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Artikel ; Online: BaySyn: Bayesian Evidence Synthesis for Multi-system Multiomic Integration.

Bhattacharyya, Rupam / Henderson, Nicholas / Baladandayuthapani, Veerabhadran

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

2022 Band 28, Seite(n) 275–286

Abstract: The discovery of cancer drivers and drug targets are often limited to the biological systems - from cancer model systems to patients. While multiomic patient databases have sparse drug response data, cancer model systems databases, despite covering a ... ...

Abstract	The discovery of cancer drivers and drug targets are often limited to the biological systems - from cancer model systems to patients. While multiomic patient databases have sparse drug response data, cancer model systems databases, despite covering a broad range of pharmacogenomic platforms, provide lower lineage-specific sample sizes, resulting in reduced statistical power to detect both functional driver genes and their associations with drug sensitivity profiles. Hence, integrating evidence across model systems, taking into account the pros and cons of each system, in addition to multiomic integration, can more efficiently deconvolve cellular mechanisms of cancer as well as learn therapeutic associations. To this end, we propose BaySyn - a hierarchical Bayesian evidence synthesis framework for multi-system multiomic integration. BaySyn detects functionally relevant driver genes based on their associations with upstream regulators using additive Gaussian process models and uses this evidence to calibrate Bayesian variable selection models in the (drug) outcome layer. We apply BaySyn to multiomic cancer cell line and patient datasets from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas, respectively, across pan-gynecological cancers. Our mechanistic models implicate several relevant functional genes across cancers such as PTPN6 and ERBB2 in the KEGG adherens junction gene set. Furthermore, our outcome model is able to make higher number of discoveries in drug response models than its uncalibrated counterparts under the same thresholds of Type I error control, including detection of known lineage-specific biomarker associations such as BCL11A in breast and FGFRL1 in ovarian cancers. All our results and implementation codes are freely available via an interactive R Shiny dashboard at tinyurl.com/BaySynApp. The supplementary materials are available online at tinyurl.com/BaySynSup.
Mesh-Begriff(e)	Humans ; Multiomics ; Computational Biology ; Bayes Theorem ; Neoplasms/drug therapy ; Neoplasms/genetics ; Biomarkers
Chemische Substanzen	Biomarkers
Sprache	Englisch
Erscheinungsdatum	2022-12-14
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2335-6936
ISSN (online)	2335-6936
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Comparative impact assessment of COVID-19 policy interventions in five South Asian countries using reported and estimated unreported death counts during 2020-2021.

Ritoban Kundu / Jyotishka Datta / Debashree Ray / Swapnil Mishra / Rupam Bhattacharyya / Lauren Zimmermann / Bhramar Mukherjee

PLOS Global Public Health, Vol 3, Iss 12, p e

2023 Band 0002063

Abstract: There has been raging discussion and debate around the quality of COVID death data in South Asia. According to WHO, of the 5.5 million reported COVID-19 deaths from 2020-2021, 0.57 million (10%) were contributed by five low and middle income countries ( ... ...

Abstract	There has been raging discussion and debate around the quality of COVID death data in South Asia. According to WHO, of the 5.5 million reported COVID-19 deaths from 2020-2021, 0.57 million (10%) were contributed by five low and middle income countries (LMIC) countries in the Global South: India, Pakistan, Bangladesh, Sri Lanka and Nepal. However, a number of excess death estimates show that the actual death toll from COVID-19 is significantly higher than the reported number of deaths. For example, the IHME and WHO both project around 14.9 million total deaths, of which 4.5-5.5 million were attributed to these five countries in 2020-2021. We focus our gaze on the COVID-19 performance of these five countries where 23.5% of the world population lives in 2020 and 2021, via a counterfactual lens and ask, to what extent the mortality of one LMIC would have been affected if it adopted the pandemic policies of another, similar country? We use a Bayesian semi-mechanistic model developed by Mishra et al. (2021) to compare both the reported and estimated total death tolls by permuting the time-varying reproduction number (Rt) across these countries over a similar time period. Our analysis shows that, in the first half of 2021, mortality in India in terms of reported deaths could have been reduced to 96 and 102 deaths per million compared to actual 170 reported deaths per million had it adopted the policies of Nepal and Pakistan respectively. In terms of total deaths, India could have averted 481 and 466 deaths per million had it adopted the policies of Bangladesh and Pakistan. On the other hand, India had a lower number of reported COVID-19 deaths per million (48 deaths per million) and a lower estimated total deaths per million (80 deaths per million) in the second half of 2021, and LMICs other than Pakistan would have lower reported mortality had they followed India's strategy. The gap between the reported and estimated total deaths highlights the varying level and extent of under-reporting of deaths across the ...
Schlagwörter	Public aspects of medicine ; RA1-1270
Thema/Rubrik (Code)	306 ; 950
Sprache	Englisch
Erscheinungsdatum	2023-01-01T00:00:00Z
Verlag	Public Library of Science (PLoS)
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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Artikel ; Online: Comparative impact assessment of COVID-19 policy interventions in five South Asian countries using reported and estimated unreported death counts during 2020-2021.

