News and Events

How BREATH works


DCC programmers prepared a presentation called Using Semantic Web Technologies to Power LungMAP, a Molecular Data Repository at the International Workshop on Semantic Big Data. The goal of the workshop is to bring together academic researchers and industry practitioners to address the challenges and report and exchange the research findings in Semantic Big Data, including new approaches, techniques and applications, make substantial theoretical and empirical contributions to, and significantly advance the state of the art of Semantic Big Data. LungMAP slide presentation is available for viewing. A few slides from the presentation are shown below.


sbd17 presentation 12  sbd17 presentation 11

2017 Gordon Conference/Seminar: Lung Development, Injury and Repair


The Gordon Research Seminar on Lung Development, Injury and Repair is a unique forum for graduate students, post-docs, and other scientists with comparable levels of experience and education to present and exchange new data and cutting edge ideas. This 2017 meeting will focus on new frontiers in pulmonary health and disease, highlighting in vitroin vivo and clinical studies linking causes and mechanisms which are paving ways for new therapies and treatments. 

The 2017 GRC Conference is dedicated to revisiting our understanding of key processes underlying lung development, injury and repair in the context of age, environment and species, with the hope of better understanding disease development and to discover novel therapeutic approaches.

LungMAP Co-investigator Thomas Mariani from the University of Rochester Medical Center (LungMAP Human Tissue Core) will moderate a discussion on Day 2 Monday August 21 called "Layering Regulatory Networks of Differentiation into a Blueprint" which includes a presentation by Yan Xu of LungMAP research site, Cincinnati Children's Hospital Medical Center. Her talk is entitled "Transcriptional Programming of Respiratory Epithelia at Single Cell Level".

On Day 4 Thursday Aug 24, LungMAP principal investigator Naftali Kaminski from Yale University will host a session called "The Rewards of Systems Biology in an Omics Age" which features a presentation by Ziv Bar-Joseph of LungMAP research site Carnegie Mellon University called "Reconstructing Regulatory Networks from Time Series Single Cell Lung Development Data".

Presentation materials from these sessions will be provided here in the coming weeks.

For a complete program see the conference link.



Rare Pediatric Respiratory Disease Conference


Rare pediatric respiratory disorders, including childhood interstitial and diffuse lung diseases (chILD), primary ciliary dyskinesia (PCD) and lung involvement in systemic juvenile inflammatory arthritis (sJIA) are high-morbidity, often life-threatening disorders that are poorly understood, under-recognized, and have little evidence-based therapies. Adult diagnosis and treatment paradigms do not generally apply to these challenging clinical problems. Many of these rare disorders hold clues to understanding normal lung biology and may unravel aspects of more common diseases. Extremely rapid advancements in genomics and other systems biology techniques have revolutionized the diagnosis of rare diseases and in many cases led to new and unexpected treatments. Breakthroughs in other rare diseases have recently been catalyzed by the efforts of passionate patient advocacy groups working closely with research teams.


Listen to Grant Kolb, the youngest spokesperson at the conference explaining the importance of lung research in his life.

                                                             Grants Speech Photo 1 small

Scientific presentations are becoming available for listening and download. Check our Themes pages under Resources.   






We now have over 5000 high resolution lung images, transcriptomic, proteomic, and lipidomic data and need feedback from users on ways to make the site easier to use.

Once the group is set up, we will start the effort with a quick meeting via google hangouts and then ask you to track your experience as you work with the site. We will look to you for suggestions on how and where to make the data more accessible for users. We will acknowledge your contributions on the homepage of our website.

If you are interested in doing testing or have students who could help, please send a message to CONTACT US.

