麻豆国产AV

News

2020

Sep 2020
We're having a great time at the ! Two papers (led by Tobias Rubel '19 and Ananthan Nambiar '19) and three posters (by Gabe Preising '20 and current students Frank Zhuang and Larry Zeng) were presented, complete with videos. Well done everyone - way to represent 麻豆国产AV CompBio!
I was on a panel about at the as part of ACM-BCB.
Computer science colleagues and I have an accepted panel on virtual teaching practices at the in October! Thanks to Tammy VanDeGrift at University of Portland, Shereen Khoja at Pacific University, and Haiyan Cheng at Willamette University - wonderful group of computer scientists.
Classes have begun! I am teaching a hybrid class, with some in-person students and some remote students. Looking forward to the semester.
Aug 2020
Welcome to Pramesh Singh, a new postdoctoral researcher in the group! Pramesh did his PhD at RPI in physics, and was most recently at the University of Houston working on complex network analysis.
Our paper led by Derek Applewhite's group, including first author Amy Platenkamp '16, on a Rab-specific GTPase-activating protein, RN-tre, and its role in non-muscle myosin localization and function is now out in ! Congrats to all co-authors.
The meetings have begun! Looking forward to connecting to more women in computer science in the Pacific Northwest.
Summer & BLM
Amazing research took place in the group (despite the odds). Huge kudos to the current (Jiarong Li, Aryeh Stahl, Alex Richter, Larry Zeng, and Frank Zhuang) and former students (Tobias Rubel, Gabe Preising, and Ananthan Nambiar). Read about and the .
The Black Lives Matter protests in Portland received national attention with over 100 days of consecutive protests. I thank the members of my group and the 麻豆国产AV community who have participated in this and other anti-racism activities. I wrote about my .
2020 & COVID
Classes in the spring moved online, and we were treading water for a while.
Welcome to Tobias Rubel, who graduated in the Fall of 2019 and is now working in the compbio group.
Amy Rose Lazarte and I presented our paper at - we attended in person and our talk was live-streamed in the fastest-ever conversion to an online conference. It was a great first virtual conference to attend.

