Bioinformatics Jobs

Scope of Work: • Work with the Computational team to define an IO Schema. • All code will be in a GitHub repo with a Dev and main branch with the final code being a versioned released and pushed to main... • Implement automated testing for each module so that branches can be tested before being merged to dev of main. • Modularizing this code into discrete and versioned dockers, for instance: Alignment, alignment sorting and deduplication, SV calling with HiCBreakfinder, Heatmap generation with juicer, QC metric summary, ect… • Implementing the pipeline into a WDL workflow. Would be nice to see the difference in time/price for alternatives such as Nextflow and Snakemake. • Implementation on AWS with optimized instances for each module. • Automation of the analysis pipeline so that a CRON job monitors for a manifest/config file and kicks off analysis automatically. • Basic analytics from each step in the pipeline for monitoring. • Performance assessment: Demonstrate equivalent performance of the pipeline using 5 datasets. Standard QC metrics and SV calls will be compared between the original pipeline and the new pipeline and are expected to be within a reasonable tolerance. • Training and documentation: • Provide a training session to assay team on how to create a manifest and kick of the analysis. • Provide detailed training presentation to the computational team on how the new pipeline works and any things that would be important for the team to know for long term support. • Provide a schematic/diagram of how the pipeline works and the IO at each step. • Provide technical documentation on how the pipeline works and the theory of Operation in a GitHub README.md

Summary Texas Children's Hospital & Baylor College of Medicine are inviting applications for a full-time, non-tenure-track bioinformatics faculty position at the Assistant level. This position will support and meet the analysis needs of Texas Children's Hospital's hundreds of research teams. The Bioinformaticians will work with research teams at Texas Children's Hospital to provide statistical... and bioinformatics support to investigators in clinical and basic research. Texas Children's comprehensive health care network includes our primary hospital in the Texas Medical Center with expertise in over 40 pediatric subspecialties; the Jan and Dan Duncan Neurological Research Institute (NRI); the Feigin Center for pediatric research; Texas Children's Pavilion for Women, a comprehensive obstetrics/gynecology facility focusing on high-risk births; Texas Children's Hospital West Campus, a community hospital in suburban West Houston; and Texas Children's Hospital The Woodlands, the first hospital devoted to children's care for communities north of Houston. We have also created the nation's first HMO for children, established the largest pediatric primary care network in the country, and a global health program that is channeling care to children and women all over the world. Texas Children's Hospital is also academically affiliated with Baylor College of Medicine, one of tthe largest, most diverse, and successful pediatric programs in the nation. Job Duties • Performs computational analysis and interpretation of data for projects and research grants. • Implements standard and advanced bioinformatics methodology and pipelines. • Design computational strategies to answer biological and biomedical questions. • Performs other tasks as assigned by senior faculty, including protocol reviews, • statistical/analytical report generation, manuscript preparation, and review of bioinformatics • literature. • Effectively interacts and presents results to investigators. • Supervises staff data analysts to support clinical and basic researchers in the • Department/Hospital. • Contributes to the publication of peer-reviewed scientific manuscripts. • Contributes to team science and/or independent grant applications. • May assist and train users/staff/trainees on bioinformatics analysis. • Performs other job-related duties as assigned. Minimum Qualifications • A Ph.D. in bioinformatics, computational biology, or related disciplines is required. • Research experience with Omics data is required. • At least 2-3 years' experience as a bioinformatician or computational biologist in a biological • and/or health-related setting. (Postdoc training counts; Successful Ph.D. graduates with strong • publications are encouraged to apply). • Strong programming skills. • Excellent oral and written communication skills. • Working knowledge of an array of advanced bioinformatics techniques. • Experience with grant development and/or successful grant funding Baylor College of Medicine is an Equal Opportunity/Affirmative Action/Equal Access Employer. 17806

