Walter Eckalbar, PhD

Assistant Professor
Medicine
[email protected]
+1 415 514-4372
Publications: 

Author Correction: Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation.

Nature metabolism

Inoue F, Eckalbar WL, Wang Y, Murphy KK, Matharu N, Vaisse C, Ahituv N

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.

Nature communications

Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG

Host-Microbe Multiomic Profiling Reveals Age-Dependent COVID-19 Immunopathology.

medRxiv : the preprint server for health sciences

Van Phan H, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, Van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns C, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, IMPACC Network, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR

Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study.

Nature communications

Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, Dandekar R, Shannon CP, Sekaly RP, Ehrlich LIR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, van Bakel H, Kim-Schulze S, Hafler DA, Levy O, Kraft M, Bime C, Haddad EK, Calfee CS, Erle DJ, Langelier CR, Eckalbar W, Bosinger SE, IMPACC Network, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Maecker HT, Altman MC, Montgomery RR, Becker PM, Rouphael N

Single-cell and spatial multi-omics identify innate and stromal modules targeted by anti-integrin therapy in ulcerative colitis.

bioRxiv : the preprint server for biology

Mennillo E, Kim YJ, Rusu I, Lee G, Dorman LC, Bernard-Vazquez F, Bain JL, Patel R, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Naser M, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG

Host-Microbe Multi-omic Profiling Identifies a Unique Program of COVID-19 Inflammatory Dysregulation in Solid Organ Transplant Recipients.

Research square

Langelier C, Pickering H, Schaenman J, Phan H, Maguire C, Tsitsiklis A, Rouphael N, Higuita N, Atkinson M, Breckenridge S, Fung M, Messer W, Network I, Salehi-Rad R, Altman M, Becker P, Bosinger S, Eckalbar W, Hoch A, Jayavelu N, Kim-Schulze S, Jenkins M, Kleinstein S, Krammer F, Maecker H, Ozonoff A, Diray-Arce J, Shaw A, Baden L, Levy O, Reed E

Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants.

bioRxiv : the preprint server for biology

Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Network I, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf J, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Augustine AD, Sekaly RP, Ehrlich LIR, Fourati S, Peters B, Kleinstein SH, Guan L

Comparative proteomic analysis of tail regeneration in the green anole lizard, Anolis carolinensis.

Natural sciences (Weinheim, Germany)

Xu C, Hutchins ED, Eckalbar W, Pendarvis K, Benson DM, Lake DF, McCarthy FM, Kusumi K

Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19.

Research square

Fragiadakis G, Neyton L, Patel R, Sarma A, Consortium UC, Willmore A, Haller SC, Kangelaris K, Eckalbar W, Erle D, Krummel M, Hendrickson C, Woodruff P, Langelier C, Calfee C

Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients.

Cell reports. Medicine

Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K, IMPACC Network, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH

Patients with abdominal aortic aneurysms have reduced levels of microRNA 122-5p in circulating exosomes.

PloS one

Lopez JL, Ramirez JL, Phu TA, Duong P, Bouchareychas L, Kuhrau CR, Lin PY, Eckalbar WL, Barczak AJ, Rudolph JD, Maliskova L, Conte MS, Vartanian SM, Raffai RL, Oskowitz AZ

Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma.

Cell genomics

Koh KD, Bonser LR, Eckalbar WL, Yizhar-Barnea O, Shen J, Zeng X, Hargett KL, Sun DI, Zlock LT, Finkbeiner WE, Ahituv N, Erle DJ

A functional circuit formed by the autonomic nerves and myofibroblasts controls mammalian alveolar formation for gas exchange.

Developmental cell

Zhang K, Yao E, Wang SA, Chuang E, Wong J, Minichiello L, Schroeder A, Eckalbar W, Wolters PJ, Chuang PT

The Type 2 Asthma Mediator IL-13 Inhibits SARS-CoV-2 Infection of Bronchial Epithelium.

American journal of respiratory cell and molecular biology

Bonser LR, Eckalbar WL, Rodriguez L, Shen J, Koh KD, Ghias K, Zlock LT, Christenson S, Woodruff PG, Finkbeiner WE, Erle DJ

Bile acid-sensitive tuft cells regulate biliary neutrophil influx.

Science immunology

O'Leary CE, Sbierski-Kind J, Kotas ME, Wagner JC, Liang HE, Schroeder AW, de Tenorio JC, von Moltke J, Ricardo-Gonzalez RR, Eckalbar WL, Molofsky AB, Schneider C, Locksley RM

Molecular programs of fibrotic change in aging human lung.

