As of today, Sohini is officially promoted to Professor of Ecology and Evolutionary Biology, and is Director of Brown University’s Data Science Initiative. In April, her family welcomed their third child, and are enjoying seeing epistasis among all their genetic experiments. Amidst the COVID-19 pandemic, Sohini feels incredibly lucky to lead and have support from her amazing lab members, and is excited to see what scientific work and new lab members the future holds!
Graduate student Wei Cheng is first author on a paper out in PLoS Genetics, which is coadvised by our collaborator and CCMB colleague Lorin Crawford. This study entitled Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits releases our gene-level association test, gene-epsilon (pronounced “genie”), a new approach for identifying statistical associations between sets of variants and quantitative traits. Congratulations to all the authors!
Graduate student Sam Smith is joint first author on a paper out in Genetics, which is a collaboration with Bjorn Sandstede’s group from the Division of Applied Mathematics at Brown University. This study entitled Hierarchical clustering of gene-level association statistics reveals shared and differential genetic architecture among traits in the UK Biobank releases WINGS, a method for clustering and prioritizing phenotypes based on shared genetic architecture revealed by gene-level association statistics. Congratulations to all the authors!
This is no April Fool’s joke: Sahar defended her amazing dissertation entitled “Integrative Computational Approaches in Cancer Genomics” today! She is transitioning back to clinical rotations for her other doctorate (an MD from the Warren Alpert Medical School), and will be greatly missed. We were able to gather for a socially distant party to celebrate our latest lab graduate.
MD/PhD student Sahar Shahamatdar’s first paper is out in Cell Reports, resulting from a collaboration with the Van Allen Lab at Dana-Farber Cancer Institute. In this study entitled Germline features associated with immune infiltration in solid tumors we identify germline variants, genes, & pathways associated with immune infiltration phenotypes in cancer. Congratulations to all the authors!
Have you ever thought “If only I could superexponentially reduce the state space of gene genealogies I’m dealing with when I infer changes in Ne over time!” ? Then this paper, releasing the method BESTT, is for you! Led by the incredible Julia Palacios, former lab postdoc, and building off of theoretical results from her 2015 Genetics paper. Currently for independent loci, but SMC-based inference is up next!
We have a new paper out led by lab friend Shaila Musharoff in PLoS Genetics, entitled The inference of sex-biased human demography from whole-genome data. The paper releases a new method that uses comparisons of X-chromosomal versus autosomal genetic variation to infer sex-specific demographic parameters (see also https://github.com/shailamusharoff/sex-bias-inference). Congratulations to all the authors, including collaborators Suyash Shringarpure and Carlos D. Bustamante!
The last chapter of Priyanka Nakka’s dissertation is now published in American Journal of Human Genetics, entitled Characterization of Prevalence and Health Consequences of Uniparental Disomy in Four Million Individuals from the General Population. Priya led this collaboration as an intern at 23andMe, Inc. The paper focuses on estimating, for the first time, the per-chromosome rates of uniparental disomy (inheriting both copies of a chromosome from just one biological parent) in samples from 23andMe and the UK Biobank. Our paper was also covered in The Atlantic by Sarah Zhang. This study underscores that recombination is simultaneously constrained but also variable and errors can sometimes be corrected. Most surprising, and exciting, for the lab was realizing that some people have incredibly long runs of homozygosity with no clear deleterious effect, an avenue we plan to continue pursuing.
Congratulations to all the authors, especially Dr. Nakka!
Sohini has been named a recipient of the Presidential Early Career Award in Science and Engineering, nominated by the NIH! This is an honor, and a complex honor to receive under the Trump administration. Sohini joined 83 other awardees to write and sign a statement that can be found here. Below, she is accepting the award from the Director of the White House Office of Science and Technology Policy, Kelvin Drogemeier. Sohini was also covered in February 2020 by the NIGMS Biomedical Beat Blog.
