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<h1>Nikolay S. Markov</h1>
<div>
<a href="mailto:[email protected]" class="no-icon">[email protected]</a> |
<a href="https://mxposed.github.io" class="no-icon">mxposed.github.io</a> |
<a href="https://scholar.google.com/citations?user=-E-79qkAAAAJ&hl=en">Google Scholar profile</a>
<span style="float: right; font-size: 11px;" id="updated-dt">updated</span>
</div>
<section style="margin-top: 20px;">
<h2>Education</h2>
<div class="entry">
<div>Ph.D. candidate, Northwestern University, Chicago, USA
<div class="details">
Driskill Graduate Program in Life Sciences<br/>
Advisors:<br/>— Alexander Misharin, Associate Professor at Northwestern University;
<br/>— Rosemary Braun, Associate Professor at Northwestern University.
</div>
</div>
<div class="date">2022–present</div>
</div>
<div class="entry">
<div>M.S. in Bioinformatics, Newcastle University, Newcastle upon Tyne, UK
<div class="details">
<em>With distinction</em><br/>
Advisors:<br/>— Jaume Bacardit, Reader at Newcastle University;
<br/>— Alexander Misharin, Assistant Professor at Northwestern University.
</div>
</div>
<div class="date">2017–2018</div>
</div>
<div class="entry">
<div>Undergraduate coursework in Biology, Moscow State University, Moscow, Russia
<div class="details">
Genetics major
</div>
</div>
<div class="date">2003–2006</div>
</div>
</section>
<section class="publications">
<h2>
Publications
<span class="remark">(* denotes equal contribution)</span>
</h2>
<h3>1. Research articles under peer-review</h3>
<div class="entry">
<div>
Luo L, Możejko M, <b>Markov N</b>, Peltekian A, Mohsin S, Carns M, Cooper P, Lysne J, Joudi A,
Betensley A, Bemiss BC, Myers C, Bharat A, Tomic R, Arunachalam A, Szczurek E, Budinger GS,
Misharin AV, Subramani MV.
<div class="details">
Machine learning analysis of the UNOS database fails to predict lung transplant outcomes
<em>medRxiv</em>.
<a href="https://doi.org/10.1101/2024.10.19.24315817v1">https://doi.org/10.1101/2024.10.19.24315817v1</a>
</div>
</div>
<div class="date">2024</div>
</div>
<div class="entry">
<div>
Zhu M, Pickens CI, <b>Markov NS</b>, Pawlowski A, Kang M, Rasmussen LV, Walter JM, Nadig NR,
Singer BD, Wunderink RG, Gao CA, NU SCRIPT Study Investigators.
<div class="details">
Antibiotic De-escalation Patterns and Outcomes in Critically Ill Patients with
Suspected Pneumonia as Informed by Bronchoalveolar Lavage Results.
<em>medRxiv</em>.
<a href="https://doi.org/10.1101/2024.09.10.24313149v1">https://doi.org/10.1101/2024.09.10.24313149v1</a>
</div>
</div>
<div class="date">2024</div>
</div>
<div class="entry">
<div>
Fenske SW, Peltekian A, Kang M, <b>Markov NS</b>, Zhu M, Grudzinski K, Bak MJ,
Pawlowski A, Gupta V, Mao Y, Bratchikov S, Stoeger T, Rasmussen LV,
Choudhary AN, Misharin AV, Singer BD, Budinger GS, Wunderink RG, Agrawal A, Gao CA,
NU SCRIPT Study Investigators.
<div class="details">
Developing and validating a machine learning model to predict successful next-day
extubation<br/>in the ICU.
<em>medRxiv</em>.
