junior software engineer Jobs in California

junior software engineer

software developer

DataAnnotation

<div>
 We are looking for a Software Developer to join our team to train AI models. You will measure the progress of these AI chatbots, evaluate their logic, and solve problems to improve the quality of each model.
 
 
 To apply to this role, you will need to be proficient in either Python and/or JavaScript. Your role will require proficiency in at least one programming language (JavaScript, Python, C#, C++, HTML, SQL, or Swift) in order to solve coding problems (think LeetCode, HackerRank, etc). For each coding problem, you must be able to explain how your solution solves the problem.
 
 
 
 Benefits
 
 
 
 <ul>
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 This is a full-time or part-time REMOTE position
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 You&rsquo;ll be able to choose which projects you want to work on
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 You can work on your own schedule
 </li>
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 Projects are paid hourly starting at $40+ USD per hour, with bonuses on high-quality and high-volume work
 
 
 </li>
 </ul>
 
 Responsibilities
 
 
 
 <ul>
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 Give AI chatbots coding challenges and evaluate their outputs
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 Evaluate the quality produced by AI models for correctness and performance
 
 
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 </ul>
 
 Qualifications
 
 
 
 <ul>
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 Fluency in English (native or bilingual level)
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 Detail-oriented
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 Experience with algorithms, data structures, and debugging workflows
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 A current, in progress, or completed Bachelor&rsquo;s degree is preferred but not required
 
 
 </li>
 </ul>
 
 Notes
 
 
 
 Payment is made via PayPal. We will never ask for any money from you. PayPal will handle any currency conversions from USD. Only applicants in the United States will be considered for this role. This is an independent contract position.
 
 
 #coder
</div>

Software Developer

BeaconFire Inc.

<div>
 
 BeaconFire is based in Central NJ, specializing in Software Development, Web Development, and Business Intelligence; looking for candidates with a strong background in Software Engineering or Computer Science for a Java / Software Developer position.
 
 
 
 
 
 
 Job Responsibilities:
 
 
 <ul>
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 Develop applications using Java 8/JEE (and higher), Angular 2+, React.js, SQL, Spring, HTML5, CSS, JavaScript and TypeScript among other tools.
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 Write scalable, secure, maintainable code that powers our clients&rsquo; platforms.
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 Create, deploy and maintain automated system tests.
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 Works with Testers to understand defects opened and resolves them in a timely manner
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 Support continuous improvement by investigating alternatives and technologies and presenting these for architectural review
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 Collaborates effectively with other team members to accomplish shared user story and sprint goals.
 </li>
 </ul>
 
 
 
 
 
 Requirement:
 
 
 <ul>
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 Experience in a programming language Java and JavaScript
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 Decent understanding of the software development life cycle
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 Basic programming skills using object-oriented programming (OOP) languages with in-depth knowledge of common APIs and data structures like Collections, Maps, lists, Sets etc.
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 Knowledge of relational databases (e.g. SQL Server, Oracle) basic SQL query language skills
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 </ul>
 
 
 
 
 
 Preferred Qualifications:
 
 
 <ul>
 <li>
 Master&rsquo;s Degree in Computer Science (CS)
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 0-1 year of practical experience in Java coding
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 Experience using Spring, Maven, and Angular frameworks, HTML, CSS
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 Knowledge with other contemporary Java technologies (e.g. Weblogic, RabbitMQ, Tomcat, etc.) &middot; Knowledge of JSP, J2EE, and JDBC
 </li>
 </ul>
 
 
 
 
 
 Compensation:
 
 $65,000.00 to $80,000.00 /year
 
 
 
 
 
 
 BeaconFire
 
 is an
 
 E-verified
 
 company that provides equal employment opportunities (visa sponsorship provided).
 
</div>

Junior Java Developer

<div>
 
 
 Job Title:
 
 Junior Software Engineer
 
 
 
 Location:
 
 Onsite &ndash; New Jersey
 
 
 
 Employment Type:
 
 Full-time
 
 
 
 
 
 
 About the Role:
 
 
 
 We are seeking a passionate and motivated
 
 Junior Software Engineer
 
 to join our growing team in New Jersey. This role is ideal for recent graduates or early-career professionals who have a strong foundation in programming and a desire to learn and grow in a collaborative environment.
 
