Research Output

2020

Alterations of the Rectal Microbiome Are Associated with the Development of Postoperative Ileus in Patients Undergoing Colorectal Surgery

Shogan, B. D., Chen, J., Duchalais, E., Collins, D., Chang, M., Krull, K., Krezalek, M. A., Larson, D. W., Walther-Antonio, M. R., Chia, N. & Nelson, H., Jan 1 2020, (Accepted/In press) In : Journal of Gastrointestinal Surgery.

Research output: Contribution to journalArticle

Comparison of methods to collect fecal samples for microbiome studies using whole-genome shotgun metagenomic sequencing

Byrd, D. A., Sinha, R., Hoffman, K. L., Chen, J., Hua, X., Shi, J., Chia, N., Petrosino, J. & Vogtmann, E., Jan 1 2020, In : mSphere. 5, 1, e00827.

Research output: Contribution to journalArticle

Comparison of three commercial tools for metagenomic shotgun sequencing analysis

Thoendel, M., Jeraldo, P., Greenwood-Quaintance, K. E., Yao, J., Chia, N., Hanssen, A. D., Abdel, M. P. & Patel, R., Jan 1 2020, In : Journal of clinical microbiology. 58, 3, e00981-19.

Research output: Contribution to journalArticle

Core genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow

the Antibacterial Resistance Leadership Group, May 2020, In : Diagnostic Microbiology and Infectious Disease. 97, 1, 114996.

Research output: Contribution to journalArticle

Fecal Metabolomic Signatures in Colorectal Adenoma Patients Are Associated with Gut Microbiota and Early Events of Colorectal Cancer Pathogenesis

Kim, M., Vogtmann, E., Ahlquist, D. A., Devens, M. E., Kisiel, J. B., Taylor, W. R., White, B. A., Hale, V. L., Sung, J., Chia, N., Sinha, R. & Chen, J., Feb 18 2020, In : mBio. 11, 1

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2019

Application of metagenomic shotgun sequencing to detect vector-borne pathogens in clinical blood samples

Vijayvargiya, P., Jeraldo, P. R., Thoendel, M. J., Greenwood-Quaintance, K. E., Garrigos, Z. E., Rizwan Sohail, M., Chia, N., Pritt, B. S. & Patel, R., Jan 1 2019, In : PloS one. 14, 10, e0222915.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Are early screening biomarkers for endometrial cancer needed to reduce health disparities?

Walther-Antonio, M. & Mariani, A., Apr 1 2019, In : American journal of obstetrics and gynecology. 220, 4, p. 408-409 2 p.

Research output: Contribution to journalLetter

1 Scopus citations

Autologous Gene and Cell Therapy Provides Safe and Long-Term Curative Therapy in A Large Pig Model of Hereditary Tyrosinemia Type 1

Hickey, R., Nicolas, C. T., Allen, K., Mao, S., Elgilani, F., Glorioso, J., Amiot, B., VanLith, C., Guthman, R., Du, Z., Chen, H., Harding, C. O., Kaiser, R. A., Nyberg, S. & Lillegard, J. B., Jan 1 2019, In : Cell Transplantation. 28, 1, p. 79-88 10 p.

Research output: Contribution to journalArticle

3 Scopus citations

Bacterial Single Cell Whole Transcriptome Amplification in Microfluidic Platform Shows Putative Gene Expression Heterogeneity

Liu, Y., Jeraldo, P., Jang, J. S., Eckloff, B., Jen, J. & Walther-Antonio, M., Jan 1 2019, In : Analytical Chemistry.

Research output: Contribution to journalArticle

Classic chronic pancreatitis is associated with prior acute pancreatitis in only 50% of patients in a large single-institution study

Hori, Y., Vege, S. S., Chari, S. T., Gleeson, F. C., Levy, M. J., Pearson, R. K., Petersen, B. T., Kendrick, M. L., Takahashi, N. M., Truty, M., Smoot, R. & Topazian, M., Jan 1 2019, In : Pancreatology.

