Publications - Khatri Lab

Pre-prints

Xiaoai Zhao, Xin Yan, Kévin Contrepois, Francesco Vallania, Mathew Ellenberger, Chloe M. Kashiwagi, Stephanie D. Gagnon, Cynthia J. Siebrand, Matias Cabruja, Gavin M. Traber, Andrew McKay, Daniel Hornburg, Purvesh Khatri, Michael P. Snyder, Richard N. Zare, Anne Brunet. Lipidomic profiling reveals age-dependent changes in complex plasma membrane lipids that regulate neural stem cell aging. bioRxiv 2022.
Abdulvasey Mohammed, Priscila F. Slepicka, Benjamin Solomon, Kelsea M. Hubka, Michael G. Chavez, Christine Y. Yeh, Virginia D. Winn, Casey A. Gifford, Purvesh Khatri, Andrew Gentles, Katja G. Weinacht. Single cell transcriptomics of human prenatal anterior foregut-derived organs identifies distinct developmental signatures directing commitment and specialization of the thymic epithelial stroma. bioRxiv 2022.
Benjamin D Solomon, Hong Zheng, Laura W Dillon, Jason D. Goldman, Christopher S Hourigan, James R. Heath, Purvesh Khatri. Prediction of HLA genotypes from single-cell transcriptome data. bioRxiv 2022.
Yiran E. Liu, Patricia A. Darrah, Joseph J. Zeppa, Megha Kamath, Farida Laboune, Daniel C. Douek, Pauline Maiello, Mario Roederer, JoAnne L. Flynn, Robert A. Seder, Purvesh Khatri. Blood Transcriptional Correlates of BCG-Induced Protection Against Tuberculosis in Rhesus Macaques. bioRxiv 2022.
Ananthakrishnan Ganesan*, Denis Dermadi*, Laurynas Kalesinskas*, Michele Donato*, Rosalie Sowers, Paul J. Utz, Purvesh Khatri. Imputing abundances and inferring direction of associations between histone modifications using neural processes. bioRxiv 2022. *Co-first authors.
Denis Dermadi, Laurynas Kalesinskas, Ananthakrishnan Ganesan, Alex Kuo, Peggie Cheung, Sarah Cheng, Mai Dvorak, Thomas Scriba, Aida Habtezion, Michele Donato, Paul Utz^§, Purvesh Khatri^§. Crosstalk of Histone Modifications in the Healthy Human Immune System. bioRxiv 2022. ^§Co-senior authors.
Aditya M Rao*, Stephen J Popper*, Sanjana Gupta, Viengmon Davong, Krista Vaidya, Anisone Chanthongthip, Sabine Dittrich, Matthew T Robinson, Manivanh Vongsouvath, Mayfong Mayxay, Pruksa Nawtaisong, Biraj Karmacharya, Simone A Thair, Isaac Bogoch, Timothy E Sweeney, Paul N Newton, Jason R Andrews, David A Relman^§, Purvesh Khatri^§. A robust host-response-based signature distinguishes bacterial and viral infections across diverse global populations. SSRN 2021 (under review). ^§Co-senior authors.
Aram J. Krauson*, Steven Schaffert*, Elisabeth M. Walczak, Jonathan M. Nizar, Gwen M. Holdgate, Sonali Iyer, Ragwa Elsayed, Alexandre Gaudet, Purvesh Khatri^§, Vivek Bhalla^§. Proximal and distal nephron-specific adaptation to Furosemide. bioRxiv 2021 (under review). *Co-first authors, ^§Co-senior authors.

