Accepting applications for undergraduate summer interns (paid position)
February 8, 2024 The Carvunis lab is seeking undergraduate summer interns as part of the “adopt a proto-gene” initiative. This is a paid 10 week-long position from May 20th – July 26 2024, where undergraduates will learn how to design and execute a research experiment while gaining experience in techniques such as cloning, microbial phenotyping, high throughput robotics, and bioinformatics. Applications are due by March 5th. The link to the advertisement is here.
Protocol paper on iRibo published
January 18, 2023 A protocol paper on iRibo, a software program that can massively integrate ribosome profiling experiments to generate a species’s translatome, is now published in STAR Protocols here. The protocol describes the steps needed to generate the yeast translatome in Aaron’s Cell Systems paper.
New preprint on the use of Ancestral Sequence Reconstruction in studying de novo genes
January 2, 2023 A new preprint by our collaborator Nikolaos Vakirlis and former lab members Omer Acar and Vijay Cherupally formally evaluates the applicability of Ancestral Sequence Reconstruction (ASR) in the detection of de novo gene emergence. You can check it out here.
New publication on the limitations of MS to detect the noncanonical translatome
December 4, 2023
Aaron’s preprint on the substantial limitations of shotgun mass-spectrometry in finding many biologically relevant lowly expressed proteins is now published in PLOS Biology. You can find the publication here.
Saurin successfully defends his PhD thesis!
November 27, 2023
Saurin becomes the second PhD student from the Carvunis lab to successfully defend their PhD thesis this year. His work revolved around ‘Leveraging the genotype-phenotype relationship to explore the traditional and novel facets of cell biology.’ Saurin is going to join the Technology Transfer team at the University of Rochester in the new year. We wish him all the best for his future endeavors!
Carvunis Lab at SMBE Satellite Meeting on De Novo Gene Birth
November 17, 2023 Multiple members of the Carvunis lab made it to the first ever conference on de novo gene birth with multiple posters and presentations to showcase the diversity of work that is done in the lab on this topic! We hope that this was the first of many such conferences. Please reach out to us if you were there and would love to learn more!
Summer students publish a uPublication
October 23, 2023 Summer students use computational prediction tools, co-expression analysis and fluorescence microscopy to suggest that an unannotated translated open reading frame in Saccharomyces cerevisiae genome, which was systemically labeled YGR016C-A in Wacholder et al., 2023, localizes to the endoplasmic reticulum. Read more about this tremendous effort here and here.
Carvunis lab receives NIH Director’s Transformative Research Award!
October 3, 2023
It was announced on October 3rd 2023 that the Carvunis Lab is going to receive the prestigious NIH Director’s Transformative Research Award (TRA)! A part of NIH’s High-Risk, High-Reward Research program, the TRA supports “individuals or teams proposing transformative projects that are inherently risky and untested but have the potential to create or overturn fundamental paradigms” ! The Carvunis Lab is honored to have received this award along with the Joglekar, Atianand and Subramaniam Labs.
April won the Best Student Talk at the CPCB retreat
August 25, 2023
April won the Best Student Talk at the CPCB retreat! Congratulations!
April’s BioZone was featured in the Pitt Med magazine
August 21, 2023
April’s science YouTube channel bioZone was featured in the summer 2023 edition of Pitt Med magazine. Check out the Pitt Med article “These student YouTubers are in the zone ” here and check out her YouTube channel here.
Lord-Carvunis Lab Joint Lab Picnic
August 18, 2023
The Lord and Carvunis Labs take best advantage of a sunny day in the Burgh to celebrate a joint lab picnic!
Jiwon won the CEBaM Catalyst Award
June 30, 2023
Jiwon won the 2023 Catalyst Award from the Pittsburgh Center for Evolutionary Biology and Medicine (CEBaM). The Catalyst Program provides funding to PhD students and postdoctoral scholars at the University of Pittsburgh to perform research at the interface of evolutionary biology and medicine. Congratulations Jiwon!!!
Farewell party for Omer
June 22, 2023
This week is the last week for Omer, the first Ph.D. from the Carvunis lab. We got together to celebrate this big milestone for Omer (Dr. Acar!), Dr. Carvunis, and the lab. The lab prepared a little gift for him and wish him all the best for his new career in the industry.
Aaron’s yeast translatome paper is published in Cell Systems
May 18, 2023
Aaron identified the vast translatome of yeast through large-scale integration of ribosome-profiling data, and show that these translated elements are mostly evolutionarily transient. The work is published in Cell Systems. Congratulations Aaron and coauthors!!