Kundu, Ritoban / Datta, Jyotishka / Ray, Debashree / Mishra, Swapnil / Bhattacharyya, Rupam / Zimmermann, Lauren / Mukherjee, Bhramar

PLOS global public health

2023 Band 3, Heft 12, Seite(n) e0002063

Abstract	There has been raging discussion and debate around the quality of COVID death data in South Asia. According to WHO, of the 5.5 million reported COVID-19 deaths from 2020-2021, 0.57 million (10%) were contributed by five low and middle income countries (LMIC) countries in the Global South: India, Pakistan, Bangladesh, Sri Lanka and Nepal. However, a number of excess death estimates show that the actual death toll from COVID-19 is significantly higher than the reported number of deaths. For example, the IHME and WHO both project around 14.9 million total deaths, of which 4.5-5.5 million were attributed to these five countries in 2020-2021. We focus our gaze on the COVID-19 performance of these five countries where 23.5% of the world population lives in 2020 and 2021, via a counterfactual lens and ask, to what extent the mortality of one LMIC would have been affected if it adopted the pandemic policies of another, similar country? We use a Bayesian semi-mechanistic model developed by Mishra et al. (2021) to compare both the reported and estimated total death tolls by permuting the time-varying reproduction number (Rt) across these countries over a similar time period. Our analysis shows that, in the first half of 2021, mortality in India in terms of reported deaths could have been reduced to 96 and 102 deaths per million compared to actual 170 reported deaths per million had it adopted the policies of Nepal and Pakistan respectively. In terms of total deaths, India could have averted 481 and 466 deaths per million had it adopted the policies of Bangladesh and Pakistan. On the other hand, India had a lower number of reported COVID-19 deaths per million (48 deaths per million) and a lower estimated total deaths per million (80 deaths per million) in the second half of 2021, and LMICs other than Pakistan would have lower reported mortality had they followed India's strategy. The gap between the reported and estimated total deaths highlights the varying level and extent of under-reporting of deaths across the subcontinent, and that model estimates are contingent on accuracy of the death data. Our analysis shows the importance of timely public health intervention and vaccines for lowering mortality and the need for better coverage infrastructure for the death registration system in LMICs.
Sprache	Englisch
Erscheinungsdatum	2023-12-27
Erscheinungsland	United States
Dokumenttyp	Journal Article
ISSN	2767-3375
ISSN (online)	2767-3375
DOI	10.1371/journal.pgph.0002063
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Buch ; Online: Functional Integrative Bayesian Analysis of High-dimensional Multiplatform Genomic Data

Bhattacharyya, Rupam / Henderson, Nicholas / Baladandayuthapani, Veerabhadran

2022

Abstract: Rapid advancements in collection and dissemination of multi-platform molecular and genomics data has resulted in enormous opportunities to aggregate such data in order to understand, prevent, and treat human diseases. While significant improvements have ... ...