Research output: Contribution to journalArticle

4 Scopus citations

Clinicopathological features and outcomes of fibrolamellar hepatocellular carcinoma

Chakrabarti, S., Tella, S. H., Kommalapati, A., Huffman, B. M., Yadav, S., Riaz, I. B., Goyal, G., Mody, K., Borad, M. J., Cleary, S., Smoot, R. & Mahipal, A., Jan 1 2019, In : Journal of Gastrointestinal Oncology. 10, 3, p. 554-561 8 p.

Research output: Contribution to journalArticle

4 Scopus citations

Comparison of oral collection methods for studies of microbiota

Vogtmann, E., Chen, J., Kibriya, M. G., Amir, A., Shi, J., Chen, Y., Islam, T., Eunes, M., Ahmed, A., Naher, J., Rahman, A., Barmon, B., Knight, R., Chia, N., Ahsan, H., Abnet, C. C. & Sinha, R., Jan 2019, In : Cancer Epidemiology Biomarkers and Prevention. 28, 1, p. 137-143 7 p.

Research output: Contribution to journalArticle

2 Scopus citations

Early-onset gastric cancer is a distinct disease with worrisome trends and oncogenic features

Bergquist, J. R., Leiting, J. L., Habermann, E. B., Cleary, S. P., Kendrick, M. L., Smoot, R., Nagorney, D. M., Truty, M. & Grotz, T. E., Jan 1 2019, In : Surgery (United States).

Research output: Contribution to journalArticle

Erratum: The Immune Landscape of Cancer (Immunity (2018) 48(4) (812–830.e14), (S1074761318301213), (10.1016/j.immuni.2018.03.023))

The Cancer Genome Atlas Research Network, Aug 20 2019, In : Immunity. 51, 2, p. 411-412 2 p.

Research output: Contribution to journalComment/debate

Open Access
3 Scopus citations

Evaluation of the cosmosid bioinformatics platform for prosthetic joint-associated sonicate fluid shotgun metagenomic data analysis

Yan, Q., Mi Wi, Y., Thoendel, M. J., Raval, Y. S., Greenwood-Quaintance, K. E., Abdel, M. P., Jeraldo, P. R., Chia, N. & Patela, R., Feb 2019, In : Journal of clinical microbiology. 57, 2, e01182.

Research output: Contribution to journalArticle

5 Scopus citations

Extreme value analysis of gut microbial alterations in colorectal cancer

Song, S. D., Jeraldo, P., Chen, J. & Chia, N., Mar 13 2019, In : Physical Review E. 99, 3, 032413.

Research output: Contribution to journalArticle

Gut microbiome meta-analysis reveals dysbiosis is independent of body mass index in predicting risk of obesity-associated CRC

Greathouse, K. L., White, J. R., Padgett, R. N., Perrotta, B. G., Jenkins, G. D., Chia, N. & Chen, J., Feb 1 2019, In : BMJ Open Gastroenterology. 6, 1, e000247.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Hepatotoxicity and Toxicology of In Vivo Lentiviral Vector Administration in Healthy and Liver-Injury Mouse Models

Kaiser, R. A., Nicolas, C. T., Allen, K. L., Chilton, J. A., Du, Z., Hickey, R. & Lillegard, J. B., Jun 1 2019, In : Human Gene Therapy Clinical Development. 30, 2, p. 57-66 10 p.

Research output: Contribution to journalArticle

Lack of correlation of virulence gene profiles of Staphylococcus aureus bacteremia isolates with mortality

Park, K. H., Greenwood-Quaintance, K. E., Cunningham, S. A., Rajagopalan, G., Chia, N. D., Jeraldo, P. R., Mandrekar, J. & Patel, R., Aug 1 2019, In : Microbial Pathogenesis. 133, 103543.

