Department of Pathology & Immunology

2022

Infantile Fibrosarcoma and Other Spindle Cell Neoplasms of Infancy. A Review of Morphologically Overlapping yet Molecularly Distinctive Entities

Jabbari, S., Salari, B., He, M. & Dehner, L. P., 2022, In: Fetal and Pediatric Pathology. 41, 6, p. 996-1014 19 p.

Research output: Contribution to journal › Review article › peer-review

Liquid Phase Partitioning in Virus Replication: Observations and Opportunities

Wu, C., Holehouse, A. S., Leung, D. W., Amarasinghe, G. K. & Dutch, R. E., 2022, In: Annual Review of Virology. 9, p. 285-306 22 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

13 Scopus citations

Management of pouch neoplasia: consensus guidelines from the International Ileal Pouch Consortium

Kiran, R. P., Kochhar, G. S., Kariv, R., Rex, D. K., Sugita, A., Rubin, D. T., Navaneethan, U., Hull, T. L., Ko, H. M., Liu, X., Kachnic, L. A., Strong, S., Iacucci, M., Bemelman, W., Fleshner, P., Safyan, R. A., Kotze, P. G., D'Hoore, A., Faiz, O., Lo, S., & 21 othersAshburn, J. H., Spinelli, A., Bernstein, C. N., Kane, S. V., Cross, R. K., Schairer, J., McCormick, J. T., Farraye, F. A., Chang, S., Scherl, E. J., Schwartz, D. A., Bruining, D. H., Philpott, J., Bentley-Hibbert, S., Tarabar, D., El-Hachem, S., Sandborn, W. J., Silverberg, M. S., Pardi, D. S., Church, J. M. & Shen, B., Sep 2022, In: The Lancet Gastroenterology and Hepatology. 7, 9, p. 871-893 23 p.

Research output: Contribution to journal › Review article › peer-review

3 Scopus citations

Microglia states and nomenclature: A field at its crossroads

Paolicelli, R. C., Sierra, A., Stevens, B., Tremblay, M. E., Aguzzi, A., Ajami, B., Amit, I., Audinat, E., Bechmann, I., Bennett, M., Bennett, F., Bessis, A., Biber, K., Bilbo, S., Blurton-Jones, M., Boddeke, E., Brites, D., Brône, B., Brown, G. C., Butovsky, O., & 76 othersCarson, M. J., Castellano, B., Colonna, M., Cowley, S. A., Cunningham, C., Davalos, D., De Jager, P. L., de Strooper, B., Denes, A., Eggen, B. J. L., Eyo, U., Galea, E., Garel, S., Ginhoux, F., Glass, C. K., Gokce, O., Gomez-Nicola, D., González, B., Gordon, S., Graeber, M. B., Greenhalgh, A. D., Gressens, P., Greter, M., Gutmann, D. H., Haass, C., Heneka, M. T., Heppner, F. L., Hong, S., Hume, D. A., Jung, S., Kettenmann, H., Kipnis, J., Koyama, R., Lemke, G., Lynch, M., Majewska, A., Malcangio, M., Malm, T., Mancuso, R., Masuda, T., Matteoli, M., McColl, B. W., Miron, V. E., Molofsky, A. V., Monje, M., Mracsko, E., Nadjar, A., Neher, J. J., Neniskyte, U., Neumann, H., Noda, M., Peng, B., Peri, F., Perry, V. H., Popovich, P. G., Pridans, C., Priller, J., Prinz, M., Ragozzino, D., Ransohoff, R. M., Salter, M. W., Schaefer, A., Schafer, D. P., Schwartz, M., Simons, M., Smith, C. J., Streit, W. J., Tay, T. L., Tsai, L. H., Verkhratsky, A., von Bernhardi, R., Wake, H., Wittamer, V., Wolf, S. A., Wu, L. J. & Wyss-Coray, T., Nov 2 2022, In: Neuron. 110, 21, p. 3458-3483 26 p.

Research output: Contribution to journal › Review article › peer-review

193 Scopus citations

Molecular Diagnosis of Pneumonia (Including Multiplex Panels)

Buchan, B. W., Armand-Lefevre, L. & Anderson, N., Jan 1 2022, In: Clinical chemistry. 68, 1, p. 59-68 10 p.

