List of works - Jacek Błażewicz

-MSA — A GPU-based, fast and accurate algorithm for multiple sequence alignment

A Parallel Branch-and-Bound Approach to the Rectangular Guillotine Strip Cutting Problem

A comparison of solution procedures for two-machine flow shop scheduling with late work criterion

article published in 2005

A heuristic managing errors for DNA sequencing

scientific article published in May 2002

A hyper-heuristic approach to sequencing by hybridization of DNA sequences

A new algorithm for genome assembly from short reads

A note on the two machine job shop with the weighted late work criterion

A novel representation of graph structures in web mining and data analysis

A polynomial time equivalence between DNA sequencing and the exact perfect matching problem

A simulated annealing hyper-heuristic methodology for flexible decision support

A study of scheduling problems with preemptions on multi-core computers with GPU accelerators

scholarly article by Jacek Błażewicz et al published December 2015 in Discrete Applied Mathematics

Adaptive memory programming: local search parallel algorithms for phylogenetic tree construction

scholarly article by Jacek Błażewicz et al published 18 September 2010 in Annals of Operations Research

Algorithms solving the Internet shopping optimization problem with price discounts

AmiRNA Designer - new method of artificial miRNA design

scientific article published on 19 January 2016

An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes

scientific article published in January 2004

An analysis of the Petri net based model of the human body iron homeostasis process

scientific article published on 9 November 2006

An assignment walk through 3D NMR spectrum

scientific article published in March 2009

An improved approximation algorithm for the single machine total completion time scheduling problem with availability constraints

An integrated model for the transshipment yard scheduling problem

Analysis of SARS-CoV-2 RNA-Sequences by Interpretable Machine Learning Models

scientific article published on 16 May 2020

Application of tabu search strategy for finding low energy structure of protein

scientific article published in September 2005

Assembling the SARS-CoV genome -- new method based on graph theoretical approach

scientific article published in January 2004

Automated 3D RNA structure prediction using the RNAComposer method for riboswitches

scientific article

Automated 3D structure composition for large RNAs

scientific article

Automated RNA 3D Structure Prediction with RNAComposer

Berth and quay crane allocation: a moldable task scheduling model

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

Candidate mRNAs interacting with fertility protein PUMILIO2 in the human germ line.

scientific article

Clarification of lower bounds of two-machine flow-shop scheduling to minimize total late work

scientific article published on 28 December 2018

Combinatorial optimization in DNA mapping — a computational thread of the Simplified Partial Digest Problem

article by Jacek Błażewicz & Marta Kasprzak published October 2005 in RAIRO Operations Research

Combinatorial optimization issues in scheduling

Complexity Issues in Computational Biology

scientific article published in 2012

Complexity of DNA sequencing by hybridization

Complexity of late work minimization in flow shop systems and a particle swarm optimization algorithm for learning effect

Computational complexity of isothermic DNA sequencing by hybridization

Computational prediction of non-enzymatic RNA degradation patterns.

scientific article

Computer Representations of Bioinformatics Models

article published in 2016

Construction of DNA restriction maps based on a simplified experiment

scientific article published in May 2001

DNA Sequencing by Hybridization via Genetic Search

DNA Sequencing—Tabu and Scatter Search Combined

scientific article published in August 2004

DNA sequencing with positive and negative errors.

scientific article published in January 1999

Dagstuhl seminar on “Scheduling in computer and manufacturing systems”

Deadline scheduling of multiprocessor tasks

Deadline scheduling of tasks with ready times and resource constraints

Deadlock-Resistant Flow Control Procedures for Store-and-Forward Networks

Dealing with repetitions in sequencing by hybridization

scientific article published on 30 August 2006

Detecting life signatures with RNA sequence similarity measures

scientific article published on 15 December 2018

Distributed processing of divisible jobs with communication startup costs

article by Jacek Błażewicz & Maciej Drozdowski published June 1997 in Discrete Applied Mathematics

Divisible task scheduling – Concept and verification

Dna Sequence Assembly Involving an Acyclic Graph Model

article

E-Commerce Evaluation – Multi-Item Internet Shopping. Optimization and Heuristic Algorithms

scholarly article by Jacek Błażewicz & Jeędrzej Musiał published 2011 in Operations research proceedings : papers of the annual meeting = Vorträge der Jahrestagung / DGOR

Editorial

Editorial: new branches, old roots

Erratum to: Internet shopping with price-sensitive discounts

article

Evolutionary Approaches to DNA Sequencing with Errors

Evolutionary approach to NOE paths assignment in RNA structure elucidation

Exact and heuristic algorithms for scheduling on two identical machines with early work maximization

scientific article published in June 2020

Exact and heuristic approaches to solve the Internet shopping optimization problem with delivery costs

