News

New collaborative paper about translatome and annotation

July 13, 2022

A new paper about a community-led effort that produces a standardized catalog of 7,264 human Ribo-seq ORFs. Read more here!


Anne is promoted to Associate Professor with Tenure today! Congratulations!!!

July 1, 2022


New collaborative paper about RNA processing

June 4, 2022

A new paper investigating the role of the RING finger protein RNF219 in post-transcriptional regulations. Read more here!


New paper on information flow in genetic networks

June 2, 2022

A new paper from Omer Acar on identifying long-range interactions in genetic networks using elastic network models. Read more here!


2022 CEBaM retreat

May 3, 2022

We had a wonderful retreat with our colleagues in the Pittsburgh Center for Evolutionary Biology and Medicine (CEBaM)


Undergraduate Summer Research Position

March 29, 2022

Funded by an NSF Career Award, the Carvunis lab is offering a paid 10 week-long summer position running from May 31st, 2022 to August 12th, 2022. The undergraduates will learn how to design and execute a research experiment while practicing various wet-lab techniques including cloning, microbial phenotyping, high throughput robotics, and bioinformatics. The undergraduates will meet weekly with their summer mentor, participate in the laboratory’s journal clubs, attend small group meetings, local seminars, and present their research at the weekly group meeting at the end of the summer. Interested applicants should reach out to Kate McCourt with any question (kmm325 [at] pitt [dot] edu). The link to the advertisement is here.


Branden presents at Pittsburgh Area Yeast Meeting

March 25, 2022

Branden presented research from his new pre-print at the Pittsburgh Area Yeast Meeting followed by celebration afterwards on the team’s manuscript submission.


In-person lab meeting

March 18, 2022

Carvunis lab enjoys another in-person lab meeting!


Dr. Carvunis receives The Chancellor’s Distinguished Research Award

March 2, 2022

Dr. Carvnuis has been awarded the 2022 Chancellor’s Distinguished Research Award for her innovative work on novel gene emergence. The award release describing Dr. Carvunis as ‘one of just a handful of the foremost experts on this phenomenon”.

Read more here and here


Dr. Carvunis and lab receive NSF CAREER award

Jan 20, 2022
Dr. Carvunis and lab receive the National Science Foundation CAREER award to study how the widespread translation of evolutionary novel sequences impacts physiology and fitness in yeast. The research will be integrated with a far reaching educational project in collaboration with Primarily Undergraduate Institutions across the United States.

“The Faculty Early Career Development (CAREER) Program is a Foundation-wide activity that offers the National Science Foundation’s most prestigious awards in support of early-career faculty who have the potential to serve as academic role models in research and education and to lead advances in the mission of their department or organization.”

Click here for more information on the NSF CAREER award.


New preprint on sulfur metabolism in yeast

Jan 20, 2022

New preprint from Dr. Branden Van Oss et al. challenges current models of sulfur metabolism in yeast, with the discovery of another enzyme involved in homocysteine production. Read more here.


Tracing the evolution of a mammalian microprotein

Nov 23, 2021

Jiwon and Aaron have discovered SPAAR, a microprotein thought to be exclusively in placental mammals, actually exists in marsupials and monotremes like the platypus! Even though it is much more ancient than previously thought, it has changed a lot to the point of diverging almost beyond recognition, including a cool elongation in primates that appears under positive selection! Read more in out open access article which is part of a Special Issue “How do new genes originate and evolve?” with many more exciting articles on molecular innovation.


Halloween’19

Oct 19, 2021

The Carvunis Lab celebrated the fall season with a field trip to a local pumpkin patch and apple orchard! We spent the day picking out pumpkins, picking apples, wandering through a corn maze, and sipping on warm apple cider. Happy autumn!


Dr. Carvunis and Dr. Wacholder speak to Science Careers

September 16, 2021
Dr. Carvunis and Dr. Wacholder were interviewed for a recent article in Science Careers about the importance of performance reviews for early-career researchers and their advisors. Check out the article here!


Happy end of semester!

August 24, 2021
The Carvunis lab celebrates the end of the summer semester with some fun outdoors!


