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Journal Articles


COSMOS-Web: Intrinsically Luminous z ≳ 10 Galaxy Candidates Test Early Stellar Mass Assembly

C. M. Casey; H. B. Akins; M. Shuntov; O. Ilbert; L. Paquereau et al. 

Astrophysical Journal. 2024-04-01. Vol. 965, num. 1, p. 98. DOI : 10.3847/1538-4357/ad2075.

Open-source microscope add-on for structured illumination microscopy

M. T. M. Hannebelle; E. Raeth; S. M. Leitao; T. Lukes; J. Pospisil et al. 

Nature Communications. 2024-02-20. Vol. 15, num. 1, p. 1550. DOI : 10.1038/s41467-024-45567-7.

Uncovering a Massive z ∼ 7.7 Galaxy Hosting a Heavily Obscured Radio-loud Active Galactic Nucleus Candidate in COSMOS-Web

E. Lambrides; M. Chiaberge; A. S. Long; D. Liu; H. B. Akins et al. 

Astrophysical Journal Letters. 2024-01-01. Vol. 961, num. 1, p. L25. DOI : 10.3847/2041-8213/ad11ee.

Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions

J. Sollier; M. Basler; P. Broz; P. S. Dittrich; K. Drescher et al. 

Nature Microbiology. 2024-01-04. DOI : 10.1038/s41564-023-01566-w.

Mechanical morphotype switching as an adaptive response in mycobacteria

H. A. Eskandarian; Y-X. Chen; C. Toniolo; J. M. Belardinelli; Z. Palcekova et al. 

Science Advances. 2024-01-05. Vol. 10, num. 1, p. eadh7957. DOI : 10.1126/sciadv.adh7957.


CEERS Key Paper. VII. JWST/MIRI Reveals a Faint Population of Galaxies at Cosmic Noon Unseen by Spitzer

A. Kirkpatrick; G. Yang; A. Le Bail; G. Troiani; E. F. Bell et al. 

Astrophysical Journal Letters. 2023-12-01. Vol. 959, num. 1, p. L7. DOI : 10.3847/2041-8213/ad0b14.

Mechanopathology of biofilm-like Mycobacterium tuberculosis cords

R. Mishra; M. T. Hannebelle; V. P. Patil; A. Dubois; C. Garcia-Mouton et al. 

Cell. 2023-11-09. Vol. 186, num. 23, p. 5135-+. DOI : 10.1016/j.cell.2023.09.016.

Two Massive, Compact, and Dust-obscured Candidate z ≃ 8 Galaxies Discovered by JWST

H. B. Akins; C. M. Casey; N. Allen; M. B. Bagley; M. Dickinson et al. 

Astrophysical Journal. 2023-10-01. Vol. 956, num. 1, p. 61. DOI : 10.3847/1538-4357/acef21.

Investigating the composition and recruitment of the mycobacterial ImuA’-ImuB-DnaE2 mutasome

S. Gessner; Z. A-M. Martin; M. A. Reiche; J. A. Santos; R. Dinkele et al. 

Elife. 2023-08-02. Vol. 12, p. e75628. DOI : 10.7554/eLife.75628.

COSMOS-Web: An Overview of the JWST Cosmic Origins Survey

C. M. Casey; J. S. Kartaltepe; N. E. Drakos; M. Franco; S. Harish et al. 

Astrophysical Journal. 2023-09-01. Vol. 954, num. 1, p. 31. DOI : 10.3847/1538-4357/acc2bc.

Amidation of glutamate residues in mycobacterial peptidoglycan is essential for cell wall cross-linking

M. T. Shaku; K. L. Ocius; A. J. Apostolos; M. M. Pires; M. S. Vannieuwenhze et al. 

Frontiers In Cellular And Infection Microbiology. 2023-08-24. Vol. 13, p. 1205829. DOI : 10.3389/fcimb.2023.1205829.

Uptake-independent killing of macrophages by extracellular Mycobacterium tuberculosis aggregates

C. Toniolo; N. Dhar; J. D. McKinney 

Embo Journal. 2023-03-15. DOI : 10.15252/embj.2023113490.

Architecture for integrated RF photonic downconversion of electronic signals

N. p. O’malley; K. a. Mckinzie; M. s. Alshaykh; J. U. N. Q. I. U. Liu; D. e. Leaird et al. 

Optics Letters. 2023-01-01. Vol. 48, num. 1, p. 159-162. DOI : 10.1364/OL.474710.


Preexisting Heterogeneity of Inducible Nitric Oxide Synthase Expression Drives Differential Growth of Mycobacterium tuberculosis in Macrophages

O. Rutschmann; C. Toniolo; J. D. McKinney 

Mbio. 2022-09-19. DOI : 10.1128/mbio.02251-22.

Mycobacterium tuberculosis EspK Has Active but Distinct Roles in the Secretion of EsxA and EspB

Z. L. Lim; K. Drever; N. Dhar; S. T. Cole; J. M. Chen 

Journal Of Bacteriology. 2022-04-19. Vol. 204, num. 4, p. e00060-22. DOI : 10.1128/jb.00060-22.


Revealing Antibiotic Tolerance of the Mycobacterium smegmatis Xanthine/Uracil Permease Mutant Using Microfluidics and Single-Cell Analysis

M. Elitas; N. Dhar; J. D. McKinney 

Antibiotics-Basel. 2021-07-01. Vol. 10, num. 7, p. 794. DOI : 10.3390/antibiotics10070794.

Early invasion of the bladder wall by solitary bacteria protects UPEC from antibiotics and neutrophil swarms in an organoid model

K. Sharma; V. V. Thacker; N. Dhar; M. Clapés Cabrer; A. Dubois et al. 

Cell Reports. 2021-07-20. Vol. 36, num. 3, p. 109351. DOI : 10.1016/j.celrep.2021.109351.