The Bhattacharya Lab for Computational Genomics in the Department of Epidemiology current has a funded open postdoctoral position to develop and apply computational methods to study the genetic and molecular etiology of breast cancer and/or pregnancy and childhood outcomes. The prospective Postdoctoral Fellow will have the opportunity to lead one of many ongoing projects as well as sufficient... resources and multiple collaborative avenues to pursue independent research interests. The Bhattacharya Lab has ample computational resources, experimental and wet laboratory resources, access to novel genomic data, and multiple collaborators both within and outside MD Anderson. We are committed to the training of the prospective Postdoctoral Fellow for their future career goals. Applicants with a background in statistics, computer science, computational biology/bioinformatics are especially encouraged to apply. LEARNING OBJECTIVES Gain or advance skills in analysis of novel genetic and transcriptomic data using machine learning and bioinformatic approaches, surrounding the study of germline genetic effects on breast cancer risk/mammographic density or placental function/pregnancy and childhood outcomes. Analysis of genetic, transcriptomic, and methylomic data to detect susceptibility genes for breast cancer risk/mammographic density or placental function/pregnancy and childhood outcomes from patient samples. Gain or advance skills in development of scalable statistical or computational genomics tools to analysis genetic and transcriptomic data. Develop computational software for statistical methods for analysis of genetic and transcriptomic data. Learn to develop independent lines of research. With support of faculty mentor(s) independently develop new lines of research. ELIGIBILITY REQUIREMENTS We are searching for a recent (or soon-to-be) Ph.D. graduate with formal training in one or more of the following: statistical human genetics, bioinformatics, genetic/molecular epidemiology, computational genomics or biology, statistics, or biostatistics. We encourage candidates with programming experience (e.g., R, python, C++, etc). The ideal candidate will have strong input about the nature and course of research projects aligning with the lab goals of applying statistical genomics and molecular epidemiology principles to understanding breast cancer and developmental trait etiology. Applicants with experience working with genetic/sequencing data, multi-omics datasets, and/or clinical data are encouraged to apply. POSITION INFORMATION MD Anderson follows the NIH stipend levels as outlined by the Kirchstein - NRSA. This full-time trainee position will provide a salary between $56,484 to $68,604, dependent upon the years of postgraduate experience. MD Anderson offers compensated trainees: - Paid medical benefits (zero premium) starting on first day for trainees who work 30 or more hours per week - Group Dental, Vision, Life, AD&D and Disability coverage - Paid Education Vacation and Sick Leave - Paid institutional holidays, wellness leave, childcare leave and other paid leave programs - Teachers Retirement System defined-benefit pension plan and two voluntary retirement plans - Employer paid life, AD&D and an illness-related reduced salary pay program - Health Savings Account and Dependent Care Reimbursement flexible spending accounts - Fertility benefits - State of Texas longevity pay - Extensive wellness, fitness, employee health programs and employee resource groups

The Center for Precision Health (CPH) at UTHealth Houston School of Biomedical Informatics (SBMI), seeks an exceptional candidate for an open-rank research faculty, non-tenure track position in the areas of precision medicine and bioinformatics. UTHealth Houston, a leading academic health center, is in the world-renowned Texas Medical Center (TMC), located in cosmopolitan Houston, Texas, the... fourth largest city in the United States. SBMI currently offers Ph.D. and Master's degrees; it also features certificate programs in biomedical and health informatics. RESPONSIBILITIES: The successful candidate is expected to have strategic thinking and scientific rigor to plan, coordinate, and conduct research in bioinformatics, genetic and genomic medicine, and related areas within the CPH. The candidate will provide technical expertise to lead in the development of study design, sample or data collection, pipeline development, data analysis, results interpretation, manuscript writing, and grant proposal preparation. Collaborative research with other faculty in the Center for Precision Health, at SBMI, and across UTHealth Houston and the Texas Medical Center (e.g., MD Anderson Cancer Center and Baylor College of Medicine, etc.) is also strongly encouraged. This position provides opportunities to supervise postdoctoral fellows and lead projects or team research initiatives, as well as develop grant applications. QUALIFICATIONS: The candidate should possess a doctoral degree in one of the following areas: bioinformatics, genomics, genetics, computational biology, biomedical informatics, bioengineering, medicine, biostatistics, computer science, or a related discipline. A record of verifiable and published research and method development in bioinformatics, genetics, or genomics is required; Candidate who has a machine learning and single-cell omics background is desired. The potential to obtain extramural funding is strongly preferred. Excellent teamwork and communication skills are required. HOW TO APPLY: Note that all application materials must be submitted through UTHealth Houston online system. As part of the application process, the candidate should provide a current curriculum vitae, a research statement, contact information for three references, and a cover letter describing qualifications and career goals. APPOINTMENTS/BENEFITS: This position is a full-time, 12-month appointment on the non-tenure track, renewable yearly. SALARY: Competitive and dependent upon qualifications and experience