Finding Hamiltonian circuits in quasi-adjoint graphs

Foreword

scholarly article by Jacek Błażewicz et al published February 2015 in Discrete Applied Mathematics

From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems

Fully polynomial time approximation scheme to maximize early work on parallel machines with common due date

scientific article published in July 2020

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

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

GRASShopPER-An algorithm for de novo assembly based on GPU alignments

scientific article published in PLoS ONE

GeVaDSs - decision support system for novel Genetic Vaccine development process

scientific article

Genetic and Tabu search algorithms for peptide assembly problem

Genome-scale de novo assembly using ALGA

scientific article published on 20 January 2021

Good Laboratory Practice for optimization research

article

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

Guest editorial

Guest editorial: “New trends in scheduling”

Hepatitis C virus quasispecies in chronically infected children subjected to interferon-ribavirin therapy

scientific article

Heuristic algorithms for the two-machine flowshop with limited machine availability

scholarly article by Jacek Błażewicz et al published December 2001 in OMEGA International Journal of Management Science

Highly Efficient Parallel Approach to the Next-Generation DNA Sequencing

Homologous crossovers among molecules of brome mosaic bromovirus RNA1 or RNA2 segments in vivo

scientific article

Human fertility protein PUMILIO2 interacts in vitro with testis mRNA encoding Cdc42 effector 3 (CEP3).

scientific article

Hypercycle

scientific article

Internet shopping with price sensitive discounts

scientific article

Linear and quadratic algorithms for scheduling chains and opposite chains

scholarly article by Jacek Błażewicz & Zhen Liu published March 2002 in European Journal of Operational Research

MLP accompanied beam search for the resonance assignment problem

Mathematical programming formulations for machine scheduling: A survey

Metaheuristic approaches for the two-machine flow-shop problem with weighted late work criterion and common due date

article by Jacek Błażewicz et al published February 2008 in Computers and Operations Research

Metaheuristics for Late Work Minimization in Two-Machine Flow Shop with Common Due Date

scientific article published in 2005

Mirror scheduling problems with early work and late work criteria

scientific article published on 30 January 2020

ModeLang: a new approach for experts-friendly viral infections modeling

scientific article published on 18 December 2013

Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA.

scientific article published on 17 November 2016

Modeling the process of human body iron homeostasis using a variant of timed Petri nets

Multi-agent approach to sequence structure simulation in the RNA World hypothesis

scientific article published on 28 August 2020

Multi-agent model of hepatitis C virus infection

scientific article published on 11 November 2013

Multiprocessor task scheduling with resource requirements

Multistage isothermic sequencing by hybridization

scientific article published in February 2005

NMR Analysis of RNA Bulged Structures: Tabu Search Application in NOE Signal Assignment

scientific article published in 2005

NPM1 alternative transcripts are upregulated in acute myeloid and lymphoblastic leukemia and their expression level affects patient outcome

New algorithms for coupled tasks scheduling – a survey

New challenges in scheduling theory

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

scientific article published on 2 September 2015

New insights into the human body iron metabolism analyzed by a Petri net based approach

scientific article published on 27 December 2008

New perspectives in scheduling theory

Novel dual discounting functions for the Internet shopping optimization problem: new algorithms

scholarly article by Jacek Błażewicz et al published 17 August 2014 in Journal of Scheduling

On some properties of DNA graphs

On the approximability of the Simplified Partial Digest Problem

article published in 2009

On the complexity of the independent set problem in triangle graphs

On the recognition of de Bruijn graphs and their induced subgraphs

Open shop scheduling problems with late work criteria

Optimal centralized algorithms for store-and-forward deadlock avoidance

Optimal pathway reconstruction on 3D NMR maps

scholarly article by Marta Szachniuk et al published February 2015 in Discrete Applied Mathematics

PREDICTION OF RESIDUE EXPOSURE AND CONTACT NUMBER FOR SIMPLIFIED HP LATTICE MODEL PROTEINS USING LEARNING CLASSIFIER SYSTEMS