 
 
 Responsibilities:
 
 
 <ul>
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 Design, develop, test, and maintain software applications.
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 Collaborate with senior engineers and cross-functional teams to implement new features.
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 Participate in code reviews and contribute to improving code quality.
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 Debug, troubleshoot, and resolve technical issues in existing systems.
 </li>
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 Stay up to date with emerging technologies and best practices in software development.
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 </ul>
 
 
 Requirements:
 
 
 <ul>
 <li>
 
 Master&rsquo;s degree
 
 in Computer Science, Software Engineering, Information Technology, or a related field.
 </li>
 <li>
 
 0&ndash;3 years of software development experience.
 
 </li>
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 Proficiency in at least one programming language (e.g., Java, Python, C++, or JavaScript).
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 Strong understanding of data structures, algorithms, and object-oriented programming.
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 Familiarity with databases, version control systems (e.g., Git), and software development tools.
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 Excellent problem-solving and communication skills.
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 Ability to work onsite in
 
 New Jersey
 
 .
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 </ul>
 
 
 Preferred Qualifications:
 
 
 <ul>
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 Experience with web or mobile application development.
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 Knowledge of cloud platforms (AWS, Azure, or Google Cloud).
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 Internship or project experience in a software development environment.
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 </ul>
 
 
 Why Join Us:
 
 
 <ul>
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 Competitive salary and benefits package.
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 Career growth and mentorship opportunities.
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 Collaborative and learning-focused work environment.
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 </ul>
 
 
 
 
 
 
 Beaconfire is an e-verified company and provides equal employment opportunities (visa sponsorship provided).
 
 
 
 
 
</div>

Junior Software Engineer

Disney Experiences

About the Role and Team: Disney Digital Entertainment, a division of Disney Experiences, is embarking on a mission to create the 'digital front door' for The Walt Disney Company, bringing all of the magic of Disney together into a new interactive universe. Disney Digital Entertainment is looking for a Lead UI (User Interface)/UX (User Experience) Designer to join us on an ambitious and exciting new project. If you are an imaginative creator with superb game development skills, and have a love of Disney/Pixar, Star Wars and Marvel properties, you'll want to check out this opportunity! We are building an experienced development team that will help create groundbreaking game experiences that will herald the next generation of Disney to the world. Working with top-class industry talent, this role is perfect for the seasoned game developer looking to create something epic - collaborating with a robust group of developers focusing on individual experiences to create a wonderfully rich and cohesive product that is truly "Disney".This is a remote role with potential for minimal travel.What you will do:<ul><li>Work with project leads and other developers to design and create UI elements and game experiences that are fun and engaging.</li><li>Lead the development of UI and manage the work for the UI team while working in a cross-disciplinary pod structure.</li><li>Be a hands-on developer in the creation of content for several interactive games and experiences based on Disney's robust portfolio of characters and worlds including Disney/Pixar, Marvel and Star Wars.</li><li>Create wireframes and mockups for user interfaces.</li><li>Create UI content using Unreal Engine, UEFN (Unreal Editor Fortnite), and scripting in Verse in both the development and live service environments.</li><li>Work closely with the art direction to develop and maintain UI style guidelines.</li><li> Collaborate with other developers to design and build user interfaces that enhance the players gameplay experience.</li><li>Design, implement, and iterate on UI and UX systems and features.</li><li>Write, update, and maintain detailed design documentation.</li><li>Provide guidance and mentorship for other UI Designers.</li></ul>Required Qualifications & Skills:<ul><li>8 years of game development experience, including at least one shipped game in a Lead/Manager role.</li><li>Developed content using Unreal Engine and/or UEFN and adept in the use UMG (Unreal Motion Graphics), Blueprints and/or the Verse Scripting language.</li><li>Have been a leader and developer on multiple shipped products and have familiarity with developing products on various gaming platforms - Console/PC and Mobile.</li><li>Excel at partnering and collaborating with key stakeholders, working through challenging problems and reaching consensus to achieve great things.</li><li>Have a special appreciation of Disney's IP, including characters and lore, linear media and movie franchises, theme parks design, and overall aesthetics.</li><li>Enjoy creative problem-solving and building something new and innovative.</li><li>Have experience creating UI mockups and wireframes using Figma or other UI programs.</li><li>Understand best practices to create smooth and engaging user experiences.</li><li> Can communicate and understand what makes a clean, friendly, and engaging UI for games.</li><li>Understand best standards and practices of user interface design within a variety of different game styles.</li><li>Have expertise at working with 3D game engines and understanding the strengths and limitations in regards to user interface design.</li><li>Able to communicate effectively with other teams and groups.</li></ul>Education:<ul><li>A Bachelor's degree in Graphic Design or equivalent combination of education and experience.</li></ul>Additional Information:<ul><li> Please include a portfolio showcasing your work and projects you have worked on. Please share or disable any passwords for efficient review of portfolios. </li></ul>Our Benefits: Disney offers a rewards package to help you live your best life. This includes health and savings benefits, educational opportunities and special extras that only Disney can provide. Learn more about our benefits and perks at The hiring range for this remote position is $126,800 to $170,000 per year, which factors in various geographic regions. The base pay actually offered will take into account internal equity and also may vary depending on the candidate's geographic region, job-related knowledge, skills, and experience among other factors. A bonus and/or long-term incentive units may be provided as part of the compensation package, in addition to the full range of medical, financial, and/or other benefits, dependent on the level and position offered.