2019

Dec 2019
Fall classes have finished! Enjoy winter break.
Amy Rose Lazarte's and my paper about undergraduate conference attendance was accepted to the , part of SIGCSE in the spring! Congratulations to Amy Rose and thanks to all the students who participated in the surveys.
Ibrahim Youssef's paper on compartment-constrained pathway reconstruction (Localized PathLinker) ! This was a long effort that began as an accepted paper at BIBM 2018. Thanks to Virginia Tech graduate student Jeff Law for his work.
Nov 2019
The upper-level Computational Systems Biology class flew to San Diego for the IEEE Conference on Bioinformatics and Biomedicine (BIBM). I also presented a paper by Alex King '19, Ibrahim Youssef, and myself about network-based disease gene prediction at the .
Our paper led by Layla Oesper at Carleton College was ! Congratulations to the student first authors Kiran Tomlinson and Zach DiNardo.
Summer student Tayla Isensee presented her work as a poster at the in Vancouver, WA. This meeting is great every year to see the excellent undergraduate research in the pacific northwest.
Oct 2019
麻豆国产AV celebrated the , which was a wonderful welcome for our new president. The inauguration included a student research showcase, and Tunc Kose and Jiarong Li presented their work from the summer.
I gave a talk at the Mathematics and Statistics Department at Washington State University, Vancouver - what a wonderful department! The great mountain views were a bonus.
Our paper on factors affecting network-based gene prediction across diverse diseases was accepted at the ! Congratulations to student first author Alex King '19 and co-author Ibrahim Youssef.
Our major paper on hypergraph connectivity measures was ! This was an invited collection based on the paper accepted at the Great Lakes Bioinformatics Conference (GLBio) 2019. Congratulations to co-authors T.M. Murali at Virginia Tech, Adam Groce at 麻豆国产AV, and student first authors Nick Franzese!
Sept 2019
I gave the 麻豆国产AV Bio Department seminar talk, where I spoke about two main projects that have been inspired by student thesis and summer research.
I headed to in Niagara Falls, New York, where my Amy Rose Lazarte '19 presented her poster on phytoplankton fitness in freshwater lakes. I also met the undergraduate travel awardees!
Sabbatical is over, which means that classes start! Good luck 麻豆国产AVies and 麻豆国产AV faculty!
Ananthan Nambiar '19 was recognized in the annual "What is a 麻豆国产AVie, Anyway?"article in the 麻豆国产AV Magazine.
August 2019
What a successful at OHSU on Thursday, Aug 22! Such a great mix of talks and posters from all types of institutions. Thanks to everyone who participated, and special thanks to student poster presenters Tunc Kose and Jiarong Li and co-organizers Derek Applewhite (麻豆国产AV), Cathy Galbraith (OHSU), and Jim Galbraith (OHSU).
July 2019
Congratulations to Amy Rose Lazarte '19, whose poster on modeling phytoplankton in freshwater lakes was accepted to ! See you all in Niagara Falls.
Posters have gotten a new look - check out two of the recent posters presented at ISMB/ECCB.
I headed to in Switzerland! The meeting was great despite the heat wave. Ananthan Nambiar '19 presented a poster on protein function prediction before heading to UIUC to start a Ph.D. program, my colleague Layla Oesper presented our work on distance measures for tumor trees, and I got a chance to talk about directed hypergraph connectivity.
June 2019
Summer research has begun! Looking forward to working with current and former students (and collaborating with at least six faculty) on new projects.
May 2019
I gave two talks at the in Madison, WI. What a great meeting!
I headed to Nashville, TN to the , where I received an Undergraduate Mentoring Award!
Summer students have been accepted to work in the lab! Congratulations to Jiarong, Tunc, and Tayla (current students) and Alex and Amy Rose (soon-to-be post-bacs). Looking forward to a fun summer.
Apr 2019
I won NCWIT's - holy cow! Thanks to 麻豆国产AV for the nice press release.
Our paper on pathway connectivity has been accepted to ! Congrats to my co-authors, read the preprint on .
Check out our recent paper on compartment-constraint pathway reconstructions (great work by my postdoc Ibrahim) on .
Layla's paper (with a little help from me) on measures for tumor tree comparisons has been accepted to RECOMB-CCB! Congrats to her and the other Carleton College undergraduate co-authors. Read the preprint on .
Mar 2019
I attended , hosted by OHSU core services and the Epigenetics Consortium with a talk by Jonathan Bibliowicz from Illumina.
I made it to cold, snowy Minneapolis for the - the major computer science education conference.
Feb 2019
I had a great visit at in Memphis, TN, where I gave a talk on signaling pathway analysis.
Our paper on has been officially accepted to the ! Congrats to faculty co-authors Adam Groce and Andrew Bray and student co-authors Marika Swanberg, Ira Globus-Harris, and Iris Griffith. Stockholm, here we come!
I reviewed applications for the -- good luck applicants!
Jan 2019
I have updated the Opportunities page with summer research and scholarship information. I have also updated the posters have that been presented at conferences. Take a look!
I had a great visit with computational biologists at when I was in the area.
My Nifty assignment submission to SIGCSE was rejected, but I'm keeping the materials online. Check out a draft assignment to visualize animal social networks.

