#### 2011 -- 2017:

** Yu-Hong Yeung, Alex Pothen, Mahantesh Halappanavar and Zhenyu Huang,
**
* AMPS: An augmented matrix formulation for principal submatrix
updates with application to power grids,
*
SIAM J. Scientific Computing, Accepted for publication, June 2017.

**Mu Wang, Guang Lin, and Alex Pothen,**
* Using Automatic Differentiation for compressive sensing in uncertainty quantification, *
Optimization Methods and Software, accepted for publication, July 2017.

**Ariful Azad, Bartek Rajwa and Alex Pothen, **
* Immunophenotype discovery, hierarchical organization, and template-based
classification of flow cytometry samples,*
Frontiers in Oncology, August 2016.

**Arif Khan and Alex Pothen, **
* A new 3/2-approximation algorithm for the b-Edgecover problem, *
SIAM Proceedings of Combinatorial Scientific Computing (CSC16),
Nov. 2016.

**Arif Khan, Alex Pothen, Md. Mostofa Ali Patwary, Mahantesh Halappanavar,
Nadathur Rajagopalan Satish, Narayanan Sundaram, and Pradeep Dubey, **
* Designing scalable b-Matching algorithms on distributed memory multiprocessors via approximation, *
Proceedings of Supercomputing (SC16), ACM/IEEE,
11 pages, Nov. 2016.

**Mu Wang, Assefaw H. Gebremedhin, and Alex Pothen,**
* Capitalizing on Live Variables: Efficient Hessian computations for
Automatic Differentiation, *
Mathematical Programming Computation, 8(4), pp. 393-433, Dec. 2016.

**Mu Wang, Alex Pothen, and Paul Hovland,**
* Edge Pushing is equivalent to vertex elimination for computing Hessians,
*
SIAM Proceedins of Combinatorial Scientific Computing (CSC16), Nov. 2016.

** Yu-Hong Yeung, Jessica Crouch and Alex Pothen, **
* Interactively cutting and constraining nodes in a mesh by augmented matrices,
*
ACM Transactions on Graphics, 35, Article 18, 17 pp., 2016.
Presented at SIGGRAPH 2016, Anaheim CA, July 2016.

* Here is a video of our results (MP4 format)*
**Arif Khan, Alex Pothen, Md Mostofa Ali Patwary, Nadathur Satish, Narayanan Sundaram,
Fredrik Manne, Mahantesh Halappanavar and Pradeep Dubey, **
* Efficient Approximation Algorithms for Weighted b-Matching, *
SIAM Journal on Scientific Computing, 38(5), S593-S619, 2016.

** Tianying Wu, Vaithianathan "Mani" Venkatasubramanian, and
Alex Pothen,**
* Fast parallel stochastic subspace algorithms for large-scale ambient oscillation monitoring, *
IEEE Transactions on Smart Grid, 10 pp., to appear, 2016.

**Ariful Azad, Aydin Buluc and Alex Pothen, **
* Computing Maximum Cardinality Matchings in Parallel on Bipartite Graphs via Tree Grafting, *
IEEE Transactions on Distributed and Parallel Systems,
Accepted for Publication, March 2016.

**Ariful Azad, Bartek Rajwa and Alex Pothen, **
*FlowVS: Channel-Specific Variance Stabilization in Flow Cytometry,*
BMC Bioinformatics, 17:291, 2016.

**Mahantesh Halappanavar, Alex Pothen, Fredrik Manne, Ariful Azad, Johannes Langguth and
Arif Khan, **
* Codesign Lessons Learned from Implementing Graph Matching Algorithms on Multithreaded
Architectures, * IEEE Computer, pp. 46-55, August 2015.

**Ariful Azad, Aydin Buluc and Alex Pothen,**
* A parallel tree grafting algorithm for computing maximum cardinality matchings in bipartite
graphs, *
Proceedings of IPDPS, pp. 1075- 1084, 2015.

** Tianying Wu S. Arash Nezam Sarmadi, Vaithianathan "Mani" Venkatasubramanian,
Alex Pothen and Ananth Kalyanaraman,**
* Fast SVD computations for synchrophasor algorithms, *
IEEE PES Transactions on Power Systems, 31(2), 1651-1652, March 2016.

**Assefaw H. Gebremedhin, Duc Nguyen, Mostofa Ali Patwary, and Alex Pothen,**
* ColPack: Graph coloring software for derivative computation and beyond, *
ACM Transactions on Mathematical Software, 40 (1), 30 pp., 2013.