Lead UI/UX Designer

Stanford University

Stanford University, the Personalized Integrative Medicine Laboratory in the Radiology Department ( ) and the Urologic Cancer Innovation Laboratory ( ) is seeking a creative, highly motivated, Research and Development Scientist and Engineer 1 with an interest in developing platforms that integrate and deploy multimodal machine learning methods in clinical applications. The project is focused on developing a software platform to deploy our existing ultrasound-MRI models for prostate cancer detection in clinical practices. The position requires managing complex multi-modal data sets including clinical assessments, laboratory results, radiological images and pathological findings, to develop a user-friendly software that will encompass existing approaches and allows for easy integration of new models. The successful candidate will join the Department of Radiology at Stanford University and will work with a multi-disciplinary team of clinicians, statisticians, computer scientists, and trainees. This position is available immediately and has a 1-year duration, with possibility of extension based on funding availability and mutual agreement. Duties include : <ul><li> Design and develop specialized software and tools; coordinate detailed phases of work related to responsibility for part of a major project. </li><li> Develop technical and methodological solutions to complex engineering/scientific problems requiring independent analytical thinking and advanced knowledge. </li><li> Develop creative new or improved equipment, materials, technologies, processes, methods, or software important to the advancement of the field. </li><li> Contribute technical expertise, and perform basic research and development in support of programs/projects; act as advisor/consultant in area of specialty. </li><li> Optional: Contribute to portions of published articles or presentations; prepare and write reports; draft and prepare scientific papers. </li><li> Provide technical directions to other research staff, engineering associates, technicians, and/or students, as needed. </li></ul> - Other duties may also be assigned. DESIRED QUALIFICATIONS: <ul><li> Candidates should have prior experience in software and platform development and C++/python/docker/UIX programming, and be familiar with toolkits, e.g., ITK, opencv, sklearn. </li><li> Candidate should have prior experience with Designing User Interfaces, including image visualization and connect platforms with docker containers. </li><li> Candidates with experience in radiomics, segmentation, image registration are strongly encouraged to apply. </li><li> Candidates should have demonstrated ability to work independently, attention to details, be dedicated and self-motivated. </li><li> Collaborative team spirit, strong communication skills, positive attitude and adherence to highest ethical principles are necessary to be considered. </li><li> The candidate should have knowledge and experience in machine learning and deep learning, visualization, platform implementation. </li><li> The preferred candidate would also have experience with medical image processing, and traditional signal processing techniques. </li></ul> EDUCATION & EXPERIENCE (REQUIRED): Bachelor's degree and three years of relevant experience, or combination of education and relevant experience. Preferred candidates will have an M.S. with relevant experience or Ph.D. in Biomedical Engineering, Electrical Engineering, Biomedical Informatics, Computer Science or related fields. KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED): <ul><li> Thorough knowledge of the principles of engineering and related natural sciences. </li><li> Demonstrated project management experience. </li></ul> PHYSICAL REQUIREMENTS : <ul><li> Frequently grasp lightly/fine manipulation, perform desk-based computer tasks, lift/carry/push/pull objects that weigh up to 10 pounds. </li><li> Occasionally stand/walk, sit, twist/bend/stoop/squat, grasp forcefully. </li><li> Rarely kneel/crawl, climb (ladders, scaffolds, or other), reach/work above shoulders, use a telephone, writing by hand, sort/file paperwork or parts, operate foot and/or hand controls, lift/carry/push/pull objects that weigh > 40 pounds. </li></ul> - Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job. WORKING CONDITIONS: <ul><li> May be exposed to high voltage electricity, radiation or electromagnetic fields, lasers, noise > 80dB TWA, Allergens/Biohazards/Chemicals /Asbestos, confined spaces, working at heights of 10 feet, temperature extremes, heavy metals, unusual work hours or routine overtime and/or inclement weather. </li><li> May require travel. </li></ul> WORK STANDARDS: <ul><li> Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations. </li><li> Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned. </li><li> Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University's Administrative Guide, . </li></ul> The expected pay range for this position is $127,211 to $154,222 per annum. Stanford University provides pay ranges representing its good faith estimate of what the university reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location and external market pay for comparable jobs. At Stanford University, base pay represents only one aspect of the comprehensive rewards package. The Cardinal at Work website ( ) provides detailed information on Stanford's extensive range of benefits and rewards offered to employees. Specifics about the rewards package for this position may be discussed during the hiring process. Consistent with its obligations under the law, the University will provide reasonable accommodations to applicants and employees with disabilities. Applicants requiring a reasonable accommodation for any part of the application or hiring process should contact Stanford University Human Resources by submitting a contact form . Stanford is an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law. The job duties listed are typical examples of work performed by positions in this job classification and are not designed to contain or be interpreted as a comprehensive inventory of all duties, tasks, and responsibilities. Specific duties and responsibilities may vary depending on department or program needs without changing the general nature and scope of the job or level of responsibility. Employees may also perform other duties as assigned.

