This document outlines how we work, collaborate, and grow as a team. It contains expectations, lab policies, and the lab’s principal investigator (PI) approach to mentorship and the PhD process. Please read it carefully before joining the lab and refer back to it regularly.

PhD Process and Career Planning

A PhD is not about checking boxes, completing tasks, or simply publishing papers. It’s about becoming a critical, creative, and independent researcher integrated into a network of collaborators. The real outcome of your PhD is not just the thesis or a list of publications—it’s you: a rigorously trained professional capable of identifying real-world problems, generating original ideas, proposing, testing and validating solutions, and defending your work with clarity and integrity. Equally important, you’ll build a professional network, grow into a leader, an effective communicator, and a collaborative team member—skills essential in any career, whether in academia, industry, policy, or entrepreneurship.

In my experience, this transformation looks different depending on the academic system. In Europe and some other regions, PhD students often pursue highly focused, well-defined research questions. Progress is assessed through clear milestones—number and quality of publications, presentations, and committee approvals—and once these are met, the path to defense is typically straightforward. The focus here is on depth and individual contribution. In the U.S. and similar systems, the PhD journey is more commonly embedded within broader, collaborative lab efforts that align with external funding and priorities, whether from federal agencies, private foundations or industry. Your work extends beyond a single dissertation: you’re contributing tools, software, systems, or foundational knowledge. You are part of a team working toward long-term goals. In this environment, the principal investigator often functions like a startup leader—balancing grant writing, personnel management, strategic planning for the lab, and project delivery. Your progress is interwoven with that of the group, and your contributions both rely on and support the work of others.

There is no universal answer to when to graduate from your PhD. While you must meet formal program requirements, advisor expectations, and project obligations, the decision is ultimately strategic—and should align with your next steps. If you’re targeting academic jobs or postdocs, an earlier defense might help you enter the market at the right time. If you’re exploring other paths, staying enrolled while finalizing applications, securing a postdoctoral position, or completing publications might be beneficial. These decisions aren’t purely academic—they’re also personal. Factors like health, family, finances, or immigration status can play a significant role. Share these with me early. Understanding your trajectory allows me to plan for project continuity, lab resources, and future opportunities. The same applies to internships and the scientific venues you plan to attend: please communicate your interests and timelines in advance so we can coordinate lab responsibilities accordingly.

The PhD process is intellectually rigorous and emotionally complex. Don’t carry the burden alone. If you’re feeling disconnected from your project, struggling with direction, or uncertain about your fit in the lab, speak up and we can reassess, adjust, or even pivot if necessary.

Mentorship and Meetings

Mentorship is tailored to your stage in the program. Junior researchers—undergraduates and master’s students—receive more frequent guidance. For PhD students, the cadence of one-on-one meetings changes over time to make you more and more independent. In Year 1, we’ll meet weekly, covering onboarding, background skills, and any research or career questions you might have. In Year 2, we will meet biweekly. In Year 3, every three weeks. From Year 4 onward, we’ll meet monthly—at that point in your PhD, you probably won’t want to meet more often anyway. These are individual meetings with me and don’t include research team meetings, coursework, or office hours. If you ever need additional time—whether for research, career advice, or anything else—just reach out and we’ll schedule it.

Plan ahead for the support you need. If you’re requesting a recommendation letter from me or another faculty member, give at least one month’s notice. Send your most recent CV, a draft of what you’d like emphasized, and always provide context. Make it easy for your recommender to support you effectively.

Keep a professional CV and up-to-date NIH or NSF biosketches on hand, and make sure to share them with me. Funding and fellowship opportunities can come up on short notice. It’s your responsibility to keep those materials current.

If you’re giving a presentation, share your slides with me at least one week before the event. For major milestones—such as your proposal, PhD defense, or competitive fellowship applications—send your materials at least one month in advance so I can give timely feedback. Plan early and communicate early. It’s important for your career.

Communication

In office hours, I often respond to emails very quickly. But I get tons of emails per day. So, if you email me and don’t hear back right away—or even for up to a week—it’s not a bad sign. You’re probably on the right track and on top of your research, and I’m likely handling teaching, grants, reviews, or other obligations. If it’s time-sensitive, follow up. If it’s urgent, include “URGENT” in your email subject line. For major time-bound issues and deadlines, send a reminder after 24 hours.

If we need to schedule a Zoom or call to discuss research, just send me an email first. Please contact me by phone only for absolute emergencies and not for regular research updates. You can call me anytime, 24/7, for personal emergencies like safety, family, health-related, or immigration issues. For medical emergencies, always call 911 first. Emory’s LGS Student Affairs also has excellent resources you can refer to for counseling or in emergency situations.

