2025
1.
Scheduling with a discounted profit criterion on identical machines,
Discrete Applied Mathematics
367,
2025,
pp. 195-209
2.
Single machine scheduling with the total weighted late work and rejection cost,
Naval Research Logistics
75,
2025,
260-274
3.
Flexible Job Shop Scheduling Problem using graph neural networks and reinforcement learning,
Computers and Operations Research
182,
2025,
107139/1-12
2024
4.
Online early work scheduling on parallel machines,
European Journal of Operational Research
315 (3),
2024,
pp. 855-862
5.
Online and Semi-online Scheduling on Two Hierarchical Machines with a Common Due Date to Maximize the Total Early Work,
International Journal of Applied Mathematics and Computer Science
34 (2),
2024,
pp. 253-261
6.
RNA World with Inhibitors,
Entropy
26 (12),
2024,
1012
2023
7.
An improved approximation algorithm for a scheduling problem with transporter coordination,
Journal of Scheduling
26,
2023,
pp. 559-570
8.
Exact Approaches to Late Work Scheduling on Unrelated Machines,
International Journal of Applied Mathematics and Computer Science
33 (2),
2023,
pp. 285-295
9.
In silico and in vitro analysis of the impact of single substitutions within EXO-motifs on Hsa-MiR-1246 intercellular transfer in breast cancer cell,
Journal of Applied Genetics
64,
2023,
pp. 105-124
10.
Ab Initio Study of Glycine Formation in the Condensed Phase: Carbon Monoxide, Formaldimine, and Water Are Enough,
The Astrophysical Journal
956 (2),
2023,
pp. 140
11.
Single machine scheduling with due date assignment to minimize the total weighted lead time penalty and late work,
Omega
121,
2023,
pp. 102923
12.
Mathematical challenges in scheduling theory,
Journal of Scheduling
26,
2023,
pp. 519–521
13.
A DNA Algorithm for Calculating the Maximum Flow of a Network,
Foundations of Computing and Decision Sciences
48 (4),
2023,
pp. 483-506
2022
14.
RNA World Modeling: A Comparison of Two Complementary Approaches,
Entropy
24 (4),
2022,
p. 536
15.
Two-machine flow shop scheduling with a common due date to maximize total early work,
European Journal of Operational Research
300 (2),
2022,
pp.504-511
16.
Alternative algorithms for identical machines scheduling to maximize total early work with a common due date,
Computers & Industrial Engineering
2022,
17.
Learning vector quantization as an interpretable classifier for the detection of SARS-CoV-2 types based on their RNA sequences,
Neural Computing and Applications
34 ,
2022,
pp. 67-78
18.
In silico and in vitro analysis of the impact of single substitutions within EXO-motifs on Hsa-MiR-1246 intercellular transfer in breast cancer cell.,
Journal of Applied Genetics
2022,
pp.1-20
19.
Online and semi-online scheduling on two hierarchical machines with a common due date to maximize the total early work.,
arXiv
2022,
20.
RNAloops: a database of RNA multiloops.,
Bioinformatics
38 (17),
2022,
pp. 4200-4205
21.
In memoriam Moshe Dror,
Journal of Scheduling
25,
2022,
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2021
22.
Semi-online Scheduling on Two Identical Machines with a Common Due Date to Maximize Total Early Work,
Discrete Applied Mathematics
290,
2021,
pp. 71-78
23.
Genome-scale de novo assembly using ALGA,
Bioinformatics
37,
2021,
pp. 1644-1651
24.
A Fast Algorithm for Knapsack Problem with Conflict Graph,
Asia-Pacific Journal of Operational Research
38 (06),
2021,
pp. 1-34
25.
Learning vector quantization as an interpretable classifier for the detection of SARS-CoV-2 types based on their RNA sequences,
Neural Computing and Applications
2021,
pp. 1-12
26.
Two-machine flow shop scheduling with a common due date to maximize total early work,
European Journal of Operational Research
2021,
27.
New Perspectives in Scheduling Theory,
Journal of Scheduling
24 (5),
2021,
pp. 455-457
28.
