Manikandan (Mani) Narayanan's academic website
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Manikandan Narayanan
Assoc. Prof., Dept. of Computer Science and Engineering (CSE) PI, Bioinformatics and Integrative Data Science (BIRDS) Group Co-ordinator, Multiscale Digital Neuroanatomy (MDN) Core Faculty, Initiative for Biological Systems Engineering (IBSE) Faculty Member, Robert Bosch Center for Data Science and AI (RBC-DSAI) IIT Madras Email: nmanik at cse dot iitm dot ac dot in Office: BSB 346 | Phone: 4375 Google scholar page Teaching: Jan-May 2024/2023, Jul-Nov 2020: Algor. Apprchs. to Computational Biology Nov 2022 - Feb 2023: Introduction to Programming Jan-Nov 2023/2021: Pattern Recognition and Machine Learning Jan-May 2020: Probabilistic Graphical Models Jan-May 2018: Multilayer Network Models & Algorithms Jan-May 2023: Algorithmic Thinking in Bioinformatics (IITM Online BS Degree Elective - Online videos playlist) |
Education
2007 Ph.D. in Computer Science (Computational & Genomic Biology), Univ. of California at Berkeley, CA
2003 M.S. in Computer Science, Univ. of California at Berkeley, CA
2001 B.E. in Computer Science & Engineering, College of Engineering at Guindy, Anna Univ.,
Chennai, TN
Research experience
2010-2017 Sr. Research Scientist / Staff Research Scientist, Systems Genomics and Bioinformatics Unit,
Laboratory of Systems Biology, NIAID, National Institutes of Health (NIH), Bethesda, MD
2007-2010 Postdoctoral Researcher (initially) / Sr. Research Scientist, Merck Research Labs,
Seattle, WA and Boston, MA
2007 Ph.D. in Computer Science (Computational & Genomic Biology), Univ. of California at Berkeley, CA
2003 M.S. in Computer Science, Univ. of California at Berkeley, CA
2001 B.E. in Computer Science & Engineering, College of Engineering at Guindy, Anna Univ.,
Chennai, TN
Research experience
2010-2017 Sr. Research Scientist / Staff Research Scientist, Systems Genomics and Bioinformatics Unit,
Laboratory of Systems Biology, NIAID, National Institutes of Health (NIH), Bethesda, MD
2007-2010 Postdoctoral Researcher (initially) / Sr. Research Scientist, Merck Research Labs,
Seattle, WA and Boston, MA
Research interests
Bioinformatics, Computational network biology, Systems biology/genomics in health and disease, Data science.
To expand briefly, I am interested in computational network models of complex cellular behaviors, especially ones that bear relevance to local diseases. Central to my research is the development and application of computational methods involving probabilistic models or graph-theoretic algorithms, which have shown promise in my current research in revealing how networks of interacting genes rewire during neurodegenerative disease or immune states. My future research at the interface of computer science and biology would tackle new combinatorial/inference problems that arise when analyzing genomic data from two emerging areas: multi-tissue diseases and single-cell behaviors..
Bioinformatics, Computational network biology, Systems biology/genomics in health and disease, Data science.
To expand briefly, I am interested in computational network models of complex cellular behaviors, especially ones that bear relevance to local diseases. Central to my research is the development and application of computational methods involving probabilistic models or graph-theoretic algorithms, which have shown promise in my current research in revealing how networks of interacting genes rewire during neurodegenerative disease or immune states. My future research at the interface of computer science and biology would tackle new combinatorial/inference problems that arise when analyzing genomic data from two emerging areas: multi-tissue diseases and single-cell behaviors..
Honors and Awards
- Wellcome Trust/DBT India Alliance Intermediate Fellowship Award, 2017+. Award recommended for proposed 5-year research program on "Computational methods for multi-tissue models of health and disease".
- Performance Award, 2013-2015. Sustained high-quality work, and outstanding performance and contribution in the Laboratory of Systems Biology, NIAID, NIH, Bethesda, MD.
- Siebel Scholar, 2003. Academic performance at the Computer Science Division, University of California, Berkeley, CA.
(Siebel Scholars Program recognizes talented students and leaders in top business, computer science, bioengineering, and energy science schools) - University Gold Medal and Colgate Endowment Gold Medal, 2001. B.E. Program. College of Engineering, Guindy, Anna University, Chennai, TN.