2022

Kalani Ratnasiri, Aaron J Wilk, Madeline J Lee, Purvesh Khatri^§, Catherine Blish^§. Single-cell RNA-seq methods to interrogate virus-host interactions. Seminars in Immunopathology 2022. ^§Co-senior authors.
Rachel J. Hagey, Menashe Elazar, Edward A. Pham, Siqi Tian, Lily Ben-Avi, Claire Bernardin-Souibgui, Matthew F. Yee, Fernando R. Moreira, Meirav Vilan Rabinovitch, Rita M. Meganck, Benjamin Fram, Aimee Beck, Scott A. Gibson, Grace Lam, Josephine Devera, Wipapat Kladwang, Khanh Nguyen, Anming Xiong, Steven Schaffert, Talia Avisar, Ping Liu, Arjun Rustagi, Carl J. Fichtenbaum, Phillip S. Pang, Purvesh Khatri, Chien-Te Tseng, Jeffery K. Taubenberger, Catherine A. Blish, Brett L. Hurst, Timothy P. Sheahan, Rhiju Das & Jeffrey S. Glenn. Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2. Nature Medicine 2022, 28(9):1944–1955.
Andrea C Bohrer, Ehydel Castro, Claire E Tocheny, Maike Assmann, Benjamin Schwarz, Eric Bohrnsen, Michelle A Makiya, Fanny Legrand, Kerry L Hilligan, Paul J Baker, Flor Torres-Juarez, Zhidong Hu, Hui Ma, Lin Wang, Liangfei Niu, Zilu Wen, Sang H Lee, Olena Kamenyeva, Tuberculosis Imaging Program, Keith D Kauffman, Michele Donato, Alan Sher, Daniel L Barber, Laura E Via, Thomas J Scriba, Purvesh Khatri, Yanzheng Song, Ka-Wing Wong, Catharine M Bosio, Amy D Klion, Katrin D Mayer-Barber. Rapid GPR183-mediated recruitment of eosinophils to the lung after Mycobacterium tuberculosis infection. Cell Reports 2022, 40(4):111144.
Laurynas Kalesinskas, Sanjana Gupta, Purvesh Khatri. Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology. PLOS Computational Biology 2022, 18(6):e1010260.
Melodi Anahtar, Leslie W. Chan, Henry Ko, Aditya Rao, Ava P. Soleimany, Purvesh Khatri^§, Sangeeta N. Bhatia^§. Host protease activity classifies pneumonia etiology. Proceedings of the National Academy of Sciences USA 2022, 119(25):e2121778119. ^§Co-senior authors.
Yiran E. Liu*, Sirle Saul*, Aditya Manohar Rao, Makeda Lucretia Robinson, Olga Lucia Agudelo Rojas, Ana Maria Sanz, Michelle Verghese, Daniel Solis, Mamdouh Sibai, ChunHong Huang, Malaya Kumar Sahoo, Rosa Margarita Gelvez, Nathalia Bueno, Maria Isabel Estupiñan Cardenas, Luis Angel Villar Centeno, Elsa Marina Rojas Garrido, Fernando Rosso, Michele Donato, Benjamin A. Pinsky, Shirit Einav^§, Purvesh Khatri^§. An 8-gene machine learning model outperforms clinical warning signs for predicting severe dengue progression. Genome Medicine 2022, 14:33. *Co-first authors, ^§Co-senior authors.
Juan Aguilera, Xiaorui Han, Shu Cao, John Balmes, Fred Lurmann, Tim Tyner, Liza Lutzker, Elizabeth Noth, S Katharine Hammond, Vanitha Sampath, Trevor Burt, PJ Utz, Purvesh Khatri, Nima Aghaeepour, Holden Maecker, Mary Prunicki, Kari Nadeau. Increases in ambient air pollutants during pregnancy are linked to increases in methylation of IL4, IL10, and IFNγ. Clinical Epigenetics 2022, 14:40.
Chunfeng Li, Audrey Lee, Lilit Grigoryan, Prabhu S. Arunachalam, Madeleine K. D. Scott, Meera Trisal, Florian Wimmers, Mrinmoy Sanyal, Payton A. Weidenbacher, Yupeng Feng, Julia Z. Adamska, Erika Valore, Yanli Wang, Rohit Verma, Noah Reis, Diane Dunham, Ruth O’Hara, Helen Park, Wei Luo, Alexander D. Gitlin, Peter Kim, Purvesh Khatri, Kari C. Nadeau and Bali Pulendran. Mechanisms of innate and adaptive immunity to the Pfizer-BioNTech BNT162b2 vaccine. Nature Immunology 2022 (online ahead of print).
Guangbo Chen, Gail Deutsch, Grant Schulert, Hong Zheng, SoRi Jang, Bruce Trapnell, Claudia Macaubas, Katherine Ho, Corinne Schneider, Vivian E. Saper, Adriana Almeida de Jesus, Mark Krasnow, Alexei Grom, Raphaela Goldbach-Mansky, Purvesh Khatri^§, Elizabeth D, Mellins^§, Scott W. Canna^§. Serum proteome analysis of systemic JIA and related pulmonary alveolar proteinosis identifies distinct inflammatory programs. Arthritis & Rheumatology 2022 (ePub ahead of print). ^§Co-senior authors.
Neeraja Ravi, Sarah E. Chang, Luis M. Franco, Sandesh C.S. Nagamani, Purvesh Khatri, Paul J. Utz, Shan X. Wang. A GMR-based assay for quantification of the human response to influenza. Biosensors and Bioelectronics 2022 (ePub ahead of print).
Yehudit Hasin-Brumshtein, Suraj Sakaram, Purvesh Khatri, Yudong He, Timothy E Sweeney. A Robust Gene Expression Signature for NASH in Liver Expression. Scientific Reports 2022, 12:2571.
Kathleen D. Kolstad*, Avani Khatri*, Michele Donato, Sarah E. Chang, Shufeng Li, Virginia D. Steen, Paul J. Utz, Purvesh Khatri and Lorinda Chung. Cytokine signatures differentiate systemic sclerosis patients at high versus low risk for pulmonary arterial hypertension. Arthritis Research & Therapy 2022, 24:39.
Dharmesh Hirani, Cristina M. Alvira, Soula Danopoulos, Carlos Milla, Michele Donato, Lu Tian, Jasmine Mohr, Katharina Dinger, Christina Vohlen, Jaco Selle, Silke v. Koningsbruggen-Rietschel, Verena Barbarino, Christian Pallasch, Stefan Rose-John, Margarete Odenthal, Gloria S. Pryhuber, Siavash Mansouri, Rajkumar Savai, Werner Seeger, Purvesh Khatri, Denise Al Alam, Jörg Dötsch, Miguel A. Alejandre Alcazar. Macrophage-derived IL-6 trans-signaling as a novel target in the pathogenesis of bronchopulmonary dysplasia. European Respiratory Journal 2022, 59:2002248.
Audrey Lee*, Madeleine KD Scott*, Florian Wimmers, Prabhu S Arunachalam, Wei Luo, Christopher B. Fox, Mark Tomai, Purvesh Khatri§, Bali Pulendran§. A molecular atlas of innate immunity to adjuvanted and live attenuated vaccines, in mice. Nature Communications 2022, 13:549. *Co-first authors, ^§Co-senior authors.
Erin F. McCaffrey, Michele Donato, Leeat Keren, Zhenghao Chen, Megan Fitzpatrick, Alea Delmastro, Noah F. Greenwald, Alex Baranski, William Graf, Rashmi Kumar, Marc Bosse, Christine Camacho, Pratista K. Ramdial, Erna Forgo, Vladimir Jojic, David Van Valen, Sean C. Bendall, Matt van de Rijn, Daniel Kalman, Deepak Kaushal, Robert L. Hunter, Niaz Banaei, Adrie J.C. Steyn, Purvesh Khatri, Michael Angelo. Multiplexed imaging of human tuberculosis granulomas uncovers immunoregulatory features conserved across tissue and blood. Nature Immunology 2022 (ePub ahead of print).
Ljubomir Buturovic*, Hong Zheng*, Benjamin Tang, Kevin Lai, Win Sen Kuan, Mark Gillett, Rahul Santram, Maryam Shojaei, Raquel Almansa, Jose Ángel Nieto, Sonsoles Muñoz, Carmen Herrero, Nikolaos Antonakos, Panayiotis Koufargyris, Marina Kontogiorgi, Georgia Damoraki, Oliver Liesenfeld, James Wacker, Uros Midic, Roland Luethy, David Rawling, Melissa Remmel, Sabrina Coyle, Yiran E. Liu, Aditya M Rao, Denis Dermadi, Jiaying Toh, Lara Murphy Jones, Michele Donato, Purvesh Khatri^§, Evangelos J. Giamarellos-Bourboulis^§, Timothy E Sweeney^§. A 6-mRNA host response whole-blood classifier trained on pre-pandemic data accurately predicts severity in COVID-19 and other acute viral infections. Scientific Reports 2022, 12(1):889. *Co-first authors, ^§Co-senior authors.
Afroza Akter, Tasnuva Ahmed, Imam Tauheed, Marjahan Akhtar, Sadia Isfat Ara Rahman, Fatema Khaton, Faisal Ahmmed, Jannatul Ferdous, Mokibul Hassan Afrad, Zannat Kawser, Mohabbat Hossain, Rabeya Khondaker, Mohammad Abul Hasnat, Mostafa Aziz Sumon, Asif Rashed, Shuvro Ghosh, Stephen B. Calderwood, Richelle C. Charles, Edward T. Ryan, Purvesh Khatri, Holden Terry Maecker, Gerlinde Obermoser, Bali Pulendran, John D. Clemens, Sayera Banu, Tahmina Shirin, Regina C. LaRocque, Jason B. Harris, Taufiqur Rahman Bhuiyan, Fahima Chowdhury, Firdausi Qadri. Disease characteristics and serological responses in patients with differing severity of COVID-19 infection: A longitudinal cohort study in Dhaka, Bangladesh. PLOS Neglected Tropical Diseases 2022, 16(1):e0010102.

