Joshua D. Welch

Department of Computer Science,
The University of North Carolina at Chapel Hill

Education

Bachelor of Science in Computer Science with Specialization in Bioinformatics, Ohio University, major GPA: 4.0 (degree awarded June 2012)
Bioinformatics Certificate, Ohio University, certificate GPA: 4.0 (certificate awarded June 2012)
Bachelor of Music in Piano Performance, Ohio University, major GPA: 4.0 (degree awarded June 2012)
Cumulative GPA: 3.99 (331 hours earned)

Doctor of Philosophy in Computer Science, The University of North Carolina at Chapel Hill (Anticipated graduation: May 2017)

Graduate Courses

BIOS 661 – Probability and Statistical Inference
BCB 716 – Sequence Analysis
BCB 717 – Structural Bioinformatics
BCB 720 – Math Models for Network Biology
COMP 555 – Bioalgorithms
COMP 633 – Parallel Computing
COMP 715 – Visualization in the Sciences
COMP 750 – Advanced Algorithms
COMP 790 – Machine Learning in Computational Biology
STOR  757 – Bayesian Statistics and Generalized Linear Models
CompSci 590 – Computational Structural Biology (Duke)
CompSci 662 – Computational Systems Biology (Duke)

Teaching

COMP 790-201: Predictive Models for High-Dimensional Data Analysis (Spring 2016)

Publications [Google Scholar] [PubMed]


Welch JD*, Williams LA*, DiSalvo M*, Brandt AT, Marayati R, Sims CE, Allbritton NL, Prins JF, Yeh JJ, Jones CD. Selective Single Cell Isolation for Genomics Using Microraft Arrays. Nucleic Acids Research (major revisions)

 

Lackey P, Welch JD, Marzluff WM. TUT7 Catalyzes the Uridylation of the 3’ End of Histone mRNA for Rapid Degradation of Histone mRNA. RNA (major revisions)

 

Lyons SM, Cunningham CH, Groh B, Guo AY, Wei B, Welch JD, Whitfield ML, Xiong Y, Marzluff WF. A subset of replication-dependent histone mRNAs are expressed

as polyadenylated RNAs in terminally differentiated tissues. Nucleic Acids Research (under review).

Welch JD, Liu Z, Wang L, Lu J, Lerou P, Purvis J, Qian L, Hartemink A, Prins JF. SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data. RECOMB 2016.

Welch JD, Hu Y, Prins JF. Robust Detection of Alternative Splicing in a Population of Single Cells. Nucleic Acids Research 2016. doi: 10.1093/nar/gkv1525 [PDF]

 

Brooks L, Lyons SM, Mahoney JM, Welch JD, Liu Z, Marzluff WM, Whitfield ML. A multi-protein occupancy map of the mRNP on the 3' end of histone mRNAs. RNA 2015. [PDF]

 

Welch JD*, Slevin MK*, Tatomer D, Duronio RJ, Prins JF, Marzluff WF. EnD-Seq and AppEnD: Sequencing 3' ends to identify nontemplated tails and degradation intermediates. RNA 2015. [PDF]

Welch JD, Baran-Gale J, Perou C, Sethupathy P, Prins JF. Pseudogenes Transcribed in Breast Invasive Carcinoma Show Subtype-Specific Expression and ceRNA Potential. BMC Genomics 2015. [PDF]

Welch, JD. Decoding the Symbols of Life: Learning Cell Types and Properties from RNA Sequencing Data. Dagstuhl Reports. (“Neural-Symbolic Learning and Reasoning”, Seminar 14381) Volume 4, 2014. [PDF]

 

Slevin MK, Meaux S, Welch JD, Bigler R, Miliani de Marval PL, Su W, Rhoads RE, Prins JF, Marzluff WF Deep Sequencing Shows Multiple Oligouridylations Are Required for 3′ to 5′ Degradation of Histone mRNAs on Polyribosomes. Molecular cell 53 (6), 1020-1030. March 2014. [HTML]

 

Lichtenberg J, Kurz K, Liang X, Al-ouran R, Neiman L, Nau LJ, Welch JD, Jacox E, Bitterman T, Ecker K, Elnitski L, Drews F, Lee SS, Welch LR. WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and

word-based genomic signatures. BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S6. [PDF]

 

Lichtenberg J, Yilmaz A, Welch JD, Kurz K, Liang X, Drews F, Ecker K, Lee SS, Geisler M, Grotewold E, Welch LR. The word landscape of the non-coding segments of the Arabidopsis thaliana genome. BMC Genomics. 2009 Oct 8;10:463. [PDF]

 

Lichtenberg J, Jacox E, Welch JD, Kurz K, Liang X, Yang MQ, Drews F, Ecker K, Lee SS, Elnitski L, Welch LR. Word-based characterization of promoters involved in human DNA repair pathways. BMC Genomics. 2009 Jul 7;10 Suppl 1:S18. [PDF]

 

Presentations

 

Welch JD, Liu Z, Wang L, Lu J, Lerou P, Purvis J, Qian L, Hartemink A, Prins JF. SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data. RECOMB 2016, Santa Monica, CA.

