Lab notes on Spakowicz Lab

Are you a graduate student interested in joining the lab?

Sat, 12 Sep 2026 00:00:00 -0400

Are you a graduate student interested in joining the lab?

We welcome graduate students who want to contribute to our work at the intersection of cancer, the microbiome, and human health. The path into the lab is different from undergraduate joining in several important ways: you will typically evaluate the lab through a rotation, I prefer to co-mentor with another PI, and the remaining requirements are set by your program.

Are you a postdoc interested in joining the lab?

Sat, 12 Sep 2026 00:00:00 -0400

Are you a postdoc interested in joining the lab?

We welcome postdoctoral researchers who want to contribute to our work at the intersection of cancer, the microbiome, and human health. The process is different from undergraduate or graduate joining on purpose. It involves a few online discussions and then a formal interview day, because the goal of a postdoc is the next job. We treat that professional development seriously.

Where Lab Files Live: A Guide to Data Storage

Wed, 09 Sep 2026 00:00:00 +0900

Our lab uses Teams, the Ohio Supercomputer Center (OSC), GitHub, and the T drive to organize our work. Each location serves a different purpose. Keeping files in the right place makes it easier to find what we need, reproduce analyses, and work together as a project moves toward a manuscript. This page expands the “locations of data” item on the onboarding checklist.

Are you an undergraduate interested in joining the lab?

Thu, 20 Aug 2026 23:42:44 -0400

Are you an undergraduate interested in joining the lab?

We welcome undergraduate students who are interested in gaining research experience and contributing to our work at the intersection of cancer, the microbiome, and human health. We use a deliberate onboarding process to ensure that students understand our research, meet the people they will be working with, and feel that the lab is a good environment for them to learn and grow.

Inside the Lab: How We Use Slack to Drive Collaboration, Code, and Consistency

Fri, 27 Mar 2026 09:26:52 -0400

Inside the Lab: How We Use Slack to Drive Collaboration, Code, and Consistency

Slack is the primary communication tool for the lab. It fills the gap between updates and announcements at gpmtg and data deep dives (project-based meetings). It provides a site where wetlab-based and drylab-based members of the lab can synchronize and stay apprised of progress. This post intends to clarify how the lab has adapted its use to serve our mission.

Scheduling meetings

Mon, 16 Feb 2026 16:29:04 -0500

Scheduling meetings

I want you to be able to get time with me without waiting on an email reply. How you schedule depends on whether I have already shared my Outlook calendar with your OSUMC account (i.e., whether you’re officially “in the lab”). Once you have access, this video tutorial walks through the process. The user manual for Dan explains why I share the calendar this way, including that Focus Time is for people in the lab.

gpmtg

Sat, 13 Dec 2025 22:48:36 -0500

gpmtg

Goals and Purpose

Meeting Type: Weekly “All Attend” Stand-up Duration: ~2.5 hrs Focus: Operational alignment, triage, and high-level progress tracking.

Primary Objectives

The “gpmtg” serves as the central synchronization point for the Spakowicz Lab. It is designed to move quickly through administrative and high-level updates to ensure the lab operates as a cohesive unit. Attendance matters; the user manual for Dan has what I expect if you cannot be there. The specific goals are:

User manual for Dan

Sat, 13 Dec 2025 11:03:44 -0500

User manual for Dan

Intro

This page details processes specific to working with me. The page is intended to be helpful and to accelerate our collaboration. If there are things here that seem unclear or overbearing, please raise them so we can discuss and adapt them.

Establishing microbiome collection support with the Biospecimen Shared Resource

Tue, 28 Jan 2025 13:44:12 -0500

Establishing microbiome collection support with the Biospecimen Shared Resource

This is one of the clinical trial logistics notes. Kit mailing is covered separately in Business Reply Mail shipping of gut microbiome samples.

Business Reply Mail shipping of gut microbiome samples

Wed, 29 May 2024 22:05:21 -0400

Business Reply Mail shipping of gut microbiome samples

Our preferred method of shipping microbiome kits from patients’ homes to processing sites uses business reply mail labels. The cost per kit is about $4, and patients can put the collection box directly in their USPS mailbox without arranging a pickup or bringing the sample to a drop-off location. However, BRM-shipping is slow and is NOT TRACKED. These details make it unacceptable for some organizations, such as cooperative groups. Please contact Dan about details for such trails.

Onboarding

Sun, 07 May 2023 22:44:57 -0400

Welcome to the lab! We’ll work through these steps together during 1:1 meetings. Complete what you can independently and bring questions to your next meeting. Confirm with Dan which tasks apply to your role.

Spakowicz Lab Research Training

Thu, 06 Apr 2023 18:44:17 -0400

Spakowicz Lab Research Training

Welcome! Researching with the Spakowicz lab requires the following training. Please complete the sections relevant to your project using the instructions below. If you have questions about which training is required for your project, please get in touch with Dan. If you have questions about the training logistics, including links on this page, please get in touch with Lane Nevers at lane.nevers@osumc.edu. This page is part of Onboarding; confirm with Dan which sections apply to your work.

Protocol language for microbiome collection

Thu, 26 Jan 2023 17:04:57 -0500

Protocol language for microbiome collection

Last updated 2023-04-04 by DS

Below is the text we’ve used in protocols for microbiome collection and sequencing. Related notes on kits, shipping, and processing are collected on Clinical Trials.

The lab was featured on the PBS show QED with Dr. B!

Fri, 16 Dec 2022 15:20:27 -0500

The lab was featured on the PBS show QED with Dr. B!

https://youtu.be/fI_vaPORMNw?list=PLXo2mTq4AYbIYtmbGsZ1_nCWqSHik8MrE

Check out Dan and Nye on the Emmy Award-winning science show, which aired on December 14, 2022.

Introduction to Microbiome Science: OSU College of Medicine Resources

Tue, 15 Nov 2022 15:14:56 -0500

Introduction to Microbiome Science: OSU College of Medicine Resources

Full video presentation (approx. 32 minutes)

The purpose of the Center of Microbiome Science is to galvanize and organize the community around the broad types of microbiome science going on around OSU across the different colleges and faculty members and to find some way that we can all work together. It turns out that many of the logistics for actually getting started are specific to your college, and that includes the details of how to collect samples. There’s a lot of overlap with how to generate data from those samples, as well as how to analyze them, but the initial part—the process for collecting samples—is unique to the College of Medicine. Given the number of requests for information that we’ve received, I put together some basic information to get you started.

Dan featured in the Center for Microbiome Science spotlight

Wed, 20 Jan 2021 10:28:27 -0500

Dan featured in the Center for Microbiome Science spotlight

Scientist Spotlight:
Dan Spakowicz, PhD

OSU researcher directory

Position: Assistant Professor
Department: Internal Medicine, Division of Medical Oncology
Website: Spakowicz Lab
Email: daniel.spakowicz@osumc.edu
Research Keywords: microbiome, cancer, immunotherapy, bioinformatics