Kaileigh, Wei, Sam, and Sahar all passed their respective qualifying exams, fielding questions from across the fields of molecular biology, evolutionary biology, mathematical biology, and computational biology. So excited for our graduate students as they become doctoral candidates! Congrats!
Our postdoc Kate Brunson has a new paper out in Trends in Genetics, coauthored with David Reich at Harvard University. The paper is entitled “The Promise of Paleogenomics Beyond Our Own Species” and is a wonderful review of available ancient DNA samples form humans and non-human species. Congratulations!
Postdoc Kate Brunson (who is also Visiting Assistant Professor in Biomolecular Archaeology) led organizing the 2019 Joukowsky Institute for Archaeology and the Ancient World State of the Field conference on “The Ancient DNA Revolution in Archaeology”.
The conference goals are to address the many issues surrounding the development and uses of ancient DNA methods around the world and to promote discussion between archaeologists, anthropologists, and geneticists in order to examine new opportunities and challenges for collaborative ancient DNA research in archaeology.
Looking forward to an exciting and productive interdisciplinary meeting!
During Spring 2019, Sohini is a Natural Sciences Fellow at the Swedish Collegium for Advanced Study (SCAS) in Uppsala, Sweden. While continuing her duties with her Lab and in graduate training, being at SCAS offers an interdisciplinary environment to focus on her research and to learn more about ancient DNA research from the Human Evolution Group and Mattias Jakobsson at the Evolutionary Biology Center, Uppsala University.
Vi ses i Juli Providence!
SWIF(r) is discussed among other machine learning approaches to detect selection in genomes in this Nature News piece by Amy Maxmen!
A new paper the Ramachandran Lab collaborated on (Sohini and Julia Palacios are coauthors) is out in Cell, led by collaborators Elizabeth Atkinson and Brenna Henn! The paper is entitled “No Evidence for Recent Selection at FOXP2 among Diverse Human Populations”, and also involved Brown University colleagues Ashley Webb and postdoc Amanda Audesse. The work uses sequence data and diverse human samples to reanalyze so-called “language gene” FOXP2, previously thought to have undergone a selective sweep in the modern human lineage. We show that there is not evidence for this, revising the history of how humans acquired language. This work was funded by Sohini’s NIH R01 GM118652, on which Brenna is a co-investigator.
Other coverage of the paper can be found at Nature News and in Cell’s press release.
Congratulations to all the authors!
Kate Brunson has joined the lab to do postdoctoral research, and is Visiting Assistant Professor in Biomolecular Archaeology through the Joukowsky Institute for Archaeology and the Ancient World at Brown University. Her interests in the Ramachandran Lab include ancient DNA analysis, mitochondrial sequence analysis, and inference of the history of domesticated animals from genomic data. Welcome to Kate!
The lab went kayaking in downtown Providence’s Venetian Canals, and was featured in the Providence Journal website! If you want to work with a dynamic group of quantitative biologists who like to hang out together, think about joining the Ramachandran Lab.
Sohini and Emilia Huerta-Sanchez, who will be joining the Brown University faculty in Ecology and Evolutionary Biology and CCMB in July 2018, are the co-organizers of the Society of Molecular Biology and Evolution (SMBE) Satellite Meeting on Modern Methods for Study of Ancient DNA (4/4-4/7/2018) in Providence, RI. 60 participants from seven countries will arrive in Providence for an exciting lineup of talks and posters.
The main goal of the meeting is to bring together early career scientists (junior faculty, postdocs and graduate students) interested in discussing state-of-the-art methods and the challenges of studying population-genetic processes across time using ancient and extant DNA. As with most areas in genomics, this is one where there is an urgent need for new quantitative tools for analysis; we look forward to discussing the technical and methodological challenges facing population genetic researchers studying ancient DNA, as well as the ethics of data generation and of direct-to-consumer testing.