LungMAP publication (2017)


In human neonates rapid adaptation from an aqueous intrauterine environment to permanent air breathing is the rate-limiting step for extrauterine life, failure of which justifies the existence of neonatal intensive care units. The lung develops at about 4-6 weeks' gestation in humans as a ventral outpouching of the primitive foregut into the surrounding ventral mesenchyme, termed the laryngotracheal groove. At its posterior end lie progenitor cells that form a pair of bronchial tubes, from which arise all the distal epithelial structures of the lung. In humans, formation of the distal gas exchange surfaces begins in utero at about 20 weeks' gestation and is substantially established by term. Stereotypic branching of the proximal airway ends relatively early at 16-18 weeks at the bronchoalveolar duct junctions. Distally, about 5 finger-like alveolar ducts arise from each bronchoalveolar duct junction and ramify outwards towards the pleura. The majority of alveolar air sacs arise from the sides of the alveolar ducts and each of these alveoli can have up to 5 daughter alveoli arising from the outer surface as subsequent buds. At the end of each alveolar duct lie the mouths of 5 interconnected alveoli. Each family of alveoli arising from each bronchoalveolar duct junction has a different shape depending upon the limitations imposed by the pleural surface as well as the interstitial fascial planes. To obtain full article, visit the journal.

3D MMVR Human Datasets for viewing


Explore in MMVR

LungMAP at ATS 2017


See the inclusive listing of all presentations by LungMAP members at ATS Conference 2017.

New LungMAP publication (2017)


Many studies have investigated the source and role of epithelial progenitors during lung development; such information is limited for fibroblast populations and their complex role in the developing lung. In this study, we characterized the spatial location, mRNA expression and Immunophenotyping of PDGFRα+ fibroblasts during sacculation and alveolarization. Confocal microscopy identified spatial association of PDGFRα expressing fibroblasts with proximal epithelial cells of the branching bronchioles and the dilating acinar tubules at E16.5; with distal terminal saccules at E18.5; and with alveolar epithelial cells at PN7 and PN28. Immunohistochemistry for alpha smooth muscle actin revealed that PDGFRα+ fibroblasts contribute to proximal peribronchiolar smooth muscle at E16.5 and to transient distal alveolar myofibroblasts at PN7. Time series RNA-Seq analyses of PDGFRα+ fibroblasts identified differentially expressed genes that, based on gene expression similarity were clustered into 7 major gene expression profile patterns. The presence of myofibroblast and smooth muscle precursors at E16.5 and PN7 was reflected by at wo-peak gene expression profile on these days and gene ontology enrichment in muscle contraction. Additional molecular and functional differences between peribronchiolar smooth muscle cells at E16.5 and transient intraseptal myofibroblasts at PN7 were suggested by a single peakingeneexpressionatPN7 with functional enrichment in cell projection and muscle cell differentiation. Immunophenotyping of subsets of PDGFRα+ fibroblasts by flowcytometry confirmed the predicted increase in proliferation at E16.5 and PN7, and identified subsets of CD29+ myofibroblasts and CD34+ lipofibroblasts. These data can be further mined to develop novel hypotheses and valuable understanding of the molecular and cellular basis of alveolarization.

This important publication is now available!

Images from the research

sma gfp (40x) 

 sma gfp pro spc 40x stack 1 30 2014 001 pic 3


sms gfp (40x) 

sms gfp prosapc 40x zstack 2 1 30 2014 001 2



New LungMAP publication (2017)


Lung immaturity is a major cause of morbidity and mortality in premature infants. Understanding the molecular mechanisms driving normal lung development could provide insights on how to ameliorate disrupted development. While transcriptomic and proteomic analyses of normal lung development have been previously reported, characterization of changes in the lipidome is lacking. Lipids play significant roles in the lung, such as dipalmitoylphosphatidylcholine in pulmonary surfactant; however, many of the roles of specific lipid species in normal lung development, as well as in disease states, are not well defined. In this study, we used liquid chromatography-mass spectrometry (LC-MS/MS) to investigate the murine lipidome during normal postnatal lung development. Lipidomics analysis of lungs from post-natal day 7, day 14 and 6–8 week mice (adult) identified 924 unique lipids across 21 lipid subclasses, with dramatic alterations in the lipidome across developmental stages. Our data confirmed previously recognized aspects of post-natal lung development and revealed several insights, including in sphingolipid-mediated apoptosis, inflammation and energy storage/usage. Complementary proteomics, metabolomics and chemical imaging corroborated these observations. This multi-omic view provides a unique resource and deeper insight into normal pulmonary development. See the entire paper.

