Profile Details

Create Project

★★★★★

☆☆☆☆☆

USD 500 /hr

★★★★★

☆☆☆☆☆

Hire Dr. Andrew R.

United States

USD 500 /hr

Associate Professor, CSO and freelance. Next-Generation Sequencing. Bioinformatics, genomics and computational biology.

Profile Summary

Expert in Virus Genomics (20+ years), RNAseq (13+ years) Transcriptomics, bulk and single-cell (8+ years) and structural biology (20+ years). Familiar with short read (e.g. Illumina) tech and long read (e.g. nanopore) tech. 50+ peer reviewed publication in broad fields (Nature, PNAS, Mol Cell, Bioinformatics, NAR, etc). Multiple patents. Published computational pipelines and generated bespoke bioinformatic workflows/solutions for academic and biotech labs. Raised >$5M in direct funds. Received Tenure in 2022. Genomics/bioinformatics leader and core director for multiple NIH-funded centers.

Subject Matter Expertise

• ★ Molecular Virology
• ★ Genomics
• ★ Next Generation Sequencing (NGS)
• ☆ Microbiology
• ☆ Virology
• ☆ Coronaviruses
• ☆ Coxsackie B Virus
• ☆ Enteroviruses
• ☆ Zika Virus
• ☆ Retrovirology
• ☆ Biochemistry
• ☆ Molecular Biology
• ☆ Omics
• ☆ Gene Expression Analysis
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Structural Bioinformatics
• ☆ Pathogenesis
• ☆ Python

Services

• Research

Research User Research, Feasibility Study, Fact Checking, Scientific and Technical Research

Work Experience

Assistant Professor

University of Texas Medical Branch at Galveston

November 2015 - Present

Post-Doctoral Researcher

Scripps Research Institute

October 2010 - August 2015

Education

PhD (MRC Laboratory of Molecular Biology)

UNIVERSITY OF CAMBRIDGE

October 2005 - August 2010

MBioc (Lady Margaret Hall)

University of Oxford

2001 - 2005

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Andrew Routh, Stephanea Sotcheff, John Yun-Chung Chen, Nathan Elrod, Jun Cao, Elizabeth Jaworski, Muge N. Kuyumcu-Martinez, Pei-Yong Shi (2022). Zika Virus Infection Alters Gene Expression and Poly-Adenylation Patterns in Placental Cells . Pathogens.

(2020). Microbial interactions in the mosquito gut determine Serratia colonization and blood-feeding propensity . The ISME journal.

(2020). Differential Alphavirus Defective RNA Diversity between Intracellular and Extracellular Compartments Is Driven by Subgenomic Recombination Events . mBio.

Andrew Routh, Tiffany Kautz, Elizabeth Jaworski, Naomi L. Forrester (2020). A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene . Viruses.

(2020). Understanding Flavivirus Capsid Protein Functions: The Tip of the Iceberg . Pathogens (Basel, Switzerland).

(2020). Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing . Nucleic acids research.

(2019). Dengue NS2A Protein Orchestrates Virus Assembly . Cell host & microbe.

(2019). Whole-Genome Sequence of Rickettsia parkeri Strain Atlantic Rainforest, Isolated from a Colombian Tick . Microbiology resource announcements.

(2019). DPAC: A Tool for Differential Poly(A)-Cluster Usage from Poly(A)-Targeted RNAseq Data . G3 (Bethesda, Md.).

(2019). Mosquito cells persistently infected with dengue virus produce viral particles with host-dependent replication . Virology.

(2019). Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients . Oncogene.

(2019). Development of Poly(A)-ClickSeq as a tool enabling simultaneous genome-wide poly(A)-site identification and differential expression analysis . Methods (San Diego, Calif.).

(2018). Better Safe than Sorry: A Dual-Function Viral Protein Inhibiting Host Defense . Cell host & microbe.

(2018). ClickSeq: Replacing Fragmentation and Enzymatic Ligation with Click-Chemistry to Prevent Sequence Chimeras . Methods in molecular biology (Clifton, N.J.).