- JNCASR Summer Research Fellowship, 2000. Jawaharlal Nehru Center for Advanced Scientific Research/Indian Institute of Science, Bangalore, KA.
Research Group (BIRDS) Members
We are an enthusiastic group of inter-disciplinary researchers interested in computation/data-driven approaches to understand tissue-tissue communication, disease-disease interactions and beyond; we call ourselves BIRDS for Bioinformatics and Integrative Data Science.
PI: Manikandan Narayanan
Project Researchers: Dr. Sanga Mitra (Sr. Research Scientist)
PhD Students: Brintha VP (latent variable models for TB multi-drug resistance), Sugyani Mahapatra (algorithms on collections of graphs), Nilesh Subramanian (IDRP, joint with Raghunathan Rengasamy; previously IBSE Postbacc Fellow working on systems biology of helminth-diabetes comorbidity), Ritwiz Kamal, Nency Bansal, Saish Jaiswal (joint with Hema Murthy), T Anand (joint with Hema Murthy), Rakshika Raveendran (IDRP, joint with Mohanasankar Sivaprakasam)
MS Students: Dipra Bhagat (multi-modal data imputation and integration), Aravind Easwar (non-linear causal discovery), Naga Venkata Sai Kumar (multi-target regression for robust cellular deconvolution)
MTech Students: Kartik Arvindbhai Gondaliya (MultiCens website), Siddharth Sanjay Vartha
BTech-MTech DD Students:
Interns:
Alumni (PhD): Tarun Kumar (joint with B. Ravindran; multilayer network centrality and inter-tissue communication)
Alumni (Project Researchers): Dr. Philge Philip (Sr. Project Officer @ IBSE; computational genomics/epigenomics), Tamizhini Loganathan (IBSE Postbacc Fellow), Dr. Shrayashi Biswas (Postdoctoral researcher), Dr. Debasmita Paul (Postdoctoral research fellow at MDN), Abhishek Pandey (Research associate - Computational Genomics at MDN)
Alumni (DD Students): BP Kailash (DD; inter-tissue gene networks in Alzheimer's disease), Aditya Jeevannavar, Amol Dumrewal, Neeraj Rajkumar Parmaar, Burhanuddin Sabuwala (single-cell multi-modal imputation), Shreya Nema
Alumni (interns): Advaith N Narayanan (intern), K.S. Sneha (intern), Nandhakishore CS (intern), Ashwin Rajendran, Mohit Raghavendra
Alumni (MS/MTech Students): Rahul Biswas (MS: causal discovery in the face of noise for gene network reconstruction), Siddhant Yogesh Bhatt (MTech), Manas Ranjan Sahoo (MTech), Jadhav Aditya Dinkar (MTech; word embeddings and inter-tissue gene signaling), Dodiya Keval (MTech), Karan Prafulbhai Jivani (MTech), Ravi Kumar (MTech; MultiCens website)
PI: Manikandan Narayanan
Project Researchers: Dr. Sanga Mitra (Sr. Research Scientist)
PhD Students: Brintha VP (latent variable models for TB multi-drug resistance), Sugyani Mahapatra (algorithms on collections of graphs), Nilesh Subramanian (IDRP, joint with Raghunathan Rengasamy; previously IBSE Postbacc Fellow working on systems biology of helminth-diabetes comorbidity), Ritwiz Kamal, Nency Bansal, Saish Jaiswal (joint with Hema Murthy), T Anand (joint with Hema Murthy), Rakshika Raveendran (IDRP, joint with Mohanasankar Sivaprakasam)
MS Students: Dipra Bhagat (multi-modal data imputation and integration), Aravind Easwar (non-linear causal discovery), Naga Venkata Sai Kumar (multi-target regression for robust cellular deconvolution)
MTech Students: Kartik Arvindbhai Gondaliya (MultiCens website), Siddharth Sanjay Vartha
BTech-MTech DD Students:
Interns:
Alumni (PhD): Tarun Kumar (joint with B. Ravindran; multilayer network centrality and inter-tissue communication)
Alumni (Project Researchers): Dr. Philge Philip (Sr. Project Officer @ IBSE; computational genomics/epigenomics), Tamizhini Loganathan (IBSE Postbacc Fellow), Dr. Shrayashi Biswas (Postdoctoral researcher), Dr. Debasmita Paul (Postdoctoral research fellow at MDN), Abhishek Pandey (Research associate - Computational Genomics at MDN)
Alumni (DD Students): BP Kailash (DD; inter-tissue gene networks in Alzheimer's disease), Aditya Jeevannavar, Amol Dumrewal, Neeraj Rajkumar Parmaar, Burhanuddin Sabuwala (single-cell multi-modal imputation), Shreya Nema
Alumni (interns): Advaith N Narayanan (intern), K.S. Sneha (intern), Nandhakishore CS (intern), Ashwin Rajendran, Mohit Raghavendra
Alumni (MS/MTech Students): Rahul Biswas (MS: causal discovery in the face of noise for gene network reconstruction), Siddhant Yogesh Bhatt (MTech), Manas Ranjan Sahoo (MTech), Jadhav Aditya Dinkar (MTech; word embeddings and inter-tissue gene signaling), Dodiya Keval (MTech), Karan Prafulbhai Jivani (MTech), Ravi Kumar (MTech; MultiCens website)
News
17 APR 2024 Our manuscript "Alzheimer’s disease rewires gene coexpression networks coupling different brain regions" has now been accepted for publication in npj Systems Biology and Applications. Congratulations Sanga and Kailash and all co-authors!