Research output: Contribution to journalArticle

2 Scopus citations

Late-life time-restricted feeding and exercise differentially alter healthspan in obesity

Schafer, M. J., Mazula, D. L., Brown, A. K., White, T. A., Atkinson, E., Pearsall, V. M., Aversa, Z., Verzosa, G. C., Smith, L. A., Matveyenko, A., Miller, J. D. & LeBrasseur, N. K., Aug 2019, In : Aging Cell. 18, 4, e12966.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Length-independent telomere damage drives post-mitotic cardiomyocyte senescence

Anderson, R., Lagnado, A., Maggiorani, D., Walaszczyk, A., Dookun, E., Chapman, J., Birch, J., Salmonowicz, H., Ogrodnik, M., Jurk, D., Proctor, C., Correia-Melo, C., Victorelli, S., Fielder, E., Berlinguer-Palmini, R., Owens, A., Greaves, L. C., Kolsky, K. L., Parini, A., Douin-Echinard, V. & 14 others, LeBrasseur, N. K., Arthur, H. M., Tual-Chalot, S., Schafer, M. J., Roos, C. M., Miller, J. D., Robertson, N., Mann, J., Adams, P. D., Tchkonia, T., Kirkland, J. L., Mialet-Perez, J., Richardson, G. D. & Passos, J. F., Mar 1 2019, In : EMBO Journal. 38, 5, e100492.

Research output: Contribution to journalArticle

Open Access
32 Scopus citations

Neoadjuvant vs. adjuvant chemotherapy for cholangiocarcinoma: A propensity score matched analysis

Yadav, S., Xie, H., Bin-Riaz, I., Sharma, P., Durani, U., Goyal, G., Borah, B. J., Borad, M. J., Smoot, R., Roberts, L. R., Go, R. S., Mc Williams, R. R. & Mahipal, A., Jan 1 2019, In : European Journal of Surgical Oncology.

Research output: Contribution to journalArticle

5 Scopus citations

Network Tomography for Understanding Phenotypic Presentations in Aortic Stenosis

Casaclang-Verzosa, G., Shrestha, S., Khalil, M. J., Cho, J. S., Tokodi, M., Balla, S., Alkhouli, M., Badhwar, V., Narula, J., Miller, J. D. & Sengupta, P. P., Feb 1 2019, In : JACC: Cardiovascular Imaging. 12, 2, p. 236-248 13 p.

Research output: Contribution to journalArticle

9 Scopus citations

Patient-Derived Xenografts Can Be Reliably Generated from Patient Clinical Biopsy Specimens

Hernandez, M. C., Bergquist, J. R., Leiting, J. L., Ivanics, T., Yang, L., Smoot, R., Nagorney, D. M. & Truty, M., Jan 1 2019, In : Journal of Gastrointestinal Surgery.

Research output: Contribution to journalArticle

Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome)

Walsh, D. M., Hokenstad, A. N., Chen, J., Sung, J., Jenkins, G. D., Chia, N., Nelson, H., Mariani, A. & Walther-Antonio, M. R. S., Dec 1 2019, In : Scientific reports. 9, 1, 19213.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Prediction and Inference With Missing Data in Patient Alert Systems

Storlie, C., Therneau, T. M., Carter, R. E., Chia, N. D., Bergquist, J. R., Huddleston, J. M. & Romero-Brufau, S., Jan 1 2019, In : Journal of the American Statistical Association.

Research output: Contribution to journalArticle

Re: Geobiology reveals how human kidney stones dissolve in vivo

Sivaguru, M., Saw, J. J., Williams, J. C., Lieske, J. C., Krambeck, A. E., Romero, M. F., Chia, N., Schwaderer, A. L., Alcalde, R. E., Bruce, W. J., Wildman, D. E., Fried, G. A., Werth, C. J., Reeder, R. J., Yau, P. M., Sanford, R. A. & Fouke, B. W., Apr 1 2019, In : Journal of Urology. 201, 4, p. 663-664 2 p.

Research output: Contribution to journalComment/debate

Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations

Byrd, D. A., Chen, J., Vogtmann, E., Hullings, A., Song, S. J., Amir, A., Kibriya, M. G., Ahsan, H., Chen, Y., Nelson, H., Knight, R., Shi, J., Chia, N. & Sinha, R., Jan 1 2019, In : PloS one. 14, 11, e0224757.