Summary Our brain tumor research laboratory is currently seeking outstanding young scientists to join our group as Postdoctoral Associate - Bioinformatic focused on computational cancer genomics. Successful candidates will be recent PhD graduates with high levels of energy and curiosity, and who are interested in making fundamental discoveries in understanding the molecular biology of brain... tumors, and in pursuing eventual independent careers in academic research. We have very large multi-omics datasets from hundreds of patient samples that we want you to mine to increase our understanding of recurrent and metastatic cancer. Fellows from our lab publish in very high impact journals (Nature, Cancer Cell, Cell) and routinely go on to run their own labs as independent PI’s. This position will be responsible for evaluation and analyzing data. Come and join us, and be part of a fun, dynamic, and dedicated world-renowned team. Job Duties • Quantifies and models tumor evolution and statistical modeling of outcome following treatment. • Develops new and innovative strategies for the analysis of cutting-edge single cell transcriptomic datasets to investigate gene function during normal mammalian brain development, and how abnormalities in normal brain development lead to the development of brain cancers. • Conducts mining, analysis, and interpretation of data (whole-genome, whole-exome, ChIP-seq and RNAseq) in light of tumor evolution, with the aim of understanding the underlying dynamics of tumor growth, relapse, metastases and progression. • Collects and analyzes data and present at national/international meetings. • Summarizes research findings and prepare manuscripts to publish results in research journals. • Applies for external fellowships. • Mentors junior lab members and supervise research staff. • Maintains laboratory operations. Minimum Qualifications • MD or Ph.D. in Basic Science, Health Science, or a related field. • No experience required. Preferred Qualifications • PhD or MD with previous training in biochemistry or cell biology and possess exceptional computational skills. The most advanced degree must have been conferred within the last 3 years. • Experience with large-scale genomic datasets. • Prior experience with brain development, and/or cancer cell biology would be an asset. • Prior first author publications are highly desirable. • Must be self-motivated, well-organized, highly independent, and willing to train new students. • Excellent communication, written and interpersonal skills are mandatory. • A detailed CV and the names and contact information for at least three references should accompany the application. • Candidates with external funding or scholarships to help support their salary will be highly recruited. Baylor College of Medicine is an Equal Opportunity/Affirmative Action/Equal Access Employer

Postdoctoral positions are available in the department of Bioinformatics and Computational Biology at the University of Texas MD Anderson Cancer Center (MDACC) in Anil Korkut's laboratory. We study resistance to targeted therapies and aim to discover combination therapies to overcome or forestall the resistance in cancer. Our laboratory combines advanced network inference and machine learning... algorithms with drug perturbation and profiling experiments. LEARNING OBJECTIVES The candidate will receive extensive training and hands on research opportunities in the development and application of algorithms for the analysis of multi-omic data for drug target identification against cancers. The trainee will learn about applications of statistical algorithms to identify driver oncogenic processes associated with resistance to therapy. The candidate will also gain expertise in the preparation of original research articles as well as grant applications in cancer genomics and therapeutic fields. ELIGIBILITY REQUIREMENTS Candidates must have a PhD in a relevant field (e.g., bioinformatics, biophysics, genomics, computer science, statistics) and a strong track record. A good understanding of statistics, experience in algorithm development, and programming skills (e.g., R, Matlab, C++, Fortran, Python) are required. Knowledge of cancer biology, signaling pathways, and drug response mechanisms is highly preferred. FACULTY MENTOR Dr. Anil Korkut