New LungMAP publication (2017)


Biological systems are increasingly being studied by high throughput profiling of molecular data over time. Determining the set of time points to sample in studies that profile several different types of molecular data is still challenging. Here we present the Time Point Selection (TPS) method that solves this combinatorial problem in a principled and practical way. TPS utilizes expression data from a small set of genes sampled at a high rate. As we show by applying TPS to study mouse lung development, the points selected by TPS can be used to reconstruct an accurate representation for the expression values of the non selected points. Further, even though the selection is only based on gene expression, these points are also appropriate for representing a much larger set of protein, miRNA and DNA methylation changes over time. TPS can thus serve as a key design strategy for high throughput time series experiments. Supporting Website:

See the whole paper.

Introduction to LungMAP


Dr. Jeffrey Whitsett from the LungMAP Research Center at Cincinnati Children’s Hospital Medical Center gives a brief overview of the LungMAP Consortium and its progress.

2017 Stem Cells, Cell Therapies, and Bioengineering in Lung Biology and Diseases Conference


The conference features an exciting faculty and cutting edge presentations on the current issues in the field. A continuing focus of this meeting is to promote rising young junior faculty and trainees. 

Experience the mouse lung in 3D




Data+ is a project conducted by select faculty and students at Duke University. The project is designed to produce an automated process for anatomical annotation of lung tissue images. Image data and descriptive metadata used in the project are from research centers working in the LungMAP consortium. To develop algorithms for machine based annotation, the Duke students worked with staff conducting a similar effort at LungMAP Research Center, CCHMC. Data+ generated de novo segmentation rules based on metadata and image properties. For a summary and results of Data+, see this poster. To see the tool in action, see identifier-v3.mp4

A complete weekly summary of progress on development can be found here.

This effort will augment the LungMAP image annotation tool that allows a user to notate specific anatomical features directly onto an image within the web environment by placing a graphic indicator (arrow, dot or by circling an area of interest within the image) within the image. The tool links the graphic indicator to a selected ontology term to enrich a viewer experience of the image. In later release of the LungMAP website, these annotated images will be highlighted.

Gordon Research Conference


Gordon Research Conference "Tissues Niches & Resident Stem Cells in Adult Epithelia" - August 7-13, 2016, Hong Kong, China


Meeting Description

Adult epithelia regenerate during adult life due to the constant activity of stem cell pools. Stem cells maintain tissue homeostasis and repair injury by close communication with their tissue environment, known as "niche". Niches are complex, structured arrays of different cell types that guide tissue stem cell dynamics. The ultimate goal of understanding epithelial stem cell regulation is to repair or replace cells or organs damaged by injury, disease, and aging. The strategies vary from generating cell types and tissues in a dish for transplantation purposes, to directly stimulating the damaged organ in the living organism. This field has been exponentially growing for the past decade. Tissues such as human skin and cornea have already been grown in 3D cultured and used in clinics to fight otherwise incurable medical conditions. The GRC "Tissue Niches and Resident Stem Cells in Adult Epithelia” will focus on comparative principles of adult epithelial stem cell dynamics and niche signaling in the homeostasis of different tissues. This conference will include work on the molecular control of stem cell function from the epidermis and its appendages, intestine, lung, mammary gland, cornea and retina, epithelial transition zones, and emerging work from other epithelial tissues. All model organisms are welcome. We strongly believe in being inclusive, and hope to inspire a principle of alternating speakers that will allow a variety of participants to contribute to this exciting meeting over the coming years.



FASEB – The Lung Epithelium in Health and Disease – July 31 - August 5 2016, Saxtons River, VT


Conference Summary

This SRC presents emerging areas of scientific interest in lung epithelial biology in development, homeostasis, and disease. It again addresses critical issues on lung epithelial biology such as stem cells and regenerative medicine, while expanding sessions to encompass themes such as single cell analytical approaches, cell-cell communication within the epithelial compartments as well as between epithelia and stroma, and immune interactions—current subjects of high interest to the lung community with many great advances pending. It will provide opportunities not only for scientists working on lung epithelial biology, but also synergize interactions among attendees in all these fields.