PUM1 and PUM2 exhibit different modes of regulation for SIAH1 that involve cooperativity with NANOS paralogues

scientific article published on 29 September 2018

Parallel DNA sequence assembly

Parallel Implementation of the Novel Approach to Genome Assembly

Petri net based model of the body iron homeostasis

scientific article published on 19 December 2006

Poseidon: An information retrieval and extraction system for metagenomic marine science

scientific article published in 2012

Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations

scientific article published on 04 June 2019

Predicting secondary structures of proteins. Recognizing properties of amino acids with the logical analysis of data algorithm

scientific article

Preemptable malleable task scheduling problem

Preface

article published in 2011

Preprocessing and Storing High-Throughput Sequencing Data

article published in 2014

ProCKSI: a decision support system for Protein (structure) Comparison, Knowledge, Similarity and Information

scientific article

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

scientific article

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

scientific article

RNA Partial Degradation Problem: Motivation, Complexity, Algorithm ⬇️

scientific article published on May 12, 2011

RNA tertiary structure determination: NOE pathways construction by tabu search.

scientific article published on 24 February 2005

RNAlyzer--novel approach for quality analysis of RNA structural models

scientific article published on 25 April 2013

RNApdbee 2.0: multifunctional tool for RNA structure annotation.

scientific article published in July 2018

RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

scientific article

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

scientific article published on 11 June 2015

RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs

scientific article published on 01 January 2019

Recent advances in computational biology, bioinformatics, medicine, and healthcare by modern OR

article

Reduced-by-matching Graphs: Toward Simplifying Hamiltonian Circuit Problem

scientific article published in 2012

Reference Alignment Based Methods for Quality Evaluation of Multiple Sequence Alignment - A Survey

Review of properties of different precedence graphs for scheduling problems

article

Scheduling Malleable Tasks on Parallel Processors to Minimize the Makespan

Scheduling a divisible task in a two-dimensional toroidal mesh

Scheduling complete intrees on two uniform processors with communication delays

Scheduling jobs in open shops with limited machine availability

Scheduling multiprocessor tasks on a dynamic configuration of dedicated processors

Scheduling multiprocessor tasks on parallel processors with limited availability

Scheduling multiprocessor tasks on two parallel processors

Scheduling of coupled tasks with unit processing times

Scheduling on parallel identical machines with late work criterion: Offline and online cases

Scheduling preemptable tasks on parallel processors with limited availability

Scheduling subject to resource constraints: classification and complexity

article by Jacek Błażewicz et al published January 1983 in Discrete Applied Mathematics

Scheduling tasks and vehicles in a flexible manufacturing system

scientific article published in 1991

Scheduling with resource management in manufacturing systems

Selected combinatorial problems of computational biology

Selected papers from the Dagstuhl workshop

Semi-online scheduling on two identical machines with a common due date to maximize total early work

scientific article published in February 2021

Sequencing by Hybridization with Positive Faults

scientific article published on 01 January 1997

Sequencing by hybridization with isothermic oligonucleotide libraries

article published in 2004

Sequential and parallel algorithms for DNA sequencing.

scientific article published on April 1997

Simplified partial digest problem: enumerative and dynamic programming algorithms.

scientific article published in October 2007

Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution

scientific article published on 10 July 2017

Simultaneous detection of mutations and copy number variation of NPM1 in the acute myeloid leukemia using multiplex ligation-dependent probe amplification

scientific article published on 04 February 2016

Some aspects of the anemia of chronic disorders modeled and analyzed by petri net based approach

scientific article published on 8 January 2011

Some operations research methods for analyzing protein sequences and structures

Some preemptive open shop scheduling problems with a renewable or a nonrenewable resource

Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark

scholarly article by Jacek Błażewicz et al published 1 December 2009 in International Journal of Applied Mathematics and Computer Science

Sorting signal targeting mRNA into hepatic extracellular vesicles

scientific article

Structural alignment of protein descriptors - a combinatorial model

scientific article

Tabu Search for the RNA Partial Degradation Problem

Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries

scientific article published in February 2004

Tabu search for DNA sequencing with false negatives and false positives

The Orderly Colored Longest Path Problem – a survey of applications and new algorithms

The clinical consequences of changes occurring in HCV population during the first weeks of chronic hepatitis C treatment with interferon and ribavirin

scientific article published in January 2005

The complexity of two group scheduling problems

The job shop scheduling problem: Conventional and new solution techniques

The simplified partial digest problem: Approximation and a graph-theoretic model

The two-machine flow-shop problem with weighted late work criterion and common due date

article by Jacek Błażewicz et al published September 2005 in European Journal of Operational Research

Time-Stamp Approach to Prevention of Different Deadlock Types in Store-and-Forward Networks

Time-Stamp Approach to Store-and-Forward Deadlock Prevention

article published in 1987

Towards prediction of HCV therapy efficiency

scientific article published in June 2010

List of works by Jacek Błażewicz

-MSA — A GPU-based, fast and accurate algorithm for multiple sequence alignment

A Parallel Branch-and-Bound Approach to the Rectangular Guillotine Strip Cutting Problem

