## Publications

**Year:**2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003

**Author:**S. Al Seesi F. Alqahtani S. Dinakar J. Duitama P. Ghimire A. Gusev G. Ilie J. Jun J. Kennedy J. Lindsay I.I. Mandoiu M. Nicolae B. Pasaniuc C. Prajescu E. Sherafat D. Trinca

### Edited Books & Proceedings:

I.I. Mandoiu and A.Z. Zelikovsky (Eds.),

**Computational Methods for Next Generation Sequencing Data Analysis**, John Wiley & Sons (to appear) , 2016, publisher url, bibtex

R. Harrison and Y. Li and I.I. Mandoiu (Eds.),

**Proc. 11th International Symposium on Bioinformatics Research and Applications**, Springer-Verlag Lecture Notes in Bioinformatics vol. 9096, 2015, publisher url, bibtex

L. Bleris and I.I. Mandoiu and R. Schwartz and J. Wang (Eds.),

**Proc. 8th International Symposium on Bioinformatics Research and Applications**, Springer-Verlag Lecture Notes in Bioinformatics vol. 7292, 2012, publisher url, bibtex

S. Istrail and I.I. Mandoiu and M. Pop and S. Rajasekaran and J. Spouge (Eds.),

**Proc. 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences**, IEEE , 2012, publisher url, bibtex

B. Chen, ..., I.I. Mandoiu, et al. (Eds.),

**2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops Proceedings**, IEEE , 2011, publisher url, bibtex

I.I. Mandoiu and S. Miyano and T. Przytycka and S. Rajasekaran (Eds.),

**Proc. 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences**, IEEE , 2011, publisher url, bibtex

I.I. Mandoiu and G. Narasimhan and Y.-Q. Zhang (Eds.),

**Proc. 5th International Symposium on Bioinformatics Research and Applications**, Springer-Verlag Lecture Notes in Bioinformatics vol. 5542, 2009, publisher url, bibtex

I.I. Mandoiu and A.Z. Zelikovsky (Eds.),

**Bioinformatics Algorithms: Techniques and Applications**, John Wiley & Sons , 2008, publisher url, bibtex

I.I. Mandoiu and R. Sunderraman and A. Zelikovsky (Eds.),

**Proc. 4th International Symposium on Bioinformatics Research and Applications**, Springer-Verlag Lecture Notes in Bioinformatics vol. 4983, 2008, publisher url, bibtex

X. Hu and I.I. Mandoiu and Z. Obradovic and J. Xia (Eds.),

**Proc. 2007 IEEE International Conference on Bioinformatics and Biomedicine**, IEEE Computer Society Press , 2007, publisher url, bibtex

I.I. Mandoiu and A.Z. Zelikovsky (Eds.),

**Proc. 3rd International Symposium on Bioinformatics Research and Applications**, Springer-Verlag Lecture Notes in Bioinformatics vol. 4463, 2007, publisher url, bibtex

### Book Chapters:

O. Glebova and Y. Temate-Tiagueu and A. Caciula and S. Al Seesi and A. Artyomenko and S. Mangul and J. Lindsay and I.I. Mandoiu and A. Zelikovsky,

**Transcriptome Quantification and Differential Expression from NGS Data**, In I.I. Mandoiu and A. Zelikovsky,

*Computational Methods for Next Generation Sequencing Data Analysis*, John Wiley & Sons (to appear), 2016, bibtex

P. Skums and A. Artyomenko and O. Glebova and S. Ramachandran and D.S. Campo and Z. Dimitrova and I.I. Mandoiu and A. Zelikovsky and Y. Khudyakov,

**Pooling Strategy for Massive Viral Sequencing**, In I.I. Mandoiu and A. Zelikovsky,

*Computational Methods for Next Generation Sequencing Data Analysis*, John Wiley & Sons (to appear), 2016, bibtex

E. Nenastyeva and B. Tork and A. Artyomenko and N. Mancuso and M.I. Khan and R. O'Neill and I.I. Mandoiu and A. Zelikovsky,

**Reconstruction of Infectious Bronchitis Virus Quasispecies from NGS Data**, In I.I. Mandoiu and A. Zelikovsky,

*Computational Methods for Next Generation Sequencing Data Analysis*, John Wiley & Sons (to appear), 2016, bibtex

