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Nikolay S. Markov

dblp:309/3871 · DBLP profile ↗
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2ranked-venue papers
0as first author
2since 2021 · last 2025
0000-0002-3659-4387ORCID · corroborated

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 2 · 2 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
single-cell analysis		 0.512021
UCSC Cell Browser: visualize your single-cell data · Bioinform. 2021
Bioinformatics and computational biology › single-cell analysis
single-cell visualization		 0.512021
UCSC Cell Browser: visualize your single-cell data · Bioinform. 2021
Bioinformatics and computational biology › gene expression analysis
gene expression visualization		 0.112021
UCSC Cell Browser: visualize your single-cell data · Bioinform. 2021

Methods — techniques the papers use, named apart from their topics

web-based visualization · 0.5python package · 0.5
YearPublicationVenuePosition
2025 Large language models accurately identify immunosuppression in intensive care unit patients
abstract
OBJECTIVE: Rule-based structured data algorithms and natural language processing (NLP) approaches applied to unstructured clinical notes have limited accuracy and poor generalizability for identifying immunosuppression. Large language models (LLMs) may effectively identify patients with heterogenous types of immunosuppression from unstructured clinical notes. We compared the performance of LLMs applied to unstructured notes for identifying patients with immunosuppressive conditions or immunosuppressive medication use against 2 baselines: (1) structured data algorithms using diagnosis codes and medication orders and (2) NLP approaches applied to unstructured notes. MATERIALS AND METHODS: We used hospital admission notes from a primary cohort of 827 intensive care unit (ICU) patients at Northwestern Memorial Hospital and a validation cohort of 200 ICU patients at Beth Israel Deaconess Medical Center, along with diagnosis codes and medication orders from the primary cohort. We evaluated the performance of structured data algorithms, NLP approaches, and LLMs in identifying 7 immunosuppressive conditions and 6 immunosuppressive medications. RESULTS: In the primary cohort, structured data algorithms achieved peak F1 scores ranging from 0.30 to 0.97 for identifying immunosuppressive conditions and medications. NLP approaches achieved peak F1 scores ranging from 0 to 1. GPT-4o outperformed or matched structured data algorithms and NLP approaches across all conditions and medications, with F1 scores ranging from 0.51 to 1. GPT-4o also performed impressively in our validation cohort (F1 = 1 for 8/13 variables). DISCUSSION: LLMs, particularly GPT-4o, outperformed structured data algorithms and NLP approaches in identifying immunosuppressive conditions and medications with robust external validation. CONCLUSION: LLMs can be applied for improved cohort identification for research purposes.
Vijeeth Guggilla, Mengjia Kang, Melissa J. Bak, Steven D. Tran, Anna Pawlowski, Prasanth Nannapaneni, Luke V. Rasmussen, Helen K. Donnelly, Ankit Agrawal 0001, David M. Liebovitz, Alexander V. Misharin, G. R. Scott Budinger, Richard G. Wunderink, Theresa Walunas, Catherine A. Gao, Alan R. Hauser, Alec Peltekian, Alexis Rose Wolfe, Alison L. Szabo, Alok N. Choudhary, Amy Ludwig, Anahid Amani Moghadam, Anjana V. Yeldandi, Ankit Bharat, Anna E. Pawlowski, Anthony M. Joudi, Arjun Prakash Tambe, Ashley J. Smith-Nunez, Benjamin D. Singer, Benjamin J. Ulrich, Betty Tran, Cara J. Gottardi, Chiagozie O. Pickens, Clara J. Schroedl, Daniel Meza, Dulce Sarai Garcia, Egon A. Ozer, Elen Gusman, Elisheva D. Shanes, Emily Mower Provost, Emily M. Olson, Erica Marie Hartmann, Erin A. Korth, Estefani Diaz, Estefany R. Guzman, Francisco J. Martinez, Gabrielle Matias, Hiam Abdala-Valencia, Jack T. Sumner, Jacob I Sznajder, Jacqueline M. Kruser, Jakub Glowala, James M. Walter, Jamie H. Rowell, Jason M. Arnold, John Coleman, Jon W. Lomasney, Joseph Isaac Bailey, Judd F. Hultquist, Justin A. Fiala, Justin Starren, Karen M. Ridge, Karolina Senkow, Kathryn A. Helmin, Khalilah L. Gates, Lacy Simmons, Lesley Pinzon, Lindsey D. Gradone, Lisa F. Wolfe, Lucy Luo, Luisa Morales-Nebreda, Manu Jain, Marc Sala, Maxwell Schleck, Melissa H. Ross, Melissa Querrey, Michael J. Cuttica, Michelle Hinsch Prickett, Nandita R. Nadig, Nathaniel Rhodes, Navdeep S. Chandel, Nikolay S. Markov, Peter H. S. Sporn, Qianli Liu, Rachel B. Kadar, Rachel L. Medernach, Ramon Lorenzo-Redondo, Ravi Kalhan, Rebecca K. Clepp, Richard I. Morimoto, Rogan A. Grant, Ruben J. Mylvaganam, Samuel Fenske, Scott A. Laurenzo, Seung Hye Han, Sophia Nozick, Srinivas Panchamukhi, Stephanie C. Eisenbarth, Suchitra Swaminathan, Susan R. Russell, Taylor A. Poor, Thaddeus Cybulski, Theresa A. Lombardo, Thomas Bolig, Thomas Stoeger, Tien Doan, Timothy Rowe, Wan-Ting Liao, Yuan Luo 0001, Yuliana Sokolenko, Ziyan Lu
 J. Am. Medical Informatics Assoc.84
2021 UCSC Cell Browser: visualize your single-cell data
abstract
SUMMARY: As the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets. AVAILABILITY AND IMPLEMENTATION: We provide the UCSC Cell Browser as a free website where scientists can explore a growing collection of single-cell datasets and a freely available python package for scientists to create stable, self-contained visualizations for their own single-cell datasets. Learn more at https://cells.ucsc.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Matthew L. Speir, Aparna Bhaduri, Nikolay S. Markov, Pablo A. Moreno, Tomasz J. Nowakowski, Irene Papatheodorou, Alex A. Pollen, Brian J. Raney, Lucas Seninge, W. James Kent, Maximilian Haeussler
 Bioinform.3