This conference will (1) highlight the latest developments in epithelial barrier maintenance and its disruption during acute lung injury; (2) promote the understanding the impact of the cystic fibrosis gene on host defense to pulmonary infections; (3) connect new insights in the fields of ER stress and cell senescence to the vulnerable pulmonary epithelium of individuals at risk for pulmonary fibrosis; (4) dissect the biological distinctions between epithelial proliferation as a repair mechanism and tumorigenesis; (5) present the impact of the newest tools in single cell analysis on understanding lung development, repair, and disease; and (6) characterize epithelial-mesenchymal interrelationships that maintain lung homeostasis and orchestrate repair and regeneration. The entire program has been designed to achieve a better understanding of the key clinical research issues and how they relate to basic mechanistic investigation.

Fetal and Neonatal Lung Development


Clinical Correlates and Technologies for the Future



Alan Jobe, University of Cincinnati
Jeffrey Whitsett, Cincinnati Children's Hospital
Steven Abman, University of Colorado School of Medicine


Published: April 2016

Aspen Lung Conference


Aspen Lung Conference "Lung Transplantation: Opportunities for Repair and Regeneration" – June 8-11, 2016, Aspen, CO

Objectives of the Thomas L. Petty Aspen Lung Conference

  • To provide an international forum for leading clinicians and researchers to exchange of ideas relating to clinical problems and research of the lung.
  • To fill a recognized need in a field where knowledge is doubling every five years.
  • To focus on a single topic, exhaustively reviewing it with significant time allowed for discussion.
  • To provide the stimulus and impetus to further research in pulmonary medicine.

New publication from LungMAP research center...


New publication from LungMAP research center, Cincinnati Children's Hospital Medical Center, presents a generally applicable analytic pipeline (SINCERA) for processing single cell RNA-seq data from a whole organ or sorted cells.

2015 Gordon Research Conference


Translating Lung Biology to Respiratory Medicine

August 16-21, 2015
Proctor Academy
Andover, NH

Chair: Thomas Mariani

Thomas Mariani is a LungMAP investigator working with the Human Tissue Core at University of Rochester Medical Center.

Vice Chairs: Andreas Guenther & Jason Rock

The 2015 Gordon Research Conference on Lung Development, Injury and Repair will assemble and immerse a group of world-class investigators (and trainees) in translational scientific sessions that simultaneously address basic developmental and homeostatic lung biology mechanisms and their impact upon respiratory health and disease. The theme for the 2015 conference is "Translating Lung Biology to Respiratory Medicine" and will include sessions focused upon facilitating interaction between basic and clinician scientists. By bringing together a diverse and outstanding group of investigators, who will present cutting-edge scientific and technical advances in these related fields, we hope to encourage creative and multidisciplinary approaches necessary for the development of innovative and effective therapies.

Unique features of this conference include the breadth of concepts and mechanisms to be considered, spanning topics from respiratory infections to personalized medicine, with an emphasis upon controversies in the field and future research needs. Exceptional abstracts submissions will be considered for short platform presentations, providing a chance for new investigators to present their research. Furthermore, an associated Gordon Research Seminar (GRS) will be held prior to the GRC. This venue is an outstanding and unique opportunity for a small number of trainees and junior professionals to interact, and to discuss their research, while under the stewardship of senior leaders in the field.

LungMAP Steering Committee Chair and LungMAP Principal Investigator Jeffrey Whitsett will give a presentation on Monday August 17: 

7:30 pm - 8:00 pm Jeffrey Whitsett (Cincinnati Children's Hospital Medical Center, USA)
"LungMAP: A Molecular Atlas for Lung Development"

Related Meeting

This GRC will be held in conjunction with the "Lung Development, Injury & Repair" Gordon Research Seminar (GRS). Those interested in attending both meetings must submit an application for the GRS in addition to an application for the GRC. Refer to the associated GRS program page for more information.


Aspen Lung: 2015 Annual Meeting


Thomas L. Petty Aspen Lung Conference
58th Annual Meeting
June 10-13, 2015
"Asthma 2015: Mechanisms to Personalized Medicine"
Monica Kraft, M.D., Chair
Anthony N. Gerber, M.D., Ph.D., Co-Chair Stanley J. Szefler, M.D., Co-Chair Michael E. Wechsler, M.D., MMSc, Co-Chair

2015 ATS International Conference


The ATS 2015 President Symposium: "How to Cure a Disease: The Cystic Fibrosis Story"

Whether cystic fibrosis is your primary research or clinical focus or you have dedicated yourself to other respiratory diseases, this symposium will describe how our research into CF may serve as a roadmap and how partnerships between patient organizations, clinicians, scientists, and industry can be transformative.