Dynamic persistence of UPEC intracellular bacterial communities in a human bladder-chip model of urinary tract infection

K. Sharma; N. Dhar; V. V. Thacker; T. M. Simonet; F. Signorino-Gelo et al. 

eLife. 2021-07-05. Vol. 10, p. e66481. DOI : 10.7554/eLife.66481.

Seeing and Touching the Mycomembrane at the Nanoscale

A. Viljoen; E. Räth; J. D. Mckinney; G. Fantner; Y. F. Dufrêne et al. 

Journal of Bacteriology. 2021-04-21. Vol. 203, num. 10, p. e00547-20. DOI : 10.1128/JB.00547-20.

Rapid endotheliitis and vascular damage characterize SARS‐CoV‐2 infection in a human lung‐on‐chip model

V. V. Thacker; V. V. Thacker; K. Sharma; N. Dhar; G. Mancini et al. 

EMBO reports. 2021-04-28. Vol. 22, num. 6, p. e52744. DOI : 10.15252/embr.202152744.

Microfluidic-assisted bioprinting of tissues and organoids at high cell concentrations

L. Serex; K. Sharma; V. Rizov; A. Bertsch; J. D. McKinney et al. 

Biofabrication. 2021-04-01. Vol. 13, num. 2, p. 025006. DOI : 10.1088/1758-5090/abca80.


A lung-on-chip model of early Mycobacterium tuberculosis infection reveals an essential role for alveolar epithelial cells in controlling bacterial growth

V. V. Thacker; N. Dhar; K. Sharma; R. Barrile; K. Karalis et al. 

eLife. 2020-11-24. Vol. 9, p. e59961. DOI : 10.7554/eLife.59961.

Elicitation of efficient, protective immune responses by using DNA vaccines against tuberculosis (vol 23, pg 5655, 2005)

A. Khera; R. Singh; H. Shakila; V. Rao; N. Dhar et al. 

Vaccine. 2020-11-17. Vol. 38, num. 49, p. 7874-7875. DOI : 10.1016/j.vaccine.2020.10.011.

Do chance encounters between heterogeneous cells shape the outcome of tuberculosis infections?

C. Toniolo; O. Rutschmann; J. McKinney 

Current Opinion in Microbiology. 2020-10-10. Vol. 59, p. 72-78. DOI : 10.1016/j.mib.2020.08.008.

Bacteria: Driving polar growth

N. Dhar 

eLife. 2020-05-07. Vol. 9, p. e57043. DOI : 10.7554/eLife.57043.

A biphasic growth model for cell pole elongation in mycobacteria

M. T. M. Hannebelle; J. X. Y. Ven; C. Toniolo; H. A. Eskandarian; G. Vuaridel-Thurre et al. 

Nature Communications. 2020-01-23. Vol. 11, p. 452. DOI : 10.1038/s41467-019-14088-z.

Overlapping and essential roles for molecular and mechanical mechanisms in mycobacterial cell division

P. D. Odermatt; M. T. M. Hannebelle; H. A. Eskandarian; A. P. Nievergelt; J. D. McKinney et al. 

Nature Physics. 2020. Vol. 16, p. 57–62. DOI : 10.1038/s41567-019-0679-1.


Computational Analysis of the Mutual Constraints between Single‐Cell Growth and Division Control Models

G. Vuaridel‐Thurre; A. R. Vuaridel; N. Dhar; J. D. McKinney 

Advanced Biosystems. 2019-12-16. Vol. 3, num. 12, p. 1900103. DOI : 10.1002/adbi.201900103.

Preexisting variation in DNA damage response predicts the fate of single mycobacteria under stress

G. Manina; A. Griego; L. K. Singh; J. D. McKinney; N. Dhar 

EMBO Journal. 2019-10-04.  p. e101876. DOI : 10.15252/embj.2019101876.


Maturing Mycobacterium smegmatis peptidoglycan requires non-canonical crosslinks to maintain shape

C. Baranowski; M. A. Welsh; L-T. Sham; H. A. Eskandarian; H. C. Lim et al. 

Elife. 2018-10-16. Vol. 7, p. e37516. DOI : 10.7554/eLife.37516.

Fluorescent Benzothiazinone Analogues Efficiently and Selectively Label Dpre1 in Mycobacteria and Actinobacteria

R. Sommer; J. Neres; J. Piton; N. Dhar; A. van der Sar et al. 

ACS Chemical Biology. 2018-11-01. Vol. 13, num. 11, p. 3184-3192. DOI : 10.1021/acschembio.8b00790.

Elucidating the role of (p)ppGpp in mycobacterial persistence against antibiotics

A. Bhaskar; C. De Piano; E. Gelman; J. McKinney; N. Dhar 

IUBMB LIFE. 2018. Vol. 70, num. 9, p. 836-844. DOI : 10.1002/iub.1888.

Photothermal Off-Resonance Tapping for Rapid and Gentle Atomic Force Imaging of Live Cells

A. P. Nievergelt; C. Brillard; H. A. Eskandarian; J. McKinney; G. Fantner 

International Journal of Molecular Sciences. 2018-09-30. Vol. 19, num. 10, p. 2984. DOI : 10.3390/ijms19102984.


Division site selection linked to inherited cell surface wave troughs in mycobacteria

H. A. Eskandarian; P. D. Odermatt; J. X. Y. Ven; M. T. M. Hannebelle; A. P. Nievergelt et al. 

Nature Microbiology. 2017. Vol. 2, p. 17094. DOI : 10.1038/nmicrobiol.2017.94.

The studies of ParA and ParB dynamics reveal asymmetry of chromosome segregation in mycobacteria

K. Ginda; I. Santi; D. Bousbaine; J. Zakrzewska-Czerwinska; D. Jakimowicz et al. 

Molecular Microbiology. 2017. Vol. 105, num. 3, p. 453-468. DOI : 10.1111/mmi.13712.

An Amidase_3 domain-containing N-acetylmuramyl-L-alanine amidase is required for mycobacterial cell division

S. Senzani; D. Li; A. Bhaskar; C. Ealand; J. Chang et al. 

Scientific Reports. 2017. Vol. 7, p. 1140. DOI : 10.1038/s41598-017-01184-7.