New preprint investigating the evolutionarily transient translatome

August 23, 2021
New preprint from Aaron Wacholder that identified ~19,000 noncanonical translated elements through integration of multiple ribo-sequencing datasets. Read more here


Carvunis lab meets in person!

June 21, 2021
The Carvunis lab met for lab meeting in person for the first time in over a year! Great science presented by Jiwon followed by ice cream.


New preprint on a collaboration towards a reference translatome using Ribo-seq

June 11, 2021
New preprint released discussing the challenges of ORF detection and annotation using ribo-sequencing. Read more here


New preprint on information flow in genetic networks

June 9, 2021
A new preprint from Omer Acar on identifying long-range interactions in genetic networks using elastic network models. Read more here!


April Rich awarded Graduate Research Fellowship!

March 23, 2021
April Rich has been awarded the NSF Graduate Research Fellowship for her strong research potential and scientific communication outreach! Congratulations to April for this great accomplishment.


LI detector methodology published in G3!

March 12, 2021
The LI detector method for sensitive analysis of colony fitness in high throughput screens has been published in G3! Check it out here.


Anne-Ruxandra Carvunis wins 2021 Sloan Fellowship!

February 16, 2021
Anne-Ruxandra Carvunis has been selected as a 2021 Sloan Fellow. This prestigious award is given to early-career scientists who “represent the most promising scientific researchers working today.” Congratulations to Dr. Carvunis for this remarkable achievement!


April Rich YouTube channel bioZone featured in Pittwire!

January 12, 2021
Check out this Pittwire article featuring April Rich and her educational YouTube channel bioZone, which explores a variety of fascinating biological subjects. And check out her YouTube channel itself here.


LI detector publication accepted in G3!

January 12, 2021
A new publication by Dr. Saurin Parikh and collaborators describing a novel method for analyzing mutant fitness in high throughput screens has been accepted for publication in G3. Congratulations Saurin!


New publication in Cell Systems

July 2, 2020
Check out this new publication from the Dr. Carvunis and collaborators in Cell Systems that investigates Dog-to-Human aging from a network biology perspective.


Carvunis Lab is a Green Lab now!

May 4, 2020
Carvunis Lab has been awarded with Green Lab Certificate showing our commitment to the good practices of recycling, re-use and reduce.


Where do new genes come from?

April 9, 2020
Check out this new press article in Quanta Magazine, spotlighting the recent publications in eLIFE and Nature Communications from the Carvunis lab and collaborators on the origins of new genes!


New publication in eLIFE

Feb 20, 2020
Check out this new publication from the Dr. Carvunis and collaborators in eLIFE that explores the origins of orphan genes!
Also, here is a link to spotlight in eLIFE.


Recent Nature Communications Publication from Carvunis Lab and Collaborators

Feb 10, 2020

Check out this new publication from the Carvunis Lab and collaborators in Nature Communications that investigates the De novo emergence of adaptive membrane proteins!


Two recent articles from the Carvunis Lab accepted to Nature Communications and eLIFE

Jan 23, 2020

Check out this preprint accepted to Nature Communications on the de novo  emergence of adaptive membrane proteins, and this preprint accepted to eLIFE that explores the origins of orphan genes. Stay tuned for the updated published versions!


The Recalcitrance and Resilience of Scientific Function

Jan 23, 2020

How is the concept of function shaped by the diverse perspectives of scientists within and across disciplines? Anne-Ruxandra and colleagues explore the use of function in research of de novo gene birth. Have a look at this article in the rhetorics journal Poroi to learn more!


Anne-Ruxandra gets recognized as an outstanding new PI

November 26, 2019

More good news!! Anne-Ruxandra gets recognized as the outstanding new PI of the month by an international community of early stage faculty. Find out more about her exciting profile by following this link: https://newpislack.wordpress.com/2019/11/26/anne-ruxandra-carvunis-ph-d/

Read about other talented young PIs around the globe over here: https://newpislack.wordpress.com/outstanding-new-pis/


How old is your dog in human years?

November 15, 2019

A Science news article features the work of Anne-Ruxandra and her colleagues at the Ideker Lab who have figured out a more scientific way of converting dog years to human years using DNA methylation signature. Find the news article here and the preprint here.

