Jobs in the United States

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Vice President, Senior Director / Director, R&D
The Fynder Group
Chicago, IL
…connections between genotypes and key phenotypes of Fusarium to engineer improved strains with enhanced yield, stability, and functional…
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AA
Principal Software Engineer
Alaska Airlines
WA-SeaTac
- $141,250 to $211,900 USD / year
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Lead Firmware & FPGA Engineer - Aircraft Surveillance Products
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North Phoenix, AZ
JOB TITLE: Lead Firmware & FPGA Engineer - Aircraft Surveillance Products
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Software Engineer, AWS Applied AI Solutions
Amazon Development Center U.S., Inc.
Seattle, WA
…opens up for design reviews, CR feedback, or unblocking an engineer. Some days you're deep in code; others you're on a call with a customer team working through how their system integrates…
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Software Engineer, AWS Applied AI Solutions
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Sr. Systems Development Engineer , Amazon Robotics Business Applications and Solutions Engineering
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Austin, TX · North Reading, MA
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Added 1 min ago
Test Automation Consultant - Healthcare
Infosys
United States
⦁ Ability to work from the office four days per week
Added 3 mins ago
Senior Staff Software Engineer, R&D - IntelliScript (Remote)
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Java Developer
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Workstyle: Hybrid schedule - employees work onsite a minimum of four days per week, with one remote day
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Senior Software Systems, Battery Algorithms Engineer
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Irvine, CA
- $135,100 to $179,040 USD / year
As a Senior Battery Algorithms Engineer at RV Tech (RVT), you will contribute to electric vehicle (EV) technology that serves both Rivian and Volkswagen Group programs. You will develop and…
Added 6 mins ago
VH
Senior Data Engineer
Vatica Health
Remote, United States
- $115,000 to $125,000 USD / year
As a Senior Data Engineer, you will design, build, and operate the data pipelines and APIs that support our data-driven and AI-enabled products. You will own how data moves from ingestion…
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Vice President, AI / Machine Learning Software Engineer
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New York, NY · NY
Added 6 mins ago
SW
Analyst I
State Water Resources Control Board
CA
- $3,861 to $6,276 USD / month
If the position requires driving, you must possess a current and valid driver’s license · In accordance with the Statewide Telework Policy and GC 14200, the successful candidate must reside in California upon appointment
Added 7 mins ago
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Senior Technical Bridge/QA Engineer
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Watertown, MA · Boston, MA
- $175,000 to $230,000 USD / year
PE license required
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Inpatient Medical Coder– DRG Specialist - Remote
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…strategies and agile execution, we don't just enable change - we engineer digital…
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Multi-Specialty Profee and/or Facility Medical Coder
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Remote, United States
To qualify you must possess: · CPC, CCS, or CCS-P certification required
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Manufacturing Engineer
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Senior Systems Engineer - Hyperscaler, AI, and Cloud Titans
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When you join Arista as a Senior Systems Engineer within our Hyperscaler team, you will become part of a highly technical organization supporting some of the world's largest and most…
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Principal HVAC Engineer
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Systems Engineer
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Professional Engineer (PE) license, Professional Geologist (PG) license, Certified Hazardous Materials Manager (CHMM) certification, Registered Environmental Manager (REM), and Project…
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A-Alpha Bio

Scientist II, Applied Machine Learning

Seattle, WA, United States

$139,000 to $175,000 USD / year

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Job details

Pay: $139,000 to $175,000 USD / year
Work location: Candidates must reside in the United States
Posting language: English
Posted: Nov 10, 2026

Original job description

A-Alpha Bio is an early-stage, rapidly growing biotechnology platform company headquartered in Seattle, WA. We are focused on building the foundational data layer for AI-driven protein engineering. We provide biopharma companies and model builders with access to ground truth experimental datasets, including affinity and structure, for training, benchmarking and validating AI protein models. In parallel, we apply our data and models directly with select partners to engineer next-generation dual-specific and molecular glue therapeutics, and to discover and optimize differentiated biologics.

A-Alpha Bio is headquartered in Seattle, WA, but remote applicants are welcome to apply. Candidates must reside in the United States.