2021

Minyoung Youn*, Stephanie M. Smith* , Alex Gia Lee*, Hee-Don Chae*, Elizabeth Spiteri, Jason Erdmann, Ilana Galperin, Lara Murphy Jones, Michele Donato, Parveen Abidi, Henrique Bittencourt, Norman Lacayo , Gary Dahl, Catherine Aftandilian, Kara L. Davis, Jairo A. Matthews, Steven M. Kornblau, Min Huang, Nathan Sumarsono, Michele S. Redell, Cecilia H. Fu, I-Ming Chen, Todd A. Alonzo, Elizabeth Eklund, Jason Gotlib, Purvesh Khatri, E. Alejandro Sweet-Cordero, Nobuko Hijiya and Kathleen M. Sakamoto. Comparison of the Transcriptomic Signatures in Pediatric and Adult CML. Cancers 2021, 13, 6263.
Suraj Sakaram, Yehudit Hasin-Brumshtein, Purvesh Khatri, Yudong D. He, Timothy E. Sweeney. A Multi-mRNA Prognostic Signature for Anti-TNFα Therapy Response in Patients with Inflammatory Bowel Disease. Diagnostics 2021, 11(10):1902.
Lauren E. Higdon*, Steven Schaffert*, Rachel H. Cohen, Maria E. Montez-Rath, Marc Lucia, Naresha Saligrama, Kenneth B. Margulies, Olivia M. Martinez, Jane C. Tan, Mark M. Davis, Purvesh Khatri^§ and Jonathan S. Maltzman^§. Functional Consequences of Memory Inflation after Solid Organ Transplantation. Journal of Immunology 2021, 207(8):2086-2095. *Co-first authors. ^§Co-senior authors.
Lauren E. Higdon*, Steven Schaffert*, Huang Huang, Maria E. Montez-Rath, Marc Lucia, Alokkumar Jha, Naresha Saligrama, Kenneth B. Margulies, Olivia M. Martinez, Mark M. Davis, Purvesh Khatri^§ and Jonathan S. Maltzman^§. Evolution of Cytomegalovirus-Responsive T Cell Clonality following Solid Organ Transplantation. Journal of Immunology 2021, 207(8):2077-2085. *Co-first authors, ^§Co-senior authors.
Lawrence Bai,* Madeleine K. D. Scott,* Ethan Steinberg, Laurynas Kalesinskas, Aida Habtezion, Nigam H. Shah, and Purvesh Khatri. Computational drug repositioning of atorvastatin for ulcerative colitis. Journal of the American Medical Informatics Association 2021, 28(11):2325–2335. *Co-first authors.
Prabhu S. Arunachalam*, Madeleine K. D. Scott*, Thomas Hagan*, Chunfeng Li, Florian Wimmers, Yupeng Feng, Lilit Grigoryan, Meera Trisal, Venkata Viswanadh Edara, Lilin Lai, Sarah Esther Chang, Allan Feng, Shaurya Dhingra, Mihir Shah, Allie Skye Lee, Natalia Sigal, Sangeeta Kowli, Sheena Gupta, Kathryn Pellegrini, Sofia Maysel-Auslender, Steven Bosinger, Holden T. Maecker, Scott D. Boyd, Mark M. Davis, Paul J. Utz, Mehul S. Suthar, Purvesh Khatri^§, Kari C. Nadeau^§, Bali Pulendran^§. Systems biological assessment of human immunity to BNT162b2 mRNA vaccination. Nature 2021, 596:410–416. *Co-first authors. ^§Co-senior authors.
Alexandra J. Zimmer^*, Samuel G. Schumacher^*, Erik Södersten, Anna Mantsoki, Romain Wyss, David H. Persing, Sara Banderby, Linda Strömqvist Meuzelaar, Jacqueline Prieto, Devasena Gnanashanmugam, Purvesh Khatri, Stefano Ongarello, Morten Ruhwald^§, Claudia M. Denkinger^§. A novel blood-based assay for treatment monitoring of tuberculosis. BMC Research Notes 2021, 14:247. *Co-first authors, ^§Co-senior authors.
Florian Wimmers, Michele Donato*, Alex Kuo*, Tal Ashuach*, Shakti Gupta, Chunfeng Li, Mai Dvorak, Mariko Hinton Foecke, Sarah E. Chang, Sanne E. De Jong, Holden T. Maecker, Robbert van der Most, Peggie Cheung, Mario Cortese, Thomas L. Hagan, Steve Bosinger, Mark Davis, Nadine Rouphael, Shankar Subramaniam, Nir Yosef, Paul J. Utz, Purvesh Khatri, Bali Pulendran. Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans. Cell 2021, 184:1-21.
Andrew R. Moore, Jonasel Roque, Brian T. Shaller, Tola Asuni, Melissa Remmel, David Rawling, Oliver Liesenfeld, Purvesh Khatri, Jennifer G. Wilson, Joseph E. Levitt, Timothy E. Sweeney & Angela J. Roger. Prospective validation of an 11-gene mRNA host response score for mortality risk stratification in the intensive care unit. Scientific Reports 2021, 11:13062.
Peggie Cheung*, Steven Schaffert*, Sarah E. Chang*, Mai Dvorak, Michele Donato, Claudia Macaubas, Mariko H. Foecke, Tie-Mei Li, Lichao Zhang, John P. Coan, Grant S. Schulert, Alexei A. Grom, Lauren A. Henderson, Peter A. Nigrovic, Joshua E. Elias, Or Gozani, Elizabeth D. Mellins^§, Purvesh Khatri^§, Paul J. Utz^§ & Alex J. Kuo^§. Repression of CTSG, ELANE and PRTN3-mediated histone H3 proteolytic cleavage promotes monocyte-to-macrophage differentiation. Nature Immunology 2021, 22:711-722. *Co-first authors, ^§Co-senior authors.
Kerui Peng, Yana Safonova, Mikhail Shugay, Alice B. Popejoy, Oscar L. Rodriguez, Felix Breden, Petter Brodin, Amanda M. Burkhardt, Carlos Bustamante, Van-Mai Cao-Lormeau, Martin M. Corcoran, Darragh Duffy, Macarena Fuentes-Guajardo, Ricardo Fujita, Victor Greiff, Vanessa D. Jönsson, Xiao Liu, Lluis Quintana-Murci, Maura Rossetti, Jianming Xie, Gur Yaari, Wei Zhang, Malak S. Abedalthagafi, Khalid O. Adekoya, Rahaman A. Ahmed, Wei-Chiao Chang, Clive Gray, Yusuke Nakamura, William D. Lees, Purvesh Khatri, Houda Alachkar, Cathrine Scheepers, Corey T. Watson, Gunilla B. Karlsson Hedestam and Serghei Mangul. Diversity in immunogenomics: the value and the challenge. Nature Methods 2021, 18:588–591.
Francesco Vallania, Liron Zisman, Claudia Macaubas, Shu-Chen Hung, Narendiran Rajasekaran, Sonia Mason, Jonathan Graf, Mary Nakamura, Elizabeth D. Mellins* and Purvesh Khatri*. Multicohort Analysis Identifies Monocyte Gene Signatures to Accurately Monitor Subset-Specific Changes in Human Diseases. Frontiers in Immunology 2021, 12:1732.
Mingxia Gu, Michele Donato, Minzhe Guo, Neil Wary, Yifei Miao, Shuai Mao, Toshie Saito, Shoichiro Otsuki, Lingli Wang, Rebecca L. Harper, Silin Sa, Purvesh Khatri, Marlene Rabinovitch. iPSC–endothelial cell phenotypic drug screening and in silico analyses identify tyrphostin-AG1296 for pulmonary arterial hypertension. Science Translational Medicine 2021, 13:eaba6480.
Simone Thair*, Caspar Mewes*, José Hinz, Ingo Bergmann, Benedikt Büttner, Stephan Sehmisch, Konrad Meissner, Michael Quintel, Timothy E Sweeney, Purvesh Khatri^§, Ashham Mansur^§. Gene Expression–Based Diagnosis of Infections in Critically Ill Patients—Prospective Validation of the SepsisMetaScore in a Longitudinal Severe Trauma Cohort. Critical Care Medicine 2021, 49(8):e751-e760 . *Co-first authors. ^§Co-senior authors.
Lara Murphy Jones and Purvesh Khatri. Multisystem inflammatory syndrome in children: a microcosm of challenges and opportunities for translational bioinformatics in pediatric research. Current Opinions in Pediatrics 2021, 33(3):325-330.
Cesar J. Lopez Angel, Edward A. Pham, Huixun Du, Francesco Vallania, Benjamin J. Fram, Kevin Perez, Thai Nguyen, Yael Rosenberg-Hasson, Aijaz Ahmed, Cornelia L. Dekker, Philip M. Grant, Purvesh Khatri, Holden T. Maecker, Jeffrey S. Glenn, Mark M. Davis, and David Furman. Signatures of immune dysfunction in HIV and HCV infection share features with chronic inflammation in aging and persist after viral reduction or elimination. Proceedings of the National Academy of Sciences 2021, 18(14):e2022928118.
Hong Zheng*, Aditya M Rao*, Denis Dermadi*, Jiaying Toh*, Lara Murphy Jones*, Michele Donato*, Yiran Liu, Yapeng Su, Minas Karagiannis, Theodoros Marantos, Yehudit Hasin-Brumshtein, Yudong D He, Evangelos J Giamarellos-Bourboulis, Jim Heath, Purvesh Khatri. Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses. Immunity 2021, 54:753-768.
Flora Martinez Figueira Moreira, Renu Verma, Paulo Cesar Pereira dos Santos, Alessandra Leite, Andrea da Silva Santos, Rafaele Carla Pivetta de Araujo, Bruna Oliveira da Silva, Júlio Henrique Ferreira de Sá Queiroz, David H Persing, Erik Södersten, Devasena Gnanashanmugam, Purvesh Khatri, Julio Croda, Jason R Andrews. Blood-based host biomarker diagnostics in active case finding for pulmonary tuberculosis: A diagnostic case-control study. EClinicalMedicine 2021,33:100776.
Erik Södersten, Stefano Ongarello, Ann Mantsoki, Romain Wyss, David H Persing, Sara Banderby, Linda Strömqvist Meuzelaar, Jacqueline Prieto, Devasena Gnanashanmugam, Purvesh Khatri, Samuel G Schumacher, Samuel G, Claudia M Denkinger. Diagnostic accuracy study of a novel blood-based assay for identification of TB in people living with HIV. Journal of Clinical Microbiology 2021, 59(3):e01643-20.
Adriana Tomic,* Ivan Tomic,* Levi Waldron, Ludwig Geistlinger, Max Kuhn, Rachel L. Spreng, Lindsay C. Dahora, Kelly E. Seaton, Georgia Tomaras, Jennifer Hill, Niharika A. Duggal, Ross D. Pollock, Norman R. Lazarus, Stephen D.R. Harridge, Janet M. Lord, Purvesh Khatri, Andrew J. Pollard, and Mark M. Davis. SIMON: Open-Soure Knowledge Discovery Platform. Patterns 2021, 2(1):100178.
Madeleine K. D. Scott, Michael G. Ozawa, Pauline Chu, Maneesha Limaye, Viswam S. Nair, Steven Schaffert, Albert C. Koong, Robert West, Purvesh Khatri. A multi-scale integrated analysis identifies KRT8 as a pan-cancer early biomarker. Pacific Symposium on Biocomputing 2021. 26:297-308.