UTHealth Houston School of Biomedical Informatics (SBMI) is accepting applications for the position of Chair of a new Department of Bioinformatics and Systems Medicine. The Chair of the Department of Bioinformatics and Systems Medicine at the School of Biomedical Informatics (SBMI) will lead approximately 20 departmental faculty and is expected to bring effective leadership, fiscal, and... management skills to cultivate existing strengths of the School. The Chair will lead the rapidly expanding research enterprise and foster research collaborations within the Department, across the School of Biomedical Informatics, and with other UTHealth Houston departments and schools, as well as specialty institutes and centers of UTHealth Houston, as appropriate. External to the School and University, this position will promote and facilitate training and research activities at the local, national, and global levels. This position will also reinforce the Department’s commitment to education by helping to strengthen and/or expand graduate curricula and programs in Bioinformatics and Systems Medicine. This position is also expected to work closely with the Dean in devising and executing strategies that advance the School’s mission and strategic vision that supports the goals of the faculty within the Department of Bioinformatics and Systems Medicine, the Dean of the School of Biomedical Informatics (SBMI), and UTHealth Houston. Position Requirements: • Ph.D., MD, or equivalent and must have a distinguished record of research, teaching, service, and academic accomplishments that meet the criteria and high standards warranting appointment as a tenured full professor. • Experience in assisting in the development and oversight of education programs that train and mentor the next generation of students, researchers, faculty, and professionals; • Experience in creating a collaborative, positive, and productive work environment for all personnel, including faculty, staff, and students. Qualifications of the Ideal Candidate: • Expertise in any area of Bioinformatics and Systems Medicine, broadly defined, including but not limited to: Precision Health, Genomic Medicine, Cancer Genomics, Omics, Pharmacogenomics, Single Cell Sequencing, Computational Drug Discovery, Imaging Informatics, Imaging Genomics, Systems Biology, Metagenomics for Microbiomes, Biological Pathways, Network Analysis, and Multimodality Modeling; • Outstanding track record of research productivity in one or more of the aforementioned areas, as demonstrated by extramural funding, publications, mentoring, and engagement; • Consistent record of successful leadership and fiscal and program management; • Demonstrated track record of excellence in research, teaching, and service; • Demonstrated success in mentoring and training junior faculty members to help them obtain grants/funding and achieve career growth; • Commitment to the core values of communication, collaboration, innovation, action, and equity The Chair of the Department of Bioinformatics and Systems Medicine at the School of Biomedical Informatics is a full-time faculty position. Experience in the administration of externally supported research centers and training grants is desirable. Resources for intra- and trans-departmental program development, faculty recruitment, and cross-campus collaborations are available. The salary is competitive and commensurate with the applicant’s experience and qualifications. The review of applications will begin immediately and continue until the position is filled. The candidate should submit: 1) a letter of interest that addresses his/her motivation to apply and summarizes qualifications and professional achievements suitable to the Chair position, including an abbreviated vision for the department; 2) a statement that summarizes research, teaching, and service activities; 3) a full CV; and 5) contact information for three references, inclusive of titles and institutions

The research intern will be training and collaborating with Dr. Su's Lab within the Department of Bioinformatics and Computational Biology. The research intern will be exposed to a variety of projects that are conducted in Dr. Su's Lab, ranging from projects on performing alignment for NGS data such as RNA-Seq, DNA-Seq, ChIP-Seq, and ATAC-Seq data; implementation of R scripts to perform... clustering analysis for scRNA-Seq data; or writing scientific manuscripts for publications. LEARNING OBJECTIVES Learn how to use high-performance computing cluster for bioinformatics data analysis. Specifically, write HPC job submission scripts for different bioinformatics data analyses, and perform alignment for NGS data such as RNA-Seq, DNA-Seq, ChIP-Seq, and ATAC-Seq data by using HPC cluster. Implement R scripts to perform clustering analysis for scRNA-Seq data. Improve scientific writing skills. Improve verbal communication skills. ELIGIBILITY REQUIREMENTS Bachelor degree in Computer or related field. ADDITIONAL APPLICATION INFORMATION This is an unpaid research opportunity

Summary The Cheng Lab at Baylor College of Medicine is searching for highly motivated and talented postdoctoral candidates to work on Bioinformatics and Computational Biology in Cancer Genomics and Immunology. The position will be involved in the development and/or application of computational approaches to understand the mechanism of cancer development, progression, metastasis, and prognosis... The candidate should have experience in processing and analyzing data from the next-generation sequencing and single-cell technologies (e.g., scRNA-seq, scATAC-seq, scTR-seq, and/or spatial transcriptomics). Previous experience in both Bioinformatics/Genomics and Cancer Biology is desirable. A candidate is expected to collaborate closely with experimental biologists and clinicians. The position offers an extraordinary team-based science environment with opportunities for significant education, training, and career development. Baylor College of Medicine is located at the Texas Medical Center, which is the largest medical complex in the world and provides an ideal environment for scientific and clinical research. Job Duties • Contributes to the development and/or application of computational approaches to understand the mechanism of cancer development, progression, metastasis, and prognosis. • Collaborates closely with experimental biologists and clinicians. Minimum Qualifications • MD or Ph.D. in Basic Science, Health Science, or a related field. • No experience required. Preferred Qualifications • PhD degree in Computational Biology, Bioinformatics, or a related field (e.g. statistics, computer science, or quantitative biology) • Experience in the application and development of computational methods/tools or machine learning algorithms • Good computer programming skills in R/Matlab/Perl/Python/ • Knowledge of basic molecular biology, genomics, and epigenetics • Experience in next-generation sequencing data and scRNA-seq data. Baylor College of Medicine is an Equal Opportunity/Affirmative Action/Equal Access Employer