Identification of aminopyrimidine-sulfonamides as potent modulators of Wag31-mediated cell elongation in mycobacteria

V. Singh; N. Dhar; J. Pato; G. S. Kolly; J. Kordulakova et al. 

Molecular Microbiology. 2017. Vol. 103, num. 1, p. 13-25. DOI : 10.1111/mmi.13535.

The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis

V. Singh; S. Donini; A. Pacitto; C. Sala; R. C. Hartkoorn et al. 

Acs Infectious Diseases. 2017. Vol. 3, num. 1, p. 5-17. DOI : 10.1021/acsinfecdis.6b00102.

Dielectrophoresis as a single cell characterization method for bacteria

M. Elitas; N. Dhar; K. Schneider; A. Valero; T. Braschler et al. 

Biomedical Physics & Engineering Express. 2017. Vol. 3, num. 1, p. 015005. DOI : 10.1088/2057-1976/3/1/015005.


Phenotypic Heterogeneity in Mycobacterium tuberculosis

N. Dhar; J. Mckinney; G. Manina 

Microbiology Spectrum. 2016. Vol. 4, num. 6, p. TBTB2-0021-2016. DOI : 10.1128/microbiolspec.TBTB2-0021-2016.

Mycobacterium tuberculosis Phosphate Uptake System Component PstA2 Is Not Required for Gene Regulation or Virulence

A. D. Tischler; R. L. Leistikow; P. Ramakrishnan; M. I. Voskuil; J. D. Mckinney 

Plos One. 2016. Vol. 11, num. 8, p. e0161467. DOI : 10.1371/journal.pone.0161467.

A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria

P. Murima; M. Zimmermann; T. Chopra; F. Pojer; G. Fonti et al. 

Nature Communications. 2016. Vol. 7, p. 12527. DOI : 10.1038/ncomms12527.

A microfluidic cell-trapping device for single-cell tracking of host-microbe interactions

M. J. Delince; J-B. Bureau; A. T. Lopez-Jimenez; P. Cosson; T. Soldati et al. 

Lab On A Chip. 2016. Vol. 16, num. 17, p. 3276-3285. DOI : 10.1039/c6lc00649c.

Antitubercular drugs for an old target: GSK693 as a promising InhA direct inhibitor

M. Martinez-Hoyos; E. Perez-Herran; G. Gulten; L. Encinas; D. Alvarez-Gomez et al. 

Ebiomedicine. 2016. Vol. 8, p. 291-301. DOI : 10.1016/j.ebiom.2016.05.006.

Mycobacterium tuberculosis Resists Stress by Regulating PE19 Expression

P. Ramakrishnan; A. M. Aagesen; J. D. Mckinney; A. D. Tischler 

Infection And Immunity. 2016. Vol. 84, num. 3, p. 735-746. DOI : 10.1128/Iai.00942-15.


Whole Cell Target Engagement Identifies Novel Inhibitors of Mycobacterium tuberculosis Decaprenylphosphoryl-beta-D-ribose Oxidase

S. M. Batt; M. Cacho Izquierdo; J. Castro Pichel; C. J. Stubbs; L. Vela-Glez Del Peral et al. 

Acs Infectious Diseases. 2015. Vol. 1, num. 12, p. 615-626. DOI : 10.1021/acsinfecdis.5b00065.

Bioluminescence for Assessing Drug Potency against Nonreplicating Mycobacterium tuberculosis

A. Vocat; R. C. Hartkoorn; B. Lechartier; M. Zhang; N. Dhar et al. 

Antimicrobial Agents And Chemotherapy. 2015. Vol. 59, num. 7, p. 4012-4019. DOI : 10.1128/Aac.00528-15.

Combinations of beta-Lactam Antibiotics Currently in Clinical Trials Are Efficacious in a DHP-I-Deficient Mouse Model of Tuberculosis Infection

J. Rullas; N. Dhar; J. D. Mckinney; A. Garcia-Perez; J. Lelievre et al. 

Antimicrobial Agents And Chemotherapy. 2015. Vol. 59, num. 8, p. 4997-4999. DOI : 10.1128/Aac.01063-15.

Rapid Cytolysis of Mycobacterium tuberculosis by Faropenem, an Orally Bioavailable beta-Lactam Antibiotic

N. Dhar; V. Dubee; L. Ballell; G. Cuinet; J-E. Hugonnet et al. 

Antimicrobial Agents And Chemotherapy. 2015. Vol. 59, num. 2, p. 1308-1319. DOI : 10.1128/Aac.03461-14.

2-Carboxyquinoxalines Kill Mycobacterium tuberculosis through Noncovalent Inhibition of DprE1

J. Neres; R. C. Hartkoorn; L. R. Chiarelli; R. Gadupudi; M. R. Pasca et al. 

Acs Chemical Biology. 2015. Vol. 10, num. 3, p. 705-714. DOI : 10.1021/cb5007163.

Chromosome Organization and Replisome Dynamics in Mycobacterium smegmatis

I. Santi; J. D. Mckinney 

Mbio. 2015. Vol. 6, num. 1, p. e01999-14. DOI : 10.1128/mBio.01999-14.

Single-Cell Tracking Reveals Antibiotic-Induced Changes in Mycobacterial Energy Metabolism

Z. Maglica; E. Oezdemir; J. D. Mckinney 

Mbio. 2015. Vol. 6, num. 1, p. e02236-14. DOI : 10.1128/mBio.02236-14.

Stressed Mycobacteria Use the Chaperone ClpB to Sequester Irreversibly Oxidized Proteins Asymmetrically Within and Between Cells

J. Vaubourgeix; G. Lin; N. Dhar; N. Chenouard; X. Jiang et al. 

Cell Host & Microbe. 2015. Vol. 17, num. 2, p. 178-190. DOI : 10.1016/j.chom.2014.12.008.

