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Article ; Online: Predicting patient-specific enhancer-promoter interactions.

Baur, Brittany / Roy, Sushmita

Cell reports methods

2023 Volume 3, Issue 9, Page(s) 100594

Abstract: Computational methods that can predict hard-to-measure modalities from those that are easier to measure, in a patient-specific manner, play a critical role in personalized medicine. In this issue of Cell Reports Methods, Khurana et al. present ... ...

Abstract	Computational methods that can predict hard-to-measure modalities from those that are easier to measure, in a patient-specific manner, play a critical role in personalized medicine. In this issue of Cell Reports Methods, Khurana et al. present differential gene targets of accessible chromatin (DGTAC), an approach which predicts patient-specific enhancer-promoter interactions.
MeSH term(s)	Humans ; Regulatory Sequences, Nucleic Acid ; Promoter Regions, Genetic/genetics ; Chromatin/genetics ; Patients ; Precision Medicine
Chemical Substances	Chromatin
Language	English
Publishing date	2023-08-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Comment
ISSN	2667-2375
ISSN (online)	2667-2375
DOI	10.1016/j.crmeth.2023.100594
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Article ; Online: Novel sequence type of carbapenem-resistant Acinetobacter pittii ST1451 with enhanced virulence isolated from septicaemic neonates in India.

Roy, Subhasree / Morita, Daichi / Bhattacharya, Sushmita / Dutta, Shanta / Basu, Sulagna

The Journal of antimicrobial chemotherapy

2024 Volume 79, Issue 4, Page(s) 779–783

Abstract: Background: The clinical relevance of Acinetobacter pittii is increasing, but reports of this organism causing neonatal sepsis are rare.: Objectives: To understand the mechanisms of resistance and virulence of A. pittii isolated from neonatal blood ... ...

Abstract	Background: The clinical relevance of Acinetobacter pittii is increasing, but reports of this organism causing neonatal sepsis are rare. Objectives: To understand the mechanisms of resistance and virulence of A. pittii isolated from neonatal blood belonging to a novel sequence type. Materials and methods: Antibiotic susceptibility, MLST, WGS, phylogenomic comparison with a global collection of carbapenemase-harbouring A. pittii were done. To study the pathogenic potential of novel A. pittii, in vitro and in vivo assays were carried out. Results and discussion: Two novel multidrug-resistant A. pittii from neonatal blood belonging to a novel sequence type 1451 (ST1451) were isolated. WGS revealed that the isolates were almost similar (147 SNP distant) and harbouring two carbapenem resistance genes blaNDM-1 with upstream ISAba125 and downstream bleMBL along with blaOXA-58 with upstream ISAba3. Other resistance genes included blaADC-25, blaOXA-533, aph(3″)-Ib, aph(3')-VIa, aph(6)-Id, aac(3)-IId, mph(E), msr(E), sul2 and tet(39), different efflux pump genes and amino acid substitutions within GyrA (Ser81Leu) and ParC (Ser84Leu; Glu88Ala) were detected among the isolates. The study genomes were closely related to four strains belonging to ST119. The isolates showed biofilm production, serum resistance, growth under iron limiting condition, surface-associated motility and adherence to host cell. Isolates induced cytokine production in the host cell and showed mice mortality. Discussion and conclusions: This study is the first report of the presence of blaNDM-1 in A. pittii from India along with another carbapenemase blaOXA-58. Emergence of highly virulent, multidrug-resistant A. pittii with attributes similar to A. baumannii calls for surveillance to identify the novel strains and their pathogenic and resistance potential.
MeSH term(s)	Animals ; Mice ; Carbapenems/pharmacology ; Anti-Bacterial Agents/pharmacology ; Virulence ; Multilocus Sequence Typing ; Acinetobacter Infections/epidemiology ; Microbial Sensitivity Tests ; Bacterial Proteins/genetics ; beta-Lactamases/genetics ; beta-Lactamases/metabolism ; Acinetobacter baumannii/genetics ; Acinetobacter
Chemical Substances	Carbapenems ; Anti-Bacterial Agents ; Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2024-02-09
Publishing country	England
Document type	Journal Article
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dkae024
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Zs.A 1197: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: GRiNCH

Da-Inn Lee / Sushmita Roy

Genome Biology, Vol 22, Iss 1, Pp 1-

simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

2021 Volume 31

Abstract: Abstract High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of ...

Abstract	Abstract High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units. We present GRiNCH, a constrained matrix-factorization-based approach for simultaneous smoothing and discovery of TADs from sparse contact count matrices. GRiNCH shows superior performance against seven TAD-calling methods and three smoothing methods. GRiNCH is applicable to multiple platforms including SPRITE and HiChIP and can predict novel boundary factors with potential roles in genome organization.
Keywords	Three-dimensional (3D) genome organization ; High-throughput chromosomal conformation capture (Hi-C) ; Topologically associating domains (TADs) ; Matrix factorization ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
Subject code	518
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization.