Research output: Contribution to journal › Review article › peer-review

4 Scopus citations

Navigating Critical Challenges Associated with Immunopeptidomics-Based Detection of Proteasomal Spliced Peptide Candidates

Lichti, C. F., Vigneron, N., Clauser, K. R., Van den Eynde, B. J. & Bassani-Sternberg, M., Mar 2022, In: Cancer immunology research. 10, 3, p. 275-284 10 p.

Research output: Contribution to journal › Review article › peer-review

9 Scopus citations

Pancreatic neuroendocrine neoplasms: a 2022 update for radiologists

Galgano, S. J., Morani, A. C., Gopireddy, D. R., Sharbidre, K., Bates, D. D. B., Goenka, A. H., Arif-Tiwari, H., Itani, M., Iravani, A., Javadi, S., Faria, S., Lall, C., Bergsland, E., Verma, S., Francis, I. R., Halperin, D. M., Chatterjee, D., Bhosale, P. & Yano, M., Dec 2022, In: Abdominal Radiology. 47, 12, p. 3962-3970 9 p.

Research output: Contribution to journal › Review article › peer-review

1 Scopus citations

Pulse/hyaline ring granuloma revisited: etiologic role of seed-derived storage cells

Rosen, Y., Garcia, P. M. & Navale, P., Mar 2022, In: Virchows Archiv. 480, 3, p. 499-508 10 p.

Research output: Contribution to journal › Review article › peer-review

4 Scopus citations

Spontaneous and induced adaptive immune responses in Alzheimer's disease: new insights into old observations

Chen, Y. & Colonna, M., Aug 2022, In: Current Opinion in Immunology. 77, 102233.

Research output: Contribution to journal › Review article › peer-review

2 Scopus citations

Technological features of blast identification in the cerebrospinal fluid: A systematic review of flow cytometry and laboratory haematology methods

Frater, J. L., Shirai, C. L. & Brestoff, J. R., Sep 2022, In: International Journal of Laboratory Hematology. 44, S1, p. 45-53 9 p.

Research output: Contribution to journal › Review article › peer-review

1 Scopus citations

The enigma of picobirnaviruses: viruses of animals, fungi, or bacteria?

Wang, D., Jun 2022, In: Current Opinion in Virology. 54, 101232.

Research output: Contribution to journal › Review article › peer-review

Open Access

6 Scopus citations

The germinal centre B cell response to SARS-CoV-2

Laidlaw, B. J. & Ellebedy, A. H., Jan 2022, In: Nature Reviews Immunology. 22, 1, p. 7-18 12 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

83 Scopus citations

The potential of artificial intelligence-based applications in kidney pathology

Bullow, R. D., Marsh, J. N., Swamidass, S. J., Gaut, J. P. & Boor, P., May 1 2022, In: Current Opinion in Nephrology and Hypertension. 31, 3, p. 251-257 7 p.

Research output: Contribution to journal › Review article › peer-review

1 Scopus citations

The resistance within: Antibiotic disruption of the gut microbiome and resistome dynamics in infancy

Thänert, R., Sawhney, S. S., Schwartz, D. J. & Dantas, G., May 11 2022, In: Cell Host and Microbe. 30, 5, p. 675-683 9 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

9 Scopus citations

Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group

Jean, S., Wallace, M. J., Dantas, G. & Burnham, C. A. D., Sep 21 2022, In: Journal of clinical microbiology. 60, 9, p. e0236120

Research output: Contribution to journal › Review article › peer-review

4 Scopus citations

Treatment of pouchitis, Crohn's disease, cuffitis, and other inflammatory disorders of the pouch: consensus guidelines from the International Ileal Pouch Consortium

Shen, B., Kochhar, G. S., Rubin, D. T., Kane, S. V., Navaneethan, U., Bernstein, C. N., Cross, R. K., Sugita, A., Schairer, J., Kiran, R. P., Fleshner, P., McCormick, J. T., D'Hoore, A., Shah, S. A., Farraye, F. A., Kariv, R., Liu, X., Rosh, J., Chang, S., Scherl, E., & 17 othersSchwartz, D. A., Kotze, P. G., Bruining, D. H., Philpott, J., Abraham, B., Segal, J., Sedano, R., Kayal, M., Bentley-Hibbert, S., Tarabar, D., El-Hachem, S., Sehgal, P., Picoraro, J. A., Vermeire, S., Sandborn, W. J., Silverberg, M. S. & Pardi, D. S., Jan 2022, In: The Lancet Gastroenterology and Hepatology. 7, 1, p. 69-95 27 p.

