(* indicates co-first author)
J16: Bhattacharyya S, Figueroa D S, Georgopoulos K, and Ay F; DiffHiChIP: Identifying differential chromatin contacts from HiChIP data, bioRxiv 2025 (accepted at Cell Reports Methods)
(RECOMB 2022 Poster) (ISMB 2022 slides) (GitHub) (Manuscript)
J15: Bhattacharyya S, and Ay F; Identifying genetic variants associated with chromatin looping and genome function, Nature Communications, 2024, (also a corresponding author).
(ISMB 2023 Oral presentation) (RSGDREAM 2023 Poster) (GitHub) (Manuscript)
J14: Reyna J, Fetter K, Ignacio R, Marandi C, Rao N, Jiang Z, Figueroa D S, Bhattacharyya S, and Ay F, Loop Catalog: a comprehensive HiChIP database of human and mouse samples, bioRxiv 2024 (Accepted at Genome Biology) (Website) (Manuscript)
J13: Hu Y, Salgado-Figueroa D, Zhang Z, Veselits M, Bhattacharyya S, Kashiwagi M, Clark M R, Morgan B A, Ay F, and Georgopoulos K; Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS, Cell, 2023, 186(24):5269-5289.e22.
(RSGDREAM 2023 Oral presentation) (Manuscript)
J12: Schmiedel B*, Gonzalez-Colin C*, Fajardo V*, Rocha J, Madrigal A, Ramírez-Suástegui C, Bhattacharyya S, Simon H, Greenbaum J, Peters B, Seumois G, Ay F, Chandra V and Vijayanand P; Single-cell eQTL analysis of activated T cell subsets reveals activation and cell-type-dependent effects of disease-risk variants, Science Immunology 2022, Vol 7, No 68, DOI: 10.1126/sciimmunol.abm2508
J11: Schmiedel B*, Rocha J*, Gonzalez-Colin C*, Bhattacharyya S*, Madrigal A, Ottensmeier C, Ay F, Chandra V, and Vijayanand P; COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types, Nature Communications 2021, Vol 12, No 6760, DOI: https://doi.org/10.1038/s41467-021-26888-3
(manuscript) (GitHub) (News Articles)
J10: Chandra V*, Bhattacharyya S*, Schmiedel B, Madrigal A, Gonzalez-Colin C, Fotsing S, Crinklaw A, Seumois G, Mohammadi P, Kronenberg M, Peters B, Ay F and Vijayanand P; Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants, Nature Genetics 2020, DOI: 10.1038/s41588-020-00745-3
(manuscript) (GitHub) (ISMB 2020 Poster) (ISMB 2020 Slides) (News Articles)
J9: Bhattacharyya S, Chandra V, Vijayanand P, and Ay F; Identification of significant chromatin contacts from HiChIP data by FitHiChIP, Nature Communications 2019, Vol 10, No 4221, DOI: 10.1038/s41467-019-11950-y
(Dovetails Genomics Kit) (manuscript) (GitHub) (RECOMB 2019 poster) (ISMB 2018 Slides) (ISMB 2018 presentation video)
J8: Kaul A*, Bhattacharyya S*, and Ay F; Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2, Nature Protocols 2020, DOI: 10.1038/s41596-019-0273-0
(manuscript) (GitHub)
J7: Lhoumaud P, Badri S, Rodriguez Hernaez J, Sakellaropoulos T, Sethia G, Kloetgen A, Cornwell M, Bhattacharyya S, Ay F, Bonneau R, Tsirigos A, and Skok J; NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains, Nature Communications 2019, Vol 10, No 4843, DOI: 10.1038/s41467-019-12811-4
J6: Clarke J, Panwar B, Madrigal A, Singh D, Gujar R, Wood O, Chee S, Eschweiler S, King E, Awad A, Hanley C, McCann K, Bhattacharyya S, Woo E, Alzetani A, Seumois G, Thomas G, Ganesan AP, Friedmann P, Sanchez-Elsner T, Ay F, Ottensmeier C, and Vijayanand P; Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer Journal of Experimental Medicine, 2019, DOI: 10.1084/jem.20190249
J5: Svensson MN, Doody KM, Schmiedel BJ, Bhattacharyya S, Panwar B, Wiede F, Yang S, Santelli E, Wu DJ, Sacchetti C, Gujar R, Seumois G, Kiosses WB, Aubry I, Kim G, Mydel P, Sakaguchi S, Kronenberg M, Tiganis T, Tremblay ML, Ay F, Vijayanand P, and Bottini N; Reduced expression of phosphatase PTPN2 promotes pathogenic conversion of Tregs in autoimmunity, Journal of Clinical Investigation. 2019 129(3):1193-1210, doi: 10.1172/JCI123267
J4: Bhattacharyya S, and Mukherjee J; IDXL: Species Tree Inference Using Internode Distance and Excess Gene Leaf Count, Journal of Molecular Evolution (Springer), 2017, volume 85, issue 1-2, pp. 57-78, DOI: 10.1007/s00239-017-9807-7
J3: Bhattacharyya S, and Mukherjee J; COSPEDTree: COuplet Supertree by Equivalence Partitioning of taxa set and DAG formation, IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2015, Vol 12, no 3, pp. 590-603
(manuscript) (GitHub) (slides at ACM-BCB 2014)
J2: Bhattacharyya S, Biswas A, Mukherjee J, Majumdar A K, Majumdar B, Mukherjee S, and Singh A K.; Detection of artifacts from high energy bursts in neonatal EEG, Computers in Biology and Medicine, 2013, 43(11), pp. 1804-14.
