Murray Patterson Assistant Professor Department of Computer Science College of Arts and Sciences Georgia State University 1 Park Place Atlanta, Georgia (USA) 30303 office: Room 636 tel: (+1) 475 330 0978 email: mpatterson[at]cs[dot]gsu[dot]edu

**Note** Please read the following advertisement if you are interested in working in my lab as a grad student: particularly if you looking for a master's project **Note**

Since the fall of 2020, I am a tenure track Assistant Professor of the Bioinformatics Cluster in the Computer Science Department at Georgia State University, Atlanta, Georgia.

In the 2019—2020 academic year, I was a Visiting Assistant Professor of Computer Science in the School of Engineering at Fairfield University.

From the summer of 2016 until the summer of 2019, I was a postdoctoral fellow in the Experimental Algorithmics Lab at the University of Milano-Bicocca with Gianluca Della Vedova and Paola Bonizzoni. My project was on haplotyping and cancer phylogenies.

From the spring of 2014 I did a 2-year postdoctoral fellowship at the LBBE as part of the Ancestrome Project with Daniel Kahn and Vincent Daubin. My project was on the evolution of metabolic networks from the perspective of the enzymes that catalyse reactions, but also of the structure of the network itself.

From the beginning of 2012 I was an ERCIM fellow with a 2-year Marie Curie ABCDE fellowship. I held my first year of the fellowship with the INRIA at the Laboratoire de Biométrie et Biologie Évolutive (LBBE) of the Université de Lyon in France with Eric Tannier. I held my second year in the Life Sciences Group at the CWI with Alexander Schoenhuth and Gunnar Klau.

Teaching

Fall 2020

• a senior year / masters-level programming language concepts course.

Spring 2020

• an introductory programming course in Java, and
• a junior year theory of programming languages course using Haskell and Prolog.

Fall 2019

• an introductory programming course in Java,
• an intermediate programming course, focusing on the object-oriented features of Java, and
• a senior year / masters-level course on database management systems.

Publications

View also at Google Scholar, DBLP or see my full CV, among a list of supporting documents

Journal Articles

1.

Zahra Tayebi, Sarwan Ali, and Murray Patterson. Robust representation and efficient feature selection allows for effective clustering of SARS-CoV-2 variants. Algorithms, 2021. doi:10.3390/a14120348.

2.

Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, and Murray Patterson. Simpler and faster development of tumor phylogeny pipelines. Journal of Computational Biology, 28(11):1142–1155, 2021. doi:10.1089/cmb.2021.0271.

3.

Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky*, and Murray Patterson*. From alpha to zeta: Identifying variants and subtypes of SARS-CoV-2 via clustering. Journal of Computational Biology, 28(11):1113–1129, 2021. doi:10.1089/cmb.2021.0302.

4.

Simone Ciccolella*, Murray Patterson*, Paola Bonizzoni, and Gianluca Della Vedova. Effective clustering for single cell sequencing cancer data. IEEE Journal of Biomedical and Health Informatics, 25(11):4068–4078, 2021. doi:10.1109/JBHI.2021.3081380.

5.

Simone Ciccolella, Mauricio Soto, Murray D. Patterson, Gianluca Della Vedova, Iman Hajirasouliha, and Paola Bonizzoni. Gpps: An ILP-based approach for inferring cancer progression with mutation losses from single cell data. BMC Bioinformatics, 2020. doi:10.1186/s12859-020-03736-7.

6.

Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush, Paola Bonizzoni, Iman Hajirasouliha, and Gianluca Della Vedova. Inferring cancer progression from single-cell sequencing while allowing mutation losses. Bioinformatics, 2020. doi:10.1093/bioinformatics/btaa722.

7.

Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, and Paola Bonizzoni. Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era. Quantitative Biology, 7(4):278–292, 2019. doi:10.1007/s40484-019-0181-x.

8.

Stefano Beretta*, Murray Patterson*, Simone Zaccaria, Gianluca Della Vedova, and Paola Bonizzoni. HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC Bioinformatics, 2018. doi:10.1186/s12859-018-2253-8.

9.

Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Sèverine Bérard, Cedric Chauve, Celine Scornavacca, Vincent Daubin, and Eric Tannier. DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies. Genome Biology and Evolution, 9(5):1312–1319, 2017. doi:10.1093/gbe/evx069.

10.

Andrea Bracciali, Marco Aldinucci, Murray Patterson, Tobias Marschall, Nadia Pisanti, Ivan Merelli, and Massimo Torquati. PWhatsHap: Efficient haplotyping for future generation sequencing. BMC Bioinformatics, 2016. doi:10.1186/s12859-016-1170-y.

11.

Murray Patterson*, Tobias Marschall*, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau$^\dagger $, and Alexander Schonhuth$^\dagger $. WhatsHap: Weighted haplotype assembly for future-generation sequencing reads. Journal of Computational Biology, 22(6):498–509, 2015. doi:10.1089/cmb.2014.0157.

12.

Murray Patterson, Gergely Szöllősi, Vincent Daubin, and Eric Tannier. Lateral gene transfer, rearrangement, reconciliation. BMC Bioinformatics, 2013. doi:10.1186/1471-2105-14-S15-S4.

13.

Mohammed El-Kebir*, Tobias Marschall*, Inken Wohlers*, Murray Patterson, Jaap Heringa, Alexander Schönhuth, and Gunnar W. Klau. Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinformatics, 2013. doi:10.1186/1471-2105-14-S15-S18.

14.

Ján Maňuch*, Murray Patterson*, Roland Wittler*, Cedric Chauve, and Eric Tannier. Linearization of ancestral multichromosomal genomes. BMC Bioinformatics, 2012. doi:10.1186/1471-2105-13-S19-S11.

15.

Ján Maňuch*, Murray Patterson*, and Cedric Chauve. Hardness results on the gapped consecutive-ones property problem. Discrete Applied Mathematics, 160(18):2760–2768, 2012. doi:10.1016/j.dam.2012.03.019.

16.

Ján Maňuch* and Murray Patterson*. The complexity of the gapped consecutive-ones property problem for matrices of bounded maximum degree. Journal of Computational Biology, 18(9):1243–1253, 2011. doi:10.1089/cmb.2011.0128.

17.

Roland Wittler, Ján Maňuch*, Murray Patterson*, and Jens Stoye. Consistency of sequence-based gene clusters. Journal of Computational Biology, 18(9):1023–1039, 2011. doi:10.1089/cmb.2011.0083.

Conference Proceedings

18.

Sarwan Ali, Bikram Sahoo, Naimat Ullah, Alex Zelikovsky, Murray Patterson*, and Imdadullah Khan. A k-mer based approach for SARS-CoV-2 variant identification. In the 17th International Symposium on Bioinformatics Research and Applications (ISBRA, Shenzhen, China, 2021), volume 13064 of LNCS, 153–164. 2021. doi:10.1007/978-3-030-91415-8_14.

19.

Brendan Smith, Cristian Navarro-Martinez, Rebecca Buonopane, S. Ashley Byun*, and Murray Patterson*. Correlated evolution in the small parsimony framework. In the 17th International Symposium on Bioinformatics Research and Applications (ISBRA, Shenzhen, China, 2021), volume 13064 of LNCS, 608–619. 2021. doi:10.1007/978-3-030-91415-8_51.

20.

Sarwan Ali and Murray Patterson. Spike2Vec: An efficient and scalable embedding approach for COVID-19 spike sequences. In the 2021 IEEE International Conference on Big Data (IEEE BigData, Virtual Conference, 2021), 1533–1530. 2021. doi:10.1109/BigData52589.2021.9671848.

21.

Sarwan Ali, Tamkanat-E-Ali, Muhammad Asad Khan, Imdadullah Khan, and Murray Patterson. Effective and scalable clustering of SARS-CoV-2 sequences. In the 5th International Conference on Big Data Research (ICBDR, Virtual Conference, 2021). 2021. to appear.

22.

Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky*, and Murray Patterson*. Clustering based identification of SARS-CoV-2 subtypes. In the 10th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS, Virtual Conference, 2020), volume 12686 of LNCS, 127–141. 2021. doi:10.1007/978-3-030-79290-9_11.

23.