I. Mandric and J. Lindsay and I.I. Mandoiu and A. Zelikovsky,

**Scaffolding Algorithms**, In I.I. Mandoiu and A. Zelikovsky,

*Computational Methods for Next Generation Sequencing Data Analysis*, John Wiley & Sons (to appear), 2016, bibtex

S. Al Seesi and F. Duan and I.I. Mandoiu and P.K. Srivastava and A. Kueck,

**Genomics-guided immunotherapy of human epithelial ovarian cancer**, In Annabelle Rodriguez-Oquendo,

*Translational Cardiometabolic Genomic Medicine*, Academic Press, pp. 237-250, 2015, publisher url, bibtex

S. Al Seesi and S. Mangul and A. Caciula and A. Zelikovsky and I.I. Mandoiu,

**Transcriptome reconstruction and quantification from RNA sequencing data**, In Maria Poptsova,

*Genome Analysis: Current Procedures and Applications*, Caister Academic Press, pp. 39-60, 2014, publisher url, bibtex

I. Astrovskaya and N. Mancuso and B. Tork and S. Mangul and A. Artyomenko and P. Skums and L. Ganova-Raeva and I.I. Mandoiu and A. Zelikovsky,

**Inferring Viral Quasispecies Spectra from Shotgun and Amplicon Next-Generation Sequencing Reads**, In Maria Poptsova,

*Genome Analysis: Current Procedures and Applications*, Caister Academic Press, pp. 231-262, 2014, publisher url, bibtex

B. DasGupta and M.-Y. Kao and I.I. Mandoiu,

**Algorithmic Issues in DNA Barcoding Problems**, In M. Elloumi and A. Zomaya,

*Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications*, Wiley, pp. 129-142, 2011, pdf preprint, publisher url, bibtex

K.M. Konwar and I.I. Mandoiu and A. Russell and A. Shvartsman,

**Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints**, In I.I. Mandoiu and A.Z. Zelikovsky,

*Bioinformatics Algorithms: Techniques and Applications*, Wiley, pp. 241-258, 2008, pdf preprint, publisher url, bibtex

I.I. Mandoiu and A. Olshevsky and A.Z. Zelikovsky,

**QoS Multimedia Multicast Routing**, In T.E. Gonzalez,

*Approximation Algorithms and Metaheuristics*, Chapman & Hall/CRC, 2007, pdf preprint, publisher url, bibtex

C. Albrecht and A.B. Kahng and I.I. Mandoiu and A.Z. Zelikovsky,

**Multicommodity Flow Algorithms for Buffered Global Routing**, In T.E. Gonzalez,

*Approximation Algorithms and Metaheuristics*, Chapman & Hall/CRC, 2007, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and A.Z. Zelikovsky,

**Practical Approximations of Steiner Trees in Uniform Orientation Metrics**, In T.E. Gonzalez,

*Approximation Algorithms and Metaheuristics*, Chapman & Hall/CRC, 2007, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and S. Reda and X. Xu and A.Z. Zelikovsky,

**Computer-Aided Optimization of DNA Array Design and Manufacturing**, In K. Chakrabarty and J. Zeng,

*Design Automation Methods and Tools for Microfluidics-Based Biochips*, Springer Verlag, pp. 235-269, 2006, pdf preprint, publisher url, bibtex

### Journal Articles:

Y. Temate-Tiagueu and S. Al Seesi and M. Mathew and I. Mandric and A. Rodriguez and K. Bean and Q. Cheng and O. Glebova and I.I. Mandoiu and N.B. Lopanik and A. Zelikovsky,

**Inferring metabolic pathway activity levels from RNA-Seq data**,

*BMC Genomics*(to appear), 2016, pdf preprint, bibtex

D.K.P. Karunakaran and S. Al Seesi and A.R. Banday and M. Baumgartner and A. Olthof and C. Lemoine and I.I. Mandoiu and R.N. Kanadia,

**Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development**,

*BMC Genomics*(to appear), 2016, pdf preprint, bibtex

M Mathew and KI Bean and YT Tiagueu and A Caciula and I.I. Mandoiu and A Zelikovsky and NB Lopanik,

**Influence of symbiont-produced bioactive natural product on holobiont fitness in the marine bryozoan, Bugula neritina via protein kinase C (PKC)**,

*Marine Biology*163:44, 2016, publisher url, bibtex

M. Baumgartner and C. Lemoine and S. Al Seesi and D.K.P. Karunakaran and N. Sturrock and A. Rouf Banday and A.M. Kilcollins and I.I. Mandoiu and R.N. Kanadia,