   


The meanings of ‘function’ in biology

November 1, 2019

Anne-Ruxandra and colleagues explore the various meanings of ‘function’ in biology and its implications on the field of de novo gene birth. Have a look at this thought provoking article and let’s start a conversation on ‘function’.


Halloween’19

November 1, 2019

Carvunis Lab celebrated Halloween in style this year! We not only had a costume-style lab meeting but also hosted this years Halloween party at work. It is important to remind everyone that doing science is not the only scary part of life!

 


Carvunis Lab members featured in the departmental newsletter

October 30, 2019

Anne-Ruxandra made news for receiving the prestigious NIH Director’s New Innovator Award and Carly was the ‘Student Highlight’ in the latest edition of the Computational & Systems Biology Department’s newsletter. Find out more about Anne-Ruxandra’s award and Carly’s life in science, Pittsburgh and the CPBP Program over here.


Tiny proteins, huge impact

October 18, 2019

Ubiquitous tiny little proteins that can boost or block the impact of their bigger kin! Read all about this fascinating phenomenon and how some of these can indeed be proto-genes in this Science feature.


News feature on de novo gene birth

October 16, 2019

Want to know “how evolution builds genes from scratch”? Follow this link to read what some of the leading researchers in the field of de novo gene birth have to say.


Anne-Ruxandra receives the NIH Director’s New Innovator Award

October 7, 2019

Anne-Ruxandra was named one of the awardees of the highly prestigious NIH Director’s New Innovator Award for 2019. This award supports “exceptionally creative early career investigators who propose innovative, high-impact projects” and will help further the Carvunis Lab’s efforts to understand how DNA sequences go “From Non-Coding to Coding”.


John’s Send-off

October 4, 2019

It was a bitter-sweet day for the Carvunis Lab to see our oldest member move on. John has been an integral part of the lab since even before there was one. During his time with us he has initiated multiple projects, both bioinformatic and experimental, and helped established a variety of protocols and mutant collections that will continue to help the current and future members of the lab for years to come.  He is going to continue his quest in science at Susana da Silva‘s lab where he will investigate fovea development using retinal organoids!! It is difficult to see him go but we can find some relief in the fact that he is not going too far from us. We wish him all the good luck for his future endeavors and hope that he continues to do great science!

We all celebrated his last day at the pizza joint where he worked part-time when he first joined the lab! He continues to remain a great salesperson for them…

     

   


EPiC Conference

September 14, 2019

Omer and Saurin took a road trip to Philly for the Evolution in Philadelphia Conference. Omer had a great poster on “Exploring de novo gene emergence through genetic interaction networks” and Saurin gave a 5 min talk on the LI Detector, a bioinformatic tool to measure small fitness effects in colony-based high-throughout screens.

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Retreat Week!

August 23, 2019

Doing science is difficult and hence we retreat! The Carvunis Lab members took a break from the lab and decide to have some fun outdoors, but that doesn’t mean there wasn’t any science happening! Same thing, the same week, for the entire CPCB PhD program!


Goodbye Summer’19 Students

August 19, 2019

Today we said goodbye to our amazing summer students – Jake, Kate and Tanvi! All of them did a wonderful job over the summer with projects ranging from figuring out new metabolic pathways in yeast, to creating mutants using CRISPR, to cataloging all possible phenotypic data of yeast mutants present in the SGD database. Carly made this occasion extra special with her hummingbird cake.


Mega Journal Club

June 7, 2019

We experimented with a new way to learn about a topic: what happens when you put random sequences into cells? We had a potluck picnic at a nearby park, then sat in a circle and each presented a paper on the topic, spanning decades, techniques and model organisms. It was a ton of fun and a great way to gain a general understanding of how research is progressing in an interdisciplinary field. Highly recommend!




Gene birth Wiki

May 24, 2019

Everything you were dreaming to learn about de novo gene birth now at your finger tips in this invited review written with postdoctoral fellow Branden Van Oss, available at PLOS Genetics and on Wikipedia!


New Carvunis Lab Manual

March 11, 2019

We were inspired by great team leaders like Angela DePace, Prachee Avasthi and others to put together a document that lays out our lab culture, training expectations, safety rules etc. Basically everything you need to know if you are joining or thinking of joining the lab! It’s so nice to have it in writing, I hope that will help strengthen our productivity and avoid any misunderstanding in the future. Thanks all lab members for their input! Any prospective lab member interested in looking at the document can request access by emailing Dr Carvunis or Nelson Coelho.