Research output: Contribution to journal › Review article › peer-review

18 Scopus citations

TREM2 dependent and independent functions of microglia in Alzheimer’s disease

Hou, J., Chen, Y., Grajales-Reyes, G. & Colonna, M., Dec 2022, In: Molecular neurodegeneration. 17, 1, 84.

Research output: Contribution to journal › Review article › peer-review

Open Access

7 Scopus citations

Tumor microenvironment heterogeneity an important mediator of prostate cancer progression and therapeutic resistance

Ge, R., Wang, Z. & Cheng, L., Dec 2022, In: npj Precision Oncology. 6, 1, 31.

Research output: Contribution to journal › Review article › peer-review

Open Access

21 Scopus citations

Tumor microenvironment in pancreatic ductal adenocarcinoma: Implications in immunotherapy

Smith, C., Zheng, W., Dong, J., Wang, Y., Lai, J., Liu, X. & Yin, F., Jul 21 2022, In: World Journal of Gastroenterology. 28, 27, p. 3297-3313 17 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

3 Scopus citations

Using the Alzheimer's Disease Neuroimaging Initiative to improve early detection, diagnosis, and treatment of Alzheimer's disease

Alzheimer’s Disease Neuroimaging Initiative, Apr 2022, In: Alzheimer's and Dementia. 18, 4, p. 824-857 34 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

27 Scopus citations

2021

A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows: A Report of the Association for Molecular Pathology Training and Education Committee

Rosenbaum, J. N., Berry, A. B., Church, A. J., Crooks, K., Gagan, J. R., López-Terrada, D., Pfeifer, J. D., Rennert, H., Schrijver, I., Snow, A. N., Wu, D. & Ewalt, M. D., Oct 2021, In: Journal of Molecular Diagnostics. 23, 10, p. 1218-1240 23 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

2 Scopus citations

Acute kidney injury pathology and pathophysiology: A retrospective review

Gaut, J. P. & Liapis, H., Feb 1 2021, In: Clinical Kidney Journal. 14, 2, p. 526-536 11 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

29 Scopus citations

A long road/read to rapid high-resolution HLA typing: The nanopore perspective

Liu, C., Jul 2021, In: Human Immunology. 82, 7, p. 488-495 8 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

19 Scopus citations

A microbiota-directed food intervention for undernourished children

Chen, R. Y., Mostafa, I., Hibberd, M. C., Das, S., Mahfuz, M., Naila, N. N., Munirul Islam, M., Huq, S., Ashraful Alam, M., Zaman, M. U., Raman, A. S., Webber, D., Zhou, C., Sundaresan, V., Ahsan, K., Meier, M. F., Barratt, M. J., Ahmed, T. & Gordon, J. I., Apr 22 2021, In: New England Journal of Medicine. 384, 16, p. 1517-1528 12 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

109 Scopus citations

Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria

Blake, K. S., Choi, J. H. & Dantas, G., Mar 2021, In: Cellular and Molecular Life Sciences. 78, 6, p. 2585-2606 22 p.

Research output: Contribution to journal › Review article › peer-review

14 Scopus citations

Associating SARS-CoV-2 Serological Assays with Protection: Where the Field Stands

Tang, M. S. & Farnsworth, C. W., May 1 2021, In: Clinical chemistry. 67, 5, p. 707-709 3 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

5 Scopus citations

Breast neuroendocrine neoplasms: practical applications and continuing challenges in the era of the 5th edition of the WHO classification of breast tumours

Bean, G. R. & Lin, C. Y., Apr 2021, In: Diagnostic Histopathology. 27, 4, p. 139-147 9 p.

Research output: Contribution to journal › Review article › peer-review

1 Scopus citations

Cancer of the Vulva: A Review

Michalski, B. M., Pfeifer, J. D., Mutch, D. & Council, M. L., Feb 1 2021, In: Dermatologic Surgery. 47, 2, p. 174-183 10 p.

Research output: Contribution to journal › Review article › peer-review

6 Scopus citations

Cellular plasticity at the nexus of development and disease

Spatz, L. B., Jin, R. U. & Mills, J. C., Feb 2021, In: Development (Cambridge). 148, 3, dev197392.

Research output: Contribution to journal › Review article › peer-review

Open Access

5 Scopus citations

Cerebrovascular Anomalies: Perspectives from Immunology and Cerebrospinal Fluid Flow

Rustenhoven, J., Tanumihardja, C. & Kipnis, J., Jun 25 2021, In: Circulation research. 129, 1, p. 174-194 21 p.