**Minor splicing snRNAs are enriched in the developing mouse CNS and are crucial for survival of differentiating retinal neurons**,

*Developmental Neurobiology*75, pp. 895-907, 2015, publisher url, bibtex

M. Hamdalla and S. Rajasekaran and D. Grant and I.I. Mandoiu,

**Metabolic pathway predictions for metabolomics: a molecular structure matching approach**,

*Journal of Chemical Information and Modeling*55, pp. 709-718, 2015, pdf preprint, publisher url, bibtex

P. Skums and A. Artyomenko and O. Glebova and S. Ramachandran and I.I. Mandoiu and D.S. Campo and Z. Dimitrova and A. Zelikovsky and Y. Khudyakov,

**Computational Framework for Next-Generation Sequencing of Heterogeneous Viral Populations using Combinatorial Pooling**,

*Bioinformatics*31, pp. 682-690, 2015, pdf preprint, publisher url, bibtex

A. Rouf Banday and M. Baumgartner and S. Al Seesi and D.K.P. Karunakaran and A. Venkatesh and S. Congdon and C. Lemoine and A.M. Kilcollins and I.I. Mandoiu and C. Punzo and R.N. Kanadia,

**Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons**,

*Cell Cycle*13(16), pp. 2526-2541, 2014, publisher url, bibtex

F. Duan and J. Duitama and S. Al Seesi and C. Ayres and S. Corcelli and A. Pawashe and T. Blanchard and D. McMahon and J. Sidney and A. Sette and B. Baker and I.I. Mandoiu and P.K. Srivastava,

**Genomic and bioinformatic profiling of mutational neo-epitopes reveals new rules to predict anti-cancer immunogenicity**,

*Journal of Experimental Medicine*211, pp. 2231-2248, 2014, publisher url, bibtex

S. Al Seesi and Y.T. Tiagueu and A. Zelikovsky and I.I. Mandoiu,

**Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates**,

*BMC Genomics*15(Suppl 8):S2 , 2014, pdf preprint, publisher url, bibtex

E. Hemphill and J. Lindsay and C. Lee and I.I. Mandoiu and C.E. Nelson,

**Feature selection and classifier performance on diverse biological datasets**,

*BMC Bioinformatics*15(Suppl 13):S4, 2014, pdf preprint, publisher url, bibtex

J. Lindsay and H. Salooti and I.I. Mandoiu and A. Zelikovsky,

**ILP-based maximum likelihood genome scaffolding**,

*BMC Bioinformatics*15(Suppl 9):S9, 2014, pdf preprint, publisher url, bibtex

S. Mangul and S. Al Seesi and A. Caciula and D. Brinza and I.I. Mandoiu and A. Zelikovsky,

**Transcriptome Assembly and Quantification from Ion Torrent RNA-Seq Data**,

*BMC Genomics*15(Suppl 5):S7, 2014, pdf preprint, publisher url, bibtex

Y. Huang and M. Khan and I.I. Mandoiu,

**Neuraminidase subtyping of Avian influenza viruses with PrimerHunter-designed primers and quadruplicate primer pools**,

*PLOS ONE*Volume 8, Issue 11, e81842, 2013, publisher url, bibtex

L. Menikarachchi and D. Hill and M. Hamdalla and I.I. Mandoiu and D. Grant,

**In silico enzymatic synthesis of a 400,000 compound biochemical database for non-targeted metabolomics**,

*Journal of Chemical Information and Modeling*53, pp. 2483-2492, 2013, publisher url, bibtex

P. Skums and N. Mancuso and A. Artyomenko and B. Tork and I.I. Mandoiu and Y. Khudyakov and A. Zelikovsky,

**Reconstruction of Viral Population Structure from Next-Generation Sequencing Data Using Multicommodity Flows**,

*BMC Bioinformatics*14(Suppl 9):S2, 2013, pdf preprint, publisher url, bibtex

M. Hamdalla and I.I. Mandoiu and D. Hill and S. Rajasekaran and D. Grant,

**BioSM: A metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space**,

*Journal of Chemical Information and Modeling*53, pp. 601-612, 2013, publisher url, bibtex