Starting Salary Range: $139,000 - $175,000 annually

Exemption Status: Exempt

Location Expectations: Remote-Eligible (expected travel to Seattle HQ once per quarter)

Reporting To: Director, Applied Machine Learning

Role Description

A-Alpha Bio is seeking a Scientist II to join our Applied Machine Learning team in turning large-scale protein interaction data into insights and models that advance antibody and protein engineering. In this role, you’ll lead computational work for both internal research and external collaborations, from defining scientific questions and analysis plans to developing models and communicating results. Working with AlphaSeq datasets, you’ll connect experimental measurements with protein sequence and structural information to understand binding, evaluate computational design methods, and guide future experiments. Success in this role will depend on ability to state assumptions, clearly define goals and objectives, and explain your procedures thoughtfully.

Key Responsibilities

Lead scientific analyses:Define and execute analysis plans for large-scale protein interaction datasets (often 1M PPIs), including evaluating binding affinity, specificity, and the performance of antibody and protein design methods.
Develop and evaluate ML models: Build, train, and apply models using experimental measurements, protein sequences, and structural information. Design rigorous benchmarks and assess model performance, uncertainty, and generalization.
Connect computation with experiments: Collaborate with experimental scientists to shape study designs, interpret results, investigate unexpected findings, and recommend follow-up experiments.
Deliver results to external partners: Serve as the computational lead for assigned projects, producing clear presentations, reports, and well-documented datasets for both internal teams and external collaborators. Many projects may have open-source elements, requiring a strong eye for detail and narrative.
Build reusable methods: Translate project-specific work into reliable analytical tools and workflows. Contribute maintainable Python code, review contributions, and document methods so others can use them.
Advance our scientific capabilities: Identify and develop new computational approaches that increase the value of AlphaSeq data for protein engineering.

Qualifications & Experience

Required

PhD in a relevant field with 2+ years of experience working on large-scale data analysis using biological sequence or structure data; or a bachelor’s degree with 10+ years of relevant experience, including 5+ years working onlarge-scale data analysis using biological sequence or structure data; or an equivalent education and experience.
Demonstrated expertise in Python for scientific computing, data analysis, visualization, and ML model development.
Experience analyzing large experimental datasets and making scientifically defensible decisions about data quality, statistical methods, and interpretation.
Strong understanding of model evaluation, including appropriate baselines, data leakage, and the limits of conclusions drawn from a benchmark.
Ability to translate an open-ended scientific question into an executable plan and deliver reproducible results with limited supervision.
Clear communication skills, including the ability to explain methods, findings, and limitations to computational and experimental audiences.
Experience contributing to a shared codebase through version control, code review, and documentation.

Preferred

Experience with antibody or protein engineering, particularly the relationship between sequence, structure, and binding.
Familiarity with the structural modeling of protein complexes and evaluation of structure prediction or generative design methods.
Use of modern ML frameworks such as PyTorch, TensorFlow, or Hugging Face.
Experience processing and analyzing next-generation sequencing data, (Illumina, Oxford Nanopore, etc.).
Experience developing analytical tools or workflows used by other scientists.

In 2018, A-Alpha Bio spun out of the University of Washington’s Institute for Protein Design and Center for Synthetic Biology – both communities filled with brilliant and highly entrepreneurial scientists. Since the company’s inception, we have built and scaled AlphaSeq, our high-throughput platform for quantitatively measuring protein-protein interactions at unprecedented scale. What began as a technology for generating large, standardized affinity datasets has grown into a broader data engine for AI-driven protein engineering. New members of the team should expect a fast-paced, highly dynamic, and interdisciplinary work environment. We are building a diverse, meritocratic, and supportive team that shares our values of speaking the truth, shooting for the moon, taking the reins, playing for the team, and improving the world.

A-Alpha Bio is headquartered in a custom designed lab and office space in downtown Seattle’s Belltown neighborhood. We are fortunate to be situated in a region that is renowned for its premier outdoor activities, including hiking, biking, climbing, skiing, kayaking, sailing, and more. At A-Alpha, you’ll find many who love the outdoors, but also gamers, amateur chefs, explorers, sports fans, bakers, crafters, photographers, brewers, jetsetters, animal lovers, and artists. Whatever your passions, you belong at A-Alpha Bio!

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Jobs in the United States