Simone Ciccolella*, Murray Patterson*, Paola Bonizzoni, and Gianluca Della Vedova. Effective clustering for single cell sequencing cancer data. In the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB, Niagara Falls, NY, USA, 2019), ACM, 437–446. 2019. doi:10.1145/3307339.3342149.

24.

Giulia Bernardini*, Paola Bonizzoni*, Gianluca Della Vedova*, and Murray Patterson*. A rearrangement distance for fully-labelled trees. In the 30th Annual Symposium on Combinatorial Pattern Matching (CPM, Pisa, Italy, 2019), volume 128 of LIPIcs, 1–15. 2019. doi:10.4230/LIPIcs.CPM.2019.28.

25.

Gianluca Della Vedova*, Murray Patterson*, Raffaella Rizzi*, and Mauricio Soto*. Character-based phylogeny construction and its application to tumor evolution. In the 13th Conference on Computability in Europe (CiE, Turku, Finland, 2017), volume 10307 of LNCS, 3–13. 2017. doi:10.1007/978-3-319-58741-7_1.

26.

Marco Aldinucci, Andrea Bracciali, Tobias Marschall, Murray Patterson, Nadia Pisanti, and Massimo Torquati. High-performance haplotype assembly. In the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB, Cambridge, UK, 2014), volume 8623 of LNCS, 245–258. 2015. doi:10.1007/978-3-319-24462-4_21.

27.

Murray Patterson*, Tobias Marschall*, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau$^\dagger $, and Alexander Schönhuth$^\dagger $. WhatsHap: Haplotype assembly for future-generation sequencing reads. In the 18th Annual International Conference on Research in Computational Molecular Biology (RECOMB, Pittsburgh PA, USA, 2014), volume 8394 of LNCS, 237–249. 2014. doi:10.1007/978-3-319-05269-4_19.

28.

Cedric Chauve*, Murray Patterson*, and Ashok Rajaraman*. Hypergraph covering problems motivated by genome assembly questions. In the International Workshop on Combinatorial Algorithms (IWOCA, Rouen, France, 2013), volume 8288 of LNCS, 428–432. 2013. doi:10.1007/978-3-642-45278-9_37.

29.

Cedric Chauve*, Ján Maňuch*, Murray Patterson*, and Roland Wittler*. Tractability results for the consecutive-ones property with multiplicity. In the 22nd Annual Symposium on Combinatorial Pattern Matching (CPM, Palermo, Italy, 2011), volume 6661 of LNCS, 90–103. 2011. doi:10.1007/978-3-642-21458-5_10.

30.

Ján Maňuch*, Murray Patterson*, and Arvind Gupta. Towards a characterization of the generalized cladistic character compatibility problem for non-branching character trees. In the 7th International Symposium on Bioinformatics Research and Applications (ISBRA, Changsha, China, 2011), volume 6674 of LNCS, 440–451. 2011.

31.

Ján Maňuch*, Murray Patterson*, Sheung-Hung Poon*, and Chris Thachuk*. Complexity of finding non-planar rectilinear drawings of graphs. In the 18th International Symposium on Graph Drawing (GD, Konstanz, Germany, 2010), volume 6502 of LNCS, 305–316. 2010. doi:10.1007/978-3-642-18469-7_28.

32.

Cedric Chauve*, Ján Maňuch*, and Murray Patterson*. On the gapped consecutive-ones property. In the European Conference on Combinatorics, Graph Theory and Applications (EuroComb, Bordeaux, France, 2009), volume 34 of ENDM, 121–125. 2009. doi:10.1016/j.endm.2009.07.020.

33.

Ján Maňuch*, Murray Patterson*, and Arvind Gupta. On the generalised character compatibility problem for non-branching character trees. In the 15th Annual International Computing and Combinatorics Conference (COCOON, Niagara Falls, USA, 2009), volume 5609 of LNCS, 268–276. 2009. doi:10.1007/978-3-642-02882-3_27.

34.

Murray Patterson, Yongmei Liu, Eugenia Ternovska, and Arvind Gupta. Grounding for model expansion in $k$-guarded formulas with inductive definitions. In the 20th International Joint Conferences on Artificial Intelligence (IJCAI, Hyderabad, India, 2007), 161–166. 2007.

Education