The correctness of large scale analysis of genomic data,
Foundations of Computing and Decision Sciences
46 (4),
2021,
pp. 423-436
29.
Mirror scheduling problems with early work and late work criteria,
Journal of Scheduling
24 (5),
2021,
pp. 483-487
2020
30.
Fully polynomial time approximation scheme to maximize early work on parallel machines with common due date,
European Journal of Operational Research, North-Holland
284 (1),
2020,
pp. 67-74
31.
Recent Results on Computational Molecular Modeling of The Origins of Life,
Foundations of Computing and Decision Sciences
45 (1),
2020,
pp. 35-46
32.
Multi-agent approach to sequence structure simulation in the RNA World hypothesis,
PloS one
15 (8),
2020,
e0238253
33.
Two meta-heuristic algorithms for scheduling on unrelated machines with the late work criterion,
International Journal of applied mathematics and computer science
30 (3),
2020,
pp. 573-584
34.
Virxicon: A Lexicon Of Viral Sequences,
Bioinformatics
36 (22-23),
2020,
pp. 5507-5513
35.
Exact and Heuristic Algorithms for Scheduling on Two Identical Machines with Early Work Maximization,
Computers & Industrial Engineering
144,
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36.
A highly effective approach to cofactor regeneration and subsequent membrane separation of bioconversion products: Kinetic parameters and effect of process conditions,
Bioresource Technology Reports
9,
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37.
PUM1 and PUM2 exhibit different modes of regulation for SIAH1 that involve cooperativity with NANOS paralogues,
Cellular and Molecular Life Sciences
76 (1),
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38.
Two-machine flow-shop scheduling to minimize total late work: revisited,
Engineering Optimization
2019,
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39.
Detecting Life Signatures with RNA Sequence Similarity Measures,
Journal of Theoretical Biology
463,
2019,
pp. 110-120
40.
Clarification of lower bounds of two-machine flow-shop scheduling to minimize total late work,
Engineering Optimization
51 (7),
2019,
1-2
41.
Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinnello Ab Initio Simulations,
Life: The Origin and Early Evolution of Life: Prebiotic Chemistry of Biomolecules
9 (46),
2019,
42.
Cloud Brokering with Bundles: Multi-objective Optimization of Services Selection,
Foundations of Computing and Decision Sciences, Sciendo
44/4,
2019,
pp. 407-426
43.
VirDB: Crowdsourced Database for Evaluation of Dynamical Viral Infection Models ,
Current Bioinformatics
14 (8),
2019,
pp. 740-748(9)
2018
44.
Graph algorithms for DNA sequencing - origins, current models and the future,
European Journal of Operational Research
264 (3),
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pp. 799-812
45.
RNApdbee 2.0: multifunctional tool for RNA structure annotation,
Nucleic acids research
2018,
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46.
A note on the complexity of scheduling of communication-aware directed acyclic graph.,
Biulletin of the Polish Academy of Sciences, Technical Sciences
66 (2),
2018,
pp. 187-191
47.
RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs,
Bioinformatics
2018,
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48.
GRASShopPER—An algorithm for de novo assembly based on GPU alignments,
PloS one
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2018,
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NPM1 alternative transcripts are upregulated in acute myeloid and lymphoblastic leukemia and their expression level affects patient outcome,
Journal of Translation Medicine
16 (232),
2018,
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New challenges in scheduling theory,
Journal of Scheduling
21 (6),
2018,
pp. 581–582
2017
51.
Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA,
Computational Biology and Chemistry
66,
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52.
Computational prediction of nonenzymatic RNA degradation patterns,
Acta Biochimica Polonica
63 (4),
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53.
Understanding Life: A Bioinformatics Perspective,
European Review
25 (2),
2017,
pp. 231-245
54.
Tabu Search for the RNA Partial Degradation Problem,
International Journal of Applied Mathematics and Computer Science
27 (2),
2017,
pp. 401-415
55.
Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution,
PloS one
12 (7),
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e0180827
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Complexity of late work minimization in flow shop systems and a particle swarm optimization algorithm for learning effect,
Computers & Industrial Engineering
111,
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57.
An integrated model for the transshipment yard scheduling problem,
Journal of Scheduling
20 (1),
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pp. 57-65
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58.