2020

Simone A. Thair, Yudong D. He, Yehudit Hasin-Brumshtein, SurajSakaram, Rushika Pandya, Jiaying Toh, David Rawling, Melissa Remmel, Sabrina Coyle, George N. Dalekos, Ioannis Koutsodimitropoulos, Glykeria Vlachogianni, Eleni Gkeka, Eleni Karakike, Georgia Damoraki, Nikolaos Antonakos, Purvesh Khatri§, Evangelos J. Giamarellos-Bourboulis§, Timothy E. Sweeney§. Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections. iScience 2020, 24(1):101947. §Co-senior authors.
Prabhu S. Arunachalam*, Florian Wimmers*, Chris Ka Pun Mok*, Ranawaka A. P. M. Perera*, Madeleine Scott, Thomas Hagan, Natalia Sigal, Yupeng Feng, Laurel Bristow, Owen Tak-Yin Tsang, Dhananjay Wagh, John Coller, Kathryn L. Pellegrini, Dmitri Kazmin, Ghina Alaaeddine, Wai Shing Leung, Jacky Man Chun Chan, Thomas Shiu Hong Chik, Chris Yau Chung Choi, Christopher Huerta, Michele Paine McCullough, Huibin Lv, Evan Anderson, Srilatha Edupuganti, Amit A. Upadhyay, Steve E. Bosinger, Holden Terry Maecker, Purvesh Khatri, Nadine Rouphael, Malik Peiris, Bali Pulendran. Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science 2020, 369:6508(1210-1220).
Eli M Cahan and Purvesh Khatri. Data Heterogeneity: The Enzyme to Catalyze Translational Bioinformatics? Journal of Medical Internet Research 2020, 22(8):e18044.
Diederik E van der Feen, Guido PL Bossers, Quint AJ Hagdorn, Jan-Renier Moonen, Kondababu Kurakula, Robert Szulcek, James Chappell, Francesco Vallania, Michele Donato, Klaas Kok, Jaskaren S Kohli, Arjen H Petersen, Tom van Leusden, Marco Demaria, Marie-José TH Goumans, Rudolf A De Boer, Purvesh Khatri, Marlene Rabinovitch, Rolf MF Berger, Beatrijs Bartelds. Cellular senescence impairs the reversibility of pulmonary arterial hypertension. Science Translational Medicine 2020, 12:554(eaaw4974).
Prabhu S. Arunachalam, Tysheena P. Charles, Vineet Joag, Venkata S. Bollimpelli, Madeleine K. D. Scott, Florian Wimmers, Samantha L. Burton, Celia C. Labranche, Caroline Petitdemange, Sailaja Gangadhara, Tiffany M. Styles, Clare F. Quarnstrom , Korey A. Walter, Thomas J. Ketas, Traci Legere, Pradeep Babu Jagadeesh Reddy, Sudhir Pai Kasturi, Anthony Tsai, Bertrand Z. Yeung, Shakti Gupta, Mark Tomai, John Vasilakos, George M. Shaw, Chil-Yong Kang, John P. Moore , Shankar Subramaniam, Purvesh Khatri, David Montefiori, Pamela A. Kozlowski , Cynthia A. Derdeyn, Eric Hunter, David Masopust, Rama R. Amara and Bali Pulendran. T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers. Nature Medicine 2020, 26:932–940.
Vivian E Saper, Guangbo Chen, R Paul Guillerman, Purvesh Khatri, Randy Q Cron, Elizabeth D Mellins. Response to: ‘Successful treatment of plasma exchange for refractory systemic juvenile idiopathic arthritis complicated with macrophage activation syndrome and severe lung disease’ by Sato et al. Annals of Rheumatic Diseases 2020, 0:1–2.
Chase Correia, Seamus Mawe, Shane Lofgren, Roberta G. Marangoni, Jungwha Lee, Rana Saber, Kathleen Aren, Michelle Cheng, Shannon Teaw, Aileen Hoffmann, Isaac Goldberg, Shawn E. Cowper, Purvesh Khatri, Monique Hinchcliff & J. Matthew Mahoney. High-throughput quantitative histology in systemic sclerosis skin disease using computer vision. Arthritis Research & Therapy 2020, 22:48.
Michael B. Mayhew, Ljubomir Buturovic, Roland Luethy, Uros Midic, Andrew R. Moore, Jonasel A. Roque, Brian D. Shaller, Tola Asuni, David Rawling, Melissa Remmel, Kirindi Choi, James Wacker, Purvesh Khatri, Angela J. Rogers & Timothy E. Sweeney. A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections. Nature Communications 2020, 11:1177.
Vivian E Saper, Guangbo Chen, Purvesh Khatri, Elizabeth D Mellins. Response to: ‘Effectiveness and safety of ruxolitinib for the treatment of refractory systemic idiopathic juvenile arthritis like associated with interstitial lung disease: case report’. Annals of Rheumatic Diseases 2020, .
Winston A. Haynes, D. James Haddon, Vivian K. Diep, Avani Khatri, Erika Bongen, Gloria Yiu, Imelda Balboni, Christopher R. Bolen, Rong Mao, Paul J. Utz^§, Purvesh Khatri^§. Integrated, Multi-Cohort Analysis Reveals Unified Signature of Systemic Lupus Erythematosus. JCI Insight 2020, 5(4):e122312. ^§co-senior authors.