Research output: Contribution to journal › Review article › peer-review

6 Scopus citations

Circulating tumor cells from enumeration to analysis: Current challenges and future opportunities

Yang, Y. P., Giret, T. M. & Cote, R. J., Jun 1 2021, In: Cancers. 13, 11, 2723.

Research output: Contribution to journal › Review article › peer-review

Open Access

20 Scopus citations

Convalescent Plasma Therapy for COVID-19: A Graphical Mosaic of the Worldwide Evidence

Klassen, S. A., Senefeld, J. W., Senese, K. A., Johnson, P. W., Wiggins, C. C., Baker, S. E., van Helmond, N., Bruno, K. A., Pirofski, L. A., Shoham, S., Grossman, B. J., Henderson, J. P., Wright, R. S., Fairweather, D. L., Paneth, N. S., Carter, R. E., Casadevall, A. & Joyner, M. J., Jun 7 2021, In: Frontiers in Medicine. 8, 684151.

Research output: Contribution to journal › Review article › peer-review

Open Access

39 Scopus citations

COVID-19 convalescent plasma: Interim recommendations from the AABB

Cohn, C. S., Estcourt, L., Grossman, B. J., Pagano, M. B., Allen, E. S., Bloch, E. M., Casadevall, A., Devine, D. V., Dunbar, N. M., Foroutan, F., Gniadek, T. J., Goel, R., Gorlin, J., Joyner, M. J., Metcalf, R. A., Raval, J. S., Rice, T. W., Shaz, B. H., Vassallo, R. R., Winters, J. L., & 2 othersBeaudoin, G. & Tobian, A. A. R., Apr 2021, In: Transfusion. 61, 4, p. 1313-1323 11 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

31 Scopus citations

Creating Affirmative and Inclusive Practices When Providing Genetic and Genomic Diagnostic and Research Services to Gender-Expansive and Transgender Patients

Theisen, J. G. & Amarillo, I. E., Jan 1 2021, In: Journal of Applied Laboratory Medicine. 6, 1, p. 142-154 13 p.

Research output: Contribution to journal › Review article › peer-review

3 Scopus citations

Dendritic cells: The first step

Randolph, G. J., 2021, In: Journal of Experimental Medicine. 218, 3, jem.20202077.

Research output: Contribution to journal › Review article › peer-review

Open Access

6 Scopus citations

Diagnosis and classification of ileal pouch disorders: consensus guidelines from the International Ileal Pouch Consortium

Shen, B., Kochhar, G. S., Kariv, R., Liu, X., Navaneethan, U., Rubin, D. T., Cross, R. K., Sugita, A., D'Hoore, A., Schairer, J., Farraye, F. A., Kiran, R. P., Fleshner, P., Rosh, J., Shah, S. A., Chang, S., Scherl, E., Pardi, D. S., Schwartz, D. A., Kotze, P. G., & 17 othersBruining, D. H., Kane, S. V., Philpott, J., Abraham, B., Segal, J., Sedano, R., Kayal, M., Bentley-Hibbert, S., Tarabar, D., El-Hachem, S., Sehgal, P., McCormick, J. T., Picoraro, J. A., Silverberg, M. S., Bernstein, C. N., Sandborn, W. J. & Vermeire, S., Oct 2021, In: The Lancet Gastroenterology and Hepatology. 6, 10, p. 826-849 24 p.

Research output: Contribution to journal › Review article › peer-review

39 Scopus citations

Endoscopic evaluation of surgically altered bowel in inflammatory bowel disease: a consensus guideline from the Global Interventional Inflammatory Bowel Disease Group

Shen, B., Kochhar, G. S., Navaneethan, U., Cross, R. K., Farraye, F. A., Iacucci, M., Schwartz, D. A., Gonzalez-Lama, Y., Schairer, J., Kiran, R. P., Kotze, P. G., Kobayashi, T., Bortlik, M., Liu, X., Levy, A. N., González Suárez, B., Tang, S. J., Coelho-Prabhu, N., Lukas, M., Bruining, D. H., & 14 othersEl-Hachem, S., Charles, R. J., Chen, Y., Sood, A., Mao, R., Loras, C., Dulai, P. S., Picoraro, J. A., Chiorean, M., Lukas, M., Shergill, A., Silverberg, M. S., Sandborn, W. J. & Bernstein, C. N., Jun 2021, In: The Lancet Gastroenterology and Hepatology. 6, 6, p. 482-497 16 p.

