GEDI: Scalable Algorithms for Genotype Error Detection and Imputation (2009)
Kennedy, Justin, Mandoiu, Ion I., Pasaniuc, Bogdan
Genome-wide association studies generate very large datasets that require scalable analysis algorithms. In this report we describe the GEDI software package, which implements efficient algorithms for...
PrimerHunter: a primer design tool for PCR-based virus subtype identification (2009)
Duitama, Jorge, Kumar, Dipu Mohan, Hemphill, Edward, Khan, Mazhar, Mandoiu, Ion I., Nelson, Craig E.
Rapid and reliable virus subtype identification is critical for accurate diagnosis of human infections, effective response to epidemic outbreaks and global-scale surveillance of highly pathogenic...
Optimum extensions of pre x codes 1 (2008)
An algorithm is given for nding the minimum weight extension of a pre x code. The algorithm runs in O(n 3), where n is the number of codewords to be added, and works for arbitrary alphabets. For...
Practical Approximation Algorithms for Separable Packing Linear Programs (2008)
Feodor F. Dragan, Andrew B. Kahn, Ion I. Mandoiu, Sudhakar Muddu, Alexander Zelikovsky, Er Zelikovsky
We describefVkw polynomial time approximation schemes fm generalized multicommodity flow problems arising in VLSI applications such as Global Routing via Bu#er Blocks (GRBB). We extend...
High-Throughput SNP Genotyping by SBE/SBH (2005)
Mandoiu, Ion I., Prajescu, Claudia
Despite much progress over the past decade, current Single Nucleotide Polymorphism (SNP) genotyping technologies still offer an insufficient degree of multiplexing when required to handle...
Multicommodity Flow Algorithms for Buffered Global Routing (2005)
Albrecht, Christoph, Kahng, Andrew B., Mandoiu, Ion I., Zelikovsky, Alexander
In this paper we describe a new algorithm for buffered global routing according to a prescribed buffer site map. Specifically, we describe a provably good multi-commodity flow based algorithm that...
Exact and Approximation Algorithms for DNA Tag Set Design (2005)
Mandoiu, Ion I., Trinca, Dragos
In this paper we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we give integer linear programming formulations for two previous formalizations of the tag...
Highly Scalable Algorithms for Robust String Barcoding (2005)
DasGupta, Bhaskar, Konwar, Kishori M., Mandoiu, Ion I., Shvartsman, Alex A.
String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string...
Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays (2005)
Mandoiu, Ion I., Prajescu, Claudia, Trinca, Dragos
In this paper we address two optimization problems arising in the design of genomic assays based on universal tag arrays. First, we address the universal array tag set design problem. For this...
Drago¸s N. Trincă, Drago¸s N. Trincă, Ion I. Mandoiu, Sanguthevar Rajasekaran, Alexander Russell
In this thesis we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we establish upper bounds for an extended version of a previous formalization. Second, we...
Selecting forwarding neighbors in wireless ad hoc networks (2004)
Calinescu, G, Mandoiu, Ion I, Wan, P J, Zelikovsky, A Z
Broadcasting is a fundamental operation which is frequent in wireless ad hoc networks. A simple broadcasting mechanism, known as flooding, is to let every node retransmit the message to all its 1-hop...
On the skew-bounded minimum-buffer routing tree problem (2003)
Albrecht, C, Kahng, A B, Liu, B, Mandoiu, Ion I, Zelikovsky, A Z
Bounding the load capacitance at gate outputs is a standard element in today's electrical correctness methodologies for high-speed digital very large scale integration design. Bounds on load caps...
Minimum buffered routing with bounded capacitive load for slew rate and reliability control (2003)
Alpert, C J, Kahng, A B, Liu, B, Mandoiu, Ion I, Zelikovsky, A Z
In high-speed digital VLSI design, bounding the load capacitance at gate outputs is a well-known methodology to improve coupling noise immunity, reduce degradation of signal transition edges, and...
Improved approximation algorithms for the Quality of Service Steiner Tree Problem (2003)
Karpinski, M, Mandoiu, Ion I, Olshevsky, A, Zelikovsky, A
The Quality of Service Steiner Tree Problem is a generalization of the Steiner problem which appears in the context of multimedia multicast and network design. In this generalization, each node...
Ion I. Mandoiu, Alexander Z. Zelikovsky
We give a tight analysis of the MST heuristic recently introduced by G.-H. Lin and G. Xue for approximating the Steiner tree with minimum number of Steiner points and bounded edge-lengths. The...
Ion I. Mandoiu, Alexander Z. Zelikovsky
We give a tight analysis of the MST heuristic recently introduced by G.-H. Lin and G. Xue for approximating the Steiner tree with minimum number of Steiner points and bounded edge-lengths. The...
Optimum Extensions of Prefix Codes (1998)
An algorithm is given for finding the minimum weight extension of a prefix code. The algorithm runs in O(n 3 ), where n is the number of codewords to be added, and works for arbitrary alphabets. For...
A New Heuristic for Rectilinear Steiner Trees
Ion I. Mandoiu, Vijay V. Vazirani, Joseph L. Ganley
The minimum rectilinear Steiner tree (RST) problem is one of the fundamental problems in the field of electronic design automation. The problem is NP-hard, and much work has been devoted to designing...
A New Heuristic for Rectilinear Steiner Trees
Ion I. Mandoiu, Rectilinear Steiner Trees, Ion I. M, Vijay V. Vazirani, Joseph L. Ganley
The minimum rectilinear Steiner tree (RST) problem is one of the fundamental problems in the field of electronic design automation. The problem is NP-hard, and much work has been devoted to designing...