J1: Bhattacharyya S, Biswas A, Mukherjee J, Majumdar A K, Majumdar B, Mukherjee S, and Singh A K.; Feature Selection for Automatic Burst Detection in Neonatal Electroencephalogram, IEEE Journal on Emerging and Selected Topics in Circuits and Systems, 2011, 1(4), pp. 469-79.
C15. Bhattacharyya S, and Mukhopadhyay J. COSPEDTree-II: Improved Couplet Based Phylogenetic Supertree, IEEE international conference on bioinformatics and biomedicine (BIBM), 2016, Shenzhen, China, pp. 98-101.
(manuscript) (GitHub) (slides)
C14. Bhattacharyya S, and Mukhopadhyay J. Accumulated Coalescence Rank and Excess Gene Count for Species Tree Inference, Proceedings of 3rd International Conference on Algorithms for Computational Biology (AlCoB) 2016, Trujillo, Spain, Springer LNBI 9702, pp. 93-105.
(manuscript) (GitHub) (slides)
C13: Bhattacharyya S, and Mukhopadhyay J. Couplet Supertree based Species Tree Estimation from Incongruent Gene Trees with Deep Coalescence, Proceedings of 11th International Symposium on Bioinformatics Research and Applications (ISBRA), June 2015, Virginia, USA, Springer LNBI 9096, pages 48-59.
(manuscript) (GitHub) (slides)
C12: Bhattacharyya S, and Mukhopadhyay J. COuplet Supertree by Equivalence Partitioning of taxa set and DAG formation, Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), September 2014, Newport, California, pp. 259-268.
(manuscript) (GitHub). (slides)
C11: Biswas A, Roy R, Mukhopadhyay J, Khaneja D, Bhattacharya S D, and Bhattacharyya S. Android Application for Therapeutic Feed and Fluid Calculation in Neonatal Care - A Way to Fast, Accurate and Safe Health-care Delivery, International Workshop on Biomedical and Health Informatics (BHI), held in conjunction with IEEE international conference on bioinformatics and biomedicine (BIBM), 2016, Shenzhen, pp. 938-945. (manuscript)
C10: Das S, Bhattacharyya S, and Sen R. Life cycle analysis of a sporogenous probiotic bacterium in mammalian gastrointestinal tract with image processing analysis, International Conference on Systems in Medicine and Biology (ICSMB), Kharagpur January 2016
C9: Sharma S, Bhattacharyya S, Biswas A, Mukhopadhyay J, Purkait P K, and Deb A K. Automated detection of newborn sleep apnea using video monitoring system, 8th International Conference on Advances in Pattern Recognition (ICAPR), Indian Statistical Institute (ISI), Kolkata, India, January 4-7, 2015
C8: Bhattacharyya S, Biswas A, Pandit R, Mukhopadhyay J, Majumdar A K, Majumdar B, Mukherjee S, and Singh A K. Detection of Burst-Suppression in Neonatal EEG, International Conference on VLSI and Signal Processing (ICVSP), January 2014
C7: Bhattacharyya S, Roy A, Dogra D P, Biswas A, Mukhopadhyay J, Majumdar A K, Majumdar B, Mukherjee S, and Singh A K. Summarization of Neonatal Video EEG for Seizure and Artifact Detection, IEEE Third National Conference on Computer Vision, Pattern Recognition, Image Processing and Graphics (NCVPRIPG), 2011, pp. 134-137
C6: Bhattacharyya S, Ghoshal G, Biswas A, Mukhopadhyay J, Majumdar A K, Majumdar B, Mukherjee S, and Singh A K. Automatic sleep spindle detection in raw EEG signal of newborn babies, IEEE 3rd International Conference on Electronics Computer Technology (ICECT), 2011, pp. 73-77.
C5: Roy S, Dogra D P, Bhattacharyya S, Saha B, Biswas A, Majumdar A K, Mukhopadhyay J, Majumdar B, Singh A K, Paria A, and Mukherjee S. A Web Enabled Health Information System with an Application to Neonatal Patient Care Services, IEEE International Workshop on Web Services in Healthcare and Application (WSHA) 2011, pp. 451-458.
C4: Bhattacharyya S, Mukhopadhyay J, Majumdar A K, Majumdar B, Singh A K, and Saha C, Automated Burst Detection in Neonatal EEG International Conference on Bio-inspired System and Signal Processing (BIOSIGNALS) 2011, pp. 15-21.
C3: Bhattacharyya S, and Piccinelli E. A NOVEL FRAME SKIPPING METHOD IN TRANSCODER, WITH MOTION INFORMATION, BUFFER FULLNESS AND SCENE CHANGE CONSIDERATION, European Signal Processing Conference (EUSIPCO), Glasgow, 2009, pp. 14-18.
C2: Bhattacharyya S, Tripathi S, and Piccinelli E. Arbitrary spatial downsizing in H. 264 to MPEG4 simple profile transcoder, IEEE International Symposium on Broadband Multimedia Systems and Broadcasting (BMSB), 2009, pp. 1-5.
C1: Bhattacharyya S, Tripathi S, and Piccinelli E. HRD compliant single pass H. 264/AVC VBR Encoding Mode, 15th National Conference for Communications (NCC), 2009, pp. 1-4