Omer defends his PhD thesis!
May 11, 2023
Omer defends his PhD thesis entitled “Understanding cellular innovation and complexity with a network perspective”. Congratulations Dr. Acar!!
Carvunis lab is co-hosting online gene evolution workshop for educators
May 3, 2023
The Carvunis Lab is excited to co-host a gene evolution workshop for instructors and educators, with a special focus on proto-genes! These unannotated, evolutionary novel genes offer unique insight into molecular evolution.
During this year’s online workshop, we will cover:
- Ancestral Sequence Reconstruction – Explore the past by tracing the evolutionary history of a sequence
- Cellular Localization Algorithms – Predict where proto-proteins reside within cells
- Protein Structure Prediction Algorithms – Predict and visualize the 3D structure of proto-proteins.
Research spotlight: “Life finds a way”
April 28, 2023 Check out this article in ASBMB Today Magazine, showcasing the recent publication in Journal of Biological Chemistry from the Carvunis lab and collaborators on the function of the previously uncharacterized gene YLL058W.
Nelson receives Sustainability Award!
April 24, 2023 Nelson received the 2023 Pitt Sustainability Award, which “recognize Pitt faculty, staff, students, and groups who are making an extraordinary impact on campus sustainability. These individuals or groups could have demonstrated their impact in one or more categories of the Pitt Sustainability Plan (Stewardship, Exploration, and/or Community and Culture) via ideas, talents, and passions that contribute to a thriving culture of sustainability at Pitt.” Read more about the award here
Carvunis lab receives HFSP grant!
April 10, 2023 The Carvunis Lab is honored to have been awarded the prestigious Human Frontier Science Program (HFSP) research grant! This grant promotes international collaboration and groundbreaking research. The funded project is entitled “New Kids on the Block: how DeNovo emerged micropeptides rewire cellular networks”. Read more about the HFSP grant here
Nelson selected as a GSA Presidential Member
March 31, 2023 Nelson has been selected as a Presidential Member for the Genetics Society of America. Congratulations Nelson! Read more here
New preprint exploring the transcriptional network of noncanonical ORFs
March 20, 2023 New preprint from April and Omer looking at the transcription of noncanonical ORFs. Check out the preprint here
New preprint on the rarity of finding noncanonical ORFs in mass spectrometry
March 12, 2023 New preprint from Aaron about how the protein products of translated noncanonical ORFs in yeast can very rarely be detected using shotgun mass spectrometry data. Check out the preprint here
New perspective piece from the lab published in Nature Ecology & Evolution
January 2, 2023 New perspective piece describing the work of An et al. which show that acquiring the ability to leave the nucleus is a major hurdle to cross towards becoming a protein-coding gene and the consequence of gaining such ability in one gene played a role in human brain evolution. Check out the perspective piece here, check out An et al.’s paper here and see Science’s news covering, featuring an interview from Dr. Carvunis here.
Students can discover and “adopt” proto-genes
December 16, 2022 Carvunis Lab’s NSF-funded Adopt a Proto-Gene initiative aims to get young researchers interested in proto-genes, improve evolutionary literacy and encourage STEM careers. Read more about it from two undergraduate students who experienced it this summer over here in PITTMED’s winter 2022/23 issue.
In a collaborative paper the lab discovers a new enzyme!
November 12, 2022 New collaborative research article by Branden, Saurin and Nelson et al. explores the mysterious growth of yeast cells lacking the MET15 gene in media lacking organosulfurs like methionine. They demonstrate through structural and evolutionary modeling, in vitro kinetic assays, and genetic complementation, that an alternative homocysteine synthase encoded by the previously uncharacterized gene YLL058W enables these cells to assimilate inorganic sulfur. Read more here and here.
April’s bioZone becomes an award winning YouTube channel
August 26, 2022 April’s bioZone YouTube channel received an award for their commitment to outreach from the CMU-Pitt Computational Biology Program. Congratulations and well deserved April!!
De novo genes and Yeasts
August 12, 2022 New review article by the Carvunis lab members – Saurin, Carly, Branden and Aaron, on why the Yeasts are particularly well suited to address fundamental questions about de novo gene emergence published in the Yeast journal. Read more about it and their new evolutionary systems biology approach for de novo gene characterization over here and here.
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, 2022Today I have Tenure! An honor I owe in large part to past and current mentors and advocates, incredibly supportive department, amazing lab members, friends and family. I hope to use this newfound job stability to make our world a little better through science and advocacy!
— anne-ruxandra carvun (@carvunis) 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. 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 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…