Research and Development Scientist and Engineer (1 Year Fixed-Term)

FERMÀT

<div>
 FERM&Agrave;T is the AI native commerce platform that optimizes shopping experiences, leading to best-in-class shopper engagement and conversion. We help brands transform clicks into conversions with dynamic, personalized shopping experiences&mdash;built and optimized in minutes.
 
 
 Backed by VMG, Bain Capital Ventures, Greylock, QED, and named The Information&rsquo;s #1 commerce startup, we&rsquo;re a 70+ person team based in SF, Austin, NYC, and Bangalore. As a fast-growing Series B company, we&rsquo;re building the infrastructure for the future of online retail&mdash;and we&rsquo;re just getting started.
 
 
 About the Role:
 
 
 We're looking for
 
 New Grad Software Engineers
 
 to join FERM&Agrave;T and help build the future of AI-native commerce. You will work on challenging problems across our platform&mdash;from building scalable systems that handle millions of shoppers to creating AI-powered features that personalize shopping experiences.
 
 
 This is a
 
 generalist role
 
 where you'll rotate across different parts of our stack and product areas. You'll work alongside experienced engineers who are invested in helping you grow from a new grad into a strong engineer, while taking on real ownership of features that directly impact our customers.
 
 
 What You'll Work On:
 
 
 You'll tackle a diverse range of problems across our platform:
 
 
 
 Full-Stack Development
 
 
 
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 Build features that span from frontend interfaces to backend services
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 Create intuitive user experiences for complex commerce workflows
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 Design and implement APIs that power our platform
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 Work with databases to model and query commerce data at scale
 
 
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 AI &amp; Personalization
 
 
 
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 Build features that leverage LLMs to generate and optimize shopping experiences
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 Implement personalization systems that adapt to shopper behavior
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 Work on experimentation infrastructure to test and measure AI-driven optimizations
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 Help train and fine-tune models for commerce-specific use cases
 
 
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 Infrastructure &amp; Scale
 
 
 
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 Build systems that handle millions of requests reliably
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 Optimize performance for high-traffic commerce scenarios
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 Design data pipelines that process and analyze shopper behavior
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 Work on deployment and monitoring systems
 
 
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 You'll spend your first few months ramping up on our stack and shipping smaller features, with increasing ownership and complexity as you grow. We believe in giving engineers real problems to solve from day one.
 