2019

Blake J Schultz, Timothy Sweeney, Malcolm R DeBaun, Melissa Remmel, Uros Midic, Purvesh Khatri, Michael J Gardner. Pilot study of a novel serum mRNA gene panel for diagnosis of acute septic arthritis. World Journal of Orthopedics 2019, 10(12):424-433.
Vivian E. Saper*, Guangbo Chen*, Gail H. Deutsch^†, R Paul. Guillerman^†, Johannes Birgmeier^||, Karthik Jagadeesh^||, Scott Canna^‡, Grant Schulert^‡, Robin Deterding, Jianpeng Xu, Ann N. Leung, Layla Bouzoubaa, Khalid Abulaban, Kevin Baszis, Edward M Behrens, James Birmingham, Alicia Casey, Michal Cidon , Randy Cron, Aliva De, Fabrizio De Benedetti, Ian Ferguson, Martha P. Fishman, Steven I. Goodman, Brent Graham, Alexei Grom, Kathleen Haines, Melissa Hazen, Lauren A. Henderson, Assunta Ho, Maria Ibarra, CJ Inman, Rita Jerath, Khulood Walid Khawaja, Daniel J Kingsbury, Marisa Klein-Gitelman, Khan Lai, Sivia Lapidus, Clara Lin, Jenny Lin, Deborah R. Liptzin, Diana Milojevic, Joy Mombourquette, Karen Onel, Seza Ozen, Maria Perez, Kathryn Phillippi, Sampath Prahalad, Suhas Radhakrishna, Adam Reinhardt, Mona Riskalla, Natalie Rosenwasser, Johannes Roth, Rayfel Schneider, Dieneke Schonenberg-Meinema, Susan Shenoi, Judith A Smith, Hafize Emine Sonmez, Matthew L. Stoll, Christopher Towe, Sara O. Vargas, Richard K. Vehe, Lisa R. Young, Jacqueline Yang, Tushar Desai, Raymond Balise, Ying Lu, Lu Tian, Gil Bejerano, Mark M. Davis, Purvesh Khatri^§, Elizabeth D. Mellins^§ and the Childhood Arthritis and Rheumatology Research Alliance Registry Investigators. Emergent high fatality lung disease in systemic juvenile arthritis. Annals of Rheumatic Diseases 2019, 78(12):1722-1731. *Co-first authors. ^§co-senior authors.
Erika Bongen, Hayley Lucian, Avani Khatri, Gabriela K Fragiadakis, Zachary B Bjornson, Gary P Nolan, Paul J Utz^§, Purvesh Khatri^§. Sex Differences in the Blood Transcriptome Identify Robust Changes in Immune Cell Proportions with Aging and Influenza Infection. Cell Reports 2019, 29(7):1961-1973. ^§co-senior authors.
Mathieu Le Gars, Christof Seiler, Alexander W. Kay, Nicholas L. Bayless, Elina Starosvetsky, Lindsay Moore, Shai S. Shen-Orr, Natali Aziz, Purvesh Khatri, Cornelia L. Dekker, Gary E. Swan, Mark M. Davis, Susan Holmes, Catherine A. Blish. Pregnancy-Induced Alterations in NK Cell Phenotype and Function. Frontiers in Immunology 2019, 10:2469.
Zinaida Good, Jacob Glanville, Marvin H Gee, Mark M Davis, Purvesh Khatri. Computational and Systems Immunology: A Student’s Perspective. Trends in immunology 2019, 40(8):665-668.
Madeleine K D Scott, Katie Quinn, Qin Li, Robert Carroll, Hayley Warsinske, Francesco Vallania, Shirley Chen, Mary A Carns, Kathleen Aren, Jiehuan Sun, Kimberly Koloms, Jungwha Lee, Jessika Baral, Jonathan Kropski, Hongyu Zhao, Erica Herzog, Fernando J Martinez, Bethany B Moore, Monique Hinchcliff, Joshua Denny, Naftali Kaminski, Jose D Herazo-Maya, Nigam H Shah^§, Purvesh Khatri^§. Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study. The Lancet Respiratory Medicine 2019, 7(6):497-508. ^§co-senior authors.
Peggie Cheung, Purvesh Khatri, Paul J Utz, Alex Kuo. Single-cell technologies — studying rheumatic diseases one cell at a time. Nature Reviews Rheumatology 2019, 15:340-354.
Lauren E Higdon*, Steven Schaffert*, Purvesh Khatri^§, Jonathan S Maltzman^§. Single-cell immune profiling in transplantation research. American Journal of Transplantation 2019, 19:1278-1287 . *Contributed equally. ^§co-senior authors.
Hayley Warsinske, Rohit Vashisht, Purvesh Khatri. Host-response-based gene signatures for tuberculosis diagnosis: A systematic comparison of 16 signatures. PLoS Medicine 2019, 16(4):e1002786.
John V. Pluvinage, Michael S. Haney, Benjamin A. H. Smith, Jerry Sun, Tal Iram, Liana Bonanno, Lulin Li, Davis P. Lee, David W. Morgens, Andrew C. Yang, Steven R. Shuken, David Gate, Madeleine Scott, Purvesh Khatri, Jian Luo, Carolyn R. Bertozzi, Michael C. Bassik & Tony Wyss-Coray. CD22 blockade restores homeostatic microglial phagocytosis in ageing brains. Nature 2019, 558:187-192.
Ayelet Alpert, Yishai Pickman, Michael Leipold, Yael Rosenberg-Hasson, Xuhuai Ji, Renaud Gaujoux, Hadas Rabani, Elina Starosvetsky, Ksenya Kveler, Steven Schaffert, David Furman, Oren Caspi, Uri Rosenschein, Purvesh Khatri, Cornelia L. Dekker, Holden T. Maecker, Mark M. Davis, Shai S. Shen-Orr. A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring. Nature Medicine 2019, 25:487-495.
Andrew J. Sweatt, Haley K. Hedlin, Vidhya Balasubramanian, Andrew Hsi, Lisa K. Blum, William H. Robinson, Francois Haddad, Allan Lawrie, Mark R. Nicolls, Marlene Rabinovitch, Purvesh Khatri, Roham T. Zamanian. Identification of deep immune phenotypes in pulmonary arterial hypertension with unsupervised machine learning. Circulation Research 2019,124:904–919.
Makeda Robinson*, Timothy E. Sweeney*, Rina Barouch-Bentov, Malaya Kumar Sahoo, Larry Kalesinskas, Francesco Vallania, Ana Maria Sanz, Eliana Ortiz-Lasso, Ludwig Luis Albornoz, Fernando Rosso, Jose G. Montoya, Benjamin A. Pinsky, Purvesh Khatri^§, Shirit Einav^§. A novel prognostic gene set for the prediction of severe dengue. Cell Reports 2019, 26(5):1104-1111. *Contributed equally. ^§co-corresponding authors.
Svenja Dannewitz Prosseda, Xuefei Tian, Kazuya Kuramoto, Mario Boehm, Deepti Sudheendra, Kazuya Miyagawa, Fan Zhang, David Solow-Cordero, Joshua Saldivar, Eric Austin, James E. Loyd, Lisa Wheeler, Adam Andruska, Lingli Wang, Kay Huebner, Ross Metzger, Purvesh Khatri, Edda Spiekerkoetter. Fragile Histidine Triad (FHIT), a novel modifier gene in pulmonary arterial hypertension. American Journal of Respiratory and Critical Care Medicine 2019, 199(1):83-98.