**Ariful Azad, Arif Khan, Bartek Rajwa, Saumyadipta Pyne and Alex Pothen,**
*Classifying immunophenotypes with templates from Flow Cytometry,*
Proceedings of the ACM Conference on Bioinformatics and Computational Biology (BCB), 10 pages, 2013

**Umit Catalyurek, John Feo, Assefaw H. Gebremedhin, Mahantesh Halappanavar, and Alex Pothen,**
* Graph Coloring Algorithms for Multi-core and Massively Multithreaded Architectures, *
Parallel Computing, 38, 576-594, 2012.

**Benjamin Letschert, Kshitij Kulshreshtha, Andrea Walther, Duc Nguyen, Assefaw Gebremedhin, and Alex Pothen,**
* Exploiting sparsity in Automatic Differentiation on multicore architectures, *
Lecture Notes in Computer Science, 87, pp. 151-161, 2012.
(Proceedings of AD 2012.)

**Arif Khan, David Gleich, Mahantesh Halappanavar and Alex Pothen,**
*A multithreaded algorithm for network alignment via approximate matching,*
Proceedings of Supercomputing 2012, 11 pp., IEEE and ACM Press.

**Ariful Azad, Mahantesh Halappanavar, Siva Rajamanickam, Erik Boman, Arif Khan and Alex Pothen,**
*Multithreaded algorithms for maximum matching in bipartite graphs,*
Proceedings of 26th IPDPS, pp. 860-872, 2012.

**Mahantesh Halappanavar, John Feo, Oreste Villa, Florin Dobrian, and Alex Pothen,**
*Approximate weighted matching on emerging manycore and multithreaded architectures,*
International Journal on High Performance Computing and Applications, 26, 413-430, 2012.

**Ariful Azad, Saumyadipta Pyne and Alex Pothen,**
*Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via Flow Cytometry,*
BMC Bioinformatics, 13(Suppl 2): S10, 2012.

**Mostofa Ali Patwary, Assefaw H. Gebremedhin and Alex Pothen, **
* New multithreaded ordering and coloring algorithms for multicore architectures,*
Europar 2011, Lecture Notes in Computer Science, Vol. 6853, pp. 250-262, Springer, 2011.

** Umit Catalyurek, Florin Dobrian, Assefaw Gebremedhin, Mahantesh Halappanavar, and Alex Pothen, **
* Distributed memory algorithms for matching and coloring,*
Proceedings of IPDPS (Workshop on Parallel Computing and Optimization), 2011.

**Bruce Hendrickson and Alex Pothen,**
*Combinatorial Scientific Computing: Past Successes, Current Challenges and Future Opportunities,*
Chapter 1 in Combinatorial Scientific Computing, Uwe Naumann and Olaf Schenk (eds.),
CRC Press/Chapman and Hall, Dec. 2011.

#### 2006 -- 2010:

**Ariful Azad, Johannes Langguth, Youhan Fang, Alan Qi and Alex Pothen,**
*Identifying Rare Cell Populations in Comparative Flow Cytometry,*
Workshop on Algorithms in Bioinformatics (WABI) 2010,
Lecture Notes in Bioinformatics, 6293, pp. 162-175, 2010.

**E. Ramadan, C. Osgood, and A. Pothen,**
* Discovering overlapping modules and bridge proteins in proteomic networks,*
Proceedings of the First ACM Conference on Bioinformatics and Computational Biology,
pp. 366-369, 2010.

**A.H. Gebremedhin, A. Pothen, A. Tarafdar, and A. Walther,**
*Efficient computation of sparse Hessians using coloring and Automatic Differentiation,*
INFORMS Journal on Computing, 21(2), pp. 209-223, 2009.

**A.H. Gebremedhin, A. Pothen, and A. Walther,**
* Exploiting Sparsity in Jacobian Computation via Coloring and Automatic Differentiation: a Case Study in a Simulated Moving Bed process,*
In C. Bischof et al. (Eds.): Proceeding of AD2008, The 5th Int'l Conference on AD, Lecture Notes in Computational Science and Engineering 64, pp. 339-349, 2008, Springer.