Abstract	Rapid advancements in collection and dissemination of multi-platform molecular and genomics data has resulted in enormous opportunities to aggregate such data in order to understand, prevent, and treat human diseases. While significant improvements have been made in multi-omic data integration methods to discover biological markers and mechanisms underlying both prognosis and treatment, the precise cellular functions governing these complex mechanisms still need detailed and data-driven de-novo evaluations. We propose a framework called Functional Integrative Bayesian Analysis of High-dimensional Multiplatform Genomic Data (fiBAG), that allows simultaneous identification of upstream functional evidence of proteogenomic biomarkers and the incorporation of such knowledge in Bayesian variable selection models to improve signal detection. fiBAG employs a conflation of Gaussian process models to quantify (possibly non-linear) functional evidence via Bayes factors, which are then mapped to a novel calibrated spike-and-slab prior, thus guiding selection and providing functional relevance to the associations with patient outcomes. Using simulations, we illustrate how integrative methods with functional calibration have higher power to detect disease related markers than non-integrative approaches. We demonstrate the profitability of fiBAG via a pan-cancer analysis of 14 cancer types to identify and assess the cellular mechanisms of proteogenomic markers associated with cancer stemness and patient survival. Comment: 41 pages manuscript, 5 figures; 49 pages supplementary materials, 37 supplementary figures
Schlagwörter	Statistics - Methodology ; Quantitative Biology - Genomics ; Quantitative Biology - Quantitative Methods ; Statistics - Applications ; Statistics - Machine Learning ; 62-08 ; G.3
Thema/Rubrik (Code)	006
Erscheinungsdatum	2022-12-28
Erscheinungsland	us
Dokumenttyp	Buch ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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Artikel ; Online: The C-terminal end of mycobacterial HadBC regulates AcpM interaction during the FAS-II pathway: a structural perspective.

Singh, Bina Kumari / Biswas, Rupam / Bhattacharyya, Sudipta / Basak, Amit / Das, Amit K

The FEBS journal

2022 Band 289, Heft 16, Seite(n) 4963–4980

Abstract: Comprehending the molecular strategies employed by Mycobacterium tuberculosis (Mtb) in FAS-II regulation is of paramount significance for curbing tuberculosis progression. Mtb employs two sets of dehydratases, namely HadAB and HadBC (β-hydroxyacyl acyl ... ...

Abstract	Comprehending the molecular strategies employed by Mycobacterium tuberculosis (Mtb) in FAS-II regulation is of paramount significance for curbing tuberculosis progression. Mtb employs two sets of dehydratases, namely HadAB and HadBC (β-hydroxyacyl acyl carrier protein dehydratase), for the regulation of the fatty acid synthase (FAS-II) pathway. We utilized a sequence similarity network to discern the basis for the presence of two copies of the dehydratase gene in Mtb. This analysis groups HadC and HadA in different clusters, which could be attributed to the variability in their physiological role with respect to the acyl chain uptake. Our study reveals structural details pertaining to the crystal structure of the last remaining enzyme of the FAS-II pathway. It also provides insights into the highly flexible hot-dog helix and substrate regulatory loop. Additionally, mutational studies assisted in establishing the role of the C-terminal end in HadC of HadBC in the regulation of acyl carrier protein from Mtb-mediated interactions. Complemented with surface plasmon resonance and molecular dynamics simulation studies, the present study provides the first evidence of the molecular mechanisms involved in the differential binding affinity of the acyl carrier protein from Mtb towards both mtbHadAB and mtbHadBC.
Mesh-Begriff(e)	Acyl Carrier Protein/genetics ; Acyl Carrier Protein/metabolism ; Bacterial Proteins/metabolism ; Fatty Acid Synthase, Type II/chemistry ; Fatty Acid Synthase, Type II/genetics ; Fatty Acid Synthase, Type II/metabolism ; Fatty Acid Synthases/genetics ; Fatty Acid Synthases/metabolism ; Hydro-Lyases/metabolism ; Mycobacterium tuberculosis/metabolism ; Mycolic Acids/metabolism
Chemische Substanzen	Acyl Carrier Protein ; Bacterial Proteins ; Mycolic Acids ; Fatty Acid Synthases (EC 2.3.1.85) ; Hydro-Lyases (EC 4.2.1.-) ; Fatty Acid Synthase, Type II (EC 6.-)
Sprache	Englisch
Erscheinungsdatum	2022-03-23
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16405
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: The C‐terminal end of mycobacterial HadBC regulates AcpM interaction during the FAS‐II pathway: a structural perspective

Singh, Bina Kumari / Biswas, Rupam / Bhattacharyya, Sudipta / Basak, Amit / Das, Amit K.