F. Duan and S. Simeone and R. Wu and J. Grady and I.I. Mandoiu and P.K. Srivastava,

**Area under the curve as a tool to measure kinetics of tumor growth in experimental animals**,

*Journal of Immunological Methods*382, pp. 224-228, 2012, publisher url, bibtex

N. Mancuso and B. Tork and P. Skums and L. Ganova-Raeva and I.I. Mandoiu and A. Zelikovsky,

**Reconstructing viral quasispecies from NGS amplicon reads**,

*In Silico Biology*11, pp. 237-249, 2012, publisher url, bibtex

S. Mangul and A. Caciula and O. Glebova and I.I. Mandoiu and A. Zelikovsky,

**Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations**,

*In Silico Biology*11, pp. 251-261, 2012, publisher url, bibtex

J. Duitama and P.K. Srivastava and I.I. Mandoiu,

**Towards Accurate Detection and Genotyping of Expressed Variants from Whole Transcriptome Sequencing Data**,

*BMC Genomics*13(Suppl 2):S6, 2012, pdf preprint, publisher url, bibtex

B. Pasaniuc and R. Garfinkel and I.I. Mandoiu and A. Zelikovsky,

**Optimal Testing of Digital Microfluidic Biochips**,

*INFORMS Journal on Computing*23, pp. 518-529, 2011, pdf preprint, publisher url, bibtex

M.B. Renfree, A.T. Papenfuss, J.E. Deakin, J. Lindsay, ..., I.I. Mandoiu, et al.,

**Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development**,

*Genome Biology*12:R81, 2011, publisher url, bibtex

I. Astrovskaya and B. Tork and S. Mangul and K. Westbrooks and I.I. Mandoiu and P. Balfe and A. Zelikovsky,

**Inferring Viral Quasispecies Spectra from 454 Pyrosequencing Reads**,

*BMC Bioinformatics*12(Suppl 6):S1, 2011, pdf preprint, publisher url, bibtex

M. Nicolae and S. Mangul and I.I. Mandoiu and A. Zelikovsky,

**Estimation of alternative splicing isoform frequencies from RNA-Seq data**,

*Algorithms for Molecular Biology*6:9, 2011, pdf preprint, publisher url, bibtex

C. Lee and I.I. Mandoiu and C.E. Nelson,

**Inferring Ethnicity from Mitochondrial DNA Sequence**,

*BMC Proceedings*5(Suppl 2):S11, 2011, pdf preprint, publisher url, bibtex

J. Duitama and J. Kennedy and S. Dinakar and Y. Hernandez and Y. Wu and I.I. Mandoiu,

**Linkage Disequilibrium Based Genotype Calling from Low-Coverage Shotgun Sequencing Reads**,

*BMC Bioinformatics*12(Suppl 1):S53, 2011, pdf preprint, publisher url, bibtex

J. Duitama and D.M. Kumar and E. Hemphill and M. Khan and I.I. Mandoiu and C.E. Nelson,

**PrimerHunter: A Primer Design Tool for PCR-Based Virus Subtype Identification**,

*Nucleic Acids Research*37, pp. 2483-2492, 2009, pdf preprint, publisher url, bibtex

J. Jun and I.I. Mandoiu and C.E. Nelson,

**Identification of mammalian orthologs using local synteny**,

*BMC Genomics*10:630, 2009, pdf preprint, publisher url, bibtex

J. Jun and P. Ryvkin and E. Hemphill and I.I. Mandoiu and C.E. Nelson,

**The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution**,

*Journal of Computational Biology*16, pp. 1429-1444, 2009, publisher url, bibtex

K. Apichonbancha and B. Dasgupta and J. Jun and I.I. Mandoiu and E. Mendonca ,

**A Review of the Primer Approximation Multiplex PCR (PAMP) Technique for Detecting Large Scale Cancer Genomic Lesions**,

*Current Bioinformatics*4, pp. 1-7, 2009, publisher url, bibtex

J. Kennedy and I.I. Mandoiu and B. Pasaniuc,

**Genotype Error Detection using Hidden Markov Models of Haplotype Diversity**,

*Journal of Computational Biology*15, pp. 1155-1171, 2008, pdf preprint, publisher url, bibtex

A. Gusev and I.I. Mandoiu and B. Pasaniuc,

**Highly Scalable Genotype Phasing by Entropy Minimization**,

*IEEE/ACM Trans. on Computational Biology and Bioinformatics*5, pp. 252-261, 2008, pdf preprint, publisher url, bibtex

S. Balla and S. Rajasekaran and I.I. Mandoiu,

**Efficient Algorithms for Degenerate Primer Search**,

*International Journal of Foundations of Computer Science*18, pp. 899-910, 2007, publisher url, bibtex