<a href="https://doi.org/10.1101/2024.06.28.24309547v1">https://doi.org/10.1101/2024.06.28.24309547v1</a>
</div>
</div>
<div class="date">2024</div>
</div>
<div class="entry">
<div>
Luecken M, Gigante S, Burkhardt D, Cannoodt R, Strobl D, <b>Markov N</b>, Zappia L, Palla G,
Lewis W, Dimitrov D, Vinyard M, Magruder D, Andersson A, Dann E, Qin Q, Otto D, Klein M,
Botvinnik O,
[…],
Bloom J, Pisco A, Saez-Rodriguez J, Wulsin D, Pinello L, Saeys Y, Theis F,
<s>Krishnaswamy S.</s>
<div class="details">
Defining and benchmarking open problems in single-cell analysis.
<em>Research Square</em>.
<a href="https://doi.org/10.21203/rs.3.rs-4181617/v1">https://doi.org/10.21203/rs.3.rs-4181617/v1</a>
</div>
</div>
<div class="date">2024</div>
</div>
<div class="entry">
<div>
Gao CA, <b>Markov NS</b>, Pickens C, Pawlowski A, Kang M, Walter JM, Singer BD, Wunderink RG.
<div class="details">
An observational cohort study of bronchoalveolar lavage fluid galactomannan and Aspergillus
culture positivity in patients requiring mechanical ventilation.
<em>medRxiv</em>.
<a href="https://doi.org/10.1101/2024.02.07.24302392">https://doi.org/10.1101/2024.02.07.24302392</a>
</div>
</div>
<div class="date">2024</div>
</div>
<h3>2. Peer-reviewed research articles</h3>
<div class="entry">
<div>
<b>Markov NS</b>, Ren Z, Senkow KJ, Grant RA, Gao CA, Malsin ES, Sichizya L, Kihshen H,
[…],
Nwaezeapu J, Kang M, Rasmussen L, Ozer EA, Lorenzo-Redondo R, Hultquist JF, Simons LM,
Rios-Guzman E, Misharin AV, Wunderink RG, Budinger GRS, Singer BD, Morales-Nebreda L;
NU SCRIPT Study Investigators.
<div class="details">
A distinctive evolution of alveolar T cell responses is associated with clinical outcomes
in unvaccinated patients with SARS-CoV-2 pneumonia.
<em>Nature Immunology</em>.
<a href="https://doi.org/10.1038/s41590-024-01914-w">https://doi.org/10.1038/s41590-024-01914-w</a>
</div>
</div>
<div class="date">2024</div>
</div>
<div class="entry">
<div>
Bailey JI, Puritz CH, Senkow KJ, <b>Markov NS</b>, Diaz E, Jonasson E, Yu Z, Swaminathan S,
Lu Z, Fenske S, Grant RA, Abdala-Valencia H, […], Jain M, Bharat A, Kurihara C, Estepar Ruben SJ, Estepar Raul SJ,
Washko GR, Shilatifard A, Sznajder JI, Ridge KM, Budinger GRS, Braun R, Misharin AV, Sala MA.
<div class="details">
Profibrotic monocyte-derived alveolar macrophages are expanded in patients with persistent
respiratory symptoms and radiographic abnormalities after COVID-19.
<em>Nature Immunology</em>.
<a href="https://doi.org/10.1038/s41590-024-01975-x">https://doi.org/10.1038/s41590-024-01975-x</a>.
</div>
</div>
<div class="date">2024</div>
</div>
<div class="entry" style="margin-top: 100px; padding-top: 10px;">
<div>
Gao CA*, <b>Markov NS</b>*, Stoeger T*, Pawlowski A, Kang M, Nannapaneni P, Grant RA, Pickens C,
Walter JM, Kruser JM, Rasmussen L, Schneider D, Starren J, Donnelly HK, Donayre A, Luo Y,
Budinger GRS, Wunderink RG, Misharin AV, Singer BD, NU SCRIPT Study Investigators.
<div class="details">
Machine learning links unresolving secondary pneumonia to mortality in patients with severe
pneumonia, including COVID-19.
<em>The Journal of Clinical Investigation (JCI)</em>, 133(12).