2018

Dec 2018
I presented Ibrahim's paper on Localized PathLinker at in Madrid. Congrats on the publication Ibrahim and our co-author Jeff Law at Virginia Tech!
Nov 2018
Sol Taylor-Brill '20 and Kathy Thompson '20 presented their work on CancerLinker at the in Vancouver, WA. This will represent their efforts integrating cancer data with PathLinker over the summer.
Oct 2018
I went to the Consortium for Computing Sciences in Colleges It was great meeting other computer science faculty in the pacific northwest!
Congratulations to Ibrahim Youssef, whose paper Integrating Protein Localization with Automated Signaling Pathway Reconstruction was accepted at the ! Thank you Ibrahim and co-author Jeff Law (at Virginia Tech) for your hard work.
Amy Platenkamp will be presenting a poster on RN-tre, which regulates non-muscle myosin II localization and function, at in San Diego in December. Congratulations to Amy, Derek Applewhite, and the other co-authors of that work!
Sept 2018
I gave a lecture on molecular interaction network mining at a at Carleton College.
The 3rd annual Pacific Northwest Quantative Biology Symposium (PacNowQB) was fun! Thanks to all the faculty and student presenters.
I had a great time at the and in Washington, D.C.
Aug 2018
Summer research has wrapped up - I had a wonderful time with the students for the past ten weeks! .
Congratulations to Miriam Bern, who received a Student Travel Award for CNB-MAC!
It's official -- our has been funded! The grant (with 麻豆国产AV cryptographer Adam Groce as the PI and 麻豆国产AV statistician Andrew Bray as a fellow co-PI) will fund student research on differential privacy for the next three years.
Our work on identifying schizophrenia disease genes associated with cell motility has been selected for a talk at the 5th International Workshop on Computational Network Biology: Modeling, Analysis, and Control (). Congratulations to the joint first authors Miriam Bern '19 and Alex King '19 and co-author Derek Applewhite.
July 2018
I will be a visiting scholar in the at during my junior leave, working with Emek Demir, Guanming Wu, and continuing a collaboration with George Thomas.
I'm heading to in Chicago! Ibrahim Youssef will be presenting his poster on Localized PathLinker.
June 2018
Our paper has been accepted to the Journal of Visual Experiments (JoVE)! Congratulations to Derek Applewhite, 麻豆国产AV students Corrina Del Valle and Ruth Valsquier, and UNC Chapel Hill co-authors Kimberly Peters, Stephen Rogers, and Elizabeth Detmar.
I attended the Galaxy Community Conference and the Bioinformatics Open Source Conference (), which are co-located at 麻豆国产AV. The meeting has a great community, and I presented a poster on a Python package for hypergraphs.
Congratulations to former student Olivier Ezell '16, who is starting medical school at OHSU!
My NSF CAREER proposal . Holy cow!
May 2018
Summer research has begun! Welcome Sol, Usman, and Kathy, who are joining the lab. Welcome back Miriam and Alex, too. Check out their .
Classes are finished! Enjoy summer break.
Ibrahim Youssef's poster on Localized PathLinker has been accepted to the Network Biology track of ! Congratulations.
I visited UC Davis for a workshop on careers in the liberal arts.
April 2018
Congratulations to Nick Franzese '17, who will be starting graduate school in computer science at the University of Maryland in the fall!
I was a panelist for a 麻豆国产AV advising workshop as part of new adviser training.
Our poster describing hypergraph software was accepted to the Bioinformatics Open Source Conference (). Congratulations to my co-authors at Virginia Tech (T. M. Murali and Aditya Pratapa) and USC (Brendan Avent)!
March 2018
I met with 8th-12th grade girls interested in STEM who were visiting campus as part of the .
I attended an AWS workshop at Portland State University to learn about using cloud computing resources for research.
Happy Spring Break!
Congratulations to Simon Couch '22, who won a 麻豆国产AV Science Research Fellowship (RCSRF) for his proposal on differentially private hypothesis testing.
I'm on the Posters Committee and Faculty Scholarships Committee for the (GHC 18). Good luck applicants!
February 2018
I attended in Baltimore, MD. You can find faculty materials for my talk, "Programming the Central Dogma", on the Bio131 website as well as on .
I'm on the Program Committee for the , which will be held in Washington D.C. in late August.
I'm on the Scientific Program Committee of the , which will be held jointly with the Bioinformatics Open Source Conference (BOSC) in Portland, OR, this summer.
I'm reviewing applications for the - good luck applicants!
January 2018
Nick Franzese '17 is a co-author on a paper recently published in Bioinformatics! The paper is . Congrats to all the authors on that paper!
Spring classes have commenced! I'm trying out for my intro class.