Simultaneous detection of mutations and copy number variation of NPM1 in the acute myeloid leukemia using multiplex ligation-dependent probe amplification,
Mutation Research
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59.
Hypercycle,
PLoS Comput Biol
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G-MAPSEQ–a new method for mapping reads to a reference genome,
Foundations of Computing and Decision Sciences
41,
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61.
Exact and heuristic approaches to solve the Internet shopping optimization problem with delivery costs,
International Journal of Applied Mathematics and Computer Science
26,
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62.
Novel dual discounting functions for the Internet shopping optimization problem: new algorithms,
Journal of Scheduling
19,
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pp. 245-255
63.
AmiRNA Designer-new method of artificial miRNA design,
Acta Biochimica Polonica
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Computer representations of bioinformatics models,
Current Bioinformatics
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65.
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Acta Biochimica Polonica
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Algorithms solving the Internet shopping optimization problem with price discounts,
Bulletin of the Polish Academy of Sciences Technical Sciences
64 (3),
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67.
Understanding Life: A Bioinformatics Perspective,
European Review
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pp. 1-15
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New challenges in scheduling theory,
Journal of Scheduling
2016,
pp.1-2
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Automated RNA 3D Structure Prediction with RNAComposer,
RNA Structure Determination: Methods and Protocols
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pp. 199-215
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Structural alignment of protein descriptors - a combinatorial model,
BMC bioinformatics
17,
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pp.383, doi:10.1186/s12859-016-1237-9
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Scheduling on parallel identical machines with late work criterion: Offline and online cases,
Journal of Scheduling
19 (6),
2016,
pp. 729-736
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72.
Automated 3D RNA structure prediction using the RNAComposer method for riboswitches,
Methods in Enzymology
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73.
New Challenges in Scheduling Theory,
RAIRO-Operations Research
49 (2),
2015,
335-337, DOI: 10.1051/ro/2014047
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Special Issue: Eighth International Colloquium on Graphs and Optimization (GO VIII), 2012 Foreword,
Discrete Applied Mathematics
182,
2015,
1-1 (SI), DOI: 10.1016/j.dam.2014.11.011
75.
Optimal pathway reconstruction on 3D NMR maps,
DISCRETE APPLIED MATHEMATICS
182,
2015,
134-149 (SI), DOI: 10.1016/j.dam.2014.04.010
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A study of scheduling problems with preemptions on multi-core computers with GPU accelerators,
Discrete Applied Mathematics
196,
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pp. 72-82
77.
Cloud Brokering: Current Practices and Upcoming Challenges,
IEEE Cloud Computing
2,
2015,
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New in silico approach to assessing RNA secondary structures with non-canonical base pairs,
BMC Bioinformatics
16:276,
2015,
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Good Laboratory Practice for optimization research,
Journal of the Operational Research Society
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doi: 10.1057/jors.2015.77
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Building the Library of Rna 3D Nucleotide Conformations Using the Clustering Approach,
International Journal of Applied Mathematics and Computer Science
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RNAssess a web server for quality assessment of RNA 3D structures,
Nucleic Acids Research
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New perspectives in scheduling theory,
Journal of Scheduling
18,
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pp. 333-334.
2014
83.
Recent advances in computational biology, bioinformatics, medicine, and healthcare by modern OR,
CEJOR
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Unified encoding for hyper-heuristics with application to bioinformatics,
CEJOR
22,
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85.
Multi-agent model of hepatitis c virus infection,
Artificial Intelligence in Medicine
60,
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pp. 123-131
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The Orderly Colored Longest Path Problem - a survey of applications and new algorithms,
RAIRO Operations Research
48(1),
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87.
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4OR-A Quarterly for Operations Research
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Reference alignment based methods for quality evaluation of multiple sequence alignment - a survey,
Current Bioinformatics
9,
2014,
pp. 44-56.
89.
Preprocessing and storing high-throughput sequencing data,
Computational Methods in Science and Technology
20,
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pp. 9-20
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Optimal pathway reconstruction on 3D NMR maps,
Discrete Applied Mathematics
2014,
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91.