 
 What We're Looking For:
 
 
 
 Required:
 
 
 
 <ul>
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 Bachelor's or Master's degree in Computer Science, Software Engineering, or related field
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 Strong foundation in data structures, algorithms, and software design
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 Experience building projects with at least one programming language (Go, Python, JavaScript, Java, C++, or similar)
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 Familiarity with web development (frontend or backend)
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 Ability to write clean, well-tested code
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 Strong problem-solving skills and curiosity about how things work
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 Excellent communication and collaboration skills&mdash;you can explain technical concepts clearly
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 Excitement about learning quickly and working across the stack
 
 
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 </ul>
 
 Nice to Have:
 
 
 
 <ul>
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 Internship experience at a tech company or startup
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 Projects involving AI/ML, LLMs, or data systems
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 Experience with TypeScript, React, Go, or Python
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 Contributions to open source or personal projects you're proud of
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 Coursework or projects in distributed systems, databases, or machine learning
 
 
 </li>
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 Our Tech Stack
 
 
 Golang
 
 
 <ul>
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 Python
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 TypeScript
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 React
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 Next.js
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 PostgreSQL
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 Google Cloud
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 Various LLM APIs
 
 
 </li>
 </ul>
 Don't worry if you haven't used all of these. We're looking for engineers who can learn quickly and adapt to new technologies.
 
 
 What a Typical Week Looks Like:
 
 
 You'll spend most of your time coding&mdash;building features, fixing bugs, and learning our systems. You'll participate in daily standups, collaborate with engineers across the team, and pair program with senior engineers who can help you grow. You'll ship code regularly and see your work go live to real customers quickly.
 
 
 Early on, you'll work on well-scoped features with guidance. As you ramp up, you'll take on more complex problems and start making architectural decisions.
 
 
 How You'll Grow:
 
 
 
 Technical Skills
 
 
 
 <ul>
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 Develop full-stack engineering skills across frontend, backend, and infrastructure
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 Gain hands-on experience with AI systems in production
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 Learn to build and scale systems that serve millions of users
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 Master software engineering best practices: testing, code review, system design
 
 
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 </ul>
 
 Mentorship &amp; Support
 
 
 
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 Dedicated onboarding plan to set you up for success
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 Regular 1:1s with your manager and senior engineers
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 Code &amp; tech spec reviews focused on learning and growth
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 Quarterly goal-setting to help you progress in your career
 
 
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 </ul>
 
 Career Development
 
 
 
 <ul>
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 Exposure to different parts of the stack and product
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 Opportunities to specialize in areas that interest you (AI, infrastructure, product engineering)
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 Clear path from new grad to mid-level and senior engineer
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 Culture that values learning and experimentation
 
 
 </li>
 </ul>
 Why Join FERM&Agrave;T as a New Grad
 
 
 <ul>
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 Real impact from day one: Your code will be used by major brands and millions of shoppers
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 Learn from the best: Work with experienced engineers from companies like Stripe, Google, and top startups
 </li>
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 Cutting-edge technology: Work on AI-native products at the intersection of commerce and machine learning
 </li>
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 Fast-paced growth: Series B startup where you'll wear different hats and learn rapidly
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 Strong engineering culture: We value code quality, thoughtful design, and continuous learning
 
 
 </li>
 </ul>
 
 Benefits
 
 
 
 <ul>
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 Competitive salary + equity package
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 Comprehensive health, dental, and vision insurance for you and all your dependents.
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 Retirement benefits:
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 <ul>
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 US: 401(k) plan with 4% matching
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 India: Provident Fund with 12% matching
 </li>
 </ul>
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 4 months of paid parental leave
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 Unlimited PTO policy (with minimum 5 days PTO / quarter!)
 