Lee, Da-Inn / Roy, Sushmita

Genome biology

2021 Volume 22, Issue 1, Page(s) 164

Abstract: High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C ... ...

Abstract	High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units. We present GRiNCH, a constrained matrix-factorization-based approach for simultaneous smoothing and discovery of TADs from sparse contact count matrices. GRiNCH shows superior performance against seven TAD-calling methods and three smoothing methods. GRiNCH is applicable to multiple platforms including SPRITE and HiChIP and can predict novel boundary factors with potential roles in genome organization.
MeSH term(s)	Algorithms ; Cell Line ; Chromatin/genetics ; Chromosomes/genetics ; Databases, Genetic ; Genome ; Histones/metabolism ; Humans ; Protein Processing, Post-Translational ; Regulatory Sequences, Nucleic Acid/genetics ; Time Factors
Chemical Substances	Chromatin ; Histones
Language	English
Publishing date	2021-05-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02378-z
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Article: GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

Lee, Da-Inn / Roy, Sushmita

Genome biology. 2021 Dec., v. 22, no. 1

2021

Abstract	High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units. We present GRiNCH, a constrained matrix-factorization-based approach for simultaneous smoothing and discovery of TADs from sparse contact count matrices. GRiNCH shows superior performance against seven TAD-calling methods and three smoothing methods. GRiNCH is applicable to multiple platforms including SPRITE and HiChIP and can predict novel boundary factors with potential roles in genome organization.
Keywords	chromatin ; genes ; topology
Language	English
Dates of publication	2021-12
Size	p. 164.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02378-z
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Article ; Online: Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE.

Zhang, Shilu / Knaack, Sara / Roy, Sushmita

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2477, Page(s) 439–455

Abstract: Transcriptional regulatory networks specify context-specific patterns of genes and play a central role in how species evolve and adapt. Inferring genome-scale regulatory networks in non-model species is the first step for examining patterns of ... ...

Abstract	Transcriptional regulatory networks specify context-specific patterns of genes and play a central role in how species evolve and adapt. Inferring genome-scale regulatory networks in non-model species is the first step for examining patterns of conservation and divergence of regulatory networks. Transcriptomic data obtained under varying environmental stimuli in multiple species are becoming increasingly available, which can be used to infer regulatory networks. However, inference and analysis of multiple gene regulatory networks in a phylogenetic setting remains challenging. We developed an algorithm, Multi-species Regulatory neTwork LEarning (MRTLE), to facilitate such studies of regulatory network evolution. MRTLE is a probabilistic graphical model-based algorithm that uses phylogenetic structure, transcriptomic data for multiple species, and sequence-specific motifs in each species to simultaneously infer genome-scale regulatory networks across multiple species. We applied MRTLE to study regulatory network evolution across six ascomycete yeasts using transcriptomic measurements collected across different stress conditions. MRTLE networks recapitulated experimentally derived interactions in the model organism S. cerevisiae as well as non-model species, and it was more beneficial for network inference than methods that do not use phylogenetic information. We examined the regulatory networks across species and found that regulators associated with significant expression and network changes are involved in stress-related processes. MTRLE and its associated downstream analysis provide a scalable and principled framework to examine evolutionary dynamics of transcriptional regulatory networks across multiple species in a large phylogeny.
MeSH term(s)	Algorithms ; Evolution, Molecular ; Gene Regulatory Networks ; Genome ; Phylogeny ; Saccharomyces cerevisiae/genetics
Language	English
Publishing date	2022-05-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2257-5_24
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Article: Deciphering the Role of 3D Genome Organization in Breast Cancer Susceptibility.

Baur, Brittany / Lee, Da-Inn / Haag, Jill / Chasman, Deborah / Gould, Michael / Roy, Sushmita

Frontiers in genetics

2022 Volume 12, Page(s) 788318

Abstract: Cancer risk by environmental exposure is modulated by an individual's genetics and age at exposure. This age-specific period of susceptibility is referred to as the "Window of Susceptibility" (WOS). Rats have a similar WOS for developing breast cancer. A ...

Abstract	Cancer risk by environmental exposure is modulated by an individual's genetics and age at exposure. This age-specific period of susceptibility is referred to as the "Window of Susceptibility" (WOS). Rats have a similar WOS for developing breast cancer. A previous study in rat identified an age-specific long-range regulatory interaction for the cancer gene,
Language	English
Publishing date	2022-01-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2021.788318
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Article ; Online: Lipoprotein (a) as a Predictor of Steroid Dependence in Paediatric Steroid Sensitive Nephrotic Syndrome

Surupa Basu / Sushmita Banerjee / Pranab Roy / Apurba Ghosh

Journal of Clinical and Diagnostic Research, Vol 15, Iss 01, Pp BC05-BC

2021 Volume 08

Abstract: Introduction: Lipoprotein a {Lp(a)} increases in Nephrotic Syndrome (NS). Although the majority of paediatric NS are steroid sensitive, relpase and steroid dependence are commonly seen in this cases. Lp(a) is an LDL-like lipoprotein that consists of an ... ...