<a href="https://doi.org/10.1172/JCI170682">https://doi.org/10.1172/JCI170682</a>
</div>
</div>
<div class="date">2023</div>
</div>
<div class="entry">
<div>
Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, <b>Markov NS</b>,
Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M,
[…],
Falk CS, Meyer KB, Kropski JA, Pe’er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA,
Misharin AV, Nawijn MC, Luecken MD, Theis FJ.
<div class="details">
An integrated cell atlas of the lung in health and disease.
<em>Nature Medicine</em>. 29, 1563–1577.
<a href="https://doi.org/10.1038/s41591-023-02327-2">https://doi.org/10.1038/s41591-023-02327-2</a>
</div>
</div>
<div class="date">2023</div>
</div>
<div class="entry">
<div>
Gao CA, Howard FM, <b>Markov NS</b>, Dyer EC, Ramesh S, Luo Y, Pearson AT.
<div class="details">
Comparing scientific abstracts generated by ChatGPT to real abstracts with detectors and
blinded human reviewers.
<em>npj Digital Medicine</em>, 6(1):1–5.
<a href="https://doi.org/10.1038/s41746-023-00819-6">https://doi.org/10.1038/s41746-023-00819-6</a>
</div>
</div>
<div class="date">2023</div>
</div>
<div class="entry">
<div>
Villéger R, Chulkina M, Mifflin RC, <b>Markov NS</b>, Trieu J, Sinha M, Johnson P, Saada JI,
Adegboyega PA, Luxon BA, Beswick EJ, Powell DW, Pinchuk IV.
<div class="details">
Loss of alcohol dehydrogenase 1B in cancer-associated fibroblasts: contribution to the
increase of tumor-promoting IL-6 in colon cancer.
<em>British Journal of Cancer</em>, 128(4):537–548.
<a href="https://doi.org/10.1038/s41416-022-02066-0">https://doi.org/10.1038/s41416-022-02066-0</a>
</div>
</div>
<div class="date">2023</div>
</div>
<div class="entry">
<div>
Sala MA*, <b>Markov NS</b>*, Politanska Y, Abdala-Valencia H, Misharin AV, Jain M.
<div class="details">
Expression of <i>ACE2</i>–A Key SARS-CoV-2 Entry Factor–Is Not Increased in the Nasal Mucosa
of People with Cystic Fibrosis.
<em>American Journal of Respiratory Cell and Molecular Biology (AJRCMB)</em>, 67(1):132–137.
<a href="https://doi.org/10.1165/rcmb.2021-0341LE">https://doi.org/10.1165/rcmb.2021-0341LE</a>
</div>
</div>
<div class="date">2022</div>
</div>
<div class="entry">
<div>
Yoshida M, Worlock KB, Huang N, Lindeboom RGH, Butler CR,
[…],
<s><b>NU SCRIPT Study Investigators</b><sup>†</sup></s>, Reynolds G, Haniffa M, Bowyer GS,
Coates M, Clatworthy MR, Calero-Nieto FJ, Göttgens B, O’Callaghan C, Sebire NJ, Jolly C,
De Coppi P, Smith CM, Misharin AV, Janes SM, Teichmann SA, Nikolić MZ, Meyer KB.
<div class="details">
Local and systemic responses to SARS-CoV-2 infection in children and adults.
<em>Nature</em>, 602, 321–327.
<a href="https://doi.org/10.1038/s41586-021-04345-x">https://doi.org/10.1038/s41586-021-04345-x</a>
<br/><sup>†</sup> <b>Markov NS</b> among NU SCRIPT Study Investigators.
</div>
</div>
<div class="date">2022</div>
</div>
<div class="entry">
<div>
Koch CM, Prigge AD, Anekalla KR, Shukla A, Do Umehara HC, Setar L, Chavez J, Abdala-Valencia H,
Politanska Y, <b>Markov NS</b>, Hahn GR, Heald-Sargent T, Sanchez- Pinto LN, Muller WJ, Singer BD,
Misharin AV, Ridge KM, Coates BM.