FEBS journal. 2022 Aug., v. 289, no. 16

2022

Abstract: Comprehending the molecular strategies employed by Mycobacterium tuberculosis (Mtb) in FAS‐II regulation is of paramount significance for curbing tuberculosis progression. Mtb employs two sets of dehydratases, namely HadAB and HadBC (β‐hydroxyacyl acyl ... ...

Abstract	Comprehending the molecular strategies employed by Mycobacterium tuberculosis (Mtb) in FAS‐II regulation is of paramount significance for curbing tuberculosis progression. Mtb employs two sets of dehydratases, namely HadAB and HadBC (β‐hydroxyacyl acyl carrier protein dehydratase), for the regulation of the fatty acid synthase (FAS‐II) pathway. We utilized a sequence similarity network to discern the basis for the presence of two copies of the dehydratase gene in Mtb. This analysis groups HadC and HadA in different clusters, which could be attributed to the variability in their physiological role with respect to the acyl chain uptake. Our study reveals structural details pertaining to the crystal structure of the last remaining enzyme of the FAS‐II pathway. It also provides insights into the highly flexible hot‐dog helix and substrate regulatory loop. Additionally, mutational studies assisted in establishing the role of the C‐terminal end in HadC of HadBC in the regulation of acyl carrier protein from Mtb‐mediated interactions. Complemented with surface plasmon resonance and molecular dynamics simulation studies, the present study provides the first evidence of the molecular mechanisms involved in the differential binding affinity of the acyl carrier protein from Mtb towards both mtbHadAB and mtbHadBC.
Schlagwörter	Mycobacterium tuberculosis ; acyl carrier protein ; crystal structure ; fatty-acid synthase ; genes ; molecular dynamics ; sequence homology ; surface plasmon resonance ; tuberculosis
Sprache	Englisch
Erscheinungsverlauf	2022-08
Umfang	p. 4963-4980.
Erscheinungsort	John Wiley & Sons, Ltd
Dokumenttyp	Artikel
Anmerkung	JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16405
Datenquelle	NAL Katalog (AGRICOLA)

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Artikel ; Online: Author Correction: Incorporating false negative tests in epidemiological models for SARS-CoV-2 transmission and reconciling with seroprevalence estimates.

Bhattacharyya, Rupam / Kundu, Ritoban / Bhaduri, Ritwik / Ray, Debashree / Beesley, Lauren J / Salvatore, Maxwell / Mukherjee, Bhramar

Scientific reports

2021 Band 11, Heft 1, Seite(n) 17221

Sprache	Englisch
Erscheinungsdatum	2021-08-20
Erscheinungsland	England
Dokumenttyp	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-96603-1
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Network-based Modeling of COVID-19 Dynamics: Early Pandemic Spread in India

Bhattacharyya, Rupam / Banerjee, Sayantan / Mohammed, Shariq / Baladandayuthapani, Veerabhadran

medRxiv

Abstract: Modeling the dynamics of COVID-19 pandemic spread is a challenging and relevant problem. Established models for the epidemic spread such as compartmental epidemiological models e.g. Susceptible-Infected-Recovered (SIR) models and its variants, have been ... ...

Abstract	Modeling the dynamics of COVID-19 pandemic spread is a challenging and relevant problem. Established models for the epidemic spread such as compartmental epidemiological models e.g. Susceptible-Infected-Recovered (SIR) models and its variants, have been discussed extensively in the literature and utilized to forecast the growth of the pandemic across different hot-spots in the world. The standard formulations of SIR models rely upon summary-level data, which may not be able to fully capture the complete dynamics of the pandemic growth. Since the disease spreads from carriers to susceptible individuals via some form of contact, it inherently relies upon a network of individuals for its growth, with edges established via direct interaction, such as shared physical proximity. Using individual-level COVID-19 data from the early days (January 30 to April 15, 2020) of the pandemic in India, and under a network-based SIR model framework, we performed state-specific forecasting under multiple scenarios characterized by the basic reproduction number of COVID-19 across 34 Indian states and union territories. We validated our short-term projections using observed case counts and the long-term projections using national sero-survey findings. Based on healthcare availability data, we also performed projections to assess the burdens on the infrastructure along the spectrum of the pandemic growth. We have developed an \href{https://bayesrx.shinyapps.io/COV-N/}{interactive dashboard} summarizing our results. Our predictions successfully identified the initial hot-spots of India such as Maharashtra and Delhi, and those that emerged later, such as Madhya Pradesh and Kerala. These models have the potential to inform appropriate policies for isolation and mitigation strategies to contain the pandemic, through a phased approach by appropriate resource prioritization and allocation.
Schlagwörter	covid19
Sprache	Englisch
Erscheinungsdatum	2021-03-20
Verlag	Cold Spring Harbor Laboratory Press
Dokumenttyp	Artikel ; Online
DOI	10.1101/2021.03.16.21253772
Datenquelle	COVID19

