Real-world clinical multi-omics analyses reveal bifurcation of ER-independent and ER-dependent drug resistance to CDK4/6 inhibitors

Authors: Zhengyan Kan, Ji Wen, Vinicius Bonato, Jennifer Webster, Wenjing Yang, Vladimir Ivanov, Kimberly Hyunjung Kim, Whijae Roh, Chaoting Liu, Xinmeng Jasmine Mu, Jennifer Lapira-Miller, Jon Oyer, Todd VanArsdale, Paul A. Rejto, Jadwiga Bienkowska

Source: Nature Communications, Vol 16, Iss 1, Pp 1-19 (2025)

Subject Terms: Science

File Description: electronic resource

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

Access URL: https://doaj.org/article/a386a891e600428c99ba0e1e1867b722

Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Authors: Yeon Hee Park, Seock-Ah Im, Kyunghee Park, Ji Wen, Kyung-Hun Lee, Yoon-La Choi, Won-Chul Lee, Ahrum Min, Vinicius Bonato, Seri Park, Sripad Ram, Dae-Won Lee, Ji-Yeon Kim, Su Kyeong Lee, Won-Woo Lee, Jisook Lee, Miso Kim, Hyun Seon Kim, Scott L. Weinrich, Han Suk Ryu, Tae Yong Kim, Stephen Dann, Yu-Jin Kim, Diane R. Fernandez, Jiwon Koh, Shuoguo Wang, Song Yi Park, Shibing Deng, Eric Powell, Rupesh Kanchi Ravi, Jadwiga Bienkowska, Paul A. Rejto, Woong-Yang Park, Zhengyan Kan

Source: Genome Medicine, Vol 15, Iss 1, Pp 1-18 (2023)

Subject Terms: Advanced breast cancer, Drug resistance, Genomic profile, Gene expression profiling, Palbociclib, Homologous recombination repair deficiengy (HRD), Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/e43bea5e36154033b3975c0ba6d40d38

Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation

Authors: Kyle Ford, Brenton P. Munson, Samson H. Fong, Rebecca Panwala, Wai Keung Chu, Joseph Rainaldi, Nongluk Plongthongkum, Vinayagam Arunachalam, Jarek Kostrowicki, Dario Meluzzi, Jason F. Kreisberg, Kristen Jensen-Pergakes, Todd VanArsdale, Thomas Paul, Pablo Tamayo, Kun Zhang, Jadwiga Bienkowska, Prashant Mali, Trey Ideker

Source: Scientific Reports, Vol 13, Iss 1, Pp 1-20 (2023)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/fcd5b895626948aba19a440f77fb4bf1

Chemotherapy induces dynamic immune responses in breast cancers that impact treatment outcome

Authors: Yeon Hee Park, Samir Lal, Jeong Eon Lee, Yoon-La Choi, Ji Wen, Sripad Ram, Ying Ding, Soo-Hyeon Lee, Eric Powell, Se Kyung Lee, Jong Han Yu, Keith A. Ching, Jae-Yong Nam, Seok Won Kim, Seok Jin Nam, Ji-Yeon Kim, Soo Youn Cho, Seri Park, Jinho Kim, Soohyn Hwang, Yu Jin Kim, Vinicius Bonato, Diane Fernandez, Shibing Deng, Shuoguo Wang, Hyuntae Shin, Eun-Suk Kang, Woong-Yang Park, Paul A. Rejto, Jadwiga Bienkowska, Zhengyan Kan

Source: Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)

Subject Terms: Science

File Description: electronic resource

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

Access URL: https://doaj.org/article/d34ef5fb3216481893b451cd685dff30

TNER: a novel background error suppression method for mutation detection in circulating tumor DNA

Authors: Shibing Deng, Maruja Lira, Donghui Huang, Kai Wang, Crystal Valdez, Jennifer Kinong, Paul A. Rejto, Jadwiga Bienkowska, James Hardwick, Tao Xie

Source: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-7 (2018)

Subject Terms: ctDNA, Next-generation sequencing, Variant calling, Error suppression, Single-nucleotide variant, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-018-2428-3; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/2a29b2d994f64e8d83cd250baf282277

Model to improve specificity for identification of clinically-relevant expanded T cells in peripheral blood.

Authors: Julie Rytlewski, Shibing Deng, Tao Xie, Craig Davis, Harlan Robins, Erik Yusko, Jadwiga Bienkowska

Source: PLoS ONE, Vol 14, Iss 3, p e0213684 (2019)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/8be2100aa85f4227b39f285fd1408e16

Lymphotoxin-LIGHT pathway regulates the interferon signature in rheumatoid arthritis.

Authors: Jadwiga Bienkowska, Norm Allaire, Alice Thai, Jaya Goyal, Tatiana Plavina, Ajay Nirula, Megan Weaver, Charlotte Newman, Michelle Petri, Evan Beckman, Jeffrey L Browning

Source: PLoS ONE, Vol 9, Iss 11, p e112545 (2014)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4236099?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/5aee8698067a47a9b3e3c6ff98a387d3

Causal modeling using network ensemble simulations of genetic and gene expression data predicts genes involved in rheumatoid arthritis.

Authors: Heming Xing, Paul D McDonagh, Jadwiga Bienkowska, Tanya Cashorali, Karl Runge, Robert E Miller, Dave Decaprio, Bruce Church, Ronenn Roubenoff, Iya G Khalil, John Carulli

Source: PLoS Computational Biology, Vol 7, Iss 3, p e1001105 (2011)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3053315?pdf=render; https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/d80bf7a0804f4a0aad4ebd11b36730c2

Optimal contact map alignment of protein-protein interfaces.

Authors: Vinay Pulim, Bonnie Berger, Jadwiga Bienkowska

Source: Bioinformatics; Oct2008, Vol. 24 Issue 20, p2324-2324, 1p