2018

Steven Schaffert, Purvesh Khatri. Early life immunity in the era of systems biology: understanding development and disease. Genome Medicine 2018 10:88.
Francesco Vallania, Andrew Tam, Shane Lofgren, Steven Schaffert, Tej D Azad, Erika Bongen, Winston Haynes, Meia Alsup, Michael Alonso, Mark Davis, Edgar Engleman, Purvesh Khatri. Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases. Nature Communications 2018 9(4735).
Hayley C. Warsinske, Aditya M. Rao, Flora M. F. Moreira, Paulo Cesar P. Santos, Andrew B. Liu, Madeleine Scott, Stephaus T. Malherbe, Katharina Ronacher, Gerhard Walzl, Jill Winter, Timothy E. Sweeney, Julio Croda, Jason R. Andrews^§, Purvesh Khatri^§. Assessment of Validity of a Blood-Based 3-Gene Signature Score for Progression and Diagnosis of Tuberculosis, Disease Severity, and Treatment Response. JAMA Network Open 2018 1(6):e183779. ^§co-corresponding authors.
Roshni Roy Chowdhury, Francesco Vallania, Qiantian Yang, Fatoumatta Darboe, Adam Penn-Nicholson, Virginie Rozot, Cesar Joel Lopez Angel, Willem Hanekom, Mark M. Davis, Xinchun Chen, Thomas J. Scriba, Purvesh Khatri^§, Yueh-hsiu Chien^§. Immune system dynamics and protective correlates of M. tuberculosis infection. Nature 2018 560:644-648. ^§co-corresponding authors.
Erika Bongen, Francesco Vallania, Paul J Utz, Purvesh Khatri. KLRD1-expressing natural killer cells predict influenza susceptibility. Genome Medicine 2018 10(1):45.
Peggie Cheung*, Francesco Vallania*, Mai Dvorak, Sarah E Chang, Steven Schaffert, Michele Donato, Aditya Rao, Rong Mao, Paul J. Utz^§, Purvesh Khatri^§, Alex J. Kuo^§. Single-cell epigenetics – Chromatin modification atlas unveiled by mass cytometry. Clinical Immunology 2018 196:40-48. *Contributed equally. ^§co-corresponding authors.
Timothy E Sweeney^§, Tej D Azad, Michele Donato, Winston A Haynes, Thanneer M Perumal, Ricardo Henao, Jesús F Bermejo-Martin, Raquel Almansa, Eduardo Tamayo, Judith A Howrylak, Augustine Choi, Grant P Parnell, Benjamin Tang, Marshall Nichols, Christopher W Woods, Geoffrey S Ginsburg, Stephen F Kingsmore, Larsson Omberg, Lara M Mangravite, Hector R Wong, Ephraim L Tsalik, Raymond J Langley, Purvesh Khatri^§. Unsupervised analysis of transcriptomics in bacterial sepsis across multiple datasets reveals three robust clusters. Critical Care Medicine. 2018, 46(6):915-925. ^§co-corresponding authors.
Peggie Cheung*, Francesco Vallania*, Hayley C. Warsinske, Michele Donato, Steven Schaffert, Sarah E. Chang, Mai Dvorak, Cornelia L. Dekker, Mark M. Davis, Paul J. Utz^§,Purvesh Khatri^§, Alex J. Kuo^§. Single-cell epigenetic landscape profiling of human immune system reveals increased variations at chromatin with aging. Cell 2018, 173(6):1385-1397. *Contributed equally. ^§co-corresponding authors.
(download data)
Renaud Gaujoux*, Elina Starosvetsky*, Naama Maimon*, Francesco Vallania, Haggai Bar-Yosef, Sigal Pressman, Roni Weisshof, Idan Goren, Matti Waterman, Henit Yanai, Iris Dotan, Edmond Sabo, Yehuda Chowers^§, Purvesh Khatri^§, Shai S. Shen-Orr^§. A cell-centered meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of IBD patients. Gut 2018.*Equal contribution, ^§Co-corresponding authors.
Aurelie Tomczak, Jonathan M. Mortensen, Rainer Winnenburg, Charles Liu, Dominique T. Alessi, Varsha Swamy, Francesco Vallania, Shane Lofgren, Winston Haynes, Nigam H. Shah, Mark A. Musen, Purvesh Khatri. Interpretation of biological experiments changes with evolution of Gene Ontology and its annotations. Scientific Reports 2018, 8:5115.
Charles S. Dela Cruz, Richard G. Wunderink, David C. Christiani, Stephania A. Cormier,Kristina Crothers, Claire M. Doerschuk, Scott E. Evans, Daniel R. Goldstein, Purvesh Khatri, Lester Kobzik, Jay K. Kolls, Bruce D. Levy, Mark L. Metersky, Michael S. Niederman, Roomi Nusrat, Carlos J. Orihuela, Paula Peyrani, Alice S. Prince, Julio A. Ramírez, Karen M. Ridge, Sanjay Sethi, Benjamin T. Suratt, Jacob I. Sznajder, Ephraim L. Tsalik, Allan J. Walkey, Sachin Yende, Neil R. Aggarwal, Elisabet V. Caler,Joseph P. Mizgerd. Future Research Directions in Pneumonia: NHLBI Working Group Report. American Journal of Respiratory and Critical Care Medicine 2018.
Timothy E Sweeney*, Thanneer M Perumal*, Ricardo Henao, Marshall Nichols, Judith A Howrylak, Augustine M Choi, Jesús F Bermejo-Martin, Raquel Almansa, Eduardo Tamayo, Emma E Davenport, Katie L Burnham, Charles J Hinds, Julian C Knight, Christopher W Woods, Stephen F Kingsmore, Geoffrey S Ginsburg, Hector R Wong, Grant P Parnell, Benjamin Tang, Lyle L Moldawer, Frederick E Moore, Larsson Omberg, Purvesh Khatri^§, Ephraim L Tsalik^§, Lara M Mangravite^§, Raymond J Langley^§. A community approach to mortality prediction in sepsis via gene expression analysis. Nature Communications 2018, 9:694.*Equal contribution, ^§Co-corresponding authors.
Timothy E. Sweeney, Neal J. Thomas, Judie A. Howrylak, Hector R. Wong, MD, Angela J. Rogers^§, Purvesh Khatri^§. Multi-cohort analysis of whole-blood gene expression data does not form a robust diagnostic for Acute Respiratory Distress Syndrome. Critical Care Medicine 2018, 46(2):244-251. ^§Co-corresponding authors.
Tej D. Azad*, Michele Donato*, Line Heylen, Shai S Shen-Orr, Timothy E. Sweeney, Jonathan Scott Maltzman, Maarten Naesens, Purvesh Khatri. Early dysregulation of inflammatory macrophages is a robust predictor of subclinical allograft injury and graft survival across transplanted organs. JCI Insight 2018, 3(2):1-12. *Contributed equally.
Marvin H. Gee*, Arnold Han*, Shane M. Lofgren, John F. Beausang, Juan L. Mendoza, Michael E. Birnbaum, Michael T. Bethune, Suzanne Fischer, Xinbo Yang, Raquel Gomez-Eerland, David B. Bingham, Leah V. Sibener, Ricardo A. Fernandes, Andrew Velasco, David Baltimore, Ton N. Schumacher, Purvesh Khatri, Stephen R. Quake, Mark M. Davis, K. Christopher Garcia. Antigen identification from orphan T cell receptors expressed on tumor-infiltrating lymphocytes. Cell 2017, 172(3):549-563. *Equal contribution
Winston A Haynes, Aurelie Tomczak, Purvesh Khatri. Gene annotation bias impedes biomedical research. Scientific Reports 2018, 8(1):1362.
Zhifen Yang, Jing Zhang, Dadi Jiang, Purvesh Khatri, David E. Solow-Cordero, Diego A.S. Toesca, Constantinos Koumenis, Nicholas C. Denko, Amato J. Giaccia, Quynh-Thu Le and Albert C. Koong. A Human Genome-wide RNAi Screen Reveals Diverse Modulators that Mediate IRE1α-XBP1 Activation. Molecular Cancer Research 2018, 16(5):745-753.

2017

Hector R Wong, Timothy E Sweeney, Kimberly W Hart, Purvesh Khatri, Christopher J Lindsell. Pediatric sepsis endotypes among adults with sepsis. Crit Care Med. 2017, Dec;45(12):e1289-91.
Steven L. Raymond, María Cecilia López Henry V. Baker, Shawn D. Larson, Philip A. Efron, Timothy E. Sweeney, Purvesh Khatri, Lyle L. Moldawer, James L. Wynn. Unique transcriptomic response to sepsis is observed among patients of different age groups. PLOS One. 2017, 12(9): e0184159.
Timothy E Sweeney, Shane Lofgren, Purvesh Khatri^§, Angela J Rogers^§. Gene Expression Analysis to Assess the Relevance of Rodent Models to Human Lung Injury. American Journal of Respiratory and Cellular Molecular Biology. 2017, 57(2):184-92. ^§co-corresponding authors.
HIPC-CHI Signatures Team and HIPC-I Consortium. Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses. Science Immunology 2017, 2: eaal4656.
Dadi Jiang, Brandon Turner, Jie Song, Ruijiang Li, Maximilian Diehn, Quynh-Thu Le, Purvesh Khatri, Albert C Koong. Comprehensive Analysis of the Unfolded Protein Response in Breast Cancer Subtypes. JCO Precision Oncology 2017, 1:1-9.
Mitchell E Garber, Alok Saldanha, Joel S Parker, Wendell D Jones, Katri Kaukinen, Kaija Laurila, Marja-Leena Lähdeaho, Purvesh Khatri, Chaitan Khosla, Daniel C Adelman, Markku Mäki. A B-Cell Gene Signature Correlates with the Extent of Gluten-induced Intestinal Injury in Celiac Disease. Cellular and Molecular Gastroenterology and Hepatology. 2017, 4(1):1:17.
Timothy E Sweeney, Purvesh Khatri. Generalizable biomarkers in critical care: toward precision medicine. Critical Care Medicine. 2017, 45(6):934-9.
Timothy E. Sweeney, James L. Wynn, María Cernada, Eva Serna, Hector R. Wong, Henry V. Baker, Máximo Vento, and Purvesh Khatri. Validation of the Sepsis MetaScore for Diagnosis of Neonatal Sepsis. Journal of Pediatric Infectious Disease Society. 2017, 7(2):129-135. (Data and analysis code)
Timothy E Sweeney, Purvesh Khatri. The Authors’ Reply to Turning a New Page in Sepsis Molecular Diagnostics Necessitates Context-Specific Biomarkers. Critical Care Medicine. 2017, 45(4):e457.
Timothy E Sweeney, Purvesh Khatri. The Authors’ Reply to The Importance of Avoiding Conclusions for the Right Diagnostic in the Wrong Population. Critical Care Medicine. 2017, 45(3):e341.
William Yuan, Dadi Jiang, Dhanya K. Nambiar, Lydia P. Liew, Michael Patrick Hay, Joshua Bloomstein, Peter Lu, Brandon Turner, Quynh-The Le, Robert Tibshirani, Purvesh Khatri, Mark Gerard Moloney, and Albert C. Koong. Chemical Space Mimicry for Drug Discovery. Journal of Chemical Information and Modeling. 2017, 57(4):875-82.
Timothy E Sweeney, Purvesh Khatri. Septic Cardiomyopathy: Getting to the Heart of the Matter.Critical Care Medicine. 2017, 45(3):556-7.
Adrian Vallejo, Naiara Perurena, Elisabet Guruceaga, Pawel K Mazur, Susana Martinez-Canarias, Carolina Zandueta, Karmele Valencia, Andrea Arricibita, Dana Gwinn, Leanne C Sayles, Chen-Hua Chuang, Laura Guembe, Peter Bailey, David K Chang, Andrew Biankin, Mariano Ponz-Sarvise, Jesper B Andersen, Purvesh Khatri, Aline Bozec, E Alejandro Sweet-Cordero, Julien Sage, Fernando Lecanda, Silve Vicent. An integrative approach unveils FOSL1 as an oncogene vulnerability in KRAS-driven lung and pancreatic cancer. Nature Communications. 2017, 8:14294.
Timothy E Sweeney, Winston A Haynes, Francesco Vallania, John P Ioannidis, Purvesh Khatri. Methods to increase reproducibility in differential gene expression via meta-analysis. Nucleic Acids Res. 2017, 45(1):e1.
Timothy E Sweeney, Purvesh Khatri. Benchmarking sepsis gene expression diagnostics using public data. Critical Care Medicine. 2016, 45(1):1-10. (Data and analysis code)
Timothy E Sweeney, Purvesh Khatri. Hospital-acquired Pneumonia: A Host of Factors. American Journal of Respiratory and Critical Care Medicine. 2017, 194(11):1309-11.
Madeleine Scott, Francesco Vallania, Purvesh Khatri. Meta-analysis of continuous phenotypes identifies a gene signature that correlates with COPD disease status. Pacific Symposium on Biocomputing. 2017, 22:266-75.
Winston A Haynes, Francesco Vallania, Charles Liu, Erika Bongen, Aurelie Tomczak, Marta Andres-Terrè, Shane Lofgren, Andrew Tam, Cole A Deisseroth, Matthew D Li, Timothy E Sweeney, Purvesh Khatri. Empowering multi-cohort gene expression analysis to increase reproducibility. Pacific Symposium on Biocomputing. 2017, 22:144-53.