I.I. Mandoiu and C. Prajescu,

**High-Throughput SNP Genotyping by SBE/SBH**,

*IEEE Trans. on Nanobioscience*6, pp. 28-35, 2007, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and X. Xu and A. Zelikovsky,

**Enhanced Design Flow and Optimizations for Multi-Project Wafers**,

*IEEE Trans. on CAD*26, pp. 301-311, 2007, pdf preprint, publisher url, bibtex

E. Althaus and G. Calinescu and I.I. Mandoiu and S. Prasad and N. Tchervenski and A.Z. Zelikovsky,

**Power Efficient Range Assignment for Symmetric Connectivity in Static Ad Hoc Wireless Networks**,

*Wireless Networks*12, pp. 287-299, 2006, pdf preprint, publisher url, bibtex

I.I. Mandoiu and D. Trinca,

**Exact and Approximation Algorithms for DNA Tag Set Design**,

*Journal of Computational Biology*13, pp. 732-744, 2006, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and S. Reda and X. Xu and A. Zelikovsky,

**Computer-Aided Optimization of DNA Array Design and Manufacturing**,

*IEEE Trans. on CAD*25, pp. 305-320, 2006, pdf preprint, publisher url, bibtex

B. DasGupta and K.M. Konwar and I.I. Mandoiu and A.A. Shvartsman,

**DNA-BAR: Distinguisher Selection for DNA Barcoding**,

*Bioinformatics*21, pp. 3424-3426, 2005, pdf preprint, publisher url, bibtex

B. DasGupta and K.M. Konwar and I.I. Mandoiu and A.A. Shvartsman,

**Highly Scalable Algorithms for Robust String Barcoding**,

*International Journal of Bioinformatics Research and Applications*1, pp. 145-161, 2005, pdf preprint, publisher url, bibtex

M. Karpinski and I.I. Mandoiu and A. Olshevsky and A. Zelikovsky,

**Improved Approximation Algorithms for the Quality of Service Multicast Tree Problem**,

*Algorithmica*42, pp. 109-120, 2005, pdf preprint, publisher url, bibtex

H. Chen and C.-K. Cheng and A.B. Kahng and I.I. Mandoiu and Q. Wang and B. Yao,

**The Y-Architecture for On-Chip Interconnect: Analysis and Methodology**,

*IEEE Trans. on CAD*24, pp. 588-599, 2005, pdf preprint, publisher url, bibtex

I.I. Mandoiu and C. Prajescu and D. Trinca,

**Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays**,

*LNCS Transactions on Computational Systems Biology*II, pp. 124-137, 2005, pdf preprint, publisher url, bibtex

S.V. Babin and A.B. Kahng and I.I. Mandoiu and S. Muddu,

**Improving CD accuracy and throughput by subfield scheduling in electron beam mask writing**,

*Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures*23, pp. 3094-3100, 2005, publisher url, bibtex

P. Gupta and A.B. Kahng and I.I. Mandoiu and P. Sharma,

**Layout-Aware Scan Chain Synthesis for Improved Path Delay Fault Coverage**,

*IEEE Trans. on CAD*24, pp. 1104-1114, 2005, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and P. Pevzner and S. Reda and A. Zelikovsky,

**Scalable Heuristics for Design of DNA Probe Arrays**,

*Journal of Computational Biology*11, pp. 429-447, 2004, pdf preprint, publisher url, bibtex

G. Calinescu and I.I. Mandoiu and P.-J. Wan and A.Z. Zelikovsky,

**Selecting Forwarding Neighbors in Wireless Ad Hoc Networks**,

*ACM Mobile Networks and Applications*9, pp. 101-111, 2004, pdf preprint, publisher url, bibtex

A.B. Kahng and B. Liu and I.I. Mandoiu,

**Non-Tree Routing for Reliability and Yield Improvement**,

*IEEE Trans. on CAD*23, pp. 148-157, 2004, pdf preprint, publisher url, bibtex

### Conference Articles:

S. Mangul and A. Caciula and S. Al Seesi and D. Brinza and A. Rouf Banday and R. Kanadia and I.I. Mandoiu and A. Zelikovsky,

**Flexible Approach for Novel Transcript Reconstruction from RNA-Seq Data using Maximum Likelihood Integer Programming**,

*Proc. 5th International Conference on Bioinformatics and Computational Biology*, pp. 25-34, 2013, pdf preprint, publisher url, bibtex

