Computational Biology Specialist - Metagenomics

About the role

The Computational Biologist will independently support –omics projects, specifically metagenomics projects as well as others as needed, initiated by researchers and clinicians at the National Institute of Allergy and Infectious Diseases (NIAID) in the National Institutes of Health (NIH).

This opportunity is a full-time position with Guidehouse and can be remote or on-site at NIH in Rockville, MD.

Responsibilities

• Implement, design, develop, and innovate current and emerging computational biology and bioinformatics algorithms aimed to process, analyze, manage, interpret and visualize original scientific data
• Enter into scientific collaborations with physicians and scientists that include the potential for authorships and acknowledgements in publications
• Gather detailed information from stakeholders and identify existing tools or develop novel algorithms/tools for performing custom and novel analyses
• Develop, maintain, document, and deliver training materials and sessions that support collaborators and researchers in applying metagenomics methods and high-throughput data processing workflows
• Research, design, and deliver educational materials that promote broader adoption and effective use of computational biology techniques, tools, and software among NIH researchers
• Aid collaborators in the design of new study projects, providing advice, and guidance for sequencing methods and analytical or statistical considerations for meeting project goals
• Aid researchers and collaborators with on-demand support and troubleshooting in the use of computational biology software and pipelines related to metagenomics and high-throughput sequencing
• Stay current on computational biology literature, emerging technologies, methods, and tools
• Partner with software developers to develop and integrate metagenomics software solutions within enterprise platforms

Requirements

• Masters or Ph.D. in computational biology, microbiology, statistics or related life, physical, or computational sciences with at least TWO (2) publications demonstrating the use or development of metagenomic methods
• Good understanding of high-throughput metagenomic technologies and techniques, bioinformatics, microbial ecology, molecular biology, and metagenomics software (e.g., QIIME2, MetaPhlan, MEGAN, Kraken, Ganon, HUMAnN, etc.)
• Minimum of TWO (2) years experience in the analysis of large-scale metagenomic data (shotgun metagenomics, amplicon sequencing), metagenomics file types (FASTQ, SAM/BAM, biom, HDF5, etc.) and experienced with a broad spectrum of relevant open-source software or pipelines (DADA2, USEARCH, DIAMOND, Bowtie2, BioBakery, genomic assemblers, CheckM, etc.)
• Experience working with relevant metagenomic databases and browsers and their annotations (SILVA, RDP, Greengenes, NCBI/RefSeq, IMG/M, GTDB, UHGG, etc)
• Proficiency in the use of UNIX/Linux and its command-line environment, including scripting (Python, R, Bash, etc.) as well as experience with code repositories such as GitHub or Bitbucket
• Proficiency in functional and taxonomic annotation of metagenomic data using enrichment and annotation tools (KEGG, eggNOG, InterProScan, Pfam, MetaCyc)
• Experience with a high-performance parallel computing environment (e.g., SLURM, PBS, UGE)
• Familiarity with community analyses tools (e.g. phyloseq etc), visualization tools (e.g. ggplots) as well as common methods in multivariate statistical analyses (linear mixed models, Bayesian approaches, differential abundance) and related tools (e.g. MaASLin2)
• Strong interpersonal, presentation, written, and oral communication skills to convey computational biology principles and concepts to non-specialists in a clear and precise manner and advise on relevant software and tools with a dedication to customer satisfaction
• Excellent troubleshooting and problem-solving skills, including the ability to learn and evaluate new software for metagenomics analyses quickly
• Effective time management skills, a high level of personal and professional drive and initiative, and attention to detail
• Proficiency with the use of open-source bioinformatics applications employing ontologies, pathways, and/or networks, at both the individual organism and metagenomic community scales
• Familiarity with problems and bottlenecks associated with storage and management of metagenomics-scale data

Qualifications

• Experience with one or more other omics analysis pipelines (QC, normalization, visualization, results reporting) and technologies listed below
• Transcriptomics/RNA-seq (alignment, quantification, differential expression analysis; relevant R and Python libraries such as DESeq2, edgeR, Salmon, Kallisto, etc.)
• Metabolomics/lipidomics (LC-MS, GC-MS, CE-MS, NMR for targeted or untargeted analysis; relevant R and Python libraries such as xcms, SpectriPy, MetaboAnalystR, pyOpenMS, Asari, pcpfm, TidyMS, lipidr, LipidMS, mixOmics, Lipydomics, LipidFinder, etc.)
• Proteomics analysis (LC-MS/MS, quantitative proteomics, relevant software and open-source tools)
• Experience constructing pipelines in open architecture platforms (e.g., Snakemake, Nextflow, R targets), including end-to-end tasks for metagenomic analysis tools
• Strong background in microbiology, microbial ecology, infectious disease research, immunology, and/or environmental science, including "bench" and/or sequencing experience

Benefits

The annual salary range for this position is $98,000.00-$163,000.00. Compensation decisions depend on a wide range of factors, including but not limited to skill sets, experience and training, security clearances, licensure and certifications, and other business and organizational needs.

Pay

The annual salary range for this position is $98,000.00-$163,000.00. Compensation decisions depend on a wide range of factors, including but not limited to skill sets, experience and training, security clearances, licensure and certifications, and other business and organizational needs.

Schedule

This opportunity is a full-time position with Guidehouse and can be remote or on-site at NIH in Rockville, MD.