15 APR 2024 Preprint on our work “Demixer: A probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample” available at bioRxiv (see below).
01 MAR 2024 Brintha is selected as a Women Leading IITM 2024 awardee. Congratulations Brintha!
28 DEC 2023 Preprint on our work "Systems analysis of multiple diabetes-helminth cohorts reveals markers of disease-disease interaction" available at bioRxiv (see below).
25 JUL 2023 Our work MultiCens starts attracting popular press / media coverage. Some example news articles can be viewed here.
01 JUL 2023 Tarun is declared a joint winner of the institute's Best PhD in Data Sciences award. Congratulations Tarun!
24 APR 2023 Tarun successfully defended his PhD thesis and got called Dr. Tarun Kumar! This happened to be in the same day that his MultiCens work got accepted in PLOS Computational Biology!! Tarun (co-advised with Prof. B. Ravindran) is the first PhD student to graduate from our BIRDS group!!!
24 APR 2023 Our work “MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication" has now been published in the PLOS Computational Biology journal. Congratulations Tarun and Sanga from our BIRDS group, and all co-authors!
24 AUG 2022 Our work “Predicting cross-tissue hormone-gene relations using balanced word embeddings" has now been published in the Bioinformatics journal. Happy to share that what started out as an MTech Project of Aditya Jadhav is now in a top-ranking journal in our field -- congratulations Aditya and all co-authors!
16/22 MAY 2022 Preprints on our work “MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication” and "Alzheimer's disease rewires gene coexpression networks coupling different brain regions" available at bioRxiv (see below).
21. OCT 2021 Work on “Computational mapping of inter-brain-region gene networks dysregulated in Alzheimer's disease.” accepted for poster presentation at ROCKY 2021 conference organized by ISCB.
17. JUN 2020 Work on “Identifying cross-tissue signaling between genes from biomedical literature.” accepted for poster presentation at ICML Workshop on Computational Biology 2020.
09.DEC 2019 Study on “Dysregulation of inter-tissue gene coexpression networks in Alzheimer’s disease” presented as a poster at Cold Spring Harbor 3D Brain Meeting.
05.DEC 2019 Work on “Robust discovery of causal gene networks via measurement error estimation and correction” presented as a poster at ROCKY 2019 conference organized by ISCB.
28. AUG 2019 Welcome Nilesh, newly appointed post-bacc via the IBSE Postbacc Fellowship Award for exceptional graduates.
15 APR 2024 Preprint on our work “Demixer: A probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample” available at bioRxiv (see below).
01 MAR 2024 Brintha is selected as a Women Leading IITM 2024 awardee. Congratulations Brintha!
28 DEC 2023 Preprint on our work "Systems analysis of multiple diabetes-helminth cohorts reveals markers of disease-disease interaction" available at bioRxiv (see below).
25 JUL 2023 Our work MultiCens starts attracting popular press / media coverage. Some example news articles can be viewed here.
01 JUL 2023 Tarun is declared a joint winner of the institute's Best PhD in Data Sciences award. Congratulations Tarun!
24 APR 2023 Tarun successfully defended his PhD thesis and got called Dr. Tarun Kumar! This happened to be in the same day that his MultiCens work got accepted in PLOS Computational Biology!! Tarun (co-advised with Prof. B. Ravindran) is the first PhD student to graduate from our BIRDS group!!!