Research Environment

Projects in this lab belong to the lab, not individuals. This might sound counterintuitive, but all projects we work on are team efforts funded by grants that we as a team (within and beyond our lab) worked hard to secure. Often, several students, postdocs, faculty, and collaborators have contributed to the preliminary data and hardware/software infrastructure behind a project. As you join, you build on what others started well before you joined, just as others will build on your work later. We all get credit for our contributions in publications and patents, but this is not a solo experience—the lab is a scientific enterprise, just like a startup company. For the same reason, the intellectual property of the projects is owned by the lab and the people who contributed to it. The only exception is when the initiation of a project is by you or if you are funded by a specific fellowship or award that is independent of our existing projects. Please make sure to communicate this or any other intellectual property expectations, questions, or concerns before joining the lab or as we go. Also, check out Emory’s Copyright and Intellectual Property Policies.

Publication of code or data must be coordinated with the PI. All GitHub repositories for active projects will be private by default and may be made public based on funding agency policies or lab strategy. Patent and licensing rights are negotiated based on actual contributions. Authorship will follow standard academic guidelines based on contributions to the research question, design, implementation, analysis, and writing. Departing students and researchers remain on publications when their contributions are essential to the output.

Expectations for Growth

Innovation is a key element of your future career. It is earned at the intersection of hard work, deep knowledge, exposure to challenges and new ideas, and conversations with your peers. As a graduate student or postdoc, you should be reading at least one scientific paper per day, within or beyond your research focus. This builds the depth and awareness you’ll need to publish and go beyond your specific focus. Also, skim through well-established textbooks—at least one per week. Use the library; borrow hard copies. Digital copies never remain in our minds like good old hard copies. When you read textbooks, start by skimming through the table of contents, picking your favorite chapters and sections, and digging deeper when needed. This is, of course, different from textbooks you use for courses with homework and specific course requirements.

Attend regular talks presented by labmates, and internal and external presenters. Listening to an hour-long talk from an expert is a simple and unique opportunity to familiarize yourself with a new field or to extend your network.

Keep detailed notes from meetings—technical, talks, and career-related. Self-notes, especially handwritten ones, help track your development and remind you what needs to get done and the context in which you heard about a topic. Keep your notes organized in your cloud folder. Share the notes related to project updates and your thesis with me, and add a link to them in our one-on-one meeting calendar invites. All recurring meetings should have a single meeting note that is updated everytime we meet. Please take notes during the meeting and do not leave it to the end of the meeting.

Your skills, interests and research focus will evolve. So will the lab’s focus and priorities, which are driven by available funding. In the early years, especially during lab rotations, use this time to explore what you’re good at and what you’re excited about. If you want to shift directions, let me know soon. If possible, I’ll help you do that—but note that shifts may take time due to current project commitments, or may not be feasible.

Whether you’re heading into academia or industry, plan your career early. The conferences/workshops you attend, the skills you develop, and the internships you pursue should align with your goals. In our one-on-one meetings, we’ll discuss your future path and what you need to get there. But it’s on you to initiate those plans and stay on top of them.

Work-Life Balance

During regular work hours, I expect full availability; however, I do not expect mentees to work on weekends or holidays as our general practice. However, I understand that academic and research work can be unpredictable, and it’s not always possible to draw clear boundaries or fully unplug outside office hours. There may be times—such as grant application deadlines or critical project milestones—when work extends beyond office hours. These situations should be occasional and generally planned. It is your responsibility to manage your time effectively and maintain a healthy and realistic work-life balance. Please let me know in advance if you need to take a day (or more) off. If you are on a student visa, please ensure that you comply with Emory’s ISSS guidelines before planning any travel.

Use of AI and Large Language Models (LLMs)

The AI landscape is evolving rapidly, but in my view, the academic and professional world still demands hard skills in theory, research, engineering, critical thinking, problem solving and technical writing. If you graduate without mastering these areas, you’ll be outpaced by your peers.

LLMs (like ChatGPT, GitHub Copilot, and others) are helpful and time-saving for writing, coding, brainstorming, and summarizing. You are welcome to use them where appropriate. However, use them intentionally and with caution, and ensure you comply with all relevant training and research policies. For example, many professors, journals, and funding agencies require disclosure of LLM use. Depending on the context, I might ask you to deliver some tasks without the use of any LLMs. Please stay compliant.

LLMs should not replace your foundational skills—research design, scientific reasoning, problem-solving, coding, writing, critical thinking, or professional communication. These are essential to your future success, and no tool can substitute for them. You are training to become a Doctor of Philosophy—someone capable of independently designing and evaluating research, generating ideas, and executing them. If you outsource these core skills to an AI tool, you’re not learning what you need—and when everyone else has access to the same tools, you risk becoming replaceable in the job market. Note that AI is not a shortcut to expertise. Use it as an accelerator, not substitute. Learn to critically evaluate their outputs and correct the hallucinations or errors they may produce. You are still responsible for the work you deliver.

Technical Onboarding

When you join a project, the PI will share a cloud-hosted folder with you (on Google Drive or OneDrive). Use this folder to store all your reports, presentations, notes, and related documents. We host LaTeX documents, reports, and manuscripts on Overleaf, and codebases are exclusively hosted on GitHub.com under the lab organization.

Keep everything organized in the folders, and do not create duplicate or disorganized copies. For each project, maintain a single slide deck that you update as you go. When providing progress updates, add them to that deck and refer to it in your email. Do not send slide decks as offline email attachments. Always keep the master document online. We may pull them up and present them in meetings live. So keep them up to date and self-contained for presentation.

