Characterizing the pan-cancer role of exosomal miRNAs in metastasis across cancers

Authors: Piyush Agrawal, Gulden Olgun, Arashdeep Singh, Vishaka Gopalan, Sridhar Hannenhalli

Source: Computational and Structural Biotechnology Journal, Vol 27, Iss , Pp 252-264 (2025)

Subject Terms: Exosomal miRNA, Cancer metastasis, Pre-metastatic Niche, Survival Analysis, Machine Learning, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037024004483; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/d733d8b13b15472aa83b6ac3dc2eb505

Protocol for identifying key genes using network-based approach as an alternative to differential expression analysis

Authors: Piyush Agrawal, Sridhar Hannenhalli

Source: STAR Protocols, Vol 5, Iss 4, Pp 103472- (2024)

Subject Terms: Bioinformatics, Cancer, Genomics, Systems biology, Computer sciences, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666166724006373; https://doaj.org/toc/2666-1667

Access URL: https://doaj.org/article/64f7a938bc9245b7a00af0c61bfb6a1e

Aberrant spliceosome activity via elevated intron retention and upregulation and phosphorylation of SF3B1 in chronic lymphocytic leukemia

Authors: Manoj Kumar Kashyap, Hiren Karathia, Deepak Kumar, Roberto Vera Alvarez, Jose Vicente Forero-Forero, Eider Moreno, Juliana Velez Lujan, Carlos Ivan Amaya-Chanaga, Newton Medeiros Vidal, Zhe Yu, Emanuela M. Ghia, Paula A. Lengerke-Diaz, Daniel Achinko, Michael Y. Choi, Laura Z. Rassenti, Leonardo Mariño-Ramírez, Stephen M. Mount, Sridhar Hannenhalli, Thomas J. Kipps, Januario E. Castro

Source: Molecular Therapy: Nucleic Acids, Vol 35, Iss 2, Pp 102202- (2024)

Subject Terms: MT: RNA/DNA Editing, RNA splicing, CLL, intron retention, RNA-seq, macrolide, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2162253124000891; https://doaj.org/toc/2162-2531

Access URL: https://doaj.org/article/adf59c81f6f94126a63b606708311ab5

Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer

Authors: Piyush Agrawal, Navami Jain, Vishaka Gopalan, Annan Timon, Arashdeep Singh, Padma S. Rajagopal, Sridhar Hannenhalli

Source: iScience, Vol 27, Iss 5, Pp 109752- (2024)

Subject Terms: gene network, cancer systems biology, cancer, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S258900422400974X; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/bc76f4e91ec44d41abab0ce488f6be49

Transcriptomes of the tumor-adjacent normal tissues are more informative than tumors in predicting recurrence in colorectal cancer patients

Authors: Jinho Kim, Hyunjung Kim, Min-Seok Lee, Heetak Lee, Yeon Jeong Kim, Woo Yong Lee, Seong Hyeon Yun, Hee Cheol Kim, Hye Kyung Hong, Sridhar Hannenhalli, Yong Beom Cho, Donghyun Park, Sun Shim Choi

Source: Journal of Translational Medicine, Vol 21, Iss 1, Pp 1-15 (2023)

Subject Terms: Colorectal cancer, Normal tissues adjacent to tumors, Recurrence, Elastic net-based machine learning, Tumor-infiltrating immune cells, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1479-5876

Access URL: https://doaj.org/article/8e84462bd82d4cb0b0c61ffa12e5ebda

Broad misappropriation of developmental splicing profile by cancer in multiple organs

Authors: Arashdeep Singh, Arati Rajeevan, Vishaka Gopalan, Piyush Agrawal, Chi-Ping Day, Sridhar Hannenhalli

Source: Nature Communications, Vol 13, Iss 1, Pp 1-18 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/200a32203bd7440fb9799425cc49aa44

Transcription factors organize into functional groups on the linear genome and in 3D chromatin

Authors: Rakesh Netha Vadnala, Sridhar Hannenhalli, Leelavati Narlikar, Rahul Siddharthan

Source: Heliyon, Vol 9, Iss 8, Pp e18211- (2023)

Subject Terms: Chromatin, Transcription factors, Science (General), Q1-390, Social sciences (General), H1-99

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2405844023054191; https://doaj.org/toc/2405-8440