J. Lindsay and H. Salooti and A. Zelikovsky and I.I. Mandoiu,

**Scalable Genome Scaffolding using Integer Linear Programming**,

*Proc. ACM Conference on Bioinformatics, Computational Biology and Biomedicine*, pp. 377-383, 2012, pdf preprint, publisher url, ppt, bibtex

S. Mangul and A. Caciula and S. Al Seesi and D. Brinza and A. Rouf Banday and R. Kanadia and I.I. Mandoiu and A. Zelikovsky,

**An Integer Programming Approach to Novel Transcript Reconstruction from Paired-End RNA-Seq Reads**,

*Proc. ACM Conference on Bioinformatics, Computational Biology and Biomedicine*, pp. 369-376, 2012, pdf preprint, publisher url, ppt, bibtex

M. Hamdalla and D. Grant and I.I. Mandoiu and D. Hill and S. Rajasekaran and R. Ammar,

**The Use of Graph Matching Algorithms to Identify Biochemical Substructures in Synthetic Chemical Compounds: Application to Metabolomics**,

*Proc. 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences*, pp. 1-6, 2012, pdf preprint, publisher url, ppt, bibtex

S. Mangul and A. Caciula and I.I. Mandoiu and A. Zelikovsky,

**RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes**,

*Proc. 1st Workshop on Computational Advances in Molecular Epidemiology*, pp. 118-123, 2011, publisher url, ppt, bibtex

N. Mancuso and B. Tork and I.I. Mandoiu and P. Skums and A. Zelikovsky,

**Viral Quasispecies Reconstruction from Amplicon 454 Pyrosequencing Reads**,

*Proc. 1st Workshop on Computational Advances in Molecular Epidemiology*, pp. 94-101, 2011, publisher url, ppt, bibtex

S. Mangul and I. Astrovskaya and M. Nicolae and B. Tork and I.I. Mandoiu and A. Zelikovsky,

**Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data**,

*Proc. 11th Workshop on Algorithms in Bioinformatics*, pp. 213-224, 2011, pdf preprint, publisher url, bibtex

M. Nicolae and I.I. Mandoiu,

**Accurate Estimation of Gene Expression Levels from DGE Sequencing Data**,

*Proc. 7th International Symposium on Bioinformatics Research and Applications*, pp. 392-403, 2011, pdf preprint, publisher url, ppt, bibtex

J. Duitama and P.K. Srivastava and I.I. Mandoiu,

**Towards Accurate Detection and Genotyping of Expressed Variants from Whole Transcriptome Sequencing Data**,

*Proc. 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences*, pp. 87-92, 2011, pdf preprint, publisher url, ppt, bibtex

M. Nicolae and S. Mangul and I.I. Mandoiu and A. Zelikovsky,

**Estimation of alternative splicing isoform frequencies from RNA-Seq data**,

*Proc. 10th Workshop on Algorithms in Bioinformatics*, pp. 202-214, 2010, pdf preprint, publisher url, ppt, bibtex

B. Pasaniuc and J. Kennedy and I.I. Mandoiu,

**Imputation-based local ancestry inference in admixed populations**,

*Proc. 5th International Symposium on Bioinformatics Research and Applications/2nd Workshop on Computational Issues in Genetic Epidemiology*, pp. 221-233, 2009, pdf preprint, publisher url, ppt, bibtex

S. Balla and S. Rajasekaran and I.I. Mandoiu,

**Faster Greedy Algorithms for Multiple Degenerate Primer Selection**,

*Proc. 8th IEEE International Conference on Bioinformatics and Bioengineering*, pp. 1-4, 2008, publisher url, bibtex

J. Jun and P. Ryvkin and E. Hemphill and I.I. Mandoiu and C.E. Nelson,

**Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events During Mammalian Evolution**,

*Proc. 6th Annual RECOMB Satellite Workshop on Comparative Genomics*, pp. 40-54, 2008, pdf preprint, publisher url, bibtex

B. Dasgupta and J. Jun and I.I. Mandoiu,

**Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP**,

*Proc. 6th Asia-Pacific Bioinformatics Conference*, pp. 353-362, 2008, pdf preprint, publisher url, bibtex

J. Kennedy and I.I. Mandoiu and B. Pasaniuc,

**Genotype Error Detection using Hidden Markov Models of Haplotype Diversity**,

*Proc. 7th Workshop on Algorithms in Bioinformatics*, pp. 73-84, 2007, pdf preprint, publisher url, ppt, bibtex