 

Welch, JD. Finding Life in High-Dimensional Space: Identifying Cell Types from Single Cell Gene Expression Data. Poster presented at NSF Data Science Workshop 2015, August 2015, Seattle, WA.

 

Welch JD, Williams LA, DiSalvo M, Sims CE, Allbritton N, Prins JF, Yeh JJ, Jones CD. Selective Single Cell Isolation and RNA Sequencing Using Magnetic Microrafts. Talk presented at RNA 2015, May 2015, Madison, WI.
 

Welch, JD. Decoding the Symbols of Life: Learning Cell Types and Properties from RNA Sequencing Data. Talk at Dagstuhl Seminar 14381, “Neural-Symbolic Learning and Reasoning”, September 2014.

 

Welch JD, Slevin MK, Prins JF, Marzluff W. EnD-seq: A method for finding the 3’ ends of RNA molecules using next-generation sequencing with application to mRNA exonuclease degradation. Poster presented at Symposium on RNA Biology X, North Carolina RNA Society Meeting. October 2013, Chapel Hill, NC.

 

Welch JD, Prins JF. Investigating the Role of Transcribed Pseudogenes in Breast Cancer. Poster presented at ISMB 2013 and RegGen SIG at ISMB, July 2013, Berlin, Germany.

Jens Lichtenberg, Kyle Kurz, Xiaoyu Liang, Rami Al-ouran, Lev Neiman, Lee Nau, Joshua Welch, Edwin Jacox, Thomas Bitterman, Klaus Ecker, Laura Elnitski, Frank Drews, Stephen Lee, Lonnie Welch. Concurrent Bioinformatics Software for Discovering Genome-wide Patterns and Word-based Genomic Signatures. 11th Bioinformatics Open Source Conference (BOSC), Special Interest Group at ISMB, July 2010, Boston, MA.

 

Jens Lichtenberg, Mohit Alam, Thomas Bitterman, Frank Drews, Klaus Ecker, Laura Elnitski, Susan Evans, Matt Geisler, Erich Grotewold, Dazhang Gu, Edwin Jacox, Kyle Kurz, Stephen S. Lee, Xiaoyu Liang, Pooja M. Majmudar, Paul Morris, Chase Nelson, Eric Stockinger, Joshua Welch, Sarah Wyatt, Alper Yilmaz, and Lonnie R. Welch. Construction of Genomic Regulatory Encyclopedias: Strategies and Case Studies. Proceedings of the 2009 Ohio Collaborative Conference on Bioinformatics (OCCBIO '09). IEEE Computer Society, Washington, DC, USA, 65-70. 2009.

 

Software

AppEnD tool for mapping 3’ additions from RNA-seq data
https://github.com/jw156605/append

 

SingleSplice algorithm for detecting alternative splicing in a population of single cells
https://github.com/jw156605/SingleSplice

Honors and Awards

NIH Predoctoral Fellowship (F31) (2016). Proposal title: "Computational Modeling of Heterogeneous Gene Expression in Single Cells"
Big Data to Knowledge Fellowship (BD2K T32) (2015)
Elected President of the Computer Science Student Association (2014)
Heidelberg Laureate Forum (2014)
Graduate Student Mentoring Award, UNC Office of Undergraduate Research (2013)
National Science Foundation Graduate Research Fellowship (2012)
Outstanding Senior in Computer Science, Ohio University Russ College of Engineering (2011)
Ohio University Concerto Competition Winner (2011)
Outstanding Junior in Computer Science, Ohio University Russ College of Engineering (2009)

Service and Outreach

President, Computer Science Student Association, UNC Chapel Hill (2014-2015)
Volunteer, North Carolina DNA Day (2013, 2014)
Volunteer, UNC Science Expo (2013)

Curriculum Vita

UNC scientists reveal how cells destroy RNA, a key to understanding disease
Lock and Key: How computer science reveals the “dark matter” of the human genome
Son follows Russ College faculty member dad into bioinformatics