Research output: Contribution to journalArticle

Open Access

Safety, Diagnostic Accuracy, and Effects of Endoscopic Ultrasound Fine-Needle Aspiration on Detection of Extravascular Migratory Metastases

Rustagi, T., Gleeson, F. C., Chari, S. T., Lehrke, H. D., Takahashi, N., Malikowski, T. M., Abu Dayyeh, B. K., Chandrasekhara, V., Iyer, P. G., Kendrick, M. L., Pearson, R. K., Petersen, B. T., Rajan, E., Smoot, R. L., Storm, A. C., Topazian, M. D., Truty, M. J., Vege, S. S., Wang, K. K. & Levy, M. J., Nov 2019, In : Clinical Gastroenterology and Hepatology. 17, 12, p. 2533-2540.e1

Research output: Contribution to journalArticle

3 Scopus citations

Smooth muscle brain-derived neurotrophic factor contributes to airway hyperreactivity in a mouse model of allergic asthma

Britt, R. J., Thompson, M. A., Wicher, S. A., Manlove, L. J., Roesler, A., Fang, Y. H., Roos, C., Smith, L., Miller, J. D., Pabelick, C. M. & Prakash, Y. S., Feb 1 2019, In : FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 33, 2, p. 3024-3034 11 p.

Research output: Contribution to journalArticle

6 Scopus citations

Survival benefit of neoadjuvant therapy in patients with non-metastatic pancreatic ductal adenocarcinoma: A propensity matching and intention-to-treat analysis

Sugimoto, M., Takahashi, N. M., Farnell, M. B., Smyrk, T. C., Truty, M., Nagorney, D. M., Smoot, R., Chari, S. T., Carter, R. E. & Kendrick, M. L., Jan 1 2019, (Accepted/In press) In : Journal of Surgical Oncology.

Research output: Contribution to journalArticle

2 Scopus citations

Targeting senescent cells alleviates obesity-induced metabolic dysfunction

Palmer, A. K., Xu, M., Zhu, Y., Pirtskhalava, T., Weivoda, M. M., Hachfeld, C. M., Prata, L. G., van Dijk, T. H., Verkade, E., Casaclang-Verzosa, G., Johnson, K. O., Cubro, H., Doornebal, E. J., Ogrodnik, M., Jurk, D., Jensen, M. D., Chini, E. N., Miller, J. D., Matveyenko, A., Stout, M. B. & 13 others, Schafer, M. J., White, T. A., Hickson, L. T. J., Demaria, M., Garovic, V., Grande, J., Arriaga, E. A., Kuipers, F., von Zglinicki, T., LeBrasseur, N. K., Campisi, J., Tchkonia, T. & Kirkland, J. L., Jun 2019, In : Aging Cell. 18, 3, e12950.

Research output: Contribution to journalArticle

Open Access
33 Scopus citations
Open Access
3 Scopus citations

YAP and the Hippo pathway in cholangiocarcinoma

Sugihara, T., Isomoto, H., Gores, G. & Smoot, R., Jun 5 2019, In : Journal of gastroenterology. 54, 6, p. 485-491 7 p.

Research output: Contribution to journalReview article

Open Access
2 Scopus citations
2018

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer cell. 33, 4, p. 690-705.e9

Research output: Contribution to journalArticle

93 Scopus citations

A Curative-Intent Trimodality Approach for Isolated Abdominal Nodal Metastases in Metastatic Colorectal Cancer: Update of a Single-Institutional Experience

Johnson, B., Jin, Z., Haddock, M., Hallemeier, C., Martenson, J. A., Smoot, R., Larson, D., Dozois, E., Nagorney, D. M. & Grothey, A. F., Jun 1 2018, In : Oncologist. 23, 6, p. 679-685 7 p.

Research output: Contribution to journalArticle

1 Scopus citations

Adjuvant systemic therapy after resection of node positive gallbladder cancer: Time for a well-designed trial? (Results of a US-national retrospective cohort study)

Bergquist, J. R., Shah, H. N., Habermann, E. B., Hernandez, M. C., Ivanics, T., Kendrick, M. L., Smoot, R. L., Nagorney, D. M., Borad, M. J., McWilliams, R. R. & Truty, M. J., Apr 2018, In : International Journal of Surgery. 52, p. 171-179 9 p.