Access URL: https://doaj.org/article/25837509f2ca413ab5edea66ed705e52

Protocol for using single-cell sequencing to study the heterogeneity of NF1 nerve sheath tumors from clinical biospecimens

Authors: Xiyuan Zhang, Vishaka Gopalan, Neeraja Syed, Sridhar Hannenhalli, Jack F. Shern

Source: STAR Protocols, Vol 4, Iss 2, Pp 102297- (2023)

Subject Terms: Bioinformatics, Single Cell, Cancer, Genetics, RNAseq, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666166723002642; https://doaj.org/toc/2666-1667

Access URL: https://doaj.org/article/c5a0401d492e45cfb046197bdd174375

Immune cell gene expression signatures in diffuse glioma are associated with IDH mutation status, patient outcome and malignant cell state, and highlight the importance of specific cell subsets in glioma biology

Authors: Bharati Mehani, Saleembhasha Asanigari, Hye-Jung Chung, Karen Dazelle, Arashdeep Singh, Sridhar Hannenhalli, Kenneth Aldape

Source: Acta Neuropathologica Communications, Vol 10, Iss 1, Pp 1-18 (2022)

Subject Terms: Glioma, Tumor microenvironment, Malignant cell-state, Deconvolution, CIBERSORTx, Prognosis, Neurology. Diseases of the nervous system, RC346-429

File Description: electronic resource

Relation: https://doaj.org/toc/2051-5960

Access URL: https://doaj.org/article/bf7c9a29502f42cb8f495ae1d1b9ea52

miRSCAPE - inferring miRNA expression from scRNA-seq data

Authors: Gulden Olgun, Vishaka Gopalan, Sridhar Hannenhalli

Source: iScience, Vol 25, Iss 9, Pp 104962- (2022)

Subject Terms: Biocomputational method, Cancer systems biology, Transcriptomics, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004222012342; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/6ef80d46915747b89f0a09407a398b1b

A Path-Based Analysis of Infected Cell Line and COVID-19 Patient Transcriptome Reveals Novel Potential Targets and Drugs Against SARS-CoV-2

Authors: Piyush Agrawal, Narmada Sambaturu, Gulden Olgun, Sridhar Hannenhalli

Source: Frontiers in Immunology, Vol 13 (2022)

Subject Terms: SARS-C0V-2, transcriptome, cell lines, PBMCs (Peripheral Blood Mononuclear Cells), DEGs (Differentially Expressed Genes), network analysis, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2022.918817/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/a4dcfde205cd496da9aa054e8034ae34

Correction: Transcriptomes of the tumor-adjacent normal tissues are more informative than tumors in predicting recurrence in colorectal cancer patients

Authors: Jinho Kim, Hyunjung Kim, Min‑Seok Lee, Heetak Lee, Yeon Jeong Kim, Woo Yong Lee, Seong Hyeon Yun, Hee Cheol Kim, Hye Kyung Hong, Sridhar Hannenhalli, Yong Beom Cho, Donghyun Park, Sun Shim Choi

Source: Journal of Translational Medicine, Vol 21, Iss 1, Pp 1-1 (2023)

Subject Terms: Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1479-5876

Access URL: https://doaj.org/article/4d58f45497cf4e3a9c10e3fff4c2719e

Pathologic gene network rewiring implicates PPP1R3A as a central regulator in pressure overload heart failure

Authors: Pablo Cordero, Victoria N. Parikh, Elizabeth T. Chin, Ayca Erbilgin, Michael J. Gloudemans, Ching Shang, Yong Huang, Alex C. Chang, Kevin S. Smith, Frederick Dewey, Kathia Zaleta, Michael Morley, Jeff Brandimarto, Nicole Glazer, Daryl Waggott, Aleksandra Pavlovic, Mingming Zhao, Christine S. Moravec, W. H. Wilson Tang, Jamie Skreen, Christine Malloy, Sridhar Hannenhalli, Hongzhe Li, Scott Ritter, Mingyao Li, Daniel Bernstein, Andrew Connolly, Hakon Hakonarson, Aldons J. Lusis, Kenneth B. Margulies, Anna A. Depaoli-Roach, Stephen B. Montgomery, Matthew T. Wheeler, Thomas Cappola, Euan A. Ashley

Source: Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/2ca5a8edf42d48a4acecfce1aa70adac

Prioritizing and characterizing functionally relevant genes across human tissues.