 
 </li>
 </ul>
</div>

Software Engineer, New Grad

The Department of Medicine, Division of Cardiovascular Medicine at Stanford University is seeking a talented Bioinformatics Engineer II to join the Bioinformatics Core (BIC) of the Molecular Transducers of Physical Activity Consortium (MoTrPAC). As part of this groundbreaking national research consortium, you will help unravel the molecular mechanisms underlying the benefits of physical activity. Under the supervision of co-PIs Dr. Euan Ashley and Dr. Matthew Wheeler, you will play a crucial role in shaping the future of personalized exercise science and public health. Dr. Ashley's research focuses on applying genomics and other omics data to improve clinical care, with an emphasis on cardiovascular disease and personalized medicine. Dr. Wheeler's research centers on integrating large-scale molecular and clinical data to understand the genetic basis of diseases and to develop novel therapeutic strategies. In this role, you will focus on genome, epigenome, and transcriptome (GET) analyses (specifically WGS, ATAC-seq, and RNA-seq) running the pipelines and tools that convert raw sequencing data into clean, analysis-ready results for the consortium. You will architect and operate scalable workflows that adhere to best practices, including WGS variant calling and joint genotyping, RNA-seq quantification and differential expression, and ATAC-seq peak calling and differential accessibility. You will adapt rigorous QC frameworks across modalities; produce integrated multi-omics analyses (e.g., linking genetic variation, chromatin accessibility, and gene expression through eQTL/caQTL/colocalization); and deliver clear visualizations, genome browser tracks, and interactive dashboards that enable collaborative interpretation across teams. Your work will span data engineering and software development: building reproducible pipelines with Nextflow and/or WDL/Cromwell, containerizing and testing them for reliable deployment on cloud and HPC environments; leveraging GCP services such as Cloud Storage and BigQuery; and designing robust schemas for omics metadata and results. You will apply software engineering best practices (version control, code review, automated testing, and documentation) while implementing data governance aligned with FAIR principles and secure handling of controlled-access human genomic data. As a key contributor to our public-facing portal (), you will help push the boundaries of biomedical data analytics to accelerate discovery and translation. You will collaborate closely with wet-lab scientists, clinicians, and data engineers to translate biological questions into robust computational analyses and to communicate findings in reports, presentations, and publications. Working within our multidisciplinary team, you will be at the forefront of understanding how physical activity preserves and improves health, ultimately making a lasting impact on human well-being. This is an 18-month fixed term position. This is a hybrid eligible position. Why Join Us?<ul><li>Work on a highly exciting and innovative multi-omics project with the potential to revolutionize our understanding of physical activity and health.</li><li>Be part of a world-class research team at Stanford University, led by Dr. Euan Ashley, a pioneer in personalized medicine</li><li>Contribute to groundbreaking research with a significant impact on public health and the prevention of diseases.</li><li>Enjoy a collaborative and stimulating work environment at one of the top universities in the world.</li></ul> If you are a passionate and dedicated professional with the required qualifications and a strong interest in advancing scientific research, we encourage you to apply for this exciting opportunity. Join us in unraveling the mysteries of physical activity and making a lasting impact on human health. A complete application will include a cover letter. Duties include:<ul><li>Prioritize and extract data from a variety of sources such as notes, survey results, medical reports, and laboratory data, and maintain its accuracy and completeness.</li><li>Determine additional data collection and reporting requirements.</li><li>Design and customize reports based upon data in the database. Oversee and monitor regulatory compliance for utilization of the data.</li><li>Use system reports and analyses to identify potentially problematic data, make corrections, and eliminate root cause for data problems or justify solutions to be implemented by others.</li><li>Create complex charts and databases, perform statistical analyses, and develop graphs and tables for publication and presentation.</li><li>Serve as a resource for non-routine inquiries such as requests for statistics or surveys.</li><li>Test prototype software and participate in approval and release process for new software.