Halloween Party 2018




Happy Birthday EVERYONE

September 7, 2018

On this day we celebrated the birthdays of: John, Nelson, Branden, Saurin, Omer, and even Anthony! Almost the whole lab has birthdays within 2 weeks of each other… Happy birthday!!



Anne-Ruxandra receives 2018 Trailblazer Award from the Ladies Hospital Aid Society

September 6, 2018

The Ladies Hospital Aid Society is has been a pilar of community service in Pittsburgh since 1898. This year, they organized a Fire and Ice gala celebrating 6 Trailblazers for their outstanding contributions to science and patient care, including Dr. Carvunis. Achievements so hot, they will give you chills! This honor is very special, as it exemplifies how much Pittsburgh biomedical leadership trusts that fundamental evolutionary research will have lasting medical impact.



New: Pittsburgh Center for Evolutionary Biology and Medicine

September 1, 2018

Anne-Ruxandra co-founded this new Center together with other evolutionary biologists at the University of Pittsburgh School of Medicine. The mission of the Center is to advance the fields of evolutionary biology and medicine by catalyzing research at their interface. The Center serves to cultivate educational and scientific collaborations between evolutionary biologists and biomedical researchers. As momentum builds, the Center will offer a yearly award to catalyze research at the interface of medicine and evolutionary biology. Visit the Center’s website to learn more about this exciting initiative!


Goodbye Selin!

August 23, 2018

A bittersweet moment together, saying goodbye to Selin who returns to Turkey to finish her undergraduate studies. Selin brought a lot to our group in the two summers she spent with us. We will always remember her fondly! Best of luck Selin!!




Celebrating BaDoi

August 7, 2018

BaDoi Phan has finished his excellent rotation work in the lab – Onto Med School!


Carvunis Lab Summer Party!

May 29, 2018

Nice picnic to welcome summer students and celebrate the beginning of summer next to the cathedral of learning



Of mice, men and immunity…

April 23, 2018

Our first manuscript on evolutionary systems medicine is published in Nature Immunology. A network-based vision of how evolution complicates comparative studies between human and mouse, and what that means for biomedical research. Great collaboration with eminent immunologist and veterinarian Peter Ernst, from UCSD. Check out the publication!


Anne-Ruxandra receives Searle Scholars award

April 15, 2018

The Kinship Foundation, established by the Searle family, has named Anne-Ruxandra one of the 15 recipients of the prestigious Searle Scholars Program for High Risk / High Reward research. Anne-Ruxandra is elated that she is granted the honor of joining this group of outstanding scientists. TRIB announcement.


Evolutionary Systems Medicine

February 15, 2018

How can we improve translation of biological knowledge between mouse models and human patients? Stay tuned for a new manuscript to come out at Nature Immunology that proposes how an evolutionary systems approach may help increase the success of future clinical trials.

The Vitruvian Rat, by GreenLabRat, Image Courtesy GreenLabRat at Deviant Art, 2016


The Plate Factory

November 15, 2017

We are now pretty much a fully equipped yeast lab, and Nelson is super proud of Saurin and John working in the plate factory!


Halloween Party

October 27, 2017

Fun times with silly costumes at our Halloween Party with everyone on the 10th floor.


Selin’s See-off

September 15, 2017

Sept 15 2017, we say goodbye to Selin who visited us from Turkey for the summer. Have a safe journey, good luck for the coming school year and we all hope to see you soon 🙂


Eclipse Party!

August 21, 2017

Fun times at the Eclipse party organized by the Department of Computational and Systems Biology


First paper from The Carvunis Lab published in Mol Biol Evol

January 12, 2017

This was a very international project with Diethard Tautz (Germany), Tomislav Domazet-Lošo (Croatia), Mat Alba (Spain) and others. We asked how the technical limitations of BLAST may interfere with our ability to know when sequences have emerged in evolution. Find out more by reading the manuscript here [LINK].


The Carvunis Lab is Open!

December 15, 2016

It all begins on December 1st 2016: with an office, a desk, a gutted lab space undergoing serious renovations and a nice plaque on the wall…