Stress and Host Immunity Amplify Mycobacterium tuberculosis Phenotypic Heterogeneity and Induce Nongrowing Metabolically Active Forms

G. Manina; N. Dhar; J. D. Mckinney 

Cell Host & Microbe. 2015. Vol. 17, num. 1, p. 32-46. DOI : 10.1016/j.chom.2014.11.016.


Simple and Rapid Method To Determine Antimycobacterial Potency of Compounds by Using Autoluminescent Mycobacterium tuberculosis

S. Sharma; E. Gelman; C. Narayan; D. Bhattacharjee; V. Achar et al. 

Antimicrobial Agents And Chemotherapy. 2014. Vol. 58, num. 10, p. 5801-5808. DOI : 10.1128/Aac.03205-14.

Quantitative Mass Spectrometry Reveals Plasticity of Metabolic Networks in Mycobacterium smegmatis

T. Chopra; R. Hamelin; F. Armand; D. Chiappe; M. Moniatte et al. 

Molecular & Cellular Proteomics. 2014. Vol. 13, num. 11, p. 3014-3028. DOI : 10.1074/mcp.M113.034082.

The Phosphatidyl-myo-Inositol Mannosyltransferase PimA Is Essential for Mycobacterium tuberculosis Growth In Vitro and In Vivo (vol 196, pg 3441, 2014)

F. Boldrin; M. Ventura; G. Degiacomi; S. Ravishankar; C. Sala et al. 

Journal Of Bacteriology. 2014. Vol. 196, num. 23, p. 4197-4197. DOI : 10.1128/Jb.02332-14.

EspI regulates the ESX-1 secretion system in response to ATP levels in Mycobacterium tuberculosis

M. Zhang; J. M. Chen; C. Sala; J. Rybniker; N. Dhar et al. 

Molecular Microbiology. 2014. Vol. 93, num. 5, p. 1057-1065. DOI : 10.1111/mmi.12718.

The Phosphatidyl-myo-Inositol Mannosyltransferase PimA Is Essential for Mycobacterium tuberculosis Growth In Vitro and In Vivo

F. Boldrin; M. Ventura; G. Degiacomi; S. Ravishankar; C. Sala et al. 

Journal Of Bacteriology. 2014. Vol. 196, num. 19, p. 3441-3451. DOI : 10.1128/Jb.01346-13.

In Vitro and In Vivo Activities of Three Oxazolidinones against Nonreplicating Mycobacterium tuberculosis

M. Zhang; C. Sala; N. Dhar; A. Vocat; V. K. Sambandamurthy et al. 

Antimicrobial Agents And Chemotherapy. 2014. Vol. 58, num. 6, p. 3217-3223. DOI : 10.1128/Aac.02410-14.

4-Aminoquinolone Piperidine Amides: Noncovalent Inhibitors of DprE1 with Long Residence Time and Potent Antimycobacterial Activity

M. Naik; V. Humnabadkar; S. J. Tantry; M. Panda; A. Narayan et al. 

Journal Of Medicinal Chemistry. 2014. Vol. 57, num. 12, p. 5419-5434. DOI : 10.1021/jm5005978.

Assessing the essentiality of the decaprenyl-phospho-D-arabinofuranose pathway in Mycobacterium tuberculosis using conditional mutants

G. S. Kolly; F. Boldrin; C. Sala; N. Dhar; R. C. Hartkoorn et al. 

Molecular Microbiology. 2014. Vol. 92, num. 1, p. 194-211. DOI : 10.1111/mmi.12546.

Dielectrophoresis-based purification of antibiotic-treated bacterial subpopulations

M. Elitas; R. Martinez-Duarte; N. Dhar; J. D. Mckinney; P. Renaud 

Lab on a Chip. 2014. Vol. 14, num. 11, p. 1850-1857. DOI : 10.1039/c4lc00109e.

Delayed bactericidal response of Mycobacterium tuberculosis to bedaquiline involves remodelling of bacterial metabolism

A. Koul; L. Vranckx; N. Dhar; H. W. H. Gohlmann; M. E. Özdemir et al. 

Nature Communications. 2014. Vol. 5, p. 3369. DOI : 10.1038/ncomms4369.

Establishment and Validation of Whole-Cell Based Fluorescence Assays to Identify Anti-Mycobacterial Compounds Using the Acanthamoeba castellanii – Mycobacterium marinum Host-Pathogen System

S. Kicka; V. Trofimov; C. Harrison; H. Ouertatani-Sakouhi; J. McKinney et al. 

Plos One. 2014. Vol. 9, num. 1, p. e87834. DOI : 10.1371/journal.pone.0087834.


Phenotypic Profiling of Mycobacterium tuberculosis EspA Point Mutants Reveals that Blockage of ESAT-6 and CFP-10 Secretion In Vitro Does Not Always Correlate with Attenuation of Virulence

J. M. Chen; M. Zhang; J. Rybniker; L. Basterra; N. Dhar et al. 

Journal Of Bacteriology. 2013. Vol. 195, num. 24, p. 5421-5430. DOI : 10.1128/Jb.00967-13.

Mycobacterium tuberculosis EspB binds phospholipids and mediates EsxA-independent virulence

J. M. Chen; M. Zhang; J. Rybniker; S. Boy-Röttger; N. Dhar et al. 

Molecular Microbiology. 2013. Vol. 89, num. 6, p. 1154-1166. DOI : 10.1111/mmi.12336.

A problem of persistence: still more questions than answers?

N. Q. Balaban; K. Gerdes; K. Lewis; J. D. McKinney 

Nature Reviews Microbiology. 2013. Vol. 11, num. 8, p. 587-591. DOI : 10.1038/nrmicro3076.

Single-cell dynamics of the chromosome replication and cell division cycles in mycobacteria

I. Santi; N. Dhar; D. Bousbaine; Y. Wakamoto; J. D. McKinney 

Nature Communications. 2013. Vol. 4, p. 2470. DOI : 10.1038/ncomms3470.