2016

Shane Lofgren*, Monique Hinchcliff*, Mary Carns, Tammara Wood, Kathleen Aren, Esperanza Arroyo, Peggie Cheung, Alex Kuo, Antonia Valenzuela, Anna Haemel, Paul J Wolters, Jessica Gordon, Robert Spiera, Shervin Assassi, Francesco Boin, Lorinda Chung, David Fiorentino, Paul J Utz, Michael Whitfield, Purvesh Khatri. Integrated, Multi-cohort Analysis of Systemic Sclerosis Identifies Robust Transcriptional Signature of Disease Severity. JCI Insight. 2016, 1(21):e89073. *Contributed equally.
Brooke A Napier, Sky W Brubaker, Timothy E Sweeney, Patrick Monette, Greggory H Rothmeier, Nina A Gertsvolf, Andreas Puschnik, Jan E Carette, Purvesh Khatri, Denise M Monack. Complement pathway amplifies caspase-11–dependent cell death and endotoxin-induced sepsis severity. Journal of Experimental Medicine. 2016, 213(11): 2365-82.
Timothy E Sweeney^§, Hector R Wong, Purvesh Khatri^§. Robust classification of bacterial and viral infections via integrated host gene expression diagnosis. Science Translational Medicine. 2016, 8(346):346ra91. ^§Co-corresponding authors. (Data and analysis code)
Timothy E Sweeney, Purvesh Khatri. Blood transcriptional signatures for tuberculosis diagnosis: a glass half-empty perspective – Authors’ reply. The Lancet Respiratory Medicine. 2016, 4(6):e29.
Timothy E Sweeney, Lindsay Braviak, Cristina M Tato, Purvesh Khatri. Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis. The Lancet Respiratory Medicine. 2016, 4(3):213-24.

2015

Marta Andres-Terre*, Helen M McGuire*, Yannick Pouliot, Erika Bongen, Timothy E Sweeney, Cristina M Tato, Purvesh Khatri. Integrated, multi-cohort analysis identifies conserved transcriptional signature across multiple respiratory viruses. Immunity 2015, 43:1199-211. *Contributed equally.
Timothy E Sweeney and Purvesh Khatri. Comprehensive Validation of the FAIM3: PLAC8 Ratio in Time-matched Public Gene Expression Data. American Journal of Respiratory and Critical Care Medicine. 2015, 192(10):1260-61.
Mark Musen, Carol A Bean, Kei-Hoi Cheung, Michel Dumontier, Kim A Durante, Olivier Gevaert, Alejandra Gonzalez-Beltran, Purvesh Khatri, Steven H Kleinstein, Martin J O’Connor, Yannick Pouliot, Philippe Rocca-Serra, Susanna-Assunta Sansone, Jeffrey A Wiser. The center for expanded data annotation and retrieval. Journal of American Medical Informatics Association. 2015, 22(6):1148-52.
Pawel K Mazur, Alexander Herner, Stephano S Mello, Matthias Wirth, Simone Hausmann, Francisco J Sánchez-Rivera, Shane M Lofgren, Timo Kuschma, Stephan A Hahn, Deepak Vangala, Marija Trajkovic-Arsic, Aayush Gupta, Irina Heid, Peter B Noël, Rickmer Braren, Mert Erkan, Jörg Kleeff, Bence Sipos, Leanne C Sayles, Mathias Heikenwalder, Elisabeth Heßmann, Volker Ellenrieder, Irene Esposito, Tyler Jacks, James E Bradner, Purvesh Khatri, E Alejandro Sweet-Cordero, Laura D Attardi, Roland M Schmid, Guenter Schneider, Julien Sage, Jens T Siveke. Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma. Nature Medicine. 2015, 21:1163-71.
Timothy E. Sweeney^§, Aaditya Shidham, Hector R. Wong, Purvesh Khatri^§. A Comprehensive Time-Course-Based Multi-Cohort Analysis of Sepsis and Sterile Inflammation Reveals a Robust Diagnostic Gene Set. Science Translational Medicine. 2015, 7(287):287ra71. ^§Co-corresponding authors. (Data and analysis code)

2014

Matthew D Li^§, Terry C Burns, Alexander A Morgan, Purvesh Khatri^§. Integrated Multi-Cohort Transcriptional Meta-Analysis of Neurodegenerative Diseases. Acta Neuropathologica Communications. 2014, 2(1):1-23. ^§Co-corresponding authors.
Pawel K. Mazur*, Nicolas Reynoird*, Purvesh Khatri, Pascal W.T.C. Jansen, Alex Wilkinson, Shichong Liu, Olena Barbash, Glenn S. Van Aller, Michael Huddleston, Peter J. Tummino, Ryan G. Kruger, Benjamin Garcia, Atul J. Butte, Michiel Vermeulen, Julien Sage, and Or Gozani. SMYD3 links methylation of MAP3K2 to Ras-driven cancer. 2014, 510:283-7.
Ron Chen*,Purvesh Khatri*,Pawel K. Mazur, Melanie Polin, Yanyan Zheng, Dedeepya Vaka, Chuong D. Hoang, Joseph Shrager, Yue Xu, Silvestre Vicent, Atul Butte, and Alejandro Sweet-Cordero. A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma. Cancer Res. 2014, 74(10):2892-902. *Contributed equally.
Alexander A. Morgan, Matthew D Li, Achal S Achrol, Purvesh Khatri, and Samuel H Cheshier. Multiplex meta-analysis of medulloblastoma expression studies with external controls. Pacific Symposium on Biocomputing 2014, 19:99-109.

2013

Nadine S. Jahchan, Joel T. Dudley, Pawel K. Mazur, Natasha Flores, Dian Yang, Alec Palmerton, Anne-Flore Zmoos, Dedeepya Vaka, Kim Q.T. Tran, Margaret Zhou, Karolina Krasinska, Jonathan W. Riess, Joel W. Neal, Purvesh Khatri, Kwon S. Park, Atul J. Butte, Julien Sage. A Drug Repositioning Approach Identifies Tricyclic Antidepressants as Inhibitors of Small Cell Lung Cancer and Other Neuroendocrine Tumors. Cancer Discovery. 2013, 3(12):1364-77.
Purvesh Khatri, Silke Roedder, Naoyuki Kimura, Alexander A Morgan, Matthew Vitalone, Michael P Fischbein, Robert C Robbins, Atul J Butte and Minnie M Sarwal. A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation. Journal of Experimental Medicine. 2013, 210:2205-21.