B. Pasaniuc and I.I. Mandoiu,

**Highly Scalable Genotype Phasing by Entropy Minimization**,

*Proc. 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society*, pp. 3482-3486, 2006, pdf preprint, publisher url, ppt, bibtex

I.I. Mandoiu and C. Prajescu,

**High-Throughput SNP Genotyping by SBE/SBH**,

*Proc. 6th International Conference on Computational Science, Part II*, pp. 742-749, 2006, pdf preprint, publisher url, bibtex

M.T. Hajiaghayi and K. Jain and L.C. Lau and I.I. Mandoiu and A.C. Russell and V.V. Vazirani,

**The minimum multicolored subgraph problem in haplotyping and PCR primer set selection**,

*Proc. 6th International Conference on Computational Science, Part II*, pp. 758-766, 2006, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and X. Xu and A. Zelikovsky,

**Multi-project reticle design and wafer dicing under uncertain demand**,

*Proc. 22nd European Mask and Lithography Conference*, pp. 45-54, 2006, pdf preprint, publisher url, ppt, bibtex

A.B. Kahng and I.I. Mandoiu and X. Xu and A. Zelikovsky,

**Yield-driven multi-project reticle design and wafer dicing**,

*Proc. 25th Annual BACUS Symposium on Photomask Technology*, pp. 1247-1257, 2005, pdf preprint, publisher url, ppt, bibtex

I.I. Mandoiu and D. Trinca,

**Exact and Approximation Algorithms for DNA Tag Set Design**,

*Proc. 16th Annual Symposium on Combinatorial Pattern Matching*, pp. 383-393, 2005, pdf preprint, publisher url, ppt, bibtex

I.I. Mandoiu and C. Prajescu and D. Trinca,

**Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays**,

*Proc. 5th International Conference on Computational Science, Part II*, pp. 994-1002, 2005, pdf preprint, publisher url, ppt, bibtex

B. DasGupta and K.M. Konwar and I.I. Mandoiu and A.A. Shvartsman,

**Highly Scalable Algorithms for Robust String Barcoding**,

*Proc. 5th International Conference on Computational Science, Part II*, pp. 1020-1028, 2005, pdf preprint, publisher url, ppt, bibtex

K.M. Konwar and I.I. Mandoiu and A.C. Russell and A.A. Shvartsman,

**Improved Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints**,

*Proc. 3rd Asia-Pacific Bioinformatics Conference*, pp. 41-50, 2005, pdf preprint, publisher url, ppt, bibtex

A.B. Kahng and I.I. Mandoiu and Q. Wang and X. Xu and A.Z. Zelikovsky,

**Multi-Project Reticle Floorplanning and Wafer Dicing**,

*Proc. ACM International Symposium on Physical Design*, pp. 70-77, 2004, pdf preprint, publisher url, bibtex

G. Calinescu and C.G. Fernandes and I.I. Mandoiu and A. Olshevsky and K. Yang and A. Zelikovsky,

**Primal-Dual Algorithms for QoS Multimedia Multicast**,

*Proc. IEEE Global Communications Conference*, pp. 3631-3635, 2003, pdf preprint, publisher url, bibtex

S.V. Babin and A.B. Kahng and I.I. Mandoiu and S. Muddu,

**Resist Heating Dependence on Subfield Scheduling in 50kV Electron Beam Maskmaking**,

*Photomask and Next-Generation Lithography Mask Technology X*, pp. 718-726, 2003, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and S. Reda and X. Xu and A. Zelikovsky,

**Evaluation of Placement Techniques for DNA Probe Array Layout**,

*Proc. IEEE-ACM International Conference on Computer-Aided Design*, pp. 262-269, 2003, pdf preprint, publisher url, bibtex

P. Gupta and A.B. Kahng and I.I. Mandoiu and P. Sharma,

**Layout-Aware Scan Chain Synthesis for Improved Path Delay Fault Coverage**,

*Proc. IEEE-ACM International Conference on Computer-Aided Design*, pp. 754-759, 2003, pdf preprint, publisher url, bibtex

H. Chen and C.-K. Cheng and A.B. Kahng and I.I. Mandoiu and Q. Wang and B. Yao,

**The Y-Architecture for On-Chip Interconnect: Analysis and Methodology**,

*Proc. IEEE-ACM International Conference on Computer-Aided Design*, pp. 13-19, 2003, pdf preprint, publisher url, bibtex