Two new papers are out from the lab! Lauren’s amazing efforts led to SWIF(r)’s publication in Nature Communications; see news coverage at Brown for more details. This paper represents major progress on the research funded by our R01, furthers our collaboration with Brenna Henn (now at UC Davis) and recognizes contributions from former lab members Annie Fischer ‘17 and Stephen Rong. We are looking forward to seeing SWIF(r) - the sweep inference framework (controlling for correlation) - applied to classify adaptive mutations by our lab and others.
The second paper reviews the history of studies mapping genotypes to heritable phenotypes, by Marc Feldman and Sohini, out in Philosophical Transactions of the Royal Society B as part of a special issue entitle ‘Bridging cultural gaps: interdisciplinary studies in human cultural evolution’. The title of the paper is “Missing compared to what? Revisiting heritability, genes and culture”.
Congratulations to all the authors!
After successfully defending his dissertation in Human Genetics at the University of Chicago, Michael Turchin has arrived and joined the Ramachandran Lab as a postdoctoral fellow! His interests include human, population, and medical genetics, and methods development in multi-ethnic GWAS. Welcome!
Priya’s second first-author paper is out in Cancer Epidemiology, Biology & Prevention. This paper furthers our collaboration with St. Jude Children’s Research Hospital, and begins our collaboration with Texas Children’s Hospital. The gene and network analyses presented uncover loci associated with acute lymphoblastic leukemia (ALL) that are missed by GWA studies. The paper also reports that ALL-associated loci do not appear to interact directly with each other to influence ALL risk, and instead appear to influence leukemogenesis through multiple, complex pathways.
Congratulations to all the authors!
As of today, Sohini is officially tenured and promoted to Associate Professor of Ecology and Evolutionary Biology and Associate Professor of Computer Science. She has also been appointed Director of Brown University’s Center for Computational Molecular Biology by the Provost, after serving as Interim Director since January 2017. Looking forward to this new chapter, especially to growth in the lab and continuing to pursue collaborative, risky, creative research projects!
This summer, Priya will be working as a summer intern at 23andme.com, supervised by Dr. Joanna Mountain (who incidentally was a mentor to Sohini back at Stanford). We miss having her in the lab in person but are excited that she is pursuing this opportunity. We look forward to welcoming Priya back in the fall!
Sam Smith, who just graduated from Vanderbilt University, has joined the Ramachandran Lab and will be taking summer courses as he matriculates into the Computational Biology doctoral program. Welcome!
Tyler, Annie, and Katie have been wonderful members of the Ramachandran Lab and will be receiving their college diplomas today in Brown’s 249th Commencement Exercises.
Tyler is graduating with an Sc.B. in Applied Math-Biology, and was awarded a Class of 2017 Senior Prize in Biology in recognition of his “academic excellence, research achievement, and intellectual contributions in biological sciences”. Tyler will begin working in the San Francisco Bay Area this fall as a Software Engineer at Yelp. Annie is also receiving her Sc.B. in Applied Math-Biology, and is a co-author on Lauren’s SWeep Inference Framework (controlling for correlation); following graduation, Annie will be working in technology at Capital One in Washington, DC. Katie is graduating with an Sc.B. in Computer Science and Religious Studies; she will be moving to Seattle to join Microsoft as a software engineer on the Shell Team of the Windows and Devices group.
We will miss Tyler, Annie, and Katie, and wish them all the best in their future endeavors! They contributed a lot to the Ramachandran Lab; luckily Annie will be close by, and Tyler and Katie will work in the lab for a bit this summer on pong.
Sahar Shahamatdar ‘13 has begun her doctoral work in the lab as an MD-PhD student; Sahar is interested in identifying ancestry-informative markers using population-genomic datasets. We are very excited to have her officially join the lab!
Graduate student Stephen Rong has passed his quals! Stephen successfully defended his thesis proposal on novel methods for detecting adaptive variants from population-genomic datasets, and answered general knowledge questions on a range of subjects in evolutionary genetics and computational biology. He will now work on writing up his first chapter on supervised learning for detecting hard and soft sweeps. Congratulations to the Candidate!