Prior to 2012

Silvestre Vicent, Leanne C. Sayles, Dedeepya Vaka, Purvesh Khatri, Olivier Gevaert, Ron Chen, Yanyan Zheng, Anna K. Gillespie, Nicole Clarke, Yue Xu, Joseph Shrager, Choang Hoang, Sylvia Plevritis, Atul Butte, E. Alejandro Sweet-Cordero. Cross-species functional analysis of cancer-associated fibroblasts identifies a critical role for CLCF1 and IL6 in non-small cell lung cancer in vivo. Cancer Research. 2012, 72(22):5744-56.
Li Li*, Purvesh Khatri*, Tara Sigdel*, Tim Tran, et al. A Peripheral Blood Diagnostic Test for Acute Rejection in Renal Transplantation. American Journal of Transplant. 2012, 12(10):2710-18. *Joint first authors.
Tara K Sigdel, Li Li, Tim Q Tran, Purvesh Khatri, Maarten Naesens, Poonam Sansanwal, Hong Dai, Szu-chuan Hsieh, Minnie Sarwal. Non-HLA Antibodies to Immunogenic Epitopes Predict the Evolution of Chronic Renal Allograft Injury. Journal of The American Society of Nephrology. 2012, 23(4):750-63.
Purvesh Khatri, Marina Sirota, Atul J. Butte. Ten years of Pathway Analysis: Current Approaches and Oustanding Challenges. PLoS Computational Biolology. 2012, 8(2):e1002375.
Tara Sigdel, Sang Woo, Hong Dai, Purvesh Khatri, Bryan Myers, Minnie Sarwal, Richard Lafayette. Profiling of autoantibodies in IgA nephropathy, an integrative antibiomics approach. Clinical Journal of The American Society of Nephrology. 2011, 6(12):2775-84.
Purvesh Khatri, Minnie Sarwal, Atul Butte. Applications of Translational Bioinformatics in Transplantation. Clinical Pharmacology and Therapeutics. 2011, 90(2):323-7.
Silke Roedder, Matthew Vitalone, Purvesh Khatri, Minnie M Sarwal. Biomarkers in solid organ transplantation: establishing personalized transplantation medicine. Genome Medicine. 2011, 3:37.
Maarten Naesens, Purvesh Khatri, Li Li, Tara Sigdel, Rong Chen, Atul Butte, Oscar Silvatierra, Minnie Sarwal. Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes. Kidney International. 2011, 80:1364-76.
Alexander A. Morgan, Purvesh Khatri, Richard Hayden Jones, Minnie M. Sarwal, and Atul J. Butte. Comparison of Multiplex Meta-analysis Techniques for Understanding the Acute Rejection of Solid Organ Transplants. BMC Bioinformatics. 2010, 11(Suppl 9):S6.
Larry A. Sonna, Matthew M. Kuhlmeier, Purvesh Khatri, Dechang Chen, and Craig M. Lilly. A microarray analysis of the effects of moderate hypothermia and rewarming on gene expression by human hepatocytes (HepG2). Cell Stress and Chaperones. 2010, 15(5):687-702.
Kandasamy K, Mohan SS, [32 authors] Khatri P, [3 authors]. Leonard WJ, Pandey A. NetPath: a public resource of curated signal transduction pathways. Genome Biology. 2010, 11(1):R3.
Shai Shen-Orr*, Robert Tibshirani*, Purvesh Khatri, Dale Bodian, Frank Staedtler, Nicholas M. Perry, Trevor Hastie, Lihua Ying, Minnie M. Sarwal, Mark M. Davis, Atul J. Butte. Cell Type-Specific Gene Expression Differences in Complex Tissues. Nature Methods. 2010, 7(4):287-9.
Purvesh Khatri, Minnie Sarwal. Using Gene Arrays in Diagnosis of Rejection. Current Opinion in Organ Transplantation. 2009, 14(1):34-9.
Adi Laurentiu Tarca, Sorin Draghici, Purvesh Khatri, Sonia S Hassan, Pooja Mittal, Jung-Sun Kim, Chong Jai Kim, Juan Pedro Kusanovic, Roberto Romero. A Novel Signaling Pathway Impact Analysis. 2009, 25(1):75-82.
Bogdan Done, Purvesh Khatri, Arina Done, Sorin Draghici. Predicting novel human gene ontology annotations using semantic analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2008, 7(1):91-9.
Sorin Draghici, Purvesh Khatri, Adi Laurentiu Tarca, Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, Roberto Romero. A systems biology approach for pathway level analysis. Genome Research. 2007, 17(10):1537-45.
Purvesh Khatri, Calin Voichita, Khalid Kattan, Nadeem Ansari, Avani Khatri, Constantin Georgescu, Adi Laurentiu Tarca, Sorin Draghici. Onto-Tools: New Additions and Improvements in 2006. Nucleic Acids Research. 2007, Jul;35:W206-11.
Purvesh Khatri, Dechang Chen, Jaques Reifman, Larry Sonna. Software Tool for Analysis of Variance of DNA Microarray Data.S. Army Research Institute of Environmental Medicine Technical Report T03-1. Natick, MA 01760-5007.
Sorin Draghici, Sivakumar Sellamuthu, and Purvesh Khatri. Babel’s tower revisited: a universal resource for cross-referencing across annotation databases. 2006, 22(23):2934-9.
Purvesh Khatri, Valmik Desai, Adi L. Tarca, Sivakumar Sellamuthu, Derek E. Wildman, Roberto Romero, and Sorin Draghici. New Onto-Tools: Promoter-Express, nsSNPCounter, and Onto-Translate. Nucleic Acids Research. 2006, Jul;34:W626-31.
Sorin Draghici, Purvesh Khatri, Aron C. Eklund, Zoltan Szallasi. Reliability and reproducibility issues in DNA microarray measurements. Trends in Genetics. 2006, Feb; 22(2):101-9.
Purvesh Khatri, Sorin Draghici. Ontological analysis of gene expression data: current tools, limitations, and open problems. 2005, Sep;21(18): 3587-95.
Purvesh Khatri, Bogdan Done, Archana Rao, Arina Done, Sorin Draghici. A semantic analysis of the annotations of the human genome. 2005, Aug;21(16):3416-21.
Purvesh Khatri, Sivakumar Sellamuthu, Pooja Malhotra, Kashyap Amin, Arina Done, and Sorin Draghici. Recent additions and improvements to the Onto-Tools. Nucleic Acids Research. 2005, Jul;33:W762-5.
Sorin Draghici*,Purvesh Khatri*, Yanhong Liu, Kitty J. Chase, Elizabeth A. Bode, David A. Kulesh, Leonard P. Wasieloski, David A. Norwood, Jaques Reifman. Identification of Genomic Signatures for the Design of Assays for the Detection and Monitoring of Anthrax Threats. Pacific Symposium on Biocomputing. 2005, 248-59. *Joint first authors.
Purvesh Khatri, Pratik Bhavsar, Gagandeep Bawa, Sorin Draghici. Onto-Tools: An ensemble of web-accessible, ontology based tools for the functional design and interpretation of high throughput gene expression experiments. Nucleic Acids Research. 2004, Jul;32:W449-56.
Sorin Draghici, Purvesh Khatri, Pratik Bhavsar, Abhik Shah, Stephen A. Krawetz, Michael Tainsky. Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Research. 2003, Jul;31(13):3775-81.
Sorin Draghici, Purvesh Khatri, Abhik Shah, Michael Tainsky. Assessing the functional bias of commercial microarrays using the Onto-Compare database. 2003 Mar;Suppl:55-61.
Sorin Draghici, Purvesh Khatri, Rui P. Martins, G. Charles Ostermeier, Stephen A. Krawetz. Global functional profiling of gene expression. Genomics. 2003, Feb;81(2):98-104.
Charles Ostermeier, David J. Dix, David Miller, Purvesh Khatri, Stephen A. Krawetz. Spermatozoal RNA profiles of normal fertile men. The Lancet. 2002, Sep;360(9335):772-7.
Purvesh Khatri, Sorin Draghici, G. Charles Ostermeier, Stephen A. Krawetz. Profiling Gene Expression Utilizing Onto-Express. Genomics. 2002, Feb;79(2):266-70.