24 APR 2023 Our work “MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication" has now been published in the PLOS Computational Biology journal. Congratulations Tarun and Sanga from our BIRDS group, and all co-authors!
24 AUG 2022 Our work “Predicting cross-tissue hormone-gene relations using balanced word embeddings" has now been published in the Bioinformatics journal. Happy to share that what started out as an MTech Project of Aditya Jadhav is now in a top-ranking journal in our field -- congratulations Aditya and all co-authors!
16/22 MAY 2022 Preprints on our work “MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication” and "Alzheimer's disease rewires gene coexpression networks coupling different brain regions" available at bioRxiv (see below).
21. OCT 2021 Work on “Computational mapping of inter-brain-region gene networks dysregulated in Alzheimer's disease.” accepted for poster presentation at ROCKY 2021 conference organized by ISCB.
17. JUN 2020 Work on “Identifying cross-tissue signaling between genes from biomedical literature.” accepted for poster presentation at ICML Workshop on Computational Biology 2020.
09.DEC 2019 Study on “Dysregulation of inter-tissue gene coexpression networks in Alzheimer’s disease” presented as a poster at Cold Spring Harbor 3D Brain Meeting.
05.DEC 2019 Work on “Robust discovery of causal gene networks via measurement error estimation and correction” presented as a poster at ROCKY 2019 conference organized by ISCB.
28. AUG 2019 Welcome Nilesh, newly appointed post-bacc via the IBSE Postbacc Fellowship Award for exceptional graduates.
Publications
Preprints/presentations
Methods for multi-tissue genomics, single-cell analysis, & related manuscripts
Graph algorithms & related network analysis publications
Computational systems biology & integrative genomics publications
Thesis and earlier work
Methods for multi-tissue genomics, single-cell analysis, & related manuscripts
Graph algorithms & related network analysis publications
Computational systems biology & integrative genomics publications
Thesis and earlier work
Preprints/presentations (selected)
Demixer: A probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample
VP Brintha, M Narayanan
bioRxiv 2024.04.11.589150. 2024
VP Brintha, M Narayanan
bioRxiv 2024.04.11.589150. 2024
Systems analysis of multiple diabetes-helminth cohorts reveals markers of disease-disease interaction
N Subramanian, P Philip, A Rajamanickam, NP Kumar, S Babu, M Narayanan
bioRxiv 2023.12.27.573481. 2023
N Subramanian, P Philip, A Rajamanickam, NP Kumar, S Babu, M Narayanan
bioRxiv 2023.12.27.573481. 2023
Robust discovery of causal gene networks via measurement error estimation and correction
R Biswas, VP Brintha, A Dumrewal, M Narayanan
bioRxiv 2023.05.09.540002. 2023
R Biswas, VP Brintha, A Dumrewal, M Narayanan
bioRxiv 2023.05.09.540002. 2023
Alzheimer's disease rewires gene coexpression networks coupling different brain regions
S Mitra+, BP Kailash+, CR Srivatsan, NV Saikumar, P Philip, M Narayanan (+ equal contributions)
bioRxiv 2022.05.22.492888. 2022
S Mitra+, BP Kailash+, CR Srivatsan, NV Saikumar, P Philip, M Narayanan (+ equal contributions)
bioRxiv 2022.05.22.492888. 2022
MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication
T Kumar, R Sethuraman, S Mitra, B Ravindran, M Narayanan
bioRxiv 2022.05.15.492007. 2022
T Kumar, R Sethuraman, S Mitra, B Ravindran, M Narayanan
bioRxiv 2022.05.15.492007. 2022
Predicting cross-tissue hormone-gene relations using balanced word embeddings
A Jadhav, T Kumar+, M Raghavendra+, T Loganathan, M Narayanan (+ equal contributions)
bioRxiv 2021.01.28.428707. 2021
A Jadhav, T Kumar+, M Raghavendra+, T Loganathan, M Narayanan (+ equal contributions)
bioRxiv 2021.01.28.428707. 2021