Send me your GitHub.com ID as soon as you join the lab. I, or the project PI, will create a private repository for you under the lab’s GitHub organization. Push your code to that repository daily or several times a day as needed—even if the code is not complete. If it is on your laptop and not in the repo, it does not exist from my perspective. When deciding whether to keep something local or push it to the cloud/GitHub, ask yourself: “How much time can I afford to lose if my device crashes right now?” If it’s more than a few hours, cloud storage is not optional—it is mandatory lab practice. All results and code updates should be communicated by referring to your GitHub repo. Do not email code or data. No data, especially if patient-related, should be pushed to GitHub. The only exception is small, fully de-identified public samples used strictly for demo purposes. Make sure to seek permission for sharing any such samples before posting them online.

No PHI or sensitive medical data should leave HIPAA-compliant storage, such as Emory’s OneDrive or the Emory BMI cluster. Google Drive is not currently HIPAA-compliant for Emory. No PHI data should be stored there. All cloud work must follow institutional data security requirements. If you are working on any PHI data on a local computer (with the PI’s prior written/electronic approval), make sure that the computer’s disk is encrypted. Check out how you can encrypt your computer depending on the OS.

Do not share any datasets over email. Push them to the appropriate cloud folder and link them in your communication. Whether on the cluster or on the cloud, never overwrite the original data folder. Source and destination (result) folders should always be separated.

All project documents and reports should live on Emory OneDrive, the BMI Google Workspace, or Overleaf. If you’re writing a paper or tech report, use Overleaf and keep it shared with the PI and your collaborators. Documents should stay online until you’re ready to submit them. Offline versions lead to confusion, incompatible copies, loss of updates, and inconsistencies.

When naming documents, avoid generic names like “Document,” “Final version,” or “My Fellowship copy v3,” etc. These are not searchable or meaningful for anyone a week from now. Use filenames that include your full name and the project or submission type. For example, “reza-sameni-ecg-digitization-google-fellowship-2025” or “reza-sameni-phd-proposal-2024”. Do not date files/codes manually in the cloud; contemporary cloud platforms track all changes and commit/change times automatically. Only use dated filenames when downloading files for external submissions or archiving, or when a file/folder is for a specific call, e.g., /R21-Blood-Pressure-NIBIB-June-2023/, which refers to a specific NIH grant submission cycle.

Coding Practices

Push code to GitHub regularly. Avoid hardcoded paths in your code. Do not write file paths like /Users/alex/data. Use relative paths or configuration files when developing portable code. Whenever needed, define file names and paths in a well-documented configuration file. Code must be reproducible by others in the lab and beyond. Your code should not be written in isolation—it should be usable by the next person who joins the project and should be readable in the future by yourself and others. That means clean structure, documentation, modular design, and no reliance on local setups or local libraries.

All data and code repositories must have a README file that includes the project title, contributors, setup and utilization procedures, a license file, contact emails and citations to related publications. No need for over-documentation—just write it for your future self (in a week or months from now). We typically use the BSD 3-Clause License for our codebases, unless specified by the PI.

Systematic programming is part of being a researcher, not just a coder. To excell your programming skills and software engineering practices, refer to Clean Code by Robert C. Martin for principles on readable, maintainable code, and Clean Architecture by the same author for structuring software in a scalable and testable way. These references are not just for software engineers—they’re valuable for scientific computing, big data and biomedical informatics as well.

Code of Conduct

We are committed to maintaining an open, respectful, and inclusive environment for everyone in the Alphanumerics Lab, in alignment with Emory University’s policies on equity and nondiscrimination. This includes adherence to Title IX, which prohibits discrimination based on sex, as well as Emory’s Equal Opportunity and Discriminatory Harassment Policy, which prohibits discrimination and harassment based on race, color, religion, national origin, age, disability, and other protected characteristics.

All lab members are expected to use inclusive language, respect differing perspectives, provide and receive constructive feedback professionally, and act with empathy, integrity, and accountability. Harassment, discrimination, sexual misconduct, retaliation, or other disruptive behavior—whether in person, online, or in lab communications—is not acceptable. Consequences for violations may include informal conversations, formal warnings, removal from lab activities, or further action as appropriate.

Please note that Emory faculty are mandatory Title IX reporters. This means if a faculty member becomes aware of a situation that may involve a Title IX violation (e.g., sexual harassment, assault, or discrimination based on sex), they are legally required to notify Emory’s Title IX office. The intent of this policy is to ensure access to support, resources, and a fair process. Emory’s Title IX office maintains as much privacy as possible for both complainants and respondents—offering support without assumptions and protecting all parties involved.

Alleged violations may be reported confidentially to the lab PI or through official Emory channels, including the Office of Equity and Compliance and Title IX staff.

Our lab values transparency, collaboration, and mutual respect. The research journey includes both rewarding and challenging moments. We are committed to supporting one another and upholding the highest standards of scientific and professional conduct.

Welcome to the team! Feel free to reach out if you have any questions.

—Reza Sameni