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Artikel: Targeting PIKfyve-driven lipid homeostasis as a metabolic vulnerability in pancreatic cancer.

Cheng, Caleb / Hu, Jing / Mannan, Rahul / Bhattacharyya, Rupam / Rossiter, Nicholas J / Magnuson, Brian / Wisniewski, Jasmine P / Zheng, Yang / Xiao, Lanbo / Li, Chungen / Awad, Dominik / He, Tongchen / Bao, Yi / Zhang, Yuping / Cao, Xuhong / Wang, Zhen / Mehra, Rohit / Morlacchi, Pietro / Sahai, Vaibhav /

di Magliano, Marina Pasca / Shah, Yatrik M / Ding, Ke / Qiao, Yuanyuan / Lyssiotis, Costas A / Chinnaiyan, Arul M

bioRxiv : the preprint server for biology

2024

Abstract: Pancreatic ductal adenocarcinoma (PDAC) subsists in a nutrient-deregulated microenvironment, making it particularly susceptible to treatments that interfere with cancer ... ...

Abstract	Pancreatic ductal adenocarcinoma (PDAC) subsists in a nutrient-deregulated microenvironment, making it particularly susceptible to treatments that interfere with cancer metabolism
Sprache	Englisch
Erscheinungsdatum	2024-03-20
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.1101/2024.03.18.585580
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Selective molecular separation of lignin model compounds by reduced graphene oxide membranes from solvent-water mixture.

Aher, Ashish / Sarma, Rupam / Crocker, Mark / Bhattacharyya, Dibakar

Separation and purification technology

2019 Band 230

Abstract: Selective separation of lignin depolymerization products is key to fractionating and isolating high-value aromatic compounds from the depolymerization process. The primary aim of this study was to synthesis graphene oxide (GO) membranes for selective ... ...

Abstract	Selective separation of lignin depolymerization products is key to fractionating and isolating high-value aromatic compounds from the depolymerization process. The primary aim of this study was to synthesis graphene oxide (GO) membranes for selective separations of lignin oligomeric units from polar organic solvent-water media. GO membranes were synthesized on a polymeric substrate by a shear assisted casting of aqueous GO dispersion using a wire-wound rod. Deposited GO was then reduced to different extents by controlled thermal incubation, and the impact on membrane performance was investigated. The extent of reduction of GO was established by extensive characterization with FTIR, XPS, Raman Spectroscopy, XRD, and contact angle measurements. Impressive performance with the rejection of over 70% for the model compound trimer BMP (2,6-bis[(2-hydroxy-5-methyl phenyl) methyl]-4-methylphenol) was achieved compared to only 20% rejection for the dimer GGE (guaiacylglycerol-β-guaiacylether) with isopropanol-water (90-10% by volume) as a solvent. This corresponds to an encouraging selective separation with selective permeation of dimer (GGE) 3.5 times higher compared to trimer (BMP). rGO membranes exhibited a stable performance over 84 h of operation at a shear rate of 1.1 Pa in a cross-flow mode of operation. Selective separation of GO can be effectively modulated by controlling the O/C ratio by the extent of reduction of GO; indeed, the retention of trimeric compounds increased with increasing GO reduction. The remarkable performance of GO membranes could enable energy-efficient fractionation of lignin oligomeric compounds from polar organic solvents.
Sprache	Englisch
Erscheinungsdatum	2019-07-27
Erscheinungsland	Netherlands
Dokumenttyp	Journal Article
ZDB-ID	2022535-0
ISSN	1383-5866
ISSN	1383-5866
DOI	10.1016/j.seppur.2019.115865
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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