A vitamin B-12 transporter in Mycobacterium tuberculosis

K. Gopinath; C. Venclovas; T. R. Ioerger; J. C. Sacchettini; J. D. McKinney et al. 

Open Biology. 2013. Vol. 3. DOI : 10.1098/rsob.120175.

Mycobacterium tuberculosis Requires Phosphate-Responsive Gene Regulation To Resist Host Immunity

A. D. Tischler; R. L. Leistikow; M. A. Kirksey; M. I. Voskuil; J. D. McKinney 

Infection And Immunity. 2013. Vol. 81, num. 1, p. 317-328. DOI : 10.1128/Iai.01136-12.

Dynamic Persistence of Antibiotic-Stressed Mycobacteria

Y. Wakamoto; N. Dhar; R. Chait; K. E. Schneider; F. Signorino-Gelo et al. 

Science. 2013. Vol. 339, num. 6115, p. 91-95. DOI : 10.1126/science.1229858.


Structural Basis for Benzothiazinone-Mediated Killing of Mycobacterium tuberculosis

J. Neres; F. Pojer; E. Molteni; L. R. Chiarelli; N. Dhar et al. 

Science Translational Medicine. 2012. Vol. 4, num. 150, p. 150ra121. DOI : 10.1126/scitranslmed.3004395.

Streptomycin-Starved Mycobacterium tuberculosis 18b, a Drug Discovery Tool for Latent Tuberculosis

M. Zhang; C. Sala; R. C. Hartkoorn; N. Dhar; A. Mendoza-Losana et al. 

Antimicrobial Agents And Chemotherapy. 2012. Vol. 56, num. 11, p. 5782-5789. DOI : 10.1128/Aac.01125-12.

Malachite Green Interferes with Postantibiotic Recovery of Mycobacteria

E. Gelman; J. D. McKinney; N. Dhar 

Antimicrobial Agents And Chemotherapy. 2012. Vol. 56, p. 3610-3614. DOI : 10.1128/AAC.00406-12.

Cholesterol Catabolism by Mycobacterium tuberculosis Requires Transcriptional and Metabolic Adaptations

J. E. Griffin; A. K. Pandey; S. A. Gilmore; V. Mizrahi; J. D. Mckinney et al. 

Chemistry & Biology. 2012. Vol. 19, p. 218-227. DOI : 10.1016/j.chembiol.2011.12.016.


Dispensability of Surfactant Proteins A and D in Immune Control of Mycobacterium tuberculosis Infection following Aerosol Challenge of Mice

M. P. Lemos; J. McKinney; K. Y. Rhee 

Infection and Immunity. 2011. Vol. 79, num. 3, p. 1077-1085. DOI : 10.1128/IAI.00286-10.

EspD Is Critical for the Virulence-Mediating ESX-1 Secretion System in Mycobacterium tuberculosis

J. M. Chen; S. Boy-Röttger; N. Dhar; N. Sweeney; R. S. Buxton et al. 

Journal of bacteriology. 2011. Vol. 194, num. 4, p. 884-93. DOI : 10.1128/JB.06417-11.

Expression of the leptin receptor outside of bone marrow-derived cells regulates tuberculosis control and lung macrophage MHC expression

M. P. Lemos; K. Y. Rhee; J. D. McKinney 

Journal of immunology (Baltimore, Md. : 1950). 2011. Vol. 187, num. 7, p. 3776-84. DOI : 10.4049/jimmunol.1003226.

Spontaneous phthiocerol dimycocerosate-deficient variants of Mycobacterium tuberculosis are susceptible to gamma interferon-mediated immunity

M. A. Kirksey; A. D. Tischler; R. Siméone; K. B. Hisert; S. Uplekar et al. 

Infection and immunity. 2011. Vol. 79, num. 7, p. 2829-38. DOI : 10.1128/IAI.00097-11.

Nanoparticle conjugation and pulmonary delivery enhance the protective efficacy of Ag85B and CpG against tuberculosis

M. Ballester; C. Nembrini; N. Dhar; A. de Titta; C. de Piano et al. 

Vaccine. 2011. Vol. 29, num. 40, p. 6959-66. DOI : 10.1016/j.vaccine.2011.07.039.


Development of a repressible mycobacterial promoter system based on two transcriptional repressors

F. Boldrin; S. Casonato; E. Dainese; C. Sala; N. Dhar et al. 

Nucleic acids research. 2010. Vol. 38, num. 12, p. e134. DOI : 10.1093/nar/gkq235.

A Simple Model for Testing Drugs against Non-replicating Mycobacterium tuberculosis

C. Sala; N. Dhar; R. C. Hartkoorn; M. Zhang; Y. H. Ha et al. 

Antimicrobial agents and chemotherapy. 2010. Vol. 54, num. 10, p. 4150-4158. DOI : 10.1128/AAC.00821-10.

Mycobacterium tuberculosis persistence mutants identified by screening in isoniazid-treated mice

N. Dhar; J. D. McKinney 

Proceedings of the National Academy of Sciences of the United States of America. 2010. Vol. 107, num. 27, p. 12275-80. DOI : 10.1073/pnas.1003219107.


Boosting with a DNA vaccine expressing ESAT-6 (DNAE6) obliterates the protection imparted by recombinant BCG (rBCGE6) against aerosol Mycobacterium tuberculosis infection in guinea pigs

B. Dey; R. Jain; A. Khera; V. Rao; N. Dhar et al. 

Vaccine. 2009. Vol. 28, p. 63-70. DOI : 10.1016/j.vaccine.2009.09.121.

Benzothiazinones kill Mycobacterium tuberculosis by blocking arabinan synthesis

V. Makarov; G. Manina; K. Mikusova; U. Möllmann; O. Ryabova et al. 

Science (New York, N.Y.). 2009. Vol. 324, num. 5928, p. 801-4. DOI : 10.1126/science.1171583.


