied Mathematics and Computer Science (year: 2017, volume: 27, pages: 401-415), Publisher: Uniwersytet Zielonogórski

Status:

Published

DOI:

10.1515/amcs-2017-0028 – link to the publication

AmiRNA Designer - new method of artificial miRNA design

Authors:

Agnieszka Mickiewicz, Agnieszka Rybarczyk, Joanna Sarzyńska, Marek Figlerowicz, Jacek Błażewicz

Academic press:

Acta Biochimica Polonica (year: 2016, volume: 63, pages: Article ID 2015_989), Publisher: Polskie Towarzystwo Biochemiczne

Status:

Published

DOI:

10.18388/abp.2015_989 – link to the publication

A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly

Authors:

Michał Góralski, Paula Sobieszczańska, Aleksandra Obrępalska-Stęplowska, Aleksandra Świercz, Agnieszka Żmieńko, Marek Figlerowicz

Academic press:

Plant Methods (year: 2016, volume: 12, pages: Article ID 28), Publisher: BioMed Central

Status:

Published

DOI:

10.1186/s13007-016-0128-4 – link to the publication

G-MAPSEQ - a new method for mapping reads to a reference genome

Authors:

Paweł Wojciechowski, Wojciech Frohmberg, Michał Kierzynka, Piotr Żurkowski, Jacek Błażewicz

Academic press:

Foundations of Computing and Decision Sciences (year: 2016, volume: 41, pages: 123-142), Publisher: Politechnika Poznańska

Status:

Published

DOI:

10.1515/fcds-2016-0007 – link to the publication

DomGen - graph based method for protein domain delineation

Authors:

Maciej Miłostan, Piotr Łukasiak

Academic press:

RAIRO Operations Research (year: 2016, volume: 50, pages: online), Publisher: EDP Sciences

Status:

Published

DOI:

10.1051/ro/2015040 – link to the publication

High-order statistical compressor for long-term storage of DNA sequencing data

Authors:

Marek Chłopkowski, Maciej Antczak, Michał Ślusarczyk, Aleksander Wdowiński, Michał Zajączkowski, Marta Kasprzak

Academic press:

RAIRO Operations Research (year: 2016, volume: 50, pages: online), Publisher: EDP Sciences

Status:

Published

DOI:

10.1051/ro/2015039 – link to the publication

Computational prediction of non-enzymatic RNA degradation patterns

Authors:

Agnieszka Rybarczyk, Paulina Jackowiak, Marek Figlerowicz, Jacek Błażewicz

Academic press:

Acta Biochimica Polonica (year: 2016, volume: 63, pages: 745-751), Publisher: Polskie Towarzystwo Biochemiczne

Status:

Published

DOI:

10.18388/abp.2016_1331 – link to the publication

Classification of de Bruijn-based labeled digraphs

Authors:

Marta Kasprzak

Academic press:

Discrete Applied Mathematics (year: 2018, volume: 234, pages: 86-92), Publisher: Elsevier

Status:

Published

DOI:

10.1016/j.dam.2016.10.014 – link to the publication

ModeLang: A New Approach for Experts-Friendly Viral Infections Modeling

Authors:

Szymon Wąsik, Tomasz Prejzendanc, Jacek Błażewicz

Academic press:

Computational and Mathematical Methods in Medicine (year: 2013, volume: 2013, pages: Article ID 320715), Publisher: Hindawi Publishing Corporation

Status:

Published

DOI:

10.1155/2013/320715 – link to the publication

MCQ4Structures to compute similarity of molecule structures

Authors:

Tomasz Żok, Mariusz Popenda, Marta Szachniuk

Academic press:

Central European Journal of Operations Research (year: 2014, volume: 22, pages: 457-473), Publisher: Springer

Status:

Published

DOI:

10.1007/s10100-013-0296-5 – link to the publication

G-DNA – a highly efficient multi-GPU/MPI tool for aligning nucleotide reads

Authors:

Wojciech Frohmberg, Michał Kierzynka, Jacek Błażewicz, Piotr Gawron, Paweł Wojciechowski

Academic press:

Bulletin of the Polish Academy of Sciences - Technical Sciences (year: 2013, volume: 61, pages: 989-992), Publisher: Polska Akademia Nauk, Wydział IV Nauk Technicznych

Status:

Published

DOI:

10.2478/bpasts-2013-0106 – link to the publication

Structural alignment of protein descriptors - a combinatorial model

Authors:

Maciej Antczak, Marta Kasprzak, Piotr Łukasiak, Jacek Błażewicz

Academic press:

BMC Bioinformatics (year: 2016, volume: 17, pages: Article ID 383), Publisher: BioMed Central

Status:

Published

DOI:

10.1186/s12859-016-1237-9 – link to the publication

MLP accompanied beam search for the resonance assignment problem

Authors:

Marta Szachniuk, Mikołaj Małaczyński, Erwin Pesch, Edmund K. Burke, Jacek Błażewicz

Academic press:

Journal of Heuristics (year: 2013, volume: 19, pages: 443-464), Publisher: Springer

Status:

Published

DOI:

10.1007/s10732-013-9220-3 – link to the publication

DNA sequence assembly involving an acyclic graph model

Authors:

Jacek Błażewicz, Wojciech Frohmberg, Piotr Gawron, Marta Kasprzak, Michał Kierzynka, Aleksandra Świercz, Paweł Wojciechowski

Academic press:

Foundations of Computing and Decision Sciences (year: 2013, volume: 38, pages: 25-34), Publisher: Politechnika Poznańska

Status:

Published

DOI:

10.2478/v10209-011-0019-4 – link to the publication

Preprocessing and storing high-throughput sequencing data

Authors:

Aleksandra Świercz, Bartosz Bosak, Marek Chłopkowski, Arkadiusz Hoffa, Marta Kasprzak, Krzysztof Kurowski, Tomasz Piontek, Jacek Błażewicz

Academic press:

Computational Methods in Science and Technology (year: 2014, volume: 20, pages: 46285), Publisher: Ośrodek Wydawnictw Naukowych

Status:

Published

DOI:

10.12921/cmst.2014.20.01.9-20 – link to the publication

Multi-agent model of hepatitis C virus infection

Authors:

Szymon Wąsik, Paulina Jackowiak, Marek Figlerowicz, Jacek Błażewicz

Academic press:

Artificial Intelligence in Medicine (year: 2014, volume: 60, pages: 123-131), Publisher: Elsevier

Status:

Published

DOI:

10.1016/j.artmed.2013.11.001 – link to the publication

RNAlyzer - novel approach for quality analysis of RNA structural models

Authors:

Piotr Łukasiak, Maciej Antczak, Tomasz Ratajczak, Janusz M. Bujnicki, Marta Szachniuk, Ryszard W. Adamiak, Mariusz Popenda, Jacek Błażewicz

Academic press:

Nucleic Acids Research (year: 2013, volume: 41, pages: 5978-5990), Publisher: Oxford University Press

Status:

Published

DOI:

10.1093/nar/gkt318 – link to the publication

An integrated approach (CLuster Analysis Integration Method) to combine expression data and protein-protein interaction networks in agrigenomics: application on Arabidopsis thaliana

Authors:

Daniele Santoni, Aleksandra Świercz, Agnieszka Żmieńko, Marta Kasprzak, Marek Błażewicz, Paola Bertolazzi, Giovanni Felici

Academic press:

OMICS A Journal of Integrative Biology (year: 2014, volume: 18, pages: 155-165), Publisher: Mary Ann Liebert

Status:

Published

DOI:

10.1089/omi.2013.0050 – link to the publication

Reference alignment based methods for quality evaluation of multiple sequence alignment - a survey

Authors:

Paweł Wojciechowski, Piotr Formanowicz, Jacek Błażewicz

Academic press:

Current Bioinformatics (year: 2014, volume: 9, pages: 44-56), Publisher: Bentham Science Publishers

Status:

Published

DOI:

10.2174/15748936113080990005 – link to the publication

The orderly colored longest path problem – a survey of applications and new algorithms

Authors:

Marta Szachniuk, Maria Cristina De Cola, Giovanni Felici, Jacek Błażewicz

Academic press:

RAIRO - Operations Research (year: 2014, volume: 48, pages: 25-51), Publisher: EDP Sciences

Status:

Published

DOI:

10.1051/ro/2013046 – link to the publication

Sorting signal targeting mRNA into hepatic extracellular vesicles

Authors:

Natalia Szóstak, Felix Royo, Agnieszka Rybarczyk, Marta Szachniuk, Jacek Błażewicz, Antonio del Sol, Juan M. Falcon-Perez

Academic press:

RNA Biology (year: 2014, volume: 11, pages: 836-844), Publisher: Landes Bioscience

Status:

Published

DOI:

10.4161/rna.29305 – link to the publication

SphereGrinder - reference structure-based tool for quality assessment of protein structural models

Authors:

Piotr Łukasiak, Maciej Antczak, Tomasz Ratajczak, Jacek Błażewicz

Conference:

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (year: 2015, pages: 665-668), Publisher: IEEE (Institute of Electrical and Electronics Engineers)

Date:

conference 9-12.11.2015

Status:

Published

Turning data into folds using RNAComposer

Authors:

Marta Szachniuk, Joanna Sarzyńska, Jacek Błażewicz

Conference:

2013 International Symposium on Computational Models for Life Sciences (year: 2013, pages: AIP Conference Proceedings, Volume 1559, 353-354), Publisher: AIP Publishing, DOI: 10.1063/1.4825029

Date:

conference 27–29.11.2013

Status:

Published