Reut Shabtai, a visiting Ph.D. student from the Weizmann Institute of Science, joins the lab.

Distributional bias compromises leave-one-out cross-validation

Comparative metagenomics using pan-metagenomic graphs

A generalizable cross-continent prediction of esophageal squamous cell carcinoma using the oral microbiome

Dr. Mick Aitken joined the lab as a postdoctoral research scientist.

Identification of Sample Processing Errors in Microbiome Studies Using Host Genetic Profiles

Xiaote Liu joins the lab for a research project.

Alexander Nguyen joins the lab for a research project

Yuval Antman joins the lab for a research project.

Rebecca (RC) Christensen joins the lab for her PhD.

Jinhui Liu (re)joins the lab for her MSc

Guidelines for preventing and reporting contamination in low-biomass microbiome studies

Curt Johnson joins the lab for a research project.

Danielle Soltz joins the lab for a research project

Inneloy Polanco joins the lab for a research project

Compositional transformations can reasonably introduce phenotype-associated values into sparse features (Matters Arising to Gihawi et al., 2024)

Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models

We are grateful to The Iris Fund for supporting our research through the Preterm Birth Prevention Center.

We are thankful to the March of Dimes for supporting our research on the vaginal immune-microbiome-metabolome axis in spontaneous preterm birth.

Michael Carrion joins the lab for a research project.

Justin Mathew joins the lab as a DSI Scholar.

Domain adaptation in small-scale and heterogeneous biological datasets

Early prediction of preeclampsia using the first trimester vaginal microbiome

The lab was awarded an M-PI R01 titled "Microbial biomarkers of intestinal MDR colonization after solid organ transplantation", a collaboration with Dr. Anne-Catrin Uhlemann

Microsynteny is a powerful front for microbial strain tracking

Qinyi Fang joins the lab for a research project

Kaushal Damania joins the lab for a research project

Julia Urban was awarded an F31 by NICHD!

The lab was awarded an R01 titled "A large scale investigation of the vaginal ecosystem in preeclampsia" by NICHD

Planning and analyzing a low-biomass microbiome study: A data analysis perspective

Soomin Park joins the lab for a research project.

Martin C. Liu joins the lab for his PhD.

Distributional bias compromises leave-one-out cross-validation

Domain adaptation in small-scale and heterogeneous biological datasets

Metagenomic coverage bias at transcription start sites is correlated with gene expression

Compositional transformations can reasonably introduce phenotype-associated values into sparse features

Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models

Shahd ElNaggar joins the lab.

Jinhui Liu joins the lab for a research project

Alexander Chui joins the lab for a research project

Aziz Zafar joins the lab for a rotation.

John Papanikolaou joins the lab for a research project.

The Salivary Microbiome and Predicted Metabolite Production are Associated with Barrett’s Esophagus and High Grade Dysplasia or Adenocarcinoma

Will successfully defended his PhD thesis!

Si Chen joined the lab for an MSc project.

Microdiversity of the vaginal microbiome is associated with preterm birth

pymgpipe: microbiome metabolic modeling in Python

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The salivary microbiome and predicted metabolite production are associated with progression from Barrett’s esophagus to esophageal adenocarcinoma

Natalya Mametyarova joins the lab as a software developer.

Andrey Zaznaev joins the lab for a rotation.

Alara Sutcu joins the lab for a rotation.

Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data

We are grateful to Repro Grants for funding a collaboration co-led with Drs. Helai Hesham and Noemie Elhadad to study the microbiome of the reproductive tract in endometriosis.

George Austin has successfully defended his M.Sc. thesis.

Microdiversity of the vaginal microbiome is associated with preterm birth

Kylee Dresbach-Hill joins the lab for a rotation.

Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome

Valeria A. Sanchez Estrada was awarded the 2022 DOORS Scholarship from the Promega Corporation.

Andrew Batuure joined the lab for his MS thesis project.

Jiong (Amy) Ma joins the lab as a DSI Scholar.

Kieu-Giang Nguyen joins the lab for a research project.

Rahul Natarajan joins the lab for a research project.

Jaeweon Shin joins the lab for a rotation.

William Kindschuh was awarded an F30 fellowship from NICHD.

Ann Thanh Phan joined the lab for a research project.

Valeria A. Sanchez Estrada joins the lab as a research associate.

Dr. Jesús Luévano joins the lab.

Eric Zhang joined the lab for a rotation.

Ayushi Sharma joins the lab for a research project.

Kaylene G. Morrison joined the lab for a research project.

Julia Urban joins the lab for a rotation.

Peiwen Cai joins the lab for a rotation.

We are incredibly proud of Dr. Jingqiu Liao for accepting a faculty position at Virginia Tech, in the Department of Civil and Environmental Engineering! Exciting hiring opportunities at https://leaph-lab.github.io/

Gordon Qian, a visiting Ph.D. student from the University of Hong Kong, joins the lab.

Jain Ryu joins the lab for a research project.

Jennifer Ho joined the lab for a rotation.

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates

Hannah E. Amin joined the lab for her MS thesis project.

Yusheng Jiang joins the lab for a research project.

Nicolas Beltran joined the lab for a research project.

Noga Aharony joined the lab for a rotation.

Shaurya joined the lab for a master's research project.

Embracing metagenomic complexity with a genome-free approach
(Not often do we get to write about what we're doing, instead of what we did)

The lab was awarded an R01 titled "A large scale investigation of the vaginal metagenome and metabolome and their role in spontaneous preterm birth".

Chen (Martin) Liu wins outstanding MA thesis award from the Department of Biomedical Informatics.

Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome

Yoli Meydan joined the lab as a research assistant.

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing

A reference map of potential determinants for the human serum metabolome

Aviya Litman joined the lab for a research project as a Data Science Institute (DSI) Scholar.

Linrui Tang joined the lab for her MA project.

George Austin joined the lab for a research project (with Itsik Pe'er [CS], Liat Shenhav [Rockefeller])

Dr. Jingqiu Liao joined the lab as a postdoctoral research scientist.

We are honored to be awarded the Vagelos Precision Medicine Pilot Grant, along with our collaborators Profs. Uhlemann, Gallos and Vink. This grant will support our work on mechanisms of host-microbiome interactions in spontaneous preterm birth.

Chen (Martin) Liu joined the lab for his MA project.

Tom Cohen joined the lab for a summer project (with Prof. Itsik Pe'er, CS)

Yiwei Sun joined the lab for a rotation.

Dr. Federico Baldini joined the lab as a postdoctoral research scientist.

Harry Lee joined the lab for a research project.

Xinyi Lin joined the lab.

Lily He joined the lab for a research project as a Data Science Institute (DSI) Scholar.

Thomas Tran joined the lab for a research project.

Tal received the CIFAR Azrieli Global Scholarship in the Humans & the Microbiome program.

Dr. Aya Brown Kav joined the lab as a postdoctoral research scientist.

William Kindschuh joined the lab for a rotation.

Izaak Coleman joined the lab for a rotation.

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Dagmawi Sraj joined the lab for a research project.

We are new members of the Program for Mathematical Genomics, and are affiliated with the Department of Systems Biology and the Department of Obstetrics and Gynecology.