A comparison of solution procedures for two-machine flow shop scheduling with late work criterion

A heuristic managing errors for DNA sequencing

A hyper-heuristic approach to sequencing by hybridization of DNA sequences

A new algorithm for genome assembly from short reads

A note on the two machine job shop with the weighted late work criterion

A novel representation of graph structures in web mining and data analysis

A polynomial time equivalence between DNA sequencing and the exact perfect matching problem

A simulated annealing hyper-heuristic methodology for flexible decision support

A study of scheduling problems with preemptions on multi-core computers with GPU accelerators

Adaptive memory programming: local search parallel algorithms for phylogenetic tree construction

Algorithms solving the Internet shopping optimization problem with price discounts

AmiRNA Designer - new method of artificial miRNA design

An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes

An analysis of the Petri net based model of the human body iron homeostasis process

An assignment walk through 3D NMR spectrum

An improved approximation algorithm for the single machine total completion time scheduling problem with availability constraints

An integrated model for the transshipment yard scheduling problem

Analysis of SARS-CoV-2 RNA-Sequences by Interpretable Machine Learning Models

Application of tabu search strategy for finding low energy structure of protein

Assembling the SARS-CoV genome -- new method based on graph theoretical approach

Automated 3D RNA structure prediction using the RNAComposer method for riboswitches

Automated 3D structure composition for large RNAs

Automated RNA 3D Structure Prediction with RNAComposer

Berth and quay crane allocation: a moldable task scheduling model

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

Candidate mRNAs interacting with fertility protein PUMILIO2 in the human germ line.

Clarification of lower bounds of two-machine flow-shop scheduling to minimize total late work

Combinatorial optimization in DNA mapping — a computational thread of the Simplified Partial Digest Problem

Combinatorial optimization issues in scheduling

Complexity Issues in Computational Biology

Complexity of DNA sequencing by hybridization

Complexity of late work minimization in flow shop systems and a particle swarm optimization algorithm for learning effect

Computational complexity of isothermic DNA sequencing by hybridization

Computational prediction of non-enzymatic RNA degradation patterns.

Computer Representations of Bioinformatics Models

Construction of DNA restriction maps based on a simplified experiment

DNA Sequencing by Hybridization via Genetic Search

DNA Sequencing—Tabu and Scatter Search Combined

DNA sequencing with positive and negative errors.

Dagstuhl seminar on “Scheduling in computer and manufacturing systems”

Deadline scheduling of multiprocessor tasks

Deadline scheduling of tasks with ready times and resource constraints

Deadlock-Resistant Flow Control Procedures for Store-and-Forward Networks

Dealing with repetitions in sequencing by hybridization

Detecting life signatures with RNA sequence similarity measures

Distributed processing of divisible jobs with communication startup costs

Divisible task scheduling – Concept and verification

Dna Sequence Assembly Involving an Acyclic Graph Model

E-Commerce Evaluation – Multi-Item Internet Shopping. Optimization and Heuristic Algorithms

Editorial

Editorial: new branches, old roots

Erratum to: Internet shopping with price-sensitive discounts

Evolutionary Approaches to DNA Sequencing with Errors

Evolutionary approach to NOE paths assignment in RNA structure elucidation

Exact and heuristic algorithms for scheduling on two identical machines with early work maximization

Exact and heuristic approaches to solve the Internet shopping optimization problem with delivery costs

Finding Hamiltonian circuits in quasi-adjoint graphs

Foreword

From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems

Fully polynomial time approximation scheme to maximize early work on parallel machines with common due date

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

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

GRASShopPER-An algorithm for de novo assembly based on GPU alignments

GeVaDSs - decision support system for novel Genetic Vaccine development process

Genetic and Tabu search algorithms for peptide assembly problem

Genome-scale de novo assembly using ALGA

Good Laboratory Practice for optimization research

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

Guest editorial

Guest editorial

Guest editorial: “New trends in scheduling”

Hepatitis C virus quasispecies in chronically infected children subjected to interferon-ribavirin therapy

Heuristic algorithms for the two-machine flowshop with limited machine availability

Highly Efficient Parallel Approach to the Next-Generation DNA Sequencing

Homologous crossovers among molecules of brome mosaic bromovirus RNA1 or RNA2 segments in vivo

Human fertility protein PUMILIO2 interacts in vitro with testis mRNA encoding Cdc42 effector 3 (CEP3).

Hypercycle