Final Project Presentations - Dates, Zoom Links, and Sign-Up
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Dear students, Final project presentations will take place on: - Wednesday, April 15: 10:00–15:00 - Thursday, April 16: 10:00–12:30 Presentations will be held over Zoom: - Wednesday: https://technion.zoom.us/j/93049708489 - Thursday: https://technion.zoom.us/j/99975059278 Please make sure your webcam and microphone are working ahead of time. A few important notes: 1. All students are required to attend their full session and serve as the audience for their classmates. 2. The project submission deadline cannot be extended any further. Each team (pair) should book a single 20-minute slot here: https://docs.google.com/spreadsheets/d/13msQpq2_7C10sN2VoaykR8UBsLik6gLX5zVOuv0QOzE/edit?usp=sharing Best, Almog |
| פורסם ב-7/4/2026, 14:36:45 Created on 7/4/2026, 14:36:45 Создано7/4/2026, 14:36:45 تم النشر ب-7/4/2026, 14:36:45 |
Final Project - Updated Deadlines
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Dear students, Due to the current security situation, we have decided to postpone the final project deadlines: - Final project submission: April 11th, 2026 - Presentations: Week of April 12th (exact schedule will be announced) If you need to present earlier in order to complete your degree on time, please send me an email and we will schedule an earlier presentation for you via Zoom. Please use the extra time wisely to strengthen your analysis and presentation. If you have any questions or concerns, feel free to reach out. Stay safe, Almog |
| עדכון אחרון ב-11/3/2026, 10:25:32 Last updated on 11/3/2026, 10:25:32 Последняя модификация11/3/2026, 10:25:32 تمت الحتلنة الأخيرة ب-11/3/2026, 10:25:32 |
Invitation to My PhD Graduation Seminar - Tomorrow
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Dear students, I hope you're doing well on the final project. I'm excited to share that my PhD graduation seminar is happening tomorrow, and I would love for you to attend! Monday, March 9, 13:00 Zoom: https://technion.zoom.us/j/91997034360 (Meeting ID: 919 9703 4360) Title: Computational Characterization of the Tumor Microenvironment for Optimizing Immunotherapy Response Abstract: Immunotherapy has transformed cancer treatment, yet most patients do not achieve a durable benefit. A prevailing hypothesis is that differences in the tumor microenvironment (TME) influence therapeutic response, highlighting the need for accurate tools to characterize tumor cellular composition. In the first part of my PhD, I developed xCell 2.0, an improved computational method for inferring cell type enrichment from bulk transcriptomic data. The framework introduces a flexible training pipeline and automated handling of cell type dependencies, enabling robust performance across diverse reference datasets. In extensive benchmarking across human and mouse datasets, xCell 2.0 outperformed existing deconvolution methods and improved prediction of immunotherapy response in pan-cancer analyses. In the second part, I investigated how chemotherapy may reshape the TME to influence response to subsequent immunotherapy. I derived a transcriptomic signature that identifies tumors likely to undergo favorable immune remodeling following chemotherapy. Notably, this benefit is specific to patients receiving combined chemo-immunotherapy and not immunotherapy alone, consistent with a model of chemotherapy-mediated immune priming. Together, this work provides both a methodological advance for TME characterization and a mechanism-informed framework for identifying patients who may benefit from combined or sequential chemo-immunotherapy strategies. Best, Almog |
| פורסם ב-8/3/2026, 17:07:51 Created on 8/3/2026, 17:07:51 Создано8/3/2026, 17:07:51 تم النشر ب-8/3/2026, 17:07:51 |
Reminder: Workflow Submission Due February 14th
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Dear students, A quick reminder that the workflow for the final project is due this Saturday, February 14th. If you haven't submitted yet, please send it as soon as possible so you have more time for the main project. As a reminder, send your workflow as a PDF file (ID1_ID2.pdf) to ualmog.angelatcampus.technion.ac.il with the subject line "Workflow submission ID1 ID2". I will return comments on your workflow within 2 days of receiving it. If you have any questions, feel free to reach out. Best, Almog |
| פורסם ב-12/2/2026, 14:43:29 Created on 12/2/2026, 14:43:29 Создано12/2/2026, 14:43:29 تم النشر ب-12/2/2026, 14:43:29 |
HW1 - Grades and Feedback
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Dear students, Grades for HW1 are now available. Please check the assignment page for relevant feedback. If you cannot see your grade or feedback, or if you notice a summation error, please contact Alon. Best, Almog and Alon |