<div class="details">
Age-related Differences in the Nasal Mucosal Immune Response to SARS-CoV-2.
<em>American Journal of Respiratory Cell and Molecular Biology (AJRCMB)</em>, 66(2):206–222.
<a href="https://doi.org/10.1165/rcmb.2021-0292OC">https://doi.org/10.1165/rcmb.2021-0292OC</a>
</div>
</div>
<div class="date">2022</div>
</div>
<div class="entry">
<div>
Speir ML, Bhaduri A, <b>Markov NS</b>, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA,
Raney BJ, Seninge L, Kent WJ, Haeussler M.
<div class="details">
UCSC Cell Browser: visualize your single-cell data.
<em>Bioinformatics</em>, 37(23):4578–4580.
<a href="https://doi.org/10.1093/bioinformatics/btab503">https://doi.org/10.1093/bioinformatics/btab503</a>
</div>
</div>
<div class="date">2021</div>
</div>
<div class="entry">
<div>
Watanabe S, <b>Markov NS</b>, Lu Z, Piseaux Aillon R, Soberanes S, Runyan CE, Ren Z, Grant RA,
Maciel M, Abdala-Valencia H, Politanska Y, Nam K, Sichizya L, Kihshen HG, Joshi N,
McQuattie-Pimentel AC, Gruner KA, Jain M, Sznajder JI, Morimoto RI, Reyfman PA, Gottardi CJ,
Budinger GRS, Misharin AV.
<div class="details">
Resetting proteostasis with ISRIB promotes epithelial differentiation to attenuate pulmonary fibrosis.
<em>Proceedings of the National Academy of Sciences (PNAS)</em>, 118(20):e2101100118.
<a href="https://doi.org/10.1073/pnas.2101100118">https://doi.org/10.1073/pnas.2101100118</a>
</div>
</div>
<div class="date">2021</div>
</div>
<div class="entry">
<div>
Morales-Nebreda L, Helmin KA, Acosta MAT, <b>Markov NS</b>, Hu JYS, Joudi AM, Piseaux-Aillon R,
Abdala-Valencia H, Politanska Y, Singer BD.
Available from: https://insight.jci.org/articles/view/141690 PMID: 0
<div class="details">
Aging imparts cell-autonomous dysfunction to regulatory T cells during
recovery from influenza pneumonia.
<em>JCI Insight</em>, 6(6): e141690.
<a href="https://doi.org/10.1172/jci.insight.141690">https://doi.org/10.1172/jci.insight.141690</a>
</div>
</div>
<div class="date">2021</div>
</div>
<div class="entry">
<div>
Grant RA*, Morales-Nebreda L*, <b>Markov NS</b>*, Swaminathan S, Querrey M, Guzman ER,
Abbott DA,
[…],
Malsin ES, Pickens CO, Smith SB, Walter JM, Pawlowski AE, Schneider D, Nannapaneni P,
Abdala-Valencia H, Bharat A, Gottardi CJ, Budinger GRS, Misharin AV, Singer BD, Wunderink RG.
<div class="details">
Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia.
<em>Nature</em>, 590, 635–641.
<a href="https://doi.org/10.1038/s41586-020-03148-w">https://doi.org/10.1038/s41586-020-03148-w</a>
</div>
</div>
<div class="date">2021</div>
</div>
<div class="entry">
<div>
Bharat A, Querrey M, <b>Markov NS</b>, Kim S, Kurihara C, Garza-Castillon R, Manerikar A,
Shilatifard A, Tomic R, Politanska Y, Abdala-Valencia H, Yeldandi AV, Lomasney JW, Misharin AV,
Budinger GRS.
<div class="details">
Lung transplantation for pulmonary fibrosis secondary to severe COVID-19.
<em>Science Translational Medicine</em>, 12, eabe4282.