Nature communications

Lee S, Islam MN, Boostanpour K, Aran D, Jin G, Christenson S, Matthay MA, Eckalbar WL, DePianto DJ, Arron JR, Magee L, Bhattacharya S, Matsumoto R, Kubota M, Farber DL, Bhattacharya J, Wolters PJ, Bhattacharya M

Inhibitor Combinations Reveal Wiring of the Proteostasis Network in Prostate Cancer Cells.

Journal of medicinal chemistry

Shkedi A, Adkisson M, Schroeder A, Eckalbar WL, Kuo SY, Neckers L, Gestwicki JE

CCR2 deficiency alters activation of microglia subsets in traumatic brain injury.

Cell reports

Somebang K, Rudolph J, Imhof I, Li L, Niemi EC, Shigenaga J, Tran H, Gill TM, Lo I, Zabel BA, Schmajuk G, Wipke BT, Gyoneva S, Jandreski L, Craft M, Benedetto G, Plowey ED, Charo I, Campbell J, Ye CJ, Panter SS, Nakamura MC, Eckalbar W, Hsieh CL

Cbl-b deficiency prevents functional but not phenotypic T cell anergy.

The Journal of experimental medicine

Nguyen TTT, Wang ZE, Shen L, Schroeder A, Eckalbar W, Weiss A

Flow Cytometric Analysis and Purification of Airway Epithelial Cell Subsets.

American journal of respiratory cell and molecular biology

Bonser LR, Koh KD, Johansson K, Choksi SP, Cheng D, Liu L, Sun DI, Zlock LT, Eckalbar WL, Finkbeiner WE, Erle DJ

Genomic characterization of the adolescent idiopathic scoliosis associated transcriptome and regulome.

Human molecular genetics

Makki N, Zhao J, Liu Z, Eckalbar WL, Ushiki A, Khanshour AM, Wu J, Rios J, Gray RS, Wise CA, Ahituv N

A defect in COPI-mediated transport of STING causes immune dysregulation in COPA syndrome.

The Journal of experimental medicine

Deng Z, Chong Z, Law CS, Mukai K, Ho FO, Martinu T, Backes BJ, Eckalbar WL, Taguchi T, Shum AK

Whole Genome Sequencing Identifies Novel Functional Loci Associated with Lung Function in Puerto Rican Youth.

American journal of respiratory and critical care medicine

Lee EY, Mak AC, Hu D, Sajuthi S, White MJ, Keys KL, Eckalbar W, Bonser L, Huntsman S, Urbanek C, Eng C, Jain D, Abecasis G, Kang HM, Germer S, Zody MC, Nickerson DA, Erle D, Ziv E, Rodriguez-Santana J, Seibold MA, Burchard EG

On the cross-population generalizability of gene expression prediction models.

PLoS genetics

Keys KL, Mak ACY, White MJ, Eckalbar WL, Dahl AW, Mefford J, Mikhaylova AV, Contreras MG, Elhawary JR, Eng C, Hu D, Huntsman S, Oh SS, Salazar S, Lenoir MA, Ye JC, Thornton TA, Zaitlen N, Burchard EG, Gignoux CR

Noncoding SNPs associated with increased GDF15 levels located in a metformin-activated enhancer region upstream of GDF15.

Pharmacogenomics

Linhares ND, Pereira DA, Conceição IM, Franco GR, Eckalbar WL, Ahituv N, Luizon MR

Development of allergic airway immunity depends on MARCH1-mediated ubiquitination of MHCII and CD86 in dendritic cells.

The Journal of Immunology

Carlos A Castellanos, Xin Ren, Hong-Erh Liang, Brian J Laidlaw, Andrea Barczak, Joshua Rudolph, Walter L Eckalbar, Xiaozhu Huang, Jason G Cyster, Richard M Locksley, David J Erle, Satoshi Ishido, Jeoung-Sook Shin

Comparative genomic characterization of the multimammate mouse Mastomys coucha.

Molecular biology and evolution

Hardin A, Nevonen KA, Eckalbar WL, Carbone L, Ahituv N

CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency.

Matharu N, Rattanasopha S, Tamura S, Maliskova L, Wang Y, Bernard A, Hardin A, Eckalbar WL, Vaisse C, Ahituv N

Cell Fate Analysis in Fetal Mouse Lung Reveals Distinct Pathways for TI and TII Cell Development.

American journal of physiology. Lung cellular and molecular physiology

Gonzalez R, Leaffer D, Chapin C, Gillespie A, Eckalbar W, Dobbs LG

Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards.