Abstract	Introduction: Lipoprotein a {Lp(a)} increases in Nephrotic Syndrome (NS). Although the majority of paediatric NS are steroid sensitive, relpase and steroid dependence are commonly seen in this cases. Lp(a) is an LDL-like lipoprotein that consists of an LDL particle to which the glycoprotein apolipoprotein(a) {apo(a)} is attached.Aim: To evaluate the potential of Lp(a), measured on admission, for the prediction of relapse/steroid dependency.Materials and Methods: Children (n=36) with first episode NS were recruited in this prospective observational case-control study and followed up for one year. They were tested at presentation for Lp(a) (mg/dL) and standard tests such as haemoglobin, albumin, protein, cholesterol, triglyceride, and urine protein. Children received standard therapy for NS, and were followed for a period of one year from diagnosis to record days to initial remission, relapse episodes, steroid dependence etc. Patients were categorised as: no relapse (NR), Infrequent Relapse (IFR), frequent relapse (FR) and Steroid Dependent (SD) as per standard definitions. Fifteen healthy volunteers were also tested for lipid profile and Lp(a) levels.Results: Of 36 cases (median age 3 years, 19 males), there were 15NR, 7IFR, 2FR and 12SD. The mean Lp(a) of the NS group (165.2±120.4 mg/dL) was higher than controls (30.52±21.9 mg/dL) (p<0.0001). All the lipid parameters except HDL-cholesterol were significantly higher in the NS group. Within the NS group, Lp(a) showed significant correlation (Spearman-rho) with albumin (p=0.0062,r=0.47), but no correlation with lipid parameters or urine protein. Comparison of Lp(a)levels in the NS groups revealed that the SD patients had a high Lp(a)(222.0±115.7 mg/dL) compared to NR (129.7±120.1 mg/dL) (p=0.02).Conclusion: Concentration of plasma Lp(a) in patients with SDNS was higher compared to patients who did not suffer any relapse, and this concentration may serve as a marker for prediction of SDNS.
Keywords	child health ; glycoprotein ; lipids ; nephrotic syndrome ; predictor ; steroid dependence ; Medicine ; R
Subject code	610
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	JCDR Research and Publications Private Limited
Document type	Article ; Online
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Article ; Online: Identification of Common Dysregulated Genes in COVID-19 and Hypersensitivity Pneumonitis: A Systems Biology and Machine Learning Approach.

Dasgupta, Sanjukta / Das, Sankha Subhra / Patidar, Sankalp / Kajaria, Vaibhav / Chowdhury, Sushmita Roy / Chaudhury, Koel

Omics : a journal of integrative biology

2023 Volume 27, Issue 5, Page(s) 205–214

Abstract: A comprehensive knowledge on systems biology of severe acute respiratory syndrome coronavirus 2 is crucial for differential diagnosis of COVID-19. Interestingly, the radiological and pathological features of COVID-19 mimic that of hypersensitivity ... ...

Abstract	A comprehensive knowledge on systems biology of severe acute respiratory syndrome coronavirus 2 is crucial for differential diagnosis of COVID-19. Interestingly, the radiological and pathological features of COVID-19 mimic that of hypersensitivity pneumonitis (HP), another pulmonary fibrotic phenotype. This motivated us to explore the overlapping pathophysiology of COVID-19 and HP, if any, and using a systems biology approach. Two datasets were obtained from the Gene Expression Omnibus database (GSE147507 and GSE150910) and common differentially expressed genes (DEGs) for both diseases identified. Fourteen common DEGs, significantly altered in both diseases, were found to be implicated in complement activation and growth factor activity. A total of five microRNAs (hsa-miR-1-3p, hsa-miR-20a-5p, hsa-miR-107, hsa-miR-16-5p, and hsa-miR-34b-5p) and five transcription factors (KLF6, ZBTB7A, ELF1, NFIL3, and ZBT33) exhibited highest interaction with these common genes. Next,
MeSH term(s)	Humans ; COVID-19/genetics ; Systems Biology ; Cell Line, Tumor ; Computational Biology ; Transcription Factors ; DNA-Binding Proteins ; MicroRNAs/genetics ; Alveolitis, Extrinsic Allergic ; Machine Learning
Chemical Substances	Transcription Factors ; DNA-Binding Proteins ; MicroRNAs ; ZBTB7A protein, human
Language	English
Publishing date	2023-04-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2030312-9
ISSN	1557-8100 ; 1536-2310
ISSN (online)	1557-8100
ISSN	1536-2310
DOI	10.1089/omi.2022.0171
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Article ; Online: A prior-based integrative framework for functional transcriptional regulatory network inference.

Siahpirani, Alireza F / Roy, Sushmita

Nucleic acids research

2016 Volume 45, Issue 4, Page(s) 2221

Language	English
Publishing date	2016-11-29
Publishing country	England
Document type	Journal Article ; Published Erratum
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkw1160
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Zs.A 1067: Show issues

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Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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