Lauren Sugden’s abstract on her SWeep Inference Framework (controlling for correlation), entitled ``An interpretable, dependence-aware composite classification framework for hard sweep detection and localization, with application to a Southern African population’’ was selected for one of 16 talks at the New York Area Population Genomics Workshop 2017. We are excited for her to tell others about this project’s results!
Sohini is one of three faculty profiled by Genome Biology in A two-fold challenge: the experience of women of color in genomics. It’s an honor to be included in this piece discussing what can be done to encourage and support women of color in STEM fields.
Lauren Alpert Sugden and Sohini Ramachandran have written a review entitled “Integrating the signatures of demic expansion and archaic introgression in studies of human population genomics” out in Current Opinion in Genetics and Development. The review is part of a special issue edited by Josh Akey and Anna Di Rienzo on the genetics of human origin. We look forward to reading the entire issue!
Graduate student’s Priya Nakka’s first paper from the lab has been accepted by Genetics! The paper is entitled “Gene and network analysis of common variants reveals novel associations in multiple complex diseases” by Nakka, Raphael, and Ramachandran. PEGASUS, the new method described in this publication, is freely available at github (also see our PEGASUS project site for more information). Congratulations to all the authors!
pong has been released in an Original Paper in Bioinformatics. pong (latest version: 1.3.4) is freely available and can be installed using the Python package management system pip. pong’s source code is available at https://github.com/abehr/pong. Congratulations to all the authors!
Our postdoc, Julia Palacios, co-advised by John Wakeley at Harvard, has accepted a tenure-track faculty position at Stanford University. She will be an Assistant Professor in the Departments of Statistics and Biomedical Data Science, beginning Fall 2016. During her time in the Ramachandran Lab, Julia has been funded by our NSF CAREER award and by Brown’s CCMB. We are very excited for her next chapter, and look forward to continuing our collaboration!
Sohini has been awarded Brown’s Henry Merritt Wriston Fellowship for 2016-2017; the fellowship is named for Brown’s 11th President, and is awarded each year to junior faculty members who have achieved a record of excellence in teaching and scholarship during their first years at Brown. We are grateful for this recognition, and the award comes with one semester’s leave, which Sohini will take during Fall 2016.
Our graduate student Stephen Rong has received a 2016 NSF Graduate Research Fellowship, which will fund him for up to three years during his graduate work. Stephen won this amidst very stiff competition, which is detailed in the NSF press release. He is the third Computational Biology graduate student to receive an NSF graduate fellowship, following in the footsteps of Raphael Lab members Max Leiserson and Ashley Conard. Congratulations, Stephen!
Our R01 (PI: Ramachandran) entitled ``Novel statistical methods to localize genomic elements underlying adaptive evolution’’ will be funded by the National Institute of General Medical Sciences. The research includes collaborative efforts with the Raphael Lab at Brown University and the Henn Lab at Stony Brook University, and will allow us to gain new insight into the interaction between selection and dynamic population histories in generating human genetic diversity.
A newly updated version of pong is available (hosted on PyPI) and can be installed with pip.
This version of pong operates without internet access.
For users with previous pong installations, we recommend running the following commands:
pip uninstall pong pip install --no-cache-dir pong
These will ensure that pong’s old directory structure is eliminated and pip grabs the new version of pong instead of installing from a local cached version.
Our graduate student Priya Nakka passed her qualifying exam and advanced to candidacy on December 18, 2015, successfullying defending her thesis proposal entitled ``Understanding the evolutionary history of genes underlying complex phenotypes’’ and answering general knowledge questions on a range of subjects in computational biology and population genetics.
Here is Priya, celebrating in the lab after her exam:
pong, our new software for processing and visualizing output from clustering inference (e.g., STRUCTURE and ADMIXTURE Q matrices), has been released! pong is freely available and can be installed using the Python package management system pip. For supporting documentation and an example dataset based on the 1000 Genomes, please see the projects subpage or the Ramachandran Lab Data Repository.