Nature ecology & evolution

Lind AL, Lai YYY, Mostovoy Y, Holloway AK, Iannucci A, Mak ACY, Fondi M, Orlandini V, Eckalbar WL, Milan M, Rovatsos M, Kichigin IG, Makunin AI, Johnson Pokorná M, Altmanová M, Trifonov VA, Schijlen E, Kratochvíl L, Fani R, Velenský P, Rehák I, Patarnello T, Jessop TS, Hicks JW, Ryder OA, Mendelson JR, Ciofi C, Kwok PY, Pollard KS, Bruneau BG

The epigenetic regulator ATF7ip inhibits Il2 expression, regulating Th17 responses.

The Journal of experimental medicine

Sin JH, Zuckerman C, Cortez JT, Eckalbar WL, Erle DJ, Anderson MS, Waterfield MR

Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation.

Nature metabolism

Inoue F, Eckalbar WL, Wang Y, Murphy KK, Matharu N, Vaisse C, Ahituv N

Singling out Th2 cells in eosinophilic esophagitis.

The Journal of clinical investigation

Eckalbar WL, Erle DJ

Abstract TP130: Transcriptome Analysis of Mononuclear Cell Responses After Ischemic Stroke in Type 2 Diabetic Mice.

Stroke

Shunsuke Omodaka, Atsushi Kanoke, Christine Hsieh, Walter L Eckalbar, Jialing Liu

CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency.

Science (New York, N.Y.)

Matharu N, Rattanasopha S, Tamura S, Maliskova L, Wang Y, Bernard A, Hardin A, Eckalbar WL, Vaisse C, Ahituv N

Integrative approach identifies corticosteroid response variant in diverse populations with asthma.

The Journal of allergy and clinical immunology

Levin AM, Gui H, Hernandez-Pacheco N, Yang M, Xiao S, Yang JJ, Hochstadt S, Barczak AJ, Eckalbar WL, Rynkowski D, Samedy LA, Kwok PY, Pino-Yanes M, Erle DJ, Lanfear DE, Burchard EG, Williams LK

Tissue signals imprint ILC2 identity with anticipatory function.

Nature immunology

Ricardo-Gonzalez RR, Van Dyken SJ, Schneider C, Lee J, Nussbaum JC, Liang HE, Vaka D, Eckalbar WL, Molofsky AB, Erle DJ, Locksley RM

Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma.

American journal of respiratory and critical care medicine

Mak ACY, White MJ, Eckalbar WL, Szpiech ZA, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD, Burchard EG

Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards.

Genome biology and evolution

Tollis M, Hutchins ED, Stapley J, Rupp SM, Eckalbar WL, Maayan I, Lasku E, Infante CR, Dennis SR, Robertson JA, May CM, Crusoe MR, Bermingham E, DeNardo DF, Hsieh ST, Kulathinal RJ, McMillan WO, Menke DB, Pratt SC, Rawls JA, Sanjur O, Wilson-Rawls J, Wilson Sayres MA, Fisher RE, Kusumi K

Genomic Characterization of Metformin Hepatic Response.

PLoS genetics

Luizon MR, Eckalbar WL, Wang Y, Jones SL, Smith RP, Laurance M, Lin L, Gallins PJ, Etheridge AS, Wright F, Zhou Y, Molony C, Innocenti F, Yee SW, Giacomini KM, Ahituv N

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus.

PLoS genetics

Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N

Transcriptomic and epigenomic characterization of the developing bat wing.

Nature genetics

Eckalbar WL, Schlebusch SA, Mason MK, Gill Z, Parker AV, Booker BM, Nishizaki S, Muswamba-Nday C, Terhune E, Nevonen KA, Makki N, Friedrich T, VanderMeer JE, Pollard KS, Carbone L, Wall JD, Illing N, Ahituv N

A genome-wide association study identifies four novel susceptibility loci underlying inguinal hernia.

Nature communications

Jorgenson E, Makki N, Shen L, Chen DC, Tian C, Eckalbar WL, Hinds D, Ahituv N, Avins A

DYNAMICS IN AN SIR MODEL WHEN VACCINATION DEMAND FOLLOWS PRIOR LEVELS OF DISEASE PREVALENCE.

Advances in Complex Systems

JOHN C. ECKALBAR, PETE TSOURNOS, WALTER L. ECKALBAR

Integrated Transcriptomic, Proteomic, and MicroRNA Data Identify Key Regulators of Developmental and Repair Processes During Tail Regeneration in the Green Anole Lizard.