Parameterized algorithms for the Steiner tree problem on a directed hypercube
S Mahapatra, M Narayanan, NS Narayanaswamy, V Ramamoorthi
arXiv:2110.02830v2 [cs.DS]. 2021
S Mahapatra, M Narayanan, NS Narayanaswamy, V Ramamoorthi
arXiv:2110.02830v2 [cs.DS]. 2021
Algorithms for handling uncertainty in input graphs
S Mahapatra and M Narayanan
Paper (extended abstract) accepted for poster presentation at AAAI (Association for the Advancement of Artificial Intelligence) Workshop on GCLR (Graphs and more Complex structures for Learning and Reasoning). Virtual conference/workshop. 2021
S Mahapatra and M Narayanan
Paper (extended abstract) accepted for poster presentation at AAAI (Association for the Advancement of Artificial Intelligence) Workshop on GCLR (Graphs and more Complex structures for Learning and Reasoning). Virtual conference/workshop. 2021
Methods for multi-tissue genomics, single-cell analysis, & related manuscripts
Alzheimer's disease rewires gene coexpression networks coupling different brain regions
S Mitra+, BP Kailash+, CR Srivatsan, NV Saikumar, P Philip, M Narayanan (+ equal contributions)
(Accepted for publication by) npj Systems Biology and Applications. 2024
S Mitra+, BP Kailash+, CR Srivatsan, NV Saikumar, P Philip, M Narayanan (+ equal contributions)
(Accepted for publication by) npj Systems Biology and Applications. 2024
Predicting cross-tissue hormone-gene relations using balanced word embeddings
A Jadhav, T Kumar+, M Raghavendra+, T Loganathan, M Narayanan (+ equal contributions)
Bioinformatics, btac578. 2022.
A Jadhav, T Kumar+, M Raghavendra+, T Loganathan, M Narayanan (+ equal contributions)
Bioinformatics, btac578. 2022.
Environment tunes propagation of cell-to-cell variation in the human macrophage gene network
AJ Martins*, M Narayanan*, T Prüstel, B Fixsen, K Park, RA Gottschalk, Y Lu, C Pfannkoch, WW Lau, KV Wendelsdorf, JS Tsang (*equal contributions)
Cell Systems 4 (4), 379-392.e12. 2017.
(highlighted in a Spotlight article, and by NIAID Communications Team in a short video)
AJ Martins*, M Narayanan*, T Prüstel, B Fixsen, K Park, RA Gottschalk, Y Lu, C Pfannkoch, WW Lau, KV Wendelsdorf, JS Tsang (*equal contributions)
Cell Systems 4 (4), 379-392.e12. 2017.
(highlighted in a Spotlight article, and by NIAID Communications Team in a short video)
Robust inference of cell-to-cell expression variations from single- and k-cell profiling
M Narayanan, AJ Martins, JS Tsang
PLoS Computational Biology 12 (7), e1005016. 2016.
M Narayanan, AJ Martins, JS Tsang
PLoS Computational Biology 12 (7), e1005016. 2016.
Utilizing natural biological variation for de novo prediction of immune cell frequencies in human disease and complex perturbations
N Shah, M Narayanan, A Biancotto, Y Lu, PL Schwartzberg, A Thurm, S Swedo, JS Tsang
Manuscript in preparation
N Shah, M Narayanan, A Biancotto, Y Lu, PL Schwartzberg, A Thurm, S Swedo, JS Tsang
Manuscript in preparation
Graph algorithms & related network analysis publications
MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication
T Kumar, R Sethuraman, S Mitra, B Ravindran, M Narayanan
PLOS Computational Biology 19(4): e1011022. 2023.
T Kumar, R Sethuraman, S Mitra, B Ravindran, M Narayanan
PLOS Computational Biology 19(4): e1011022. 2023.
Effect of Interlayer Coupling on Multilayer Network Centrality Measures (review article)
T Kumar, M Narayanan, B Ravindran
To appear in Journal of the Indian Institute of Science 99 (2). 2019.
T Kumar, M Narayanan, B Ravindran
To appear in Journal of the Indian Institute of Science 99 (2). 2019.
Computational Problems in Multi-tissue Models of Health and Disease (perspective/review article)
M Narayanan
Journal of the Indian Institute of Science 97, 325-337. 2017.
M Narayanan
Journal of the Indian Institute of Science 97, 325-337. 2017.
Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases
M Narayanan+, JL Huynh, K Wang, X Yang, S Yoo, J McElwee, B Zhang, C Zhang, J Lamb, T Xie, C Suver, C Molony, S Melquist, A Johnson, G Fan, D Stone, E Schadt, P Casaccia, V Emilsson, and J Zhu+ (+joint corresponding authors)
Molecular Systems Biology 10 (7), 743. 2014.
(cross-listed below; application of graph-matching algorithm to analyze disease networks)
M Narayanan+, JL Huynh, K Wang, X Yang, S Yoo, J McElwee, B Zhang, C Zhang, J Lamb, T Xie, C Suver, C Molony, S Melquist, A Johnson, G Fan, D Stone, E Schadt, P Casaccia, V Emilsson, and J Zhu+ (+joint corresponding authors)
Molecular Systems Biology 10 (7), 743. 2014.
(cross-listed below; application of graph-matching algorithm to analyze disease networks)
The Complexity of the Simultaneous Cluster Problem
Z Li, M Narayanan, A Vetta
Journal of Graph Algorithms and Applications. 2014.
Z Li, M Narayanan, A Vetta
Journal of Graph Algorithms and Applications. 2014.
Simultaneous clustering of multiple gene expression and physical interaction datasets
M Narayanan, A Vetta, E Schadt, J Zhu
PLoS Computational Biology 6 (4), e1000742. 2010.
M Narayanan, A Vetta, E Schadt, J Zhu
PLoS Computational Biology 6 (4), e1000742. 2010.
Comparing protein interaction networks via a graph match-and-split algorithm
M Narayanan, RM Karp
Journal of Computational Biology 14 (7), 892-907. 2007.
M Narayanan, RM Karp
Journal of Computational Biology 14 (7), 892-907. 2007.
Gapped local similarity search with provable guarantees
M Narayanan, RM Karp
Algorithms in Bioinformatics, 74-86. 2004.
M Narayanan, RM Karp
Algorithms in Bioinformatics, 74-86. 2004.
Computational systems biology & integrative genomics publications
Shared mechanisms among neurodegenerative diseases: from genetic factors to gene networks (review article)
D Arneson, Y Zhang, X Yang, M Narayanan
Journal of Genetics 97 (3), 795-806. 2018.
D Arneson, Y Zhang, X Yang, M Narayanan
Journal of Genetics 97 (3), 795-806. 2018.
Equilibrative nucleoside transporter ENT1 as a biomarker of Huntington disease
X Guitart, J Bonaventura, W Rea, M Orrú, L Cellai, I Dettori, F Pedata, M Brugarolas, A Cortés, V Casadó, CP Chang, M Narayanan, Y Chern, S Ferré
Neurobiology of Disease 96, 47-53. 2016.
X Guitart, J Bonaventura, W Rea, M Orrú, L Cellai, I Dettori, F Pedata, M Brugarolas, A Cortés, V Casadó, CP Chang, M Narayanan, Y Chern, S Ferré
Neurobiology of Disease 96, 47-53. 2016.
Lineage relationship of CD8+ T cell subsets is revealed by progressive changes in the epigenetic landscape
JG Crompton*, M Narayanan*, S Cuddapah, R Roychoudhuri, Y Ji, W Yang, SJ Patel, M Sukumar, DC Palmer, W Peng, E Wang, FM Marincola, CA Klebanoff, Zhao. K, JS Tsang, L Gattinoni*, NP Restifo* (*equal contributions)
Cellular & Molecular Immunology, doi: 10.1038/cmi.2015.032. 2015.
JG Crompton*, M Narayanan*, S Cuddapah, R Roychoudhuri, Y Ji, W Yang, SJ Patel, M Sukumar, DC Palmer, W Peng, E Wang, FM Marincola, CA Klebanoff, Zhao. K, JS Tsang, L Gattinoni*, NP Restifo* (*equal contributions)
Cellular & Molecular Immunology, doi: 10.1038/cmi.2015.032. 2015.
Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases
M Narayanan+, JL Huynh, K Wang, X Yang, S Yoo, J McElwee, B Zhang, C Zhang, J Lamb, T Xie, C Suver, C Molony, S Melquist, A Johnson, G Fan, D Stone, E Schadt, P Casaccia, V Emilsson, and J Zhu+ (+joint corresponding authors)
Molecular Systems Biology 10 (7), 743. 2014.