Our submitted paper (Behr, Liu, Liu-Fang, Nakka, and Ramachandran) describing pong’s algorithm and comparing it against state-of-the-art methods can be found on bioRxiv. A screenshot of pong’s D3.js visualization is shown below:
The entire lab was able to present at the first Probabilistic Modeling in Genomics meeting, held at Cold Spring Harbor in October 2015. Julia’s abstract, entitle ``Inference of population size trajectories with Tajima’s coalescent’’ was selected as one of the 36 talks presented, while Lauren, Priya, and Stephen presented posters and got lots of great feedback. We look forward to next year’s meeting in Oxford, UK!
Here are (L to R) Henn Lab members Meng Lin and Elizabeth, Priya, Raphael Lab member Matt Reyna, Stephen, and Lauren at the lobster banquet!
Our work will be presented in a series of sessions at SMBE 2015 in Vienna, Austria:
Longtime collaborator Nicole Creanza will present poster 170C, entitled ``Detailed signatures of human evolutionary history in linguistic and genetic data” (Creanza, Feldman, and Ramachandran). Nicole is also chairing a symposium on cancer as a Darwinian process.
Postdoc Julia Palacios will present poster 545D, entitled ``Sideways demographic inference with Gaussian processes” (Palacios, Wakeley, and Ramachandran).
Shaila Musharoff, graduate student in the Bustamante group at Stanford, is co-advised by Sohini and will present talk 17.9 entitled ``Modeling population size changes leads to accurate inference of sex-biased demographic events” (Musharoff, Shringarpure, Bustamante, and Ramachandran).
Sohini will present postdoc Lauren Alpert Sugden’s work in talk 23.13, entitled ``Novel probabilistically interpretable methods for localizing targets of selective sweeps”.
Looking forward to an exciting and productive meeting!
Effective July 1, 2015, Sohini’s title will be the Manning Assistant Professor of Ecology and Evolutionary Biology. This endowed assistant professorship provides additional funding for the Ramachandran Lab, and we are grateful for the recognition it brings to the work of the Lab.
Aaron and Maya have been integral lab members for the past two years and will be receiving their college diplomas on Sunday in Brown’s 247th Commencement Exercises. Maya will receive her Sc.B. in Applied Math-Biology with Honors; her thesis was entitled “Statistical methods to distinguish classic selective sweeps from bottlenecks in genome-wide data”. Aaron will receive his A.B. in Computer Science, and his Sc.B. in Biology with Honors; his thesis was entitled “pong: a network-graphical approach to the inference of population structure”.
We will be miss Aaron and Maya, but luckily they are staying close by! After graduation, Maya will be studying at the New England Conservatory, continuing to develop her amazing talents as a violinist. Aaron will join Oracle’s Big Data Discovery team in Cambridge this July, by which time we plan to have submitted a paper based on his thesis work. Aaron will work in the lab in June and July, along with Gracie and Katie to release pong.
Congratulations, Maya and Aaron!
Two undergraduates are joining the lab for the summer, and will work on implementing the D3-based visualization of population structure to complete Aaron Behr’s thesis project. We are very excited to welcome Katie Liu (a sophomore at Brown concentrating in Computer Science) and Gracie Fang (a sophomore at Wellesley College concentrating in Computer Science) to the group. Gracie is funded by an REU supplement to our CAREER grant, NSF DBI-1452622.
Here are (L to R) Aaron, Stephen, Katie, Gracie, and Priya at a welcome dinner for our newest members!
Julia’s first paper (Palacios, Wakeley, and Ramachandran: “Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies”) has been posted to biorxiv and submitted for peer review. We are excited to share these results with other researchers, and this is our first paper developed under our NSF CAREER proposal.
The link to the paper is here.
SR and the lab have received funding from the National Science Foundation for the next 5 years (2/2015-1/2020) to support our project “CAREER: Next-generation inference of evolutionary parameters from genome-wide sequence data”. The project will lead to the development of a suite of novel statistical and computational methods for inferring detailed evolutionary histories from whole-genomes of multiple individuals. In the immediate future, the grant (totaling $1,029,319) will support postdoc Dr. Julia Palacios and our graduate students. This research will be integrated with an education plan that consists of multiple activities intended to introduce young women in high school to computer science and biology research, a core goal of the Ramachandran lab.