**Emad Ramadan, Michael Ward, Xin Guo, Sarah Durkin, Adam Sawyer, Marcelo Viela, Chris Osgood, Alex Pothen and O. John Semmes,**
*Physical and in silico approaches identify DNA-PK in a Tax DNA-damage response interactome,*
Retrovirology, 5:92, 13 pages, 2008

**E.G. Boman, D. Bozdag, U. Catalyurek, K. Devine, A.H. Gebremedhin, P. Hovland and A. Pothen,**
*Combinatorial Algorithms for Computational Science and Engineering,*
Journal of Physics: Conference Series 125 (2008) 012071, 5 pp. SciDAC 2008.

**A. Gebremedhin, A. Tarafdar, F. Manne and A. Pothen,**
* New Acyclic and Star Coloring Algorithms with Applications to Hessian Computation,*
SIAM Journal on Scientific Computing, Vol 29, No 3, pp 1042--1072, 2007.

**A. Pothen, A.H. Gebremedhin, F. Dobrian, E.G. Boman, K.D. Devine, B.A. Hendrickson, P. Hovland, B. Norris, J. Utke, U. Catalyurek, M.M. Strout,**
*Combinatorial Algorithms for Petascale Science,*
SciDAC Review, Issue 5, pp 26-35, Fall 2007.

**E.G. Boman, D. Bozdag, U.V. Catalyurek, K.D. Devine, A.H. Gebremedhin, P.D. Hovland, A. Pothen, and M.M. Strout,**
*Enabling high performance computational science through combinatorial algorithms,*
Proceedings of SciDAC 2007, Journal of Physics: Conference Series 78 (2007) 012058.

**B. Hendrickson, and A. Pothen,**
* Combinatorial Scientific Computing: The enabling power of discrete algorithms in computational science,*
Proceedings of the 7th International Meeting on High Performance Computing for Computational Science (VECPAR'06), Lecture Notes in Computer Science, Springer Verlag, 21 pp., 2006. (Invited paper)

**A. Pinar, E. Chow and A. Pothen,**
*Combinatorial Algorithms for Computing Column Space Bases that have Sparse Inverses,*
Electronic Transactions on Numerical Analysis, 22, pp. 122--145, 2006.

**S. Bhomwick, E.G. Boman, K. Devine, A.H. Gebremedhin, B. Hendrickson, P. Hovland, T. Munson and A. Pothen,**
*Combinatorial Algorithms Enabling Computational Science: Tales from the Front,*
Journal of Physics: Conference Series 46 (2006), 453-457, SciDAC 2006.

#### 2001 -- 2005:

** Assefaw Gebremedhin, Fredrik Manne and Alex Pothen,**
* What Color is Your Jacobian? Graph Coloring for Computing Derivatives,*
SIAM Review, Vol. 47 (4), pp. 629--705, 2005.

**E. Ramadan, C. Osgood, and A. Pothen,**
* The architecture of a proteomic network in the yeast,*
Proceedings of CompLife2005, Lecture Notes in Bioinformatics, Vol. 3695, pp. 265--276, 2005.

**Badr Al-Mutairy, Jolan E. Walter, Alex Pothen and Douglas K. Mitchell,**
* Genomic mapping of genome-linked viral protein (VPg) and helicase of astroviruses,*
Virus Genes, 31 (1), pp. 21--30, 2005.

This paper computationally predicted a VPg gene in a human astrovirus,
and now it has been experimentally confirmed! See

C. Fuentes, A. Bosch, R. M. Pinto and S. Guix,

* Identification of human astrovirus genome-linked protein (VPg) essential for
virus infectivity, *
Journal of Virology, Vol. 86, 18, 10070-78, 2012.

**F. Dobrian and A. Pothen,**
* Oblio: Design and Performance,*
in State of the Art in Scientific Computing, J. Dongarra, K. Madsen and J. Wasniewski (eds.), Lecture Notes in Computer Science, 3732, pp. 758--767, 2005.

**A. Pothen,**
* Dedication to Alan George,*
Electronic Transactions on Numerical Analysis, Special Volume on Combinatorial Scientific Computing, 21, pp. vii--xviii, Dec. 2005.

**M. Wagner, D. Naik, A. Pothen et al.,**
* Computational protein biomarker prediction: a case study for prostate cancer,*
BMC Bioinformatics, 5, 26 pp., March 2004.

**Emad Ramadan, Arijit Tarafdar, and A. Pothen,**
* A hypergraph model for the yeast protein complex network,*
Proceedings of the IEEE Workshop on High Performance Computational Biology, April 2004. (Presented at the HICOMB Workshop, Santa Fe, NM, IEEE)

**A. Pothen and S. Toledo,**
* Elimination structures in scientific computing, In Handbook on Data Structures and Applications,*
Chapter 59, 29 pp., Dinesh Mehta and Sartaj Sahni, editors, Chapman and Hall /CRC, 2004.