M Narayanan+, JL Huynh, K Wang, X Yang, S Yoo, J McElwee, B Zhang, C Zhang, J Lamb, T Xie, C Suver, C Molony, S Melquist, A Johnson, G Fan, D Stone, E Schadt, P Casaccia, V Emilsson, and J Zhu+ (+joint corresponding authors)
Molecular Systems Biology 10 (7), 743. 2014.
Global analyses of human immune variation reveal baseline predictors of postvaccination responses
JS Tsang+, PL Schwartzberg+, Y Kotliarov#, A Biancotto#, Z Xie#, RN Germain#, E Wang#, M Olnes#, M Narayanan*, H Golding*, S Moir*, H Dickler*, S Perl*, F Cheung*, Baylor HIPC Center, and CHI Consortium (+corresponding authors. #equal contributions. *equal contributions)
Cell 157 (2), 499-513. 2014.
(selected as one of the notable NIAID Research Advances of 2014)
JS Tsang+, PL Schwartzberg+, Y Kotliarov#, A Biancotto#, Z Xie#, RN Germain#, E Wang#, M Olnes#, M Narayanan*, H Golding*, S Moir*, H Dickler*, S Perl*, F Cheung*, Baylor HIPC Center, and CHI Consortium (+corresponding authors. #equal contributions. *equal contributions)
Cell 157 (2), 499-513. 2014.
(selected as one of the notable NIAID Research Advances of 2014)
Characterization of functional reprogramming during osteoclast development using quantitative proteomics and mRNA profiling
E An, M Narayanan, NP Manes, A Nita-Lazar
Mol. Cell. Proteomics 13, 2687-2704. 2014.
E An, M Narayanan, NP Manes, A Nita-Lazar
Mol. Cell. Proteomics 13, 2687-2704. 2014.
Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease
B Zhang, C Gaiteri, L Bodea, Z Wang, J McElwee, A Podtelezhnikov, C Zhang, T Xie, L Tran, R Dobrin, E Fluder, B Clurman, S Melquist, M Narayanan, C Suver, H Shah, M Mahajan, T Gillis, J Mysore, M MacDonald, J Lamb, D Bennett, C Molony, D Stone, V Gudnason, A Myers, E Schadt, H Neumann, J Zhu, J., and V Emilsson
Cell 153 (3), 707-720. 2013.
B Zhang, C Gaiteri, L Bodea, Z Wang, J McElwee, A Podtelezhnikov, C Zhang, T Xie, L Tran, R Dobrin, E Fluder, B Clurman, S Melquist, M Narayanan, C Suver, H Shah, M Mahajan, T Gillis, J Mysore, M MacDonald, J Lamb, D Bennett, C Molony, D Stone, V Gudnason, A Myers, E Schadt, H Neumann, J Zhu, J., and V Emilsson
Cell 153 (3), 707-720. 2013.
From Finger Pricks to Point-and-Click (preview piece)
M Narayanan, JS Tsang
Immunity 38 (4), 622-624. 2013.
M Narayanan, JS Tsang
Immunity 38 (4), 622-624. 2013.
Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases
K Wang, M Narayanan, H Zhong, M Tompa, E Schadt, J Zhu
PLoS Computational Biology 5 (12), e1000616. 2009.
K Wang, M Narayanan, H Zhong, M Tompa, E Schadt, J Zhu
PLoS Computational Biology 5 (12), e1000616. 2009.
Thesis and earlier work
Comparative and evolutionary analysis of cellular pathways
M Narayanan
PhD thesis, Computer Science Division, University of California at Berkeley, 2007.
M Narayanan
PhD thesis, Computer Science Division, University of California at Berkeley, 2007.
Generating permutation instructions from a high-level description
M Narayanan, KA Yelick
Workshop on Media and Streaming Processors (MSP), 2004.
M Narayanan, KA Yelick
Workshop on Media and Streaming Processors (MSP), 2004.
Compiling Communication Access Patterns for a Vector Processor
M Narayanan
MS thesis, Computer Science Division, University of California at Berkeley, 2003.
M Narayanan
MS thesis, Computer Science Division, University of California at Berkeley, 2003.
Performance evaluation of two emerging media processors: VIRAM and Imagine
S Chatterji, M Narayanan, J Duell, L Oliker
Parallel and Distributed Processing Symposium, 2003.
S Chatterji, M Narayanan, J Duell, L Oliker
Parallel and Distributed Processing Symposium, 2003.