2017

December 2017
Fall classes are complete! Have a good winter break.
I am reviewing applications for the High School and Collegiate - good luck applicants!
I went to the , where I gave a flash talk and a poster on Integrating Protein Localization Information in Signaling Pathway Reconstructions.
November 2017
Our paper Differentially Private ANOVA Testing. was accepted at . Congratulations to first author Zachary Campbell '18 and the other co-authors Adam Groce and Andrew Bray!
I attended the twenty-sixth in Spokane, with other 麻豆国产AV faculty and students.
October 2017
Congratulations to my collaborator - our paper Metabolic reprogramming ensures cancer cell survival despite oncogenic signaling blockade was accepted to Genes & Development.
The paper titled Programming the Central Dogma: An Integrated Unit on Computer Science and Molecular Biology Concepts has been accepted at . Thanks to the students for providing valuable feedback on the Bio131 unit.
I gave a Systems Science seminar at .
I gave a Biology seminar at .
September 2017
Derek Applewhite and I co-organized the second Pacific Northwest Quantitative Biology () Symposium on Friday, September 22. We arranged a great lineup of speakers, and had some excellent student poster presentations.
August 2017
I am teaching Bio331: Computational Systems Biology.
The group went to in Boston! My postdoctoral researcher Ibrahim Youssef presented a poster titled Breaking Ties in Weighted Interactomes. Students Gio Ramirez and Nick Egan also attended.
Check out the CREU team's blog, (kudos to Alex King for the name).
July 2017
I went to in Prague - what a great meeting.
  • I presented a poster on Hyperpath Relaxations for Signaling Pathway Analysis, which is co-authored with Adam Groce and Jim Fix in the CS Department and former students Nick Franzese and Barney Potter.
  • I lead a discussion at the Computational Biology Education (CoBE) BOF.
  • I was on the 2017 panel on Essential Skills and Networking Advice for Early-Career Researchers.
Chris Lydgate wrote a blog post about Derek's and my NSF grant: Bio Profs Win NSF Grant to Study Shapeshifting Cells
I was on the Award Selection Committee for the ACM-BCB 2017 Student Travel Grant. Congratulations to the winners!
June 2017
Ibrahim Youssef's poster abstract was accepted to ACM-BCB! He will present the poster, titled Breaking Ties in Weighted Interactomes, in Boston at the end of August.
Derek Applewhite's and my has been funded! The grant is titled RUI: Investigating the Molecular Mechanisms of Non-muscle Myosin II Contractility. Congratulations to the PI, Derek Applewhite.
We received funding from for a collaborative REU project! The project, titled Graph-Based Semi-Supervised Learning to Predict Genes Associated with Schizophrenia, will support student research for the next academic year. Congratulations to the co-PI Derek Applewhite and the two students on the team, Miriam Bern and Alex King!
The GraphSpace paper has been accepted to Bioinformatics! Congratulations to all my collaborators on that paper (in Computer Science, Human Computer Interaction, Biology, Mathematical Modeling, and Statistics. Talk about interdisciplinary!)
Check out Bio131's final projects on the class website.
May 2017
I visited UC Davis and Stanford for workshops on careers in the liberal arts.
I will be presenting a poster at the NetBio track of titled Hyperpath Relaxations for Signaling Pathway Analysis, co-authored by Nick Franzese, Barney Potter, Adam Groce, and Jim Fix.
We received summer student funding to work on a thesis database supported by the Summer Scholarship Funds at 麻豆国产AV.
Congratulations to the graduating seniors!
  • Moira Differding's thesis is titled Your Microbes are Super Models: Using Microbiome Data to Reproducibly Predict Crohn's Disease
  • Nick Franzese's thesis is titled Examining the Practicality of Shortest Hyperpaths for Signaling Pathway Analysis: The Cheating Hyperpath Algorithm as an Alternative Approach
April 2017
I am attending the NCWIT Regional Award Ceremony for the high school Aspirations in Computing award. Congratulations to the award winners!
March 2017
I reviewed poster submissions for the - good luck applicants!
I reviewed applications for the Faculty Scholarships - good luck applicants!
I attended a CRA-Women's in Seattle.
I attended in Seattle.
February 2017
Ibrahim gave a talk at the Biology Department seminar about mathematical models of disease outcome analysis in cancer.
I gave a guest lecture in Topics in Biology (Bio102) about the computational challenges of de novo genome assembly.
I am reviewing applications for the NCWIT College Award - good luck applicants!
I am a co-chair of the Biologial Modeling track of ACM-BCB'17.
January 2017
Welcome Ibrahim Youssef, a new postdoctoral researcher in my lab.
Spring classes have commenced! I am teaching Introduction to Computational Biology (Bio131) and a seminar on Computational Cancer Biology (Bio431).
Bio331 Final Projects are posted on the course web page - nice work everyone.

