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EDUCATION                                                                                                                             

• Ph.D. in Computer Science (2012 - 2018)                                                            Rice University                                           

• M.S. in Electrical and Computer Engineering (2006 - 2008)                     The Johns Hopkins University                      

• M.S. in Pattern Recognition and Intelligent Systems (2004 - 2006)      Shanghai Jiao Tong University            

• B.S. in Information Engineering (2000 - 2004)                                               Shanghai Jiao Tong University            

PROFESSIONAL EXPERIENCE                                                                                           

• Assistant Professor (Aug. 2020 - now) Florida State University

• Postdoctoral Research Associate (Jul. 2018 - Jul. 2020)  Rice University 

• Software Engineer (2011-2012)  IGS, University of Maryland in Baltimore

• Statistical Analyst (2010-2011)  The Genome Institute at Washington University 

• Intern (May. 2008 - Aug. 2008)  Siemens Corporate Research

GRANTS 

• CTSI Precision Health Initiative Pilot Funding @ University of Florida, 2023-2024 (co-PI, $50,000 in total)

• Bankhead-Coley Cancer Research Program @ Florida Department of Health, 2021-2023 (co-I, $300,000/y, 2% of salary)

• Small Grant @ FSU, July-December 2022 (PI, $3,000)

• First Year Assistant Professor Grant @ FSU, summer 2021 (PI, $20,000)

• Multidisciplinary Support Grant @ FSU, 2021 (co-PI, $25,000)

• Planning Grant @ FSU, 2021 (PI, $25,000)

• Gulf Coast Consortia CCBTP Fellowship Awardee, 2019-2020.

• Gulf Coast Consortia CCBTP Fellowship Awardee, 2018-2019.

HONORS AND AWARDS                                                                                                      

●      Travel fellowship of MBI Workshop on Evolutionary Dynamics in Cancer, OSU, 2019.

●      Rising Star of EECS, UIUC, 2019.

●      Fellowship in Computer Science Department, Rice University, 2012-2013.

●      Travel fellowship of HiTSeq/ISMB, Orlando, 2016.

INVITED LECTURES

●      Bioinformatics (GMS6001-0001.fa21) @ FSU, Nov. 2021

INVITED TALKS

●      CS Colloquium @ FSU, Dec. 2022

●      CS board meeting @ FSU, May 2022

●      Scientific Computing Colloquium @ FSU, Apr. 2022

●      CS Colluqium @ FSU, Nov 2020

●      Biomedical Sciences Seminar Series @ FSU, Sep 2020

●      Human Genome Structural Variation Consortium f2f meeting, May 2016 (CSHL), Oct 2016 

●      HiTSeq/ISMB, Orlando, 2016 (<20% oral)

●      ASHG, Vancouver, 2016 (<3% oral)

●      Southeast Texas Evolutionary Genetics and Genomics (STEGG), Houston, 2016 and 2017

●      IEEE Computer Society Workshop on MMBIA, Anchorage, 2008.

PEER-REVIEWED PUBLICATIONS                                                                                                

1. Liting Zhang, Hank W. Bass, Jerome Irianto, Xian Mallory*, Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data, Genome Research, 33(11), 2002-2017 (2023).

2. Rituparna Khan and Xian F. Mallory*, Assessing the Performance of Methods for Cell Clustering from Single-cell DNA Sequencing Data, PLoS Computational Biology, Oct 12; 19(10):e1010480 (2023).

3. Olalekan Usman, Liting Zhang, Gengqiang Xie, Hemant Kocher, Chang-il Hwang, Yue Julia Wang, Xian Mallory, Jerome Irianto, Genomic heterogeneity in pancreatic cancer organoids and its stability with culture. npj Genomic Medicine 7(1), (2022).

4. Xian F. Mallory* and Luay Nakhleh, SimSCSnTree: a simulator of single-cell DNA sequencing data, Bioinformatics, (2022).

5. Joel Mallory, Xian F. Mallory, Anatoly Kolomeisky, Oleg Igoshin, Theoretical Analysis Reveals Cost and Benefit of Proofreading in Coronavirus Genome Replication, Journal of Physical Chemistry Letters, 12(10), (2021).

6. Xian F. Mallory, Mohammadamin Edrisi, Nicholas Navin and Luay Nakhleh, Methods for copy number aberration detection from single-cell DNA-sequencing data, Genome Biology, 21(208), (2020).

7. Xian F. Mallory*, Mohammadamin Edrisi, Nicholas Navin and Luay Nakhleh, Benchmarking Tools for Copy Number Aberration Detection from Single-cell DNA Sequencing Data, PLoS Computational Biology, 16(7): e1008012, (2020).

8. Justin Zook ... Xian Fan … Marc Salit, A robust benchmark for detection of germline large deletions and insertions, Nature Biotechnology, 1-9, (2020).

9. Mark Chaisson … Xian Fan … Charles Lee, Multi-platform discovery of haplotype-resolved structural variation in human genomes, Nature communications, 10, (2019).

10. Xian Fan*, Jie Xu, Luay Nakhleh, Detecting Large Indels Using Optical Maps Data, RECOMB-International Conference on Comparative Genomics (2018).

11. Xian Fan, Mark Chaisson, Luay Nakhleh and Ken Chen, HySA: A Hybrid Structural variant Assembly approach using next generation and single-molecule sequencing technologies, Genome Research, 27(5), 793 (2017).