The FASEB Journal

Elizabeth Hutchins, Walter Eckalbar, Ken Pendarvis, Fiona McCarthy, Douglas Lake, Kenro Kusumi

A PAX1 enhancer locus is associated with susceptibility to idiopathic scoliosis in females.

Nature communications

Sharma S, Londono D, Eckalbar WL, Gao X, Zhang D, Mauldin K, Kou I, Takahashi A, Matsumoto M, Kamiya N, Murphy KK, Cornelia R, Herring JA, Burns D, Ahituv N, Ikegawa S, Gordon D, Wise CA

Genome-wide discovery of drug-dependent human liver regulatory elements.

PLoS genetics

Smith RP, Eckalbar WL, Morrissey KM, Luizon MR, Hoffmann TJ, Sun X, Jones SL, Force Aldred S, Ramamoorthy A, Desta Z, Liu Y, Skaar TC, Trinklein ND, Giacomini KM, Ahituv N

Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.

Translational psychiatry

Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N

Transcriptomic analysis of tail regeneration in the lizard Anolis carolinensis reveals activation of conserved vertebrate developmental and repair mechanisms.

PloS one

Hutchins ED, Markov GJ, Eckalbar WL, George RM, King JM, Tokuyama MA, Geiger LA, Emmert N, Ammar MJ, Allen AN, Siniard AL, Corneveaux JJ, Fisher RE, Wade J, DeNardo DF, Rawls JA, Huentelman MJ, Wilson-Rawls J, Kusumi K

Activation of musculoskeletal development and repair mechanisms in the regenerating lizard tail (344.7).

The FASEB Journal

Elizabeth Hutchins, Minami Tokuyama, Walter Eckalbar, Rebecca Fisher, Alan Rawls, Jeanne Wilson-Rawls, Kenro Kusumi

A large-scale view of the evolution of amniote development: insights from somitogenesis in reptiles.

Current opinion in genetics & development

Kusumi K, May CM, Eckalbar WL

Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes.

BMC genomics

Eckalbar WL, Hutchins ED, Markov GJ, Allen AN, Corneveaux JJ, Lindblad-Toh K, Di Palma F, Alföldi J, Huentelman MJ, Kusumi K

Scoliosis and segmentation defects of the vertebrae.

Wiley interdisciplinary reviews. Developmental biology

Eckalbar WL, Fisher RE, Rawls A, Kusumi K

Somitogenesis in the anole lizard and alligator reveals evolutionary convergence and divergence in the amniote segmentation clock.

Developmental biology

Eckalbar WL, Lasku E, Infante CR, Elsey RM, Markov GJ, Allen AN, Corneveaux JJ, Losos JB, DeNardo DF, Huentelman MJ, Wilson-Rawls J, Rawls A, Kusumi K

Major shifts in the evolution of somitogenesis: The reptile Anolis carolinensis represents a fourth type of segmentation clock among vertebrates.

Developmental biology

Walter Eckalbar, Eris Lasku, Carlos Infante, Dale DeNardo, Jonathan Losos, Alan Rawls, Jeanne Wilson-Rawls, Kenro Kusumi

Dynamics of an epidemic model with quadratic treatment.

Nonlinear Analysis Real World Applications

John C. Eckalbar, Walter L. Eckalbar

Developmental gene activation in tail regeneration in the lizard, Anolis carolinensis.

Developmental biology

Glenn J. Markov, Rajani George, Nataliya Emmert, Michael Ammar, Walter L. Eckalbar, Juli Wade, Dale DeNardo, Alan Rawls, Jeanne Wilson-Rawls, Kenro Kusumi

Identification of a divergent notch pathway delta ligand in the segmentation clock of the reptile, Anolis carolinensis.

Developmental biology

Walter L. Eckalbar, Carlos Infante, Nataliya Emmert, Jonathan Losos, Alan Rawls, Jeanne Wilson-Rawls, Kenro Kusumi

Genetic Regulation of Somite and Early Spinal Patterning.

The Genetics and Development of Scoliosis

Kenro Kusumi, Walter Eckalbar, Olivier Pourquié

How many genes are part of the oscillatory network regulating somitogenesis? Developmental analysis and mathematical modeling of genes identified in functional genomic screens.

Developmental biology

Walter Eckalbar, Will Sewell, Allanceson Smith, Eric Huynh, Joshua Gibson, Jeanne Wilson-Rawls, Michael Caplan, Kenro Kusumi