Authors: Gowthami Somepalli, Sarthak Sahoo, Arashdeep Singh, Sridhar Hannenhalli

Source: PLoS Computational Biology, Vol 17, Iss 7, p e1009194 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/ec34913d83af4be5b41ab61cfb9daf94

A transcription-centric model of SNP-age interaction.

Authors: Kun Wang, Mahashweta Basu, Justin Malin, Sridhar Hannenhalli

Source: PLoS Genetics, Vol 17, Iss 3, p e1009427 (2021)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1009427&type=printable; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/06509c22b6af47abb4ab47515d734856

Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells.

Authors: Andrey A Parkhitko, Arashdeep Singh, Sharon Hsieh, Yanhui Hu, Richard Binari, Christopher J Lord, Sridhar Hannenhalli, Colm J Ryan, Norbert Perrimon

Source: PLoS Genetics, Vol 17, Iss 2, p e1009354 (2021)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/5d7da79486b143a8a4352f9eed0f8e17

Genome‐wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy

Authors: Avinash Das Sahu, Joo S Lee, Zhiyong Wang, Gao Zhang, Ramiro Iglesias‐Bartolome, Tian Tian, Zhi Wei, Benchun Miao, Nishanth Ulhas Nair, Olga Ponomarova, Adam A Friedman, Arnaud Amzallag, Tabea Moll, Gyulnara Kasumova, Patricia Greninger, Regina K Egan, Leah J Damon, Dennie T Frederick, Livnat Jerby‐Arnon, Allon Wagner, Kuoyuan Cheng, Seung Gu Park, Welles Robinson, Kevin Gardner, Genevieve Boland, Sridhar Hannenhalli, Meenhard Herlyn, Cyril Benes, Keith Flaherty, Ji Luo, J Silvio Gutkind, Eytan Ruppin

Source: Molecular Systems Biology, Vol 15, Iss 3, Pp 1-21 (2019)

Subject Terms: drug combination, drug resistance, immunotherapy, synergy, Biology (General), QH301-705.5, Medicine (General), R5-920

File Description: electronic resource

Relation: https://doaj.org/toc/1744-4292

Access URL: https://doaj.org/article/3e0d9e37ccd24f31aaa5e8abf6557875

Analysis and correction of compositional bias in sparse sequencing count data

Authors: M. Senthil Kumar, Eric V. Slud, Kwame Okrah, Stephanie C. Hicks, Sridhar Hannenhalli, Héctor Corrada Bravo

Source: BMC Genomics, Vol 19, Iss 1, Pp 1-23 (2018)

Subject Terms: Compositional bias, Normalization, Empirical Bayes, Data integration, Count data, Metagenomics, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-018-5160-5; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/07388e3a527746048a5877c7081c3f38

Harnessing synthetic lethality to predict the response to cancer treatment

Authors: Joo Sang Lee, Avinash Das, Livnat Jerby-Arnon, Rand Arafeh, Noam Auslander, Matthew Davidson, Lynn McGarry, Daniel James, Arnaud Amzallag, Seung Gu Park, Kuoyuan Cheng, Welles Robinson, Dikla Atias, Chani Stossel, Ella Buzhor, Gidi Stein, Joshua J. Waterfall, Paul S. Meltzer, Talia Golan, Sridhar Hannenhalli, Eyal Gottlieb, Cyril H. Benes, Yardena Samuels, Emma Shanks, Eytan Ruppin

Source: Nature Communications, Vol 9, Iss 1, Pp 1-12 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/3a4240165a2541088f4b9ac5ea8738dc

Ligand dependent gene regulation by transient ERα clustered enhancers.

Authors: Bharath Saravanan, Deepanshu Soota, Zubairul Islam, Sudeshna Majumdar, Rajat Mann, Sweety Meel, Umer Farooq, Kaivalya Walavalkar, Srimonta Gayen, Anurag Kumar Singh, Sridhar Hannenhalli, Dimple Notani

Source: PLoS Genetics, Vol 16, Iss 1, p e1008516 (2020)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1008516&type=printable; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/5b925ab7e98540f4ba736bfe03e3d973