Andrew Routh, Elizabeth Jaworski, Adam S. Lauring(2017). Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus . PLOS Pathogens. 13. (5). p. e1006365. Public Library of Science ({PLoS})

Andrew Routh, Ping Ji, Elizabeth Jaworski, Zheng Xia, Wei Li, Eric J. Wagner(2017). Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation . Nucleic Acids Research. 45. (12). p. e112--e112. Oxford University Press ({OUP})

van de Waterbeemd, M., Fort, K.L., Boll, D., Reinhardt-Szyba, M., Routh, A., Makarov, A., Heck, A.J.R.(2017). High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles . Nature Methods.

Barrows, N.J., Campos, R.K., Powell, S.T., Prasanth, K.R., Schott-Lerner, G., Soto-Acosta, R., Galarza-Muñoz, G., McGrath, E.L., Urrabaz-Garza, R., Gao, J., et al.(2016). A Screen of FDA-Approved Drugs for Inhibitors of Zika Virus Infection . Cell Host and Microbe. 20. (2). p. 259-270.

Routh, A., Head, S.R., Ordoukhanian, P., Johnson, J.E.(2015). ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3′-Azido cDNAs . Journal of Molecular Biology. 427. (16). p. 2610-2616.

Routh, A., Chang, M.W., Okulicz, J.F., Johnson, J.E., Torbett, B.E.(2015). CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data . Methods. 91. p. 40-47.

Routh, A., Johnson, J.E.(2014). Discovery of functional genomic motifs in viruses with ViReMa-a virus recombination mapper-for analysis of next-generation sequencing data . Nucleic Acids Research. 42. (2).

Routh, A., Domitrovic, T., Johnson, J.E.(2012). Packaging host RNAs in small RNA viruses: An inevitable consequence of an error-prone polymerase? . Cell Cycle. 11. (20). p. 3713-3714.

Routh, A., Ordoukhanian, P., Johnson, J.E.(2012). Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing . Journal of Molecular Biology. 424. (5). p. 257-269.

Routh, A., Domitrovic, T., Johnson, J.E.(2012). Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus . Proceedings of the National Academy of Sciences of the United States of America. 109. (6). p. 1907-1912.

Andrew Routh, Sara Sandin, Daniela Rhodes(2010). Chromatin Higher Order Structure and Regulation of its Compaction . Biophysical Journal. 98. (3). p. 608a. Elsevier {BV}

Neumann, H., Hancock, S.M., Buning, R., Routh, A., Chapman, L., Somers, J., Owen-Hughes, T., van Noort, J., Rhodes, D., Chin, J.W.(2009). A Method for Genetically Installing Site-Specific Acetylation in Recombinant Histones Defines the Effects of H3 K56 Acetylation . Molecular Cell. 36. (1). p. 153-163.

Kruithof, M., Chien, F.-T., Routh, A., Logie, C., Rhodes, D., Van Noort, J.(2009). Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber . Nature Structural and Molecular Biology. 16. (5). p. 534-540.

Robinson, P.J.J., An, W., Routh, A., Martino, F., Chapman, L., Roeder, R.G., Rhodes, D.(2008). 30 nm Chromatin Fibre Decompaction Requires both H4-K16 Acetylation and Linker Histone Eviction . Journal of Molecular Biology. 381. (4). p. 816-825.

Routh, A., Sandin, S., Rhodes, D.(2008). Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure . Proceedings of the National Academy of Sciences of the United States of America. 105. (26). p. 8872-8877.

Mehnert, T., Routh, A., Judge, P.J., Lam, Y.H., Fischer, D., Watts, A., Fischer, W.B.(2008). Biophysical characterization of Vpu from HIV-1 suggests a channel-pore dualism . Proteins: Structure, Function and Genetics. 70. (4). p. 1488-1497.

Mehnert, T., Lam, Y.H., Judge, P.J., Routh, A., Fischer, D., Watts, A., Fischer, W.B.(2007). Towards a mechanism of function of the viral ion channel Vpu from HIV-1 . Journal of Biomolecular Structure and Dynamics. 24. (6). p. 589-596.