Enhanced and Enduring Protection against Tuberculosis by Recombinant BCG-Ag85C and Its Association with Modulation of Cytokine Profile in Lung

R. Jain; B. Dey; N. Dhar; V. Rao; R. Singh et al. 

Plos One. 2008. Vol. 3, num. 12, p. e3869. DOI : 10.1371/journal.pone.0003869.

Functional characterization of a vitamin B12-dependent methylmalonyl pathway in Mycobacterium tuberculosis: implications for propionate metabolism during growth on fatty acids

S. Savvi; D. F. Warner; B. D. Kana; J. D. McKinney; V. Mizrahi et al. 

Journal of bacteriology. 2008. Vol. 190, num. 11, p. 3886-95. DOI : 10.1128/JB.01767-07.


Role of the methylcitrate cycle in propionate metabolism and detoxification in Mycobacterium smegmatis

A. M. Upton; J. D. McKinney 

Microbiology (Reading, England). 2007. Vol. 153, num. 12, p. 3973-82. DOI : 10.1099/mic.0.2007/011726-0.


Role of the methylcitrate cycle in Mycobacterium tuberculosis metabolism, intracellular growth, and virulence

E. J. Muñoz-Elías; A. M. Upton; J. Cherian; J. D. McKinney 

Molecular microbiology. 2006. Vol. 60, num. 5, p. 1109-22. DOI : 10.1111/j.1365-2958.2006.05155.x.

M. tuberculosis Rv2252 encodes a diacylglycerol kinase involved in the biosynthesis of phosphatidylinositol mannosides (PIMs)

R. M. Owens; F. F. Hsu; B. C. VanderVen; G. E. Purdy; E. Hesteande et al. 

Molecular microbiology. 2006. Vol. 60, num. 5, p. 1152-63. DOI : 10.1111/j.1365-2958.2006.05174.x.

A multidrug-resistant, acr1-deficient clinical isolate of Mycobacterium tuberculosis is unimpaired for replication in macrophages

J. Timm; N. Kurepina; B. N. Kreiswirth; F. A. Post; G. B. Walther et al. 

The Journal of infectious diseases. 2006. Vol. 193, num. 12, p. 1703-10. DOI : 10.1086/504526.

Dual role of isocitrate lyase 1 in the glyoxylate and methylcitrate cycles in Mycobacterium tuberculosis

T. A. Gould; H. van de Langemheen; E. J. Muñoz-Elías; J. D. McKinney; J. C. Sacchettini 

Molecular microbiology. 2006. Vol. 61, num. 4, p. 940-7. DOI : 10.1111/j.1365-2958.2006.05297.x.


Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence

E. Munoz-Elias; J. McKinney 

Nature Medicine. 2005. Vol. 11, num. 6, p. 638-644. DOI : 10.1038/nm1252.


Role of KatG catalase-peroxidase in mycobacterial pathogenesis: countering the phagocyte oxidative burst

V. H. Ng; J. S. Cox; A. O. Sousa; J. D. MacMicking; J. D. McKinney 

Molecular microbiology. 2004. Vol. 52, num. 5, p. 1291-302. DOI : 10.1111/j.1365-2958.2004.04078.x.

Identification of Mycobacterium tuberculosis counterimmune (cim) mutants in immunodeficient mice by differential screening

K. B. Hisert; M. A. Kirksey; J. E. Gomez; A. O. Sousa; J. S. Cox et al. 

Infection and immunity. 2004. Vol. 72, num. 9, p. 5315-21. DOI : 10.1128/IAI.72.9.5315-5321.2004.

Replication dynamics of Mycobacterium tuberculosis in chronically infected mice

E. J. Muñoz-Elías; J. Timm; T. Botha; W-T. Chan; J. E. Gomez et al. 

Infection and immunity. 2004. Vol. 73, num. 1, p. 546-51. DOI : 10.1128/IAI.73.1.546-551.2005.


Life on the inside for Mycobacterium tuberculosis

J. D. McKinney; J. E. Gomez 

Nature medicine. 2003. Vol. 9, num. 11, p. 1356-7. DOI : 10.1038/nm1103-1356.

Ribonucleotide reduction in Mycobacterium tuberculosis: function and expression of genes encoding class Ib and class II ribonucleotide reductases

S. S. Dawes; D. F. Warner; L. Tsenova; J. Timm; J. D. McKinney et al. 

Infection and immunity. 2003. Vol. 71, num. 11, p. 6124-31. DOI : 10.1128/IAI.71.11.6124-6131.2003.

Immune control of tuberculosis by IFN-gamma-inducible LRG-47

J. D. MacMicking; G. A. Taylor; J. D. McKinney 

Science (New York, N.Y.). 2003. Vol. 302, num. 5645, p. 654-9. DOI : 10.1126/science.1088063.

Differential expression of iron-, carbon-, and oxygen-responsive mycobacterial genes in the lungs of chronically infected mice and tuberculosis patients

J. Timm; F. A. Post; L-G. Bekker; G. B. Walther; H. C. Wainwright et al. 

Proceedings of the National Academy of Sciences of the United States of America. 2003. Vol. 100, num. 24, p. 14321-6. DOI : 10.1073/pnas.2436197100.


Infection of mice with aerosolized Mycobacterium tuberculosis: use of a nose-only apparatus for delivery of low doses of inocula and design of an ultrasafe facility

J. R. Schwebach; B. Chen; A. Glatman-Freedman; A. Casadevall; J. D. McKinney et al. 

Applied and environmental microbiology. 2002. Vol. 68, num. 9, p. 4646-9. DOI : 10.1128/AEM.68.9.4646-4649.2002.


Recombinant bacillus Calmette-Guérin as a potential vector for preventive HIV type 1 vaccines

L. A. Falk; K. L. Goldenthal; J. Esparza; M. T. Aguado; S. Osmanov et al. 

AIDS research and human retroviruses. 2000. Vol. 16, num. 2, p. 91-8. DOI : 10.1089/088922200309421.

Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis

V. Sharma; S. Sharma; K. Hoener zu Bentrup; J. D. McKinney; D. G. Russell et al. 

Nature structural biology. 2000. Vol. 7, num. 8, p. 663-8. DOI : 10.1038/77964.

Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase

J. D. McKinney; K. Höner zu Bentrup; E. J. Muñoz-Elías; A. Miczak; B. Chen et al. 

Nature. 2000. Vol. 406, num. 6797, p. 735-8. DOI : 10.1038/35021074.


The death and resurrection of tuberculosis

B. R. Bloom; J. D. McKinney 

Nature medicine. 1999. Vol. 5, num. 8, p. 872-4. DOI : 10.1038/11309.


Ste12 and Mcm1 regulate cell cycle-dependent transcription of FAR1.

L. J. Oehlen; J. D. McKinney; F. R. Cross 

Molecular and cellular biology. 1996. Vol. 16, num. 6, p. 2830-7. DOI : 10.1128/MCB.16.6.2830.


FAR1 and the G1 phase specificity of cell cycle arrest by mating factor in Saccharomyces cerevisiae.

J. D. McKinney; F. R. Cross 

Molecular and cellular biology. 1995. Vol. 15, num. 5, p. 2509-16. DOI : 10.1128/MCB.15.5.2509.


Identification of bacteriophage T4 prereplicative proteins on two-dimensional polyacrylamide gels

E. M. Kutter; K. d’Acci; R. H. Drivdahl; J. Gleckler; J. C. McKinney et al. 

Journal of bacteriology. 1994. Vol. 176, num. 6, p. 1647-54.

Role of Swi4 in cell cycle regulation of CLN2 expression.

F. R. Cross; M. Hoek; J. D. McKinney; A. H. Tinkelenberg 

Molecular and cellular biology. 1994. Vol. 14, num. 7, p. 4779-87. DOI : 10.1128/MCB.14.7.4779.


Negative regulation of FAR1 at the Start of the yeast cell cycle.

J. D. McKinney; F. Chang; N. Heintz; F. R. Cross 

Genes & development. 1993. Vol. 7, num. 5, p. 833-43. DOI : 10.1101/gad.7.5.833.


A switch-hitter at the Start of the cell cycle

J. McKinney; F. Cross 

Current biology. 1992. Vol. 2, num. 8, p. 421-3. DOI : 10.1016/0960-9822(92)90322-2.


Histone H1 subtype-specific consensus elements mediate cell cycle-regulated transcription in vitro

F. La Bella; P. Gallinari; J. McKinney; N. Heintz 

Genes & development. 1989. Vol. 3, num. 12A, p. 1982-90. DOI : 10.1101/gad.3.12a.1982.

Expression of cloned rpoB gene of Escherichia coli: a genetic system for the isolation of dominant negative mutations and overproduction of defective beta subunit of RNA polymerase.

J. Y. Lee; K. Zalenskaya; Y. K. Shin; J. D. McKinney; J. H. Park et al. 

Journal of bacteriology. 1989. Vol. 171, num. 6, p. 3002-7. DOI : 10.1128/jb.171.6.3002-3007.1989.


Overexpression and purification of a biologically active rifampicin-resistant beta subunit of Escherichia coli RNA polymerase

J. D. McKinney; J. Y. Lee; R. E. O’Neill; A. Goldfarb 

Gene. 1987. Vol. 58, num. 1, p. 13-8. DOI : 10.1016/0378-1119(87)90024-2.

Conference Papers


Time-Lapse Atomic Force Microscopy Reveals New End Take Off (Neto) Dynamics in Mycobacteria

M. T. M. Hannebelle; J. X. Y. Ven; H. A. Eskandarian; C. Toniolo; A. P. D. Nievergelt et al. 

2019-02-15. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, Mar 02-06, 2019. p. 324A-324A. DOI : 10.1016/j.bpj.2018.11.1757.


Analysis of genome-scale metabolic model of mycobacterium tuberculosis for new combat strategies

M. E. Oezdemir; K. C. Soh; J. D. McKinney; V. Hatzimanikatis 

2009.  p. 329-BIOT.

Separation of antibiotic-treated mycobacterial subpopulations using multiple-frequency dielectrophoresis

M. Elitas; A. Valero; T. Braschler; N. Dhar; J. D. McKinney et al. 

2009. 13th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS), Jeju, Korea, Nov. 1-5, 2009.


Liquid Electrodes and Multiple-Frequency Dielectrophoresis for studying bacterial persistence to antibiotics

M. Elitas; A. Valero; T. Braschler; N. Dhar; R. Tornay et al. 

2008. NanoTech-Montreux 2008, Montreux, Switzerland, nov. 17-19, 2008. p. x-x.



Targeting Bacterial Central Metabolism for Drug Development

P. Murima; J. D. Mckinney; K. Pethe 

Chemistry & Biology. 2014. Vol. 21, num. 11, p. 1423-1432. DOI : 10.1016/j.chembiol.2014.08.020.


Contrasting persistence strategies in Salmonella and Mycobacterium

A. D. Tischler; J. D. McKinney 

Current opinion in microbiology. 2010. Vol. 13, num. 1, p. 93-9. DOI : 10.1016/j.mib.2009.12.007.


Microbial phenotypic heterogeneity and antibiotic tolerance

N. Dhar; J. D. McKinney 

Current opinion in microbiology. 2007. Vol. 10, num. 1, p. 30-8. DOI : 10.1016/j.mib.2006.12.007.


Consumed in the city Observing tuberculosis at century‘s end

J. E. Gomez; J. D. McKinney 

The journal of clinical investigation. 2005. Vol. 115, num. 3, p. 484-484. DOI : 10.1172/JCI24576.

Carbon metabolism of intracellular bacteria

E. J. Muñoz-Elías; J. D. McKinney 

Cellular microbiology. 2005. Vol. 8, num. 1, p. 10-22. DOI : 10.1111/j.1462-5822.2005.00648.x.