</li><li>Provide documentation based on audit and reporting criteria to investigators and research staff.</li></ul> DESIRED QUALIFICATIONS:<ul><li>Transcriptomics and Gene Expression Analysis: Comprehensive RNA-seq workflows including read alignment (STAR, HISAT2), quantification (Salmon, Kallisto), QC (FastQC, MultiQC, RSeQC, Picard), normalization and differential expression (DESeq2, edgeR, limma), and pathway enrichment. Isoform analysis (StringTie) and fusion detection (STAR-Fusion) are a plus.</li><li>Advanced Genomics Data Analysis Expertise: Extensive experience with WGS data from raw FASTQ through variant calling, joint genotyping, annotation, cohort-level QC, and interpretation. Proficiency with BWA-MEM/BWA, GATK Best Practices (BQSR, HaplotypeCaller, joint calling, VQSR), DeepVariant, bcftools, and scalable VCF/BCF/CRAM handling.</li><li>Structural and Copy Number Variation: Experience with SV/CNV calling and QC (e.g., Manta, Delly, LUMPY, CNVnator), sample-level QC (coverage, duplication, contamination via VerifyBamID/Peddy/Somalier), and cohort metrics (Ti/Tv, call rate, Hardy-Weinberg).</li><li>Epigenomics and Chromatin Accessibility Analysis: Expertise in ATAC-seq processing and analysis, including alignment (BWA/Bowtie2), Tn5 shifting, peak calling (MACS2), replicate concordance (IDR), QC metrics (FRiP, TSS enrichment, nucleosome signal), differential accessibility (DiffBind/DESeq2), footprinting (HINT-ATAC), motif enrichment (HOMER/MEME), and browser tracks (bigWig/bigBed for IGV/UCSC). Regulatory element annotation using ENCODE/Roadmap resources.</li><li>Multi-omics Data Integration: Experience integrating WGS, ATAC-seq, and RNA-seq to identify regulatory relationships (eQTL/aseQTL/caQTL, colocalization), linking chromatin accessibility to gene expression and variant effects.</li><li>Advanced Python and R for Genomics: Deep proficiency in Python and R/Bioconductor with strong statistical and reproducible analysis skills.</li><li>Genomics Workflow Development: Proven experience designing, testing, and deploying complex workflows using Nextflow and/or WDL/Cromwell (or Snakemake) in cloud or HPC environments, with containerization (Docker, Singularity) and CI/CD for reproducibility.</li><li>Specialized Cloud and Database Skills: Hands-on experience with GCP (Cloud Storage, BigQuery), and genomics platforms (Terra, AnVIL). SQL skills and experience designing schemas for omics metadata/results; familiarity with gnomAD, ClinVar, Ensembl/RefSeq, dbSNP, UCSC.</li><li>Genome Browser and Visualization Expertise: Proficiency creating custom track hubs and sessions for IGV/UCSC; ability to produce publication-quality visualizations and interactive dashboards for large-scale genomics data.</li><li>Software Engineering Best Practices: Version control (Git/GitHub), code review, issue tracking, semantic versioning, packaging (setuptools/Poetry), automated testing (pytest), and comprehensive documentation (Sphinx/MkDocs).</li><li>Data Governance and FAIR Principles: Demonstrated experience with data lineage, provenance, audit trails, and adherence to FAIR; secure handling of controlled-access human genomic data (HIPAA/IRB compliance, DUAs), and submissions to dbGaP/GEO/SRA.</li><li>Cross-functional Collaboration and Communication: Proven ability to work with wet-lab scientists, clinicians, and data engineers to translate biological questions into robust, actionable computational analyses.</li></ul> EDUCATION & EXPERIENCE (REQUIRED):<ul><li>Bachelor's degree and three years of relevant experience or combination of education and relevant experience. Experience in a quantitative discipline such as economics, finance, statistics or engineering.</li></ul> KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED):<ul><li>Substantial experience with MS Office and analytical programs.</li><li>Excellent writing and analytical skills.</li><li>Ability to prioritize workload.</li></ul> CERTIFICATIONS & LICENSES:<ul><li>None</li></ul> PHYSICAL REQUIREMENTS :<ul><li>Sitting in place at computer for long periods of time with extensive keyboarding/dexterity.</li><li>Occasionally use a telephone.</li><li>Rarely writing by hand.</li></ul>WORKING CONDITIONS:<ul><li>Some work may be performed in a laboratory or field setting.</li></ul>WORKING STANDARDS:<ul><li>Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations.</li><li>Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned.</li><li>Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University's Administrative Guide, </li></ul> The expected pay range for this position is $108,002 to $128 . click apply for full job details

Bioinformatics Engineer II (18 Month Fixed-Term) (Hybrid Opportunity)

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