I.I. Mandoiu,

**Recent Advances in Multicommodity Flow Algorithms for Global Routing**,

*Proc. 5th International. Conference on ASIC*, pp. 160-165, 2003, pdf preprint, publisher url, bibtex

A.B. Kahng and I.I. Mandoiu and S. Reda and X. Xu and A. Zelikovsky,

**Design Flow Enhancements for DNA Arrays**,

*Proc. IEEE International Conference on Computer Design*, pp. 116-123, 2003, pdf preprint, publisher url, bibtex

M. Karpinski and I.I. Mandoiu and A. Olshevsky and A. Zelikovsky,

**Improved Approximation Algorithms for the Quality of Service Steiner Tree Problem**,

*Proc. 8th International Workshop on Algorithms and Data Structures*, pp. 401-411, 2003, pdf preprint, publisher url, bibtex

### Technical Reports:

J. Kennedy and I.I. Mandoiu and B. Pasaniuc,

**GEDI: Scalable Algorithms for Genotype Error Detection and Imputation**, Cornell University arXiv e-print, 0911.1765, 2009, url, bibtex

I.I. Mandoiu and C. Prajescu and D. Trinca,

**Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays**, Cornell University arXiv e-print, cs/0502054, 2005, url, bibtex

B. DasGupta and K.M. Konwar and I.I. Mandoiu and A.A. Shvartsman,

**Highly Scalable Algorithms for Robust String Barcoding**, Cornell University arXiv e-print, cs/0502065, 2005, url, bibtex

I.I. Mandoiu and D. Trinca,

**Exact and Approximation Algorithms for DNA Tag Set Design**, Cornell University arXiv e-print, cs/0503057, 2005, url, bibtex

I.I. Mandoiu and C. Prajescu,

**High-Throughput SNP Genotyping by SBE/SBH**, Cornell University arXiv e-print, cs/0512052, 2005, url, bibtex

C. Albrecht and A.B. Kahng and I.I. Mandoiu and A. Zelikovsky,

**Multicommodity Flow Algorithms for Buffered Global Routing**, Cornell University arXiv e-print, cs/0508045, 2005, url, bibtex

K.M. Konwar and I.I. Mandoiu and A. Russell and A.A. Shvartsman,

**Approximation Algorithms for Minimum PCR Primer Set Selection with Amplification Length and Uniqueness Constraints**, Cornell University arXiv e-print, cs.DS/0406053, 2004, url, bibtex

### Ph.D. Thesis:

J. Lindsay,

**Scalable Optimization Algorithms for High-throughput Genomic Data**, University of Connecticut, Storrs, CT, May, 2015, pdf preprint, url, bibtex

J. Duitama,

**Bioinformatics Methods for Diagnosis and Treatment of Human Diseases**, University of Connecticut, Storrs, CT, Dec., 2010, pdf preprint, ppt, bibtex

J. Jun,

**Reconstruction and Analysis of Gene Family Evolution in Mammals**, University of Connecticut, Storrs, CT, May, 2010, pdf preprint, url, bibtex

J. Kennedy,

**Efficient Algorithms for SNP Genotype Data Analysis using Hidden Markov Models of Haplotype Diversity**, University of Connecticut, Storrs, CT, Dec., 2009, pdf preprint, ppt, bibtex

B. Pasaniuc,

**Scalable Algorithms for Analysis of Genomic Diversity Data**, University of Connecticut, Storrs, CT, May, 2008, pdf preprint, url, ppt, bibtex

### M.S. Thesis:

G. Ilie,

**Algorithms for Multisample Read Binning**, University of Connecticut, Storrs, CT, Dec., 2013, pdf preprint, ppt, bibtex

P. Ghimire,

**Detection of Genomic Inversion from Single End Reads**, University of Connecticut, Storrs, CT, Dec., 2012, pdf preprint, bibtex

M. Nicolae,

**Accurate Estimation of Isoform and Gene Expression Levels from Next Generation Sequencing Data**, University of Connecticut, Storrs, CT, September, 2011, pdf preprint, bibtex

C. Prajescu,

**Multiplexing Algorithms for High-Throughput Genomic Based Assays**, University of Connecticut, Storrs, CT, December, 2005, pdf preprint, url, bibtex

D. Trinca,

**Exact and Approximation Algorithms for DNA Tag Set Design**, University of Connecticut, Storrs, CT, December, 2005, pdf preprint, url, bibtex