SUMMARY The University of Texas MD Anderson Cancer Center in Houston is one of the world's most respected centers focused on cancer patient care, research, education and prevention. It was named the nation's No. 1 hospital for cancer care in U.S. News & World Report's 2022-2023 rankings. It is one of the nation's original three comprehensive cancer centers designated by the National Cancer... Institute. The Genetics Department is a basic science department located in the George and Cynthia Mitchell Basic Sciences Research Building at the world-renowned University of Texas MD Anderson Cancer Center in the heart of the Texas Medical Center. The focus is on advancing knowledge of the molecular genetic mechanisms that regulate normal and abnormal cellular processes. The primary purpose of the Associate Data Scientist position is to provide bioinformatics analysis of next generation sequencing (NGS) data for faculty across the institution, to process NGS data for Advanced Technology Genomics Core facility, to perform quality control (QC) analysis and to maintain QC metrics and sample records of NGS experiments on the servers, and to meet with faculty to review data analysis results. This position impacts cancer research projects by developing/maintaining programs and applications tailored to meet research objectives and makes them available to the wider cancer research community. The ideal candidate will have working experience in: • Analyzing genomic and epigenomic data. • Proficiency in at least one programming language such as R, Python, or PERL. • Experience in NGS data analysis (expression profiling, mutations and structural variations, and differential peak analysis), data integration, and data mining. KEY FUNCTIONS • Performs bioinformatics analysis of bulk RNA-Seq and scRNA-Seq datasets in terms of gene expression profiling analysis. • Performs bioinformatics analysis of DNA-Seq and scDNA-Seq in terms of detection of both mutations and structural variations. • Performs bioinformatics analysis of ChIP-Seq, ATAC-Seq, and scATAC-Seq datasets in terms of genome wide profiling of histone modifications and chromosome accessibility. • Develop software pipelines to perform standard NGS data analysis routine in an automated fashion. • Perform quality control (QC) analysis on NGS data, and maintain QC metrics and sample records of NGS experiments on the servers. • Work with bioinformatics faculty, IT personnel, and other researchers to respond to new technologies. Other Skills • Expertise in programming languages such as Python, PERL, or R. • Expertise in linux/unix based environments. • Excellent communication skills and team-working attitude will be essential. • Other duties as assigned. EDUCATION Required: Bachelor's degree in Biomedical Engineering, Electrical Engineering, Computer Engineering, Physics, Applied Mathematics, Statistics, Computer Science, Computational Biology, or related field. EXPERIENCE Required: Two years of experience in scientific software development/analysis. Preferred: • Analyzing genomic and epigenomic data. • Proficiency in at least one programming language such as R, Python, or PERL. • Experience in NGS data analysis (expression profiling, mutations and structural variations, and differential peak analysis), data integration, and data mining. It is the policy of The University of Texas MD Anderson Cancer Center to provide equal employment opportunity without regard to race, color, religion, age, national origin, sex, gender, sexual orientation, gender identity/expression, disability, protected veteran status, genetic information, or any other basis protected by institutional policy or by federal, state or local laws unless such distinction is required by law. http://www.mdanderson.org/about-us/legal-and-policy/legal-statements/eeo-affirmative-action.html Additional Information • Requisition ID: 163498 • Employment Status: Full-Time • Employee Status: Regular • Work Week: Days • Minimum Salary: US Dollar (USD) 75,000 • Midpoint Salary: US Dollar (USD) 94,000 • Maximum Salary : US Dollar (USD) 113,000 • FLSA: exempt and not eligible for overtime pay • Fund Type: Soft • Work Location: Onsite • Pivotal Position: Yes • Referral Bonus Available?: No • Relocation Assistance Available?: Yes • Science Jobs: Yes #LI-Onsite