Video: Jeff Whitsett, American Thoracic Society


Dr. Whitsett will give a Presidential Plenary Lecture at the American Thoracic Society on May 20, 2015, at 8:30 am in the Bellco Theatre Section 2. Observations about lung development research are presented here.

Dr. Whitsett will give the following presentations during the conference:




Event / Title

May 19, 2015


5 – 7 pm

Embassy Suites in the Cripple Creek, Ballroom, 2nd Floor


Neonatal and Developing Lung Interest Group  - Invited Speaker

“Neonatal Lung Research -  the Next Decade”

May 20, 2015

8:30 am


Bellco Theatre Section 2

#68697 Session: DS7 Lung Development and Disease: Lessons from Newborn Infants (speaking time: 45 min.)

May 20, 2015

12:15 pm


Room 205/207 (Street Level)

#61042 Session: L25 Single Cell RNA Analysis - Molecular Atlas of Lung Development (speaking time: 15 min.)

J. Whitsett is the 4th presentation of 5.

May 20, 2015

2:45 pm

Room 201/203 (Street Level)

#A6088 Session: D96 Building the Conducting Airways and Alveolar Gas Exchange Region of the Primate – Lung Development and Neonatal Lung Disease

(Mini Symposium – speaking time: 15 min.)

J. Whitsett is the 6th presentation of 8.

Several LungMAP submissions are accepted for presentation:

ID 67473 Identifying the Heterogeneity of Pulmonary Mesenchymal Cell Lineages Via Single Cell RNA-Seq Analysis
Mini Symposium
SUNDAY, MAY 17, 2015
2:15 PM-4:15 PM

ID 66469 Indeterminate Differentiation of Peripheral Respiratory Epithelial Cells in Idiopathic Pulmonary Fibrosis (IPF)
Poster Discussion Session
MONDAY, MAY 18, 2015
2:15 PM-4:15 PM

ID 66172 Assessing the Quality of Human Pediatric Lung Organ Sample Preparation by the Human Tissue Core for the Molecular Atlas of Lung Development (LungMAP) Program
Thematic Poster Discussion 
TUESDAY, MAY 19, 2015
9:30 AM-4:15 PM

ID 68466 Implicating a Multi-Cellular Interactome Responsible for Integrative Regulation of Cell-Specific Differentiation, Branching Morphogenesis, Vascularization, and Organ-Scale Patterning During the Saccular Phase of Lung Development
Mini Symposium
TUESDAY, MAY 19, 2015
2:15 PM-4:15 PM

ID 66770 "SCALE": A Web-Based Tool for Mapping Gene Expression Patterns and Cell Types in the Developmental Lung at Single Cell Level

Poster Discussion Session
9:30 AM-11:30 AM

ID 67523 Transcriptional Programs Distinguishing Submucosal Glands and Bronchiolar Epithelial Cells in the Mouse Lung
Poster Discussion Session
9:30 AM-11:30 AM

ID 65359 A Comprehensive Anatomical Ontology for the Developing Lung
Poster Discussion Session
9:30 AM-11:30 AM

Session Type: Outside Organization Session
Date: Wednesday, May 20, 2015
Time: 12:15 PM - 1:15 PM

ID 67653 Video Visualization of the Airways and Alveolar Structures Using High-Resolution microCT Data and Digital Rendering
Mini Symposium
1:30 PM-3:30 PM


Colorado Convention Center: 700 14th Street, Denver, CO 80202 May 17th - May 20th


American Pediatric Society/ Society for Pediatric Research (APS/SPR)


2015 Annual Meeting

April 25-28, 2015

San Diego, CA
Plenary presidential address: Jeff Whitsett
Avery Neonatal research Award: Jeff Whitsett

ISHLT International Society for Heart and Lung Transplantation


April 15-18, 2015 in Nice, France 

Endoderm Lineages in Development and Disease (B2)


Scientific Organizers: Lori Sussel, Hans-Willem E. Snoeck, James M. Wells and Aaron M. Zorn
February 8—13, 2015 Keystone Resort, Keystone, Colorado, USA

Come see LungMAP researchers present at ATS 2016!