Erratum to: Internet shopping with price-sensitive discounts,
4OR-A Quarterly for Operations Research
12,
2014,
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92.
Sorting signal targeting mRNA into hepatic extracellular vesicles,
RNA Biology
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pp. 836-844
93.
RNApdbee-a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs,
Nucleic Acid Research
42,
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pp. W368-W372
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G-MSA - GPU-based, fast and accurate algorithm for multiple sequence alignment,
Journal of Parallel and Distributed Computing
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DNA sequence assembly involving an acyclic graph model,
Foundations of Computing and Decision Sciences
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MLP accompanied beam search for the resonance assignment problem,
Journal of Heuristics
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RNAlyzer - novel approach for quality analysis of RNA structural models,
Nucleic Acid Research
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A hyper-heuristic approach to sequencing by hybridization of DNA sequences,
Annals of Operations Research
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New trends in scheduling,
Journal of Scheduling
16,
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Modelang -- a new approach for experts-friendly viral infections modeling,
Computational and Mathematical Methods in Medicine
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G-DNA - a highly efficient multi-GPU/MPI tool for aligning nucleotide reads,
Bulletin of the Polish Academy of Sciences-Technical Sciences
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pp. 989–992
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GeVaDSs - decision support system for novel Genetic Vaccine development process,
BMC Bioinformatics
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Complexity issues in computational biology,
Fundamenta Informaticae
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104.
Editorial: new branches, old roots,
Journal of Scheduling
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pp. 399-401
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A simulated annealing hyper-heuristic methodology for flexible decision support,
4OR-A Quarterly Journal of Operations Research
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Highly efficient parallel approach to the next-generation DNA sequencing,
Lecture Notes in Computer Science
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107.
Reduced-by-matching graphs: toward simplifying Hamiltonian circuit problem,
Fundamenta Informaticae
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Poseidon: An information retrieval and extraction system for metagenomic marine science,
Ecological Informatics
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New algorithms for coupled tasks scheduling- a survey,
RAIRO - Operations Research
46,
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Automated 3D structure composition for large RNAs,
Nucleic Acid Research
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G-PAS 2.0-an improved version of protein alignment tool with an efficient backtracking routine on multiple GPUs,
Bulletin of the Polish Academy of Sciences-Technical Sciences
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2011
112.
The Simplified Partial Digest Problem: approximation and a graph-theoretic model,
European Journal of Operational Research
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Adaptive memory programming: local search parallel algorithms for phylogenetic tree construction,
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pp. 75-94
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A parallel branch and bound approach to the rectangular guillotine strip cutting problem,
INFORMS J. on Computing
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RNA Partial Degradation Problem: motivation, complexity, algorithm,
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Berth and quay crane allocation: a moldable task scheduling model,
Journal of the Operational Research Society
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Some aspects of the anemia of chronic disorders modeled and analyzed by petri net based approach,
Bioprocess and Biosystems Engineering
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Protein alignment algorithms with an efficient backtracking routine on multiple GPUs,
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Combinatorial Optimization Issues in Scheduling,
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On the complexity of the independent set problem in triangle graphs,
Discrete Mathematics
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pp. 1670-1680
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DomAns - pattern based method for protein domain boundaries prediction and analysis,
Foundations of Computing and Decision Sciences
36,
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Some operations research methods for analyzing protein sequences and structures,
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pp. 9-35
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Towards prediction of HCV therapy efficiency,
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Genetic and tabu search algorithms for peptide assembly problems,
RAIRO - Operations Research
44,
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Internet Shopping Optimization problem,
International Journal of Applied Mathematics and Computer Science
20,
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Scheduling of coupled tasks with unit processing times,
Journal of Scheduling
13,
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pp. 453-461
127.
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Journal of Scheduling
13,
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pp. 451-452
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Hepatitis C virus quasispecies in chronically infected children subjected to interferon–ribavirin therapy,
Archives of Virology
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pp. 1977-1987
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RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures,
BMC Bioinformatics
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Flexibility of Dicer studied by implicit solvent molecular dynamics simulations,
Computational Methods in Science and Technology
16,
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Operations Research Models for Computational Biology, Bioinformatics and Medicine,
J Math Model Algor
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New insights into the human body iron metabolism analyzed by a Petri net based approach,
Biosystems
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pp. 104-113
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Translational and structural analysis of the shortest legume enod40 gene in Lupinus luteus.,
Acta Biochimica Polonica
56,
2009,
pp. 89-102
134.