| עדכון אחרון ב-4/1/2026, 14:09:28 Last updated on 4/1/2026, 14:09:28 Последняя модификация4/1/2026, 14:09:28 تمت الحتلنة الأخيرة ب-4/1/2026, 14:09:28 |
HW2
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Dear students, The second homework assignment is now available! This assignment covers Differential Gene Expression Analysis. **Submission deadline: Wednesday, December 24st, 2025** Note that the HW assignments are to be **submitted in pairs**. We overlooked this requirement for the first assignment, but we will begin enforcing it from this assignment forward. If you have any trouble finding a partner, don’t hesitate to reach out to us. As usual, the R Markdown file is your primary working document. Please read through it carefully, and make sure you understand it fully. If any question arises, we will be as available as possible via the piazza forum. Good luck! Almog and Alon |
| פורסם ב-10/12/2025, 20:54:23 Created on 10/12/2025, 20:54:23 Создано10/12/2025, 20:54:23 تم النشر ب-10/12/2025, 20:54:23 |
בקורס זה הייתה בעיה ייחודית בהגשת קבצי תרגיל בית 1
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הבעייה נפתרה - נבעה מהמבנה הייחודי של הקבצים שמוגשים בתרגיל כל מי שנכשל בהגשה מוזמן לנסות שוב אם הבעייה חוזרת - אנא דווחו!!! לידיעתכם GR Admin |
| עדכון אחרון ב-28/11/2025, 04:45:50 Last updated on 28/11/2025, 04:45:50 Последняя модификация28/11/2025, 04:45:50 تمت الحتلنة الأخيرة ب-28/11/2025, 04:45:50 |
HW1
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Dear students, The first homework assignment is now available! This assignment covers the material we've explored in class and tutorials so far: - Data exploration and statistical analysis - Multiple sequence alignment **Submission deadline: Wednesday, December 3rd, 2025** The R Markdown file is your primary working document. We've designed it to be fully self-explanatory, so please read through it carefully - especially the instructions section at the beginning. If you have questions, don't hesitate to reach out. Good luck! Almog and Alon |
| פורסם ב-19/11/2025, 17:20:21 Created on 19/11/2025, 17:20:21 Создано19/11/2025, 17:20:21 تم النشر ب-19/11/2025, 17:20:21 |
Monday's tutorial
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Dear students, Just a quick update about Monday's tutorial schedule: The tutorial will start shortly after Dr. Aran finishes his lecture (instead of the usual 16:30 start time). We'll have a brief 5-10 minute break and start right after, so we can all finish earlier as requested by many of you. Best, Almog |
| פורסם ב-12/11/2025, 14:27:39 Created on 12/11/2025, 14:27:39 Создано12/11/2025, 14:27:39 تم النشر ب-12/11/2025, 14:27:39 |
Welcome to Introduction to Bioinformatics – Getting Started
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Dear students, I’m excited to welcome you to Introduction to Bioinformatics and to serve as your TA this semester. In our tutorials, we’ll dive into the practical side of bioinformatics, complementing the theoretical concepts covered by Dr. Aran in the lectures. Together, we’ll work with real biological data, learning how to extract meaningful insights that drive discoveries in biology and medicine. The tools and skills you’ll gain will be essential for completing the homework assignments throughout the semester and for your final project. First Tutorial: Please note that our first tutorial will take place on Monday, November 3rd. There will not be a tutorial this Wednesday (October 29th). Preparing for Our First Session: Our main tool will be R, a widely used programming language among statisticians, data scientists, and bioinformaticians. To get ready: 1. Install R and RStudio Follow the step-by-step guide here: https://rstudio-education.github.io/hopr/starting.html 2. Familiarize Yourself with R Although we’ll cover the basics in our first session, I recommend watching a short introductory R tutorial on YouTube to get comfortable with the environment. 3. Learn About R Packages Packages extend R’s functionality. Read more here: https://rstudio-education.github.io/hopr/packages2.html We’ll start with the tidyverse package collection. You can install it in RStudio using: install.packages("tidyverse") Tutorial Materials: Before each tutorial, I will upload an R Markdown file with the code we’ll use to the course website (one day in advance). Please download the file and install any required packages beforehand. If you have any questions or need help setting up, feel free to contact me at ualmog.angelatcampus.technion.ac.il. Looking forward to an exciting semester together! Best, Almog |
| פורסם ב-26/10/2025, 09:22:38 Created on 26/10/2025, 09:22:38 Создано26/10/2025, 09:22:38 تم النشر ب-26/10/2025, 09:22:38 |