More information about the faculty members at Brown who received early career awards in 2015.
Our paper in collaboration with Merritt Ruhlen, Marcus Feldman, and Noah Rosenberg is out in the Proceedings of the National Academy of Sciences. Find the paper here; press coverage from Brown University (a conversation with SR) is here; and we got press coverage from The Atlantic. Congratulations to all the authors, especially first author Dr. Nicole Creanza!
Postdoc Dr. Lauren Alpert has had her talk accepted at the SMBE Satellite Meeting in Hameau de l’etoile, which is near Montpelier, France. The meeting topic is “Investigating biological adaptation with NGS: data and models” and Lauren will be talking about machine learning approaches she has developed for identifying loci under adaptation from genomic data. Congrats, Lauren!
Our paper in collaboration with Kate Smith and CC Chen (with undergraduate coauthors Michael Goldberg and Jane Chen) is out in the Journal of the Royal Society Interface. It received press from Yahoo!, Voice of America, New Scientist, International Business Times, Times of India, Journalist’s Resource, and Healio Infectious Disease News. Congratulations to all the authors!
Dr. Julia Palacios, a postdoc in the lab, has been named a Candidate [Candidato a Investigador Nacional] by the National System of Researchers of Mexico (SNI) from 01/01/2015-12/31/2017. If Julia becomes a PI in Mexico, her lab will gain additional funds due to this nomination. Congratulations, Julia!
Stephen Rong has just joined the lab as a graduate student. Stephen graduate from Washington University in St. Louis in 2014, and did undergraduate research in the Queller Lab while majoring in both Mathematics and Anthropology. He will be working towards his doctorate in Computational Biology and EEB. Welcome Stephen!
As part of Brown’s 250th Anniversary, many faculty members have been profiled in conversation with Professor Richard Fishman. See Sohini’s conversation with Richard about being a faculty member at Brown here on YouTube.
Dr. Lauren Alpert Sugden has joined the lab as a postdoctoral fellow. Lauren did her doctoral work with Chip Lawrence at Brown’s Division of Applied Mathematics and graduated this past May. During her dissertation work, she collaborated with Rob Reenan’s lab on modeling RNA editing. She is working on developing a probabilistically interpretable method for detecting selection from genome-wide data. Welcome Lauren!
Aaron Behr ‘15 joins the lab starting this summer to develop a computational method that aligns cluster membership inferred by programs like ADMIXTURE across multiple numbers of clusters. Aaron’s work is funded by an UTRA. Welcome Aaron!
The annual meeting of the Society of Molecular Biology and Evolution has begun, and the Ramachandran Lab is well-represented: SR is co-chairing a symposium entitled “Out of Africa: Humans, commensals, pathogens, oh my!” with collaborator Brenna Henn; Nicole Creanza is presenting work on evolution of language (SR is the senior author); Shaila Musharoff of the Bustamante Lab at Stanford is presenting a poster entitled “A Novel Likelihood Ratio Test for Sex-Biased Demography and the Effect of Cryptic Sex-Bias on the Estimation of Demographic Parameters” (SR is a senior author).
As part of her doctoral requirements, Priya is conducting research with Ben Raphael’s Lab this summer, working on applying the method HotNet to common variants. Stay tuned for the results from this collaborative project!
The lab and PI receive press in The Scientist (“Scientist to Watch”) and Nature (“Turning Point”).
Professor Ramachandran is named a 2012 Pew Scholar, which provides a $240,000 grant to support the lab’s research.
Alyna Khan, undergraduate member of the lab, graduates from Brown. Alyna’s undergraduate thesis in Biology is entitled “Analysis of linguistic variation as a means of understanding human migration”. Congratulations Alyna!
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