M. tuberculosis persistence, latency, and drug tolerance

J. E. Gomez; J. D. McKinney 

Tuberculosis. 2003. Vol. 84, num. 1-2, p. 29-44. DOI : 10.1016/


In vivo veritas: the search for TB drug targets goes live

J. D. McKinney 

Nature medicine. 2000. Vol. 6, num. 12, p. 1330-3. DOI : 10.1038/82142.


Is START a switch?

F. Cross; J. McKinney 

Ciba Foundation symposium. 1992. Vol. 170, p. 20-5.


Transcriptional regulation in the eukaryotic cell cycle

J. D. McKinney; N. Heintz 

Trends in biochemical sciences. 1991. Vol. 16, num. 11, p. 430-435. DOI : 10.1016/0968-0004(91)90170-Z.



Single-cell analysis of the interactions between Mycobacterium tuberculosis and macrophages

O. Rutschmann / J. McKinney (Dir.)  

Lausanne, EPFL, 2024. 


Identification of genes required for host-cell adhesion and antibiotic persistence of uropathogenic Escherichia coli via high-content screening

T. M. Simonet / J. McKinney (Dir.)  

Lausanne, EPFL, 2022. 


Coordination between cell growth, division and chromosome replication cycles in mycobacteria

G. M. Vuaridel / J. McKinney; N. Dhar (Dir.)  

Lausanne, EPFL, 2021. 

Microtissue models for studying the dynamics of host-pathogen interactions in the urinary bladder

K. Sharma / J. McKinney; N. Dhar (Dir.)  

Lausanne, EPFL, 2021. 


Time-lapse high-resolution microscopy to study the morphogenesis of microorganisms

M. T. M. Hannebelle / G. Fantner; J. McKinney (Dir.)  

Lausanne, EPFL, 2020. 


Single-cell studies of Mycobacterium smegmatis cell cycle using time-lapse fluorescence microscopy

J. X. Y. Ven / J. McKinney (Dir.)  

Lausanne, EPFL, 2019. 


Single-cell division and killing dynamics of bacteria exposed to isocratic and time-dependent concentrations of antibiotic

K. E. Schneider / J. McKinney; N. Dhar (Dir.)  

Lausanne, EPFL, 2018. 


A Microfluidic Platform Enables Large-Scale Single-Cell Screening to Identify Genes Involved in Bacterial Persistence

A. Verpoorte / J. McKinney; S. Maerkl (Dir.)  

Lausanne, EPFL, 2017. 


Quantitative Single-Cell Analysis of Host-Pathogen Interactions

M. J-H. Delincé / J. McKinney (Dir.)  

Lausanne, EPFL, 2016. 


Antibiotic-Induced Killing and Persistence of Mycobacteria

E. Gelman / J. McKinney; N. Dhar (Dir.)  

Lausanne, EPFL, 2014. 


Metabolic modeling and experimental studies on carbon and energy metabolism of Mycobacterium tuberculosis

M. E. Özdemir / J. McKinney; V. Hatzimanikatis (Dir.)  

Lausanne, EPFL, 2013. 

The Phosphate Specific Transport (Pst) System in Fast- and Slow-Growing Mycobacteria

C. De Piano / J. McKinney (Dir.)  

Lausanne, EPFL, 2013. 


Single-Cell Analysis of Mycobacterial Persistence Using Microfabricated Tools

M. Elitas / J. McKinney; S. Maerkl (Dir.)  

Lausanne, EPFL, 2012. 

Book Chapters


A microfluidic cell-trapping device to study dynamic host-microbe interactions at the single-cell level

C. Toniolo; M. Delince; J. D. McKinney 

Microfluidics In Cell Biology, Pt B: Microfluidics In Single Cells; San Diego: ELSEVIER ACADEMIC PRESS INC, 2018-01-01. p. 199-213.


A Single-Cell Perspective on Non-Growing but Metabolically Active (NGMA) Bacteria

G. Manina; J. D. McKinney 

Pathogenesis Of Mycobacterium Tuberculosis And Its Interaction With The Host Organism; Berlin: Springer-Verlag, 2014. p. 135-161.

Pathogenesis of Mycobacterium tuberculosis and its Interaction with the Host Organism Preface

J. Pieters; J. McKinney 

Pathogenesis Of Mycobacterium Tuberculosis And Its Interaction With The Host Organism; Berlin: Springer-Verlag, 2014. p. V-VI.


Bacterial strategies for survival in the host

A. D. Tischler; J. D. McKinney 

The immune response to infection; Washington, D.C: ASM Press, 2011. p. 425-440.


Persistence and drug tolerance

J. E. Gomez; J. D. McKinney 

Tuberculosis; Philadelphia: Lippincott Williams & Wilkins, 2004. p. 101-114.


Macrophage immunity and Mycobacterium Tuberculosis

J. D. MacMicking; J. D. McKinney 

The macrophage as therapeutic target; Berlin: Springer, 2003. p. 409-457.


Bacterial persistence: strategies for survival

E. J. Muñoz-Elías; J. D. McKinney 

Immunology of infectious diseases; Washington, D.C: ASM Press, 2002. p. 331-355.


Tuberculosis and leprosy

J. D. McKinney; B. R. Bloom; R. L. Modlin 

Samter’s immunologic diseases; Lippincott Williams & Wilkins, 2001. p. 985-1002.


Persisting problems in tuberculosis

J. D. McKinney; W. R. Jacobs; B. R. Bloom 

Emerging infections; San Diego: Academic Press, 1998. p. 51-146.


Effects on host genome and structure

E. Kutter; T. White; M. Kashlev; J. D. McKinney; B. Guttman 

Molecular biology of bacteriophage T4; Washington: American Society for Microbiology, 1994. p. 357-368.

Student Projects


The Role of c-di-AMP in Listeria monocytogenes

M. J-H. Delincé 



Mechanism of DegU-dependent activation of flagellar gene transcription in Listeria monocytogenes

D. Baer