Research output: Contribution to journal › Review article › peer-review

22 Scopus citations

Genetic models of human and mouse dendritic cell development and function

Anderson, D. A., Dutertre, C. A., Ginhoux, F. & Murphy, K. M., Feb 2021, In: Nature Reviews Immunology. 21, 2, p. 101-115 15 p.

Research output: Contribution to journal › Review article › peer-review

119 Scopus citations

Hypoxia and HIF-1 as key regulators of gut microbiota and host interactions

Pral, L. P., Fachi, J. L., Corrêa, R. O., Colonna, M. & Vinolo, M. A. R., Jul 2021, In: Trends in Immunology. 42, 7, p. 604-621 18 p.

Research output: Contribution to journal › Review article › peer-review

28 Scopus citations

IgG4-Related Disease of the Skull and Skull Base–A Systematic Review and Report of Two Cases

Cler, S. J., Sharifai, N., Baker, B., Dowling, J. L., Pipkorn, P., Yaeger, L., Clifford, D. B., Dahiya, S. & Chicoine, M. R., Jun 2021, In: World neurosurgery. 150, p. 179-196.e1

Research output: Contribution to journal › Review article › peer-review

9 Scopus citations

INSM1 Is Less Sensitive but More Specific Than Synaptophysin in Gynecologic High-grade Neuroendocrine Carcinomas: An Immunohistochemical Study of 75 Cases with Specificity Test and Literature Review

Zou, Q., Zhang, L., Cheng, Z., Guo, X. & Cao, D., Feb 2021, In: American Journal of Surgical Pathology. 45, 2, p. 147-159 13 p.

Research output: Contribution to journal › Review article › peer-review

10 Scopus citations

Intracranial metastasis from a malignant peripheral nerve sheath tumor in a patient with neurofibromatosis type 1: A case study and literature review

Griffin, S., Witt, M. C., El Tecle, N., Prim, M., Hockman, J., Schwetye, K. E. & Pierson, M. J., Apr 2021, In: Clinical Neurology and Neurosurgery. 203, 106540.

Research output: Contribution to journal › Review article › peer-review

2 Scopus citations

Killing the invaders: Nk cell impact in tumors and anti-tumor therapy

Molgora, M., Cortez, V. S. & Colonna, M., Feb 2 2021, In: Cancers. 13, 4, p. 1-16 16 p., 595.

Research output: Contribution to journal › Review article › peer-review

Open Access

15 Scopus citations

Laboratory evaluation of SARS-CoV-2 in the COVID-19 pandemic

Parikh, B. A. & Farnsworth, C. W., Mar 2021, In: Best Practice and Research: Clinical Rheumatology. 35, 1, 101660.

Research output: Contribution to journal › Review article › peer-review

2 Scopus citations

Mechanisms of damage tolerance and repair during DNA replication

Ashour, M. E. & Mosammaparast, N., Apr 6 2021, In: Nucleic acids research. 49, 6, p. 3033-3047 15 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

16 Scopus citations

Meningioma: A Pathology Perspective

Toland, A., Huntoon, K. & Dahiya, S. M., Jul 1 2021, In: Neurosurgery. 89, 1, p. 11-21 11 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

5 Scopus citations

Microglia in Alzheimer’s disease at single-cell level. Are there common patterns in humans and mice?

Chen, Y. & Colonna, M., Jul 22 2021, In: Journal of Experimental Medicine. 218, 9, e20202717.

Research output: Contribution to journal › Review article › peer-review

Open Access

78 Scopus citations

Molecular Testing in Breast Cancer: Current Status and Future Directions

Sun, L., Wu, A., Bean, G. R., Hagemann, I. S. & Lin, C. Y., Nov 2021, In: Journal of Molecular Diagnostics. 23, 11, p. 1422-1432 11 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

9 Scopus citations

NAFLD: Reporting Histologic Findings in Clinical Practice

for the American Association for the Study of Liver Diseases NASH Task Force, May 2021, In: Hepatology. 73, 5, p. 2028-2038 11 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

57 Scopus citations

Neuromodulation by the immune system: a focus on cytokines

Salvador, A. F., de Lima, K. A. & Kipnis, J., Aug 2021, In: Nature Reviews Immunology. 21, 8, p. 526-541 16 p.

Research output: Contribution to journal › Review article › peer-review

120 Scopus citations

Department of Pathology & Immunology

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