<a href="https://doi.org/10.1126/scitranslmed.abe4282">https://doi.org/10.1126/scitranslmed.abe4282</a>
</div>
</div>
<div class="date">2020</div>
</div>
<div class="entry" style="margin-top: 120px; padding-top: 10px;">
<div>
Runyan CE, Welch LC, Lecuona E, Shigemura M, Amarelle L, Abdala‐Valencia H, Joshi N, Lu Z,
Nam K, <b>Markov NS</b>, McQuattie‐Pimentel AC, Piseaux‐Aillon R, Politanska Y, Sichizya L,
Watanabe S, Williams KJN, Budinger GRS, Sznajder JI, Misharin AV.
<div class="details">
Impaired phagocytic function in CX3CR1<sup>+</sup> tissue-resident
skeletal muscle macrophages prevents muscle recovery after influenza A
virus-induced pneumonia in old mice.
<em>Aging Cell</em>, 19(9):e13180.
<a href="https://doi.org/10.1111/acel.13180">https://doi.org/10.1111/acel.13180</a>
</div>
</div>
<div class="date">2020</div>
</div>
<div class="entry">
<div>
Joshi N, Watanabe S, Verma R, Jablonski RP, Chen CI, Cheresh P, <b>Markov NS</b>, Reyfman PA,
McQuattie-Pimentel AC, Sichizya L, Lu Z, Piseaux R, Kirchenbuechler D, Flozak AS, Gottardi CJ,
Cuda CM, Perlman H, Jain M, Kamp DW, Scott Budinger GR, Misharin AV.
<div class="details">
A spatially restricted fibrotic niche in pulmonary fibrosis is
sustained by M-CSF/M-CSFR signalling in monocyte-derived
alveolar macrophages.
<em>European Respiratory Journal (ERJ)</em>, 55 (1) 1900646.
<a href="https://doi.org/10.1183/13993003.00646-2019">https://doi.org/10.1183/13993003.00646-2019</a>
</div>
</div>
<div class="date">2019</div>
</div>
</section>
<section>
<h2>Invited Talks</h2>
<div class="entry">
<div>Host response in severe pneumonia is pathogen-specific
<div class="details">
Systems Biology for Infectious Diseases Annual Meeting.
</div>
</div>
<div class="date">September 2024</div>
</div>
<div class="entry">
<div>Cellular and molecular biomarkers of successful responses to therapy in severe pneumonia,
including COVID-19
<div class="details">
CZI Single-Cell Biology 2022 Annual meeting.
<a href="https://fast.wistia.com/embed/channel/n9ne6nikz4?wchannelid=n9ne6nikz4&wmediaid=x46zqa026r">Recording</a>
</div>
</div>
<div class="date">November 2022</div>
</div>
<div class="entry">
<div>Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia
<div class="details">
American Thoracic Society Allergy, Immunology and Inflammation (AII) assembly
journal club.<br/>
<a href="https://www.thoracic.org/members/assemblies/assemblies/aii/journal-club/circuits-between-infected-macrophages-and-t-cells-in-sars-cov-2-pneumonia.php">Recording</a>
</div>
</div>
<div class="date">June 2021</div>
</div>
</section>
<section>
<h2>Awards and Grant</h2>
<div class="entry">
<div>
American Heart Association Predoctoral Fellowship
<div class="details">
Machine learning approaches to predict outcomes and complications in ICU patients.