12. Zechen Chong … Xian Fan …  Ken Chen, novoBreak: local assembly for breakpoint detection in cancer genomes, Nature Methods, 14(1), 65 (2017).

13. Matthew Wyczalkowski … Xian Fan …  Li Ding, BreakPoint Surveyor: a pipeline for structural variant visualization, Bioinformatics, 33(19), 3121 (2017).

14. 1000 Genomes Project Consortium, A global reference for human genetic variation, Nature, 526(7571), 68 (2015).

15. Peter Sudmant … Xian Fan … 1000 Genomes Project Consortium, An integrated map of structural variation in 2,504 human genomes, Nature, 526(7571), 75 (2015).

16. Malachi Griffith … Xian Fan … Richard Wilson, Genome modeling system: a knowledge management platform for genomics, PLOS Computational Biology, 11(7), e1004274 (2015).

17. Xian Fan, Wanding Zhou, Zechen Chong, Luay Nakhleh and Ken Chen, Towards accurate characterization of clonal heterogeneity based on structural variation, BMC Bioinformatics, 15(1), 299 (2014).

18. Xian Fan, Travis E. Abbott, David Larson and Ken Chen, BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping, Current Protocols in Bioinformatics, 45(1), 15-6 (2014).

19. Ken Chen, Lei Chen, Xian Fan, John Wallis, Li Ding and George Weinstock, TIGRA: A targeted iterative graph routing assembler for breakpoint assembly, Genome Research, 24(2), 310 (2014) (co-first author).

20. Xian Fan, Luay Nakhleh, Ken Chen, Integrated genotyping of structural variation, 1st IEEE Global Conference on Signal and Image Processing (2013).

21. Ken Chen … Xian Fan … Li Ding, BreakTrans: uncovering the genomic architecture of gene fusions, Genome Biology, 14(8), R87 (2013).

22. Margaret Young … Xian Fan … Timothy Ley, Background mutations in parental cells contribute to the genetic heterogeneity of Induced Pluripotent, Cell Stem Cells, 10(5), 570 (2012).

23. Matthew Walter … Xian Fan … Timothy Graubert, Clonal architecture of secondary acute myeloid leukemia, New England Journal of Medicine, 366(12), 1090 (2012).

24. Jianmin Wang … Xian Fan … Jinghui Zhang, CREST maps somatic structural variation in cancer genomes with base-pair resolution, Nature Methods, 8(8), 652 (2011).

25. Lucas Wartman ... Xian Fan ... Timothy Ley, Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression, Journal of Clinical Investigation, 121(4), 1445 (2011).

TEACHING

• Data structure, algorithm analysis and generic programming (COP4530) (Spring 2023) (88 students)

• Bioinformatics: Sequence Analysis (Fall 2022) (84 students)

• Bioinformatics: Sequence Analysis (Spring 2022) (47 students)

• Application of machine learning tools to solve a biological problem (Spring 2021) (25 students)

• Bioinformatics: Sequence Analysis (Fall 2020) (24 students)

ACADEMIC SERVICES

• Committee member of BIBM workshops:

  • (2022): workshop of Computational methods to characterize genomic variants using high-throughput sequencing data

  • (2021): workshop of Computational methods and their applications on single cell multiomic data

• Reviewer for the journals (2015-2022): BMC Bioinformatics, Bioinformatics, Nucleic Acids Research, PLoS Computational Biology, BMC Genomics

• Reviewer for the conferences (2015-2017): RECOMB’17, RECOMB-CBB’17, ICBEB’15, ACM-TCBB’17, AlCoB’16, AlCoB’17

• Research mentor for graduate students

  • (May 2021 - ): Liting Zhang (CS @ Florida State University)

  • (May 2021 – May 2023): Gyanendra Shrestha (CS @ Florida State University)

  • (May 2021 -): Rituparna Khan (CS @. Florida State University)

  • (Oct 2023 -): Shrey Choksi (CS @ Florida State University)

  • (Oct 2023 -): Teja Potu (CS @ Florida State University, Master Thesis student)

  • (Oct 2023 -): Bhavya Halasabele Shivakumaraiah (CS @ Florida State University, Master Thesis student)

• Research mentor for undergraduate students

  • (Jan 2023 - ): Anoushka Ahuja (Florida State University)

  • (May 2021 - Aug. 2021): Britnee Marius (Florida State University)

  • (June 2019 – Aug. 2019): Rufino Oregon (Texas A&M University)

  • (Oct 2023 -): Tina Tian (Florida State University)

• Thesis advisor for undergraduate students

  • (Jan 2023 - Dec 2023): Andres Candido (Florida State University)

• Committee member for graduate students

  • Shaeke Salman, Aug. 2023 (Florida State University)

  • Shweta Uddhavrao Aher, Mar. 2023 (Florida State University)

  • Zhe Li, Dec. 2022 (Florida State University)

  • Rupak Roy, Apr. 2021 (Florida State University)

• Teaching assistant at Rice University (2012-2015): COMP481 (Design and Analysis of Algorithms) and COMP571 (Bioinformatics: Sequence Analysis)

• Coach for an undergraduate project presentation (Spring, 2017)

• Coach for exchange students’ poster presentations (Summer, 2017)