Whole genome assembly from 454 sequencing output via modified DNA graph concept,
Computational Biology and Chemistry
33,
2009,
pp. 224-230
135.
The Knapsack-Lightening problem and its application to scheduling HRT tasks,
Bulletin of the Polish Academy of Sciences, Technical Sciences
57,
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pp. 71-77
136.
Modeling the process of human body iron homeostasis using a variant of timed Petri nets,
Discrete Applied Mathematics
157,
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pp. 2221-2231
137.
Two types of viral quasispecies identified in children suffering from chronic hepatitis C,
Journal of Hepatology
55:27,
2009,
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Zastosowanie sieci Petriego do modelowania procesów biologicznych,
Kosmos
58 (1-2),
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System wspomagania wytwarzania i analizy szczepionek genetycznych,
Kosmos
58 (1-2),
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pp. 113-126
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On the approximability of the Simplified Partial Digest problem,
Discrete Applied Mathematics
157,
2009,
pp. 3586-3592
141.
Sequence Similarity Based Method For Protein Function Prediction,
Foundations of Computing and Decision Sciences
34,
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Some remarks on evaluation of quality of the multiple sequence alignment based on BAliBASE benchmark,
International Journal of Applied Mathematics and Computer Science
19,
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143.
Web and Grid technologies in bioinformatics, computational and systems biology: a review,
Current Bioinformatics
3,
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Graph reduction and its application to DNA sequence assembly,
Bulletin of the Polish Academy of Sciences, Technical Sciences
56,
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Emerging scheduling applications,
Journal of Scheduling
11,
2008,
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146.
Plant phenolic secondary metabolites mass spectra database,
Acta Biochimica Polonica
55, Suppl.2,
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Finding Hamiltonian circuits in quasi-adjoint graphs,
Discrete Applied Mathematics
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pp.2573-2580
148.
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Computers & Operations Research
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An analysis of the Petri net based model of the human body iron homeostasis process,
Computational Biology and Chemistry
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Petri net based model of the body iron homeostasis,
Journal of Biomedical Informatics
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A note on two-machine job shop with weighted late work criterion,
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Selected papers from the Dagstuhl workshop - On scheduling in computer and manufacturing systems,
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A polynomial time equivalence between DNA sequencing and the exact perfect matching problem,
Discrete Optimization
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New machine learning methods for prediction of protein secondary structure,
Control and Cybernetics
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3D-Judge - A Metaserver Approach to Protein Structure Prediction,
Foundations of Computing and Decision Sciences
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ProCKSI: A Decision Support System for Protein (Structure) Comparison, Knowledge, Similarity and Information,
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Simplified partial digest problem: enumerative and dynamic programming algorithms,
IEEE/ACM Trans. on Computational Biology and Bioinformatics
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Preemptable malleable task scheduling problem,
IEEE Transactions on Computers
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From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems,
Lecture Notes in Computer Science
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Dealing with repetitions in sequencing by hybridization,
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Operations Research
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Candidate mRNAs interacting with fertility protein PUMILIO2 in the human germ line,
Reproductive Biology
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Human fertility protein PUMILIO2 interacts in vitro with testis mRNA encoding Cdc42 effector 3 (CEP3),
Reproductive Biology
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An improved approximation algorithm for the single machine total completion time scheduling problem with availability constraints,
European Journal of Operational Research
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Selected combinatiorial problems of computational biology,
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Homologous Crossovers among Molecules of Brome Mosaic Bromovirus RNA1 or RNA2 Segments in vivo,
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Application of tabu search strategy for finding low energy structure of protein,
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Predicting secondary structures of proteins,
IEEE Engineering in Medicine and Biology
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RNA tertiary structure determination: NOE pathways construction by tabu search,
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On graph theoretical models for peptide sequence assembly,
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Computational methods in diagnostics of chronic hepatitis C,
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