Research output: Contribution to journalArticle

11 Scopus citations

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 400-416.e11

Research output: Contribution to journalArticle

228 Scopus citations

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 386-399.e12

Research output: Contribution to journalArticle

43 Scopus citations

A Potent and Specific CD38 Inhibitor Ameliorates Age-Related Metabolic Dysfunction by Reversing Tissue NAD+ Decline

Tarragó, M. G., Chini, C. C. S., Kanamori, K. S., Warner, G. M., Caride, A., de Oliveira, G. C., Rud, M., Samani, A., Hein, K. Z., Huang, R., Jurk, D., Cho, D. S., Boslett, J. J., Miller, J. D., Zweier, J. L., Passos, J., Doles, J., Becherer, D. J. & Chini, E. N., Jan 1 2018, (Accepted/In press) In : Cell Metabolism.

Research output: Contribution to journalArticle

40 Scopus citations

A Rare Case of Recurrent Small Bowel Obstructions

Kamboj, A. K., Stroh, G. R., Smoot, R. & Prichard, D. O., Nov 1 2018, In : Gastroenterology. 155, 5, p. e5-e7

Research output: Contribution to journalComment/debate

A Tale of Three Tails and a Cystic Lesion: A Rare Cause of Recurrent Acute Pancreatitis

Nagpal, S. J. S., Levy, M. J., Takahashi, N., Kendrick, M. L., Smyrk, T. C., Pearson, R. K. & Majumder, S., Jul 2 2018, (Accepted/In press) In : American Journal of Gastroenterology. p. 1-2 2 p.

Research output: Contribution to journalArticle

Ca2+ Entry Through Reverse Mode Na+/Ca2+ Exchanger Contributes to Store Operated Channel-Mediated Neointima Formation After Arterial Injury

Liu, B., Zhang, B., Huang, S., Yang, L., Roos, C. M., Thompson, M. A., Prakash, Y. S., Zang, J., Miller, J. D. & Guo, R., Jan 1 2018, (Accepted/In press) In : Canadian Journal of Cardiology.

Research output: Contribution to journalArticle

2 Scopus citations

Case for a role of the microbiome in gynecologic cancers: Clinician's perspective

Mert, I., Walther-Antonio, M. & Mariani, A., Sep 1 2018, In : Journal of Obstetrics and Gynaecology Research. 44, 9, p. 1693-1704 12 p.

Research output: Contribution to journalReview article

8 Scopus citations

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

The Cancer Genome Atlas Network, Apr 5 2018, In : Cell. 173, 2, p. 291-304.e6

Research output: Contribution to journalArticle

237 Scopus citations

Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea

Battaglioli, E. J., Hale, V. L., Chen, J., Jeraldo, P., Ruiz-Mojica, C., Schmidt, B. A., Rekdal, V. M., Till, L. M., Huq, L., Smits, S. A., Moor, W. J., Jones-Hall, Y., Smyrk, T. C., Khanna, S., Pardi, D. S., Grover, M., Patel, R., Chia, N. D., Nelson, H., Sonnenburg, J. L. & 2 others, Farrugia, G. & Kashyap, P. C., Oct 24 2018, In : Science Translational Medicine. 10, 464, eaam7019.

Research output: Contribution to journalArticle

14 Scopus citations

Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens

Masters, T. L., Hilker, C. A., Jeraldo, P. R., Bhagwate, A. V., Greenwood-Quaintance, K. E., Eckloff, B. W., Chia, N. D., Hanssen, A. D., Abdel, M., Yao, J. Z., Jen, J. & Patel, R., Nov 1 2018, In : Journal of Microbiological Methods. 154, p. 55-62 8 p.

Research output: Contribution to journalArticle

2 Scopus citations

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer cell. 33, 4, p. 721-735.e8

Research output: Contribution to journalArticle

66 Scopus citations