2016

December 2016
Classes are Complete! Enjoy Winter Break.
November 2016
PathLinker made it on the at the RECOMB/ISCB Conference on Regulatory & Systems Genomics in Phoenix earlier this month.
I attended the in Spokane, WA co-hosted with Gonzaga University.
October 2016
I gave a talk at the at Washington State University (WSU) Vancouver.
Congratulations to Barney Potter for receiving the Best Poster Award at ACM-BCB!
I brought my Computational Systems Biology class to ACM-BCB in Seattle! Thanks to the organizers for putting together such a great opportunity.
I chaired a session at ACM-BCB.
August 2016
Fall classes have commenced! I am teaching Computational Systems Biology (Bio331).
Congratulations to current student Karl Menzel and recent graduates Barney Potter and Nicole Ezell for getting poster abstracts accepted to ACM-BCB!
  • Karl Menzel, Suzy CP Renn, and Anna Ritz. Copy Number Variation and Adaptive Evolutionary Radiations across the African Cichlid phylogeny.
  • Barney Potter, James Fix, and Anna Ritz. Modeling Cell Signaling Networks with Prize-Collecting Subhypernetworks.
  • Nicole Ezell and Anna Ritz. Reconstructing Neuronal Signaling Pathways With the Potential for Disruption in Schizophrenia.
July 2016
I attended in Orlando
July 2016
I am attending in Orlando - looking forward to some great talks!
Looking for a job? We are accepting applications for a postdoctoral researcher in computational biology. Please see the announcement and the . Send me any questions you may have.
June 2016
An NSF proposal for was funded! The grant is titled A Course-Based Undergraduate Conference Experience in Computational Biology.
I gave a talk at Carleton College.
May 2016
I visited collaborators at Virginia Tech, supported by the Summer Scholarship Funds at 麻豆国产AV.
I visited UC Davis and Stanford for workshops on careers in the liberal arts.
Apr 2016
Classes are complete! Happy Renn Fayre.
My work on signaling pathway reconstructions was written up in a . Congratulations to all my PathLinker co-authors.
I am a member of the Poster Committee for the (GHC) 2016.
I am on the Program Committee for the (ACM-BCB) 2016.
I received Summer Scholarship Funds from 麻豆国产AV to visit collaborators at Virginia Tech.
I attended the (NCWIT) Regional Awards reception at Lewis and Clark College. Congratulations to the award recipients!
I was on an Open Access Panel as part of the at 麻豆国产AV.
Mar 2016
My computer lab was on display when I hosted tours for the high school Junior Visit Day at 麻豆国产AV.
Congratulations to Kara Cerveny and Suzy Renn for receiving grant funding! Our success with Murdock and NSF grant awards were written up in the 麻豆国产AV Magazine.
A grant proposal submitted to the was funded! The project's title is Developing Computational Methods to Identify Candidate Driver Genes Involved in Signaling Pathway Dysregulation in Colorectal Cancer. That's a mouthful.
The PathLinker paper is now available online at .
Feb 2016
I attended an hosted by Portland State University.
Jan 2016
Spring classes have commenced! I am teaching two sections of Introduction to Computational Biology (Bio131).
I am on the program committee of the RECOMB Satellite Workshops on Massively Parallel Sequencing (RECOMB-Seq) and Computational Cancer Biology (RECOMB-CCB) 2015.
Looking to do summer research? I updated my webpage with opportunities and the CompBio Lab.
I am on the program committee of the RECOMB satellite workshops on Massively Parallel Sequencing () and Computational Cancer Biology ().

2015

Dec 2015
Classes are done! Enjoy Winter Break.
Nov 2015
Our paper on PathLinker has been accepted to NPJ Systems Biology and Applications! Congratulations to my co-authors Chris Poirel, Allison Tegge, Nick Sharp, Allison Powell, Kelsey Simmons, Shiv Kale, and T. M. Murali.
Oct 2015
I attended a Bioinformatics and Genomics Workshop at 麻豆国产AV.
Sept 2015
I attended the Pacific Northwest Quantitative Biology Meeting at OHSU.
August 2015
麻豆国产AV classes have commenced! I am teaching Introduction to Computational Biology (Bio131) and Computational Cancer Biology (Bio431).
July 2015
Our paper on signaling hypergraphs has been accepted to IEEE Transactions on Computational Biology and Bioinformatics (TCBB)! Congratulations to my co-authors Brendan Avent and T. M. Murali.
June 2015
I am on the program committee of the 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
May 2015
I gave a talk at the Workshop at Virginia Tech
I led a Bioinformatics session at the 17th Annual Women in Computing Day at Virginia Tech. The put on a great event.
I gave a chalk talk at 麻豆国产AV about student thesis ideas.
March 2015
I gave a talk at the at Virginia Tech
February 2015
I gave a talk at the University of Kansas
January 2015
I gave a talk at the BioFrontiers Institute at CU Boulder

2014

December 2014
I gave a talk at 麻豆国产AV
November 2014
I gave a talk at the (San Diego, CA)
September 2014
I gave a talk at the (Newport Beach, CA)
October 2014
I gave a talk at the Virginia Tech Computer Science Department seminar
I helped out at a community STEM workshop for middle school girls sponsored by the Chapter.

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Contact

Biology Department
麻豆国产AV
3203 SE Woodstock Blvd.
Portland, OR 97202-8199

Email icon aritz-at-reed-dot-edu

CV icon Curriculum Vitae [pdf]



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