<br/>24PRE1196998 ($67000)
<br/><a href="https://doi.org/10.58275/AHA.24PRE1196998.pc.gr.190609">https://doi.org/10.58275/AHA.24PRE1196998.pc.gr.190609</a>
</div>
</div>
<div class="date">2024–2026</div>
</div>
<div class="entry">
<div>Northwestern Institute on Complex Systems Data Science Fellow ($12500)</div>
<div class="date">2022</div>
</div>
</section>
<section>
<h2>Work Experience</h2>
<div class="entry">
<div>Post-Baccalaureate Research Fellow, Division of Pulmonary and Critical Care Medicine,<br/>
Feinberg School of Medicine, Northwestern University, Chicago, USA
<div class="details">
Analyse transcriptomic data from human samples and mouse experiments to gain insights into
<s>COVID-19</s>, pulmonary fibrosis, systemic sclerosis and other pulmonary diseases. Analyse
clinical data to correlate -omics data to clinical states and effects of treatment. Write
manuscripts, support and organize data exchange, data management infrastructure, survey and
apply new tools to RNA-seq analysis, develop in-house algorithms, design biological
experiments to test hypothesis generated from analysis of transcriptomic data.
</div>
</div>
<div class="date">2019–2022</div>
</div>
<div class="entry">
<div>Head of maintenance tools development group, Yandex, Moscow, Russia
<div class="details">
Manage a team of developers: mentoring, resolving conflicts, improving performance, code
review. Develop, design and support tools for system administrators and other employees.
</div>
</div>
<div class="date">2014–2017</div>
</div>
<div class="entry">
<div>Full-stack software engineer, Yandex, Moscow, Russia
<div class="details">
Develop, design and support web-services and console tools for improving employees’ workflows.
</div>
</div>
<div class="date">2007–2014</div>
</div>
<div class="entry">
<div>Software engineer, Art. Lebedev Studio, Moscow, Russia
<div class="details">Develop and support web-sites and a content management system.</div>
</div>
<div class="date">2006–2007</div>
</div>
</section>
<section>
<h2>Teaching Experience</h2>
<div class="entry">
<div>Summer Students Program 2022 at Division of Pulmonary and Critical Care Medicine
<div class="details">Co-mentored 1 college student in automated image
analysis. Helped develop project goals, methodology and results interpretation.
</div>
</div>
<div class="date">2022</div>
</div>
<div class="entry">
<div>Summer Students Program 2020 at Division of Pulmonary and Critical Care Medicine
<div class="details">Co-mentored a group of 4 college students on a bioinformatics
project. Contributed to project's design, teaching R programming environment, single-cell
RNA-seq experimental technology and analysis.</div>
</div>
<div class="date">2020</div>
</div>
<div class="entry">
<div>Introduction to Python, Introduction to Pandas and Matplotlib
<div class="details">Small introductory lecture series during Data Science Nights
at NICO, Northwestern University.</div>
</div>
<div class="date">2020</div>
</div>
<div class="entry">
<div>Introduction to Programming, Newcastle University, Newcastle upon Tyne, UK
<div class="details">Unofficial 5-lecture course for fellow students.</div>
</div>
<div class="date">2017</div>
</div>
<div class="entry">
<div>Introduction to Computer Science with Python 3, Yandex, Moscow, Russia
<div class="details">High-school students.</div>
</div>
<div class="date">2013</div>
</div>
</section>
<section>
<h2>Miscalleneous</h2>
<div class="entry">
<div>Open Problems for Single-Cell Analysis Jamboree
<div class="details"><a href="https://openproblems.bio/jamboree/">https://openproblems.bio/jamboree/</a></div>
</div>
<div class="date">March 2021</div>
</div>
<div class="entry">
<div>Contributor to open-source software:
<div class="details">
<tt>Seurat</tt>, <tt>CellBrowser</tt>, <tt>biopython</tt>,
<tt>funkyheatmap</tt>, <tt>statannotations</tt>, <tt>scanpy</tt>, <tt>CellBender</tt>.
</div>
</div>
<div class="date">2018–present</div>
</div>
<div class="entry">
<div>Programming languages:
<div class="details">
Python, R, Java, C++, Ruby, Perl. Linux. Latex. HTML, JavaScript.<br/>
Github: <a href="https://github.com/mxposed">https://github.com/mxposed</a>
</div>
</div>
</div>
</section>
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