**Michael Wagner, Dayanand Naik, and A. Pothen,**
* Protocols for disease classification from mass spectrometry data,*
Proteomics, Vol 3 (9), pp. 1692--1698, Sep 2003. (Presented at the First Annual Proteomics Datamining Conference at the Duke Medical School)

**Florin Dobrian and A. Pothen,**
* A comparison between three external memory algorithms for factoring sparse matrices,*
Proceedings of the SIAM Conference on Applied Linear Algebra, 11 pp, July 2003.

**Pinar Heggernes, Stan Eisenstat, Gary Kumfert and A. Pothen,**
* The computational complexity of the minimum degree algorithm,*
Proceedings of the Norwegian Conference on Computer Science NIK, 2002.

**David Hysom and A. Pothen,**
* Level-based Incomplete LU factorization: Graph Model and Algorithms,*
Tech Report UCRL-JC-150789, Lawrence Livermore National Labs, 19 pp., Nov 2002.

**D. Hysom and A. Pothen,**
* A scalable parallel algorithm for incomplete factor preconditioning,*
SIAM Journal on Scientific Computing, 22(6), 2194--2215, 2001.

**Florin Dobrian and A. Pothen,**
* The Design of I/O efficient Sparse Direct Solvers,*
Proceedings of Supercomputing 2001, IEEE and ACM.

**Florin Dobrian,**
* External memory algorithms for factoring sparse matrices,*
PhD Thesis, Old Dominion University, Dec. 2001.

**David Hysom,**
* New parallel and sequential algorithms for incomplete factor preconditioners,*
PhD Thesis, Old Dominion University, Dec. 2001.

#### 1996 -- 2000:

**F. Dobrian and A. Pothen,**
* Oblio: a sparse direct solver library for serial and parallel computations,*
Technical Report describing the OBLIO software library, 2000.

**F. Dobrian, G. Kumfert and A. Pothen,**
* The Design of Sparse Direct Solvers using Object-Oriented Techniques*
, In Modern Software Tools in Scientific Computing, A. M. Bruaset, H. P. Langtangen and E. Quak (eds.), pp. 89--131, Springer-Verlag, 2000.

**Gary Karl Kumfert,**
* An object-oriented algorithmic laboratory for ordering sparse matrices,*
PhD Thesis, Old Dominion University, Dec. 2000.

**D. Hysom and A. Pothen,**
* Efficient Parallel Computation of ILU(k) Preconditioners,*
Proceedings of Supercomputing '99 (CDROM), 1999.

**G. Kumfert and A. Pothen,**
* An object-oriented collection of minimum degree algorithms: design, implementation, and experience,s*
In Computing in Object-oriented Parallel Environments, Lecture Notes in Computer Science 1505, D.~Caromel et al (eds.), pp. 95--106, Springer Verlag, 1998. (Proceedings of the Second International Symposium on Computing in Object-oriented Parallel Environments, Santa Fe, 1998.)

**Florin Dobrian, Gary Kumfert, and Alex Pothen,**
* Object-Oriented Design for Sparse Direct Solvers,*
In Computing in Object-oriented Parallel Environments, Lecture Notes in Computer Science 1505, D.~Caromel et al (eds.), pp. 207--214, Springer Verlag, 1998. (Proceedings of the Second International Symposium on Computing in Object-oriented Parallel Environments, Santa Fe, 1998.)

**G. Kumfert and A. Pothen,**
* Two improved algorithms for envelope and wavefront reduction,*
invited paper, BIT, 37(3), 559--590, 1997.

**A. George and A. Pothen,**
* An analysis of spectral envelope-reduction via quadratic assignment problems,*
SIAM Journal of Matrix Analysis and its Applications, 18(3), pp. 706--732, 1997.

**A. Pothen,**
* Graph partitioning algorithms with applications to scientific computing,*
In Parallel Numerical Algorithms, D. E. Keyes, A. H. Sameh and V. Venkatakrishnan (eds.), Kluwer Academic Press, 1996. (46 pages)

**I. Stoica and A. Pothen,**
* A robust and flexible microeconomic scheduler for parallel computers,*
Preprint, Dec 1996. Proceedings of Third International Conference on High Performance Computing, Thiruvananthapuram, India.

#### 1990 -- 1995:

**S. T. Barnard, A. Pothen and H. D. Simon,**
* A spectral algorithm for envelope reduction of sparse matrices,*
Numerical Linear Algebra with Applications, 2, pp. 317--334, 1995.

**B. W. Peyton, A. Pothen and X. Yuan,**
* A clique tree algorithm for partitioning a chordal graph into transitive subgraphs,*
Linear Algebra and its Applications, 223/224, pp. 553--588, 1995.

**I. Stoica, H. Abdel-Wahab, and A.Pothen,**
* A microeconomic scheduler for parallel computers,*
In Load-balancing and Job Scheduling for Parallel Computers, D. G. Feitelson and L. Rudolph (eds.), Lecture Notes in Computer Science, Vol. 949, Springer-Verlag, pp. 200--218, 1995.

**R.A.Brualdi, A. Pothen and S. Friedland,**
* The sparse basis problem and multilinear algebra,*
SIAM J. Matrix Anal. Applic., 16, pp. 1--20, 1995.

**N.J. Higham and A.Pothen,**
* Stability of the partitioned inverse method for parallel solution of sparse triangular systems,*
SIAM J. Sci. Computing, 15, 139--148, 1994.

**A. Pothen,**
* Predicting the structure of sparse orthogonal factors,*
Lin. Alg. Applic., 194 (1993), 183--204.

**B. W. Peyton, A. Pothen and X. Yuan,**
* Partitioning a chordal graph into transitive subgraphs for
parallel sparse triangular solution,*
Linear Algebra and its Applications, 192, pp. 329--354, 1993.

**F. L. Alvarado, A. Pothen and R. S. Schreiber,**
* Highly parallel sparse triangular solution,*
In Graph Theory and Sparse Matrix Computation, IMA vol. in Appl. Math., 56, 141--158, 1993. (Springer Verlag)

**A. Pothen and C.Sun,**
* A mapping algorithm for parallel sparse Cholesky factorization,*
SIAM J. Sci. Computing, 14 (1993), 1253--1257.

**A. Pothen and F. Alvarado,**
* A fast reordering algorithm for parallel sparse triangular solution,*
SIAM Journal on Scientific and Statistical Computing, 13 (2), pp. 645--653, 1992.

**A. Pothen, H. D. Simon, and K. Liou,**
* Partitioning sparse matrices with eigenvectors of graphs,*
SIAM Journal on Matrix Analysis and its Applications, 11, pp. 430--452, 1990.

**A. Pothen and C. Fan,**
* Computing the block triangular form of a sparse matrix,*
ACM Transactions on Mathematical Software, 16 (4), pp. 303--324, 1990.

**A. Pothen and C. Sun,**
* Compact clique tree data structures in sparse matrix factorizations,*
SIAM Proceedings in Applied Mathematics, 46, pp. 180--204, 1990.

#### 1986 -- 1989:

**J. G. Lewis, B. W. Peyton, and A. Pothen,**
* A fast algorithm for reordering sparse matrices for parallel factorization,*
SIAM Journal on Scientific and Statistical Computing, 10, pp. 1146--1173, 1989.

**A. Pothen and P. Raghavan,**
* Distributed orthogonal factorization: Givens and Householder algorithms,*
SIAM Journal on Scientific and Statistical Computing, 10, pp. 1113--1134, 1989.

**A. Pothen,**
* Sparse null basis computations in structural optimization,*
Numerische Mathematik, 55, pp. 501--519, 1989.

**A. Pothen,**
* The complexity of optimal elimination trees,*
Technical Report CS 88-16, Department of Computer Science, Penn State, April 1988.

**A. Pothen, S. Jha, and U. B. Vemulapati,**
*Orthogonal factorization on a distributed memory multiprocessor,*
Hypercube Multiprocessors 1987, pp. 587-596, SIAM, Philadelphia, 1987.

**T. F. Coleman and A. Pothen,**
* The null space problem II: algorithms,*
SIAM Journal on Algebraic and Discrete Methods, 8, pp. 544--563, 1987.

**T. F. Coleman and A. Pothen,**
* The null space problem I: complexity,*
SIAM Journal on Algebraic and Discrete Methods, 7, pp. 527--537, 1986.

**A. Pothen and G. Basu,**
*The single crystal spectra of tetrakis-thiourea nickel (